chemical-structures-2.2.dfsg.0.orig/0000755000175000017500000000000011225622315017557 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/NEWS0000644000175000017500000000174610737173211020271 0ustar georgeskgeorgeskChemical Structures 2.1 (2008-01-03) What's new from 2.0.1: - New structures (carbohydrates, i.e.) - Many french translation added - Spanish translation available - The structure file is named according the usual name - More documentation in Python modules - MicroFormat support - New style for the html pages - All html pages are xhtml1.0-strict compliant - Bug fixes Chemical Structures 2.0.1 (2007-02-28) What's new from 2.0.0: - Dutch translation has been added - Fix formula - Fix InChI code - Fix witdh Chemical Structures 2.0.0 (2007-02-27) What's new from 1.2: - Bug fixes - The build system is based on CMake - The project has 524 structures - A new stylesheet and new pictures make the presentation better - Support of OpenBabel2 has been added - InChI semantic markup have been added (many thanks to Egon Willighagen) - SMILES code have been added - Python scripts are used to generate HTML pages - Name and formula index - Boiling and melting points are also available in K units chemical-structures-2.2.dfsg.0.orig/AUTHORS0000644000175000017500000000072511225117631020633 0ustar georgeskgeorgeskJerome Pansanel - main author Jean Brefort - debugging and feature ideas I-Yuan Chiang - traditional chinese translation and debugging George Khaznadar - debugging, feature ideas and debian package maintainer Jerome Kieffer - debugging with ghemical Patrick Lax - debugging and add-on for nucleobases Carsten Niehaus - debugging and feature ideas and german translations Noel O'Boyle - InChI bug fix Egon Willighagen - support for semantic markup and dutch translation chemical-structures-2.2.dfsg.0.orig/INSTALL0000644000175000017500000000134211112716301020602 0ustar georgeskgeorgeskRequirements ============ The chemical structures project depends on: - CMake >= 2.4 (see http://www.cmake.org) - Python >= 2.2 (see http://www.pymol.org) You can also access extended features by using: - OpenBabel >= 2.1.1 (see http://www.openbabel.org) Basic Installation ================== The project can be easily compiled in 4 steps: 1. 'cd' to the directory containing the project's source code 2. Create a 'build' directory and go in this directory 2. Type 'cmake ..' 4. Type 'make install' to build and install the data files Options ======= By default, 'make install' will install the project's files in a default directory. You can specify another path for the installation: 'cmake -DCMAKE_INSTALL_PREFIX=/another/path .' chemical-structures-2.2.dfsg.0.orig/COPYING0000644000175000017500000000245411225046520020615 0ustar georgeskgeorgeskCopyright 2006-2009 The Chemical Structures Project. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. THIS SOFTWARE IS PROVIDED BY THE CHEMICAL STRUCTURES PROJECT ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE CHEMICAL STRUCTURES PROJECT OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. chemical-structures-2.2.dfsg.0.orig/README0000644000175000017500000000340111225120102020420 0ustar georgeskgeorgesk# # Chemical-Structures: Presentation # The chemical-structures package aims to provide a complete set of molecular structures. The version 2.2 contains over 550 structures of organic compounds. In addition to structural data, each file contains complementary informations, like molecular weight, boiling point, melting point or InChI string. The structures are provided in CML format, but can easily be converted to other formats by using the OpenBabel software (http://openbabel.sourceforge.net/wiki/Main_Page). At this time, 6 languages are supported (dutch, english, french, german, spanish and traditional chinese). New languages are easy to add (a single file to edit: l10n.xml). Structures are visualized with the Jmol applet (http://jmol.sourceforge.net/) # # Chemical-Structures: Data Generation # Each structure is generated with the ghemical software, and the best conformation is chosen by using a Monte Carlo modellisation and optimized with MOPAC/PM3 method. Additional data, like molecular weight, exact molecular weight and molecular formula are calculated with Open Babel. InChI code are generated by the official InChI CLI tool. At least, boiling point and melting point are the mean-values of data found in scientific literature. # # Chemical-Structures: License # All the files are released under the BSD license (see COPYING), except: src/jmol/* (LGPL license) - http://jmol.sourceforge.net # # Chemical-Structures: Contact # If you want so add some molecules to the archive, send a mail with the list of molecule to Jerome Pansanel . # # Icon # The "Download" icon is issued from the Crystal icon set for KDE. This set is released under the GPL license. For further informations, look on this website: http://www.everaldo.com/crystal.html chemical-structures-2.2.dfsg.0.orig/src/0000755000175000017500000000000011225622315020346 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/macrocycles/0000755000175000017500000000000011225622315022652 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/macrocycles/index.xml0000644000175000017500000000125111142231213024471 0ustar georgeskgeorgesk Macrocycles Makrozyklen Macrociclos Macrocycles Grote ringsysteme Macrocycles 大環類 Porphin Porphine Porphin 卟吩/四聯吡咯環 porphin Jerome Pansanel 2006-11-21 chemical-structures-2.2.dfsg.0.orig/src/macrocycles/porphin.cml0000644000175000017500000001335510723031701025030 0ustar georgeskgeorgesk Porphyrin 310.3520 310.1218465 chemical-structures-2.2.dfsg.0.orig/src/macrocycles/CMakeLists.txt0000644000175000017500000000712711112716045025420 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "macrocycles") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/drugs/0000755000175000017500000000000011225622315021472 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/drugs/index.xml0000644000175000017500000000762611142231213023325 0ustar georgeskgeorgesk Drugs Drogen Drogas Drogues Drugs Drugs 藥物 (4-Acetamidophenyl) 2-hydroxybenzoate (4-Acetamidophenyl) 2-hydroxybenzoate 2-Hydroxybenzoate de 4-acétamidophényle (4-Acetamidophenyl) 2-hydroxybenzoate 2-羥基苯甲酸(4-乙醯氨基酚)酯 4-acetamidophenyl_2-hydroxybenzoate Acetaminosalol Acétaminosalol Acetaminosalol 醋胺沙羅 Jerome Pansanel 2006-11-09 N-(4-Hydroxyphenyl)acetamide N-(4-Hydroxyphényl)acétamide N-(4-Hydroxyphenyl)acetamide N-(4-羥苯)乙醯胺 N-4-hydroxyphenyl_acetamide Acetaminophen Paracetamol Acétaminophène Paracétamol Acetaminophen 乙醯胺苯酚 Paracetamol 乙醯胺苯酚 Jerome Pansanel 2006-11-09 Acepromazine Acepromazin Acépromazine Acepromazine 乙醯丙嗪 acepromazine Acetylpromazine Acetylpromazin Acétylpromazine Acetylpromazine 乙醯丙嗪 Jerome Pansanel 2006-11-09 D-Amphetamine D-Amphetamin D-Amphétamine D-Amphetamine D-安非他命 D-amphetamine (S)-1-Phenylpropan-2-amine Dextroamphetamine (S)-1-Phenylpropan-2-amin Dextroamphetamin (S)-1-Phénylpropan-2-amine Dextroamphétamine (S)-1-Phenylpropan-2-amine (S)-1-1–苯基丙–2–胺) Dextroamphetamine 右旋苯異丙胺 Jerome Pansanel 2006-11-24 Diazepam Diazépam Diazepam 苯甲二氮焯 diazepam 7-chloro-1-methyl-5-phenyl-1,3-dihydro-2H-1,4-benzodiazepin-2-one Valium 7-chloro-1-méthyl-5-phényl-1,3-dihydro-2H-1,4-benzodiazépin-2-one Valium 7-chloro-1-methyl-5-phenyl-1,3-dihydro-2H-1,4-benzodiazepin-2-one 7-氯-1-甲基-5-苯基-1,3-二氫-1,4-苯二氮平-2-酮 Valium 二氮平 Jerome Pansanel 2007-12-03 chemical-structures-2.2.dfsg.0.orig/src/drugs/acepromazine.cml0000644000175000017500000001477410662517661024674 0ustar georgeskgeorgesk 1-[10-(3-Dimethylaminopropyl)phenothiazin-2-yl]ethanone 326.4558 326.1452843 chemical-structures-2.2.dfsg.0.orig/src/drugs/N-4-hydroxyphenyl_acetamide.cml0000644000175000017500000000703510662517661027465 0ustar georgeskgeorgesk N-(4-Hydroxyphenyl)acetamide 151.1626 151.0633285 169 chemical-structures-2.2.dfsg.0.orig/src/drugs/diazepam.cml0000644000175000017500000001205410774671262024000 0ustar georgeskgeorgesk 7-Chloro-1-methyl-5-phenyl-1,3-dihydro-2H-1,4-benzodiazepin-2-one 284.7402 284.0716407 chemical-structures-2.2.dfsg.0.orig/src/drugs/CMakeLists.txt0000644000175000017500000000712111112716045024232 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "drugs") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/drugs/D-amphetamine.cml0000644000175000017500000000732710722000734024645 0ustar georgeskgeorgesk (S)-1-Phenylpropan-2-amine 135.2062 135.1047994 chemical-structures-2.2.dfsg.0.orig/src/drugs/4-acetamidophenyl_2-hydroxybenzoate.cml0000644000175000017500000001200110662517661031160 0ustar georgeskgeorgesk (4-Acetamidophenyl) 2-hydroxybenzoate 271.2680 271.0844579 chemical-structures-2.2.dfsg.0.orig/src/esters/0000755000175000017500000000000011225622315021653 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/esters/ethyl_butanoate.cml0000644000175000017500000000716610662517661025564 0ustar georgeskgeorgesk Ethyl butanoate 116.1583 116.0837296 -93 120 chemical-structures-2.2.dfsg.0.orig/src/esters/pentyl_propanoate.cml0000644000175000017500000001053510662517661026132 0ustar georgeskgeorgesk Pentyl propanoate 144.2114 144.1150298 -75 168 chemical-structures-2.2.dfsg.0.orig/src/esters/butyl_propanoate.cml0000644000175000017500000000747110662517661025763 0ustar georgeskgeorgesk Butyl propanoate 130.1849 130.0993797 146 chemical-structures-2.2.dfsg.0.orig/src/esters/propyl_propanoate.cml0000644000175000017500000000716710662517661026153 0ustar georgeskgeorgesk Propyl propanoate 116.1583 116.0837296 -76 123 chemical-structures-2.2.dfsg.0.orig/src/esters/propyl_formate.cml0000644000175000017500000000561610662517661025435 0ustar georgeskgeorgesk Propyl formate 88.1051 88.0524295 -93 81 chemical-structures-2.2.dfsg.0.orig/src/esters/pentyl_acetate.cml0000644000175000017500000000774310662517661025377 0ustar georgeskgeorgesk Pentyl acetate 130.1849 130.0993797 -100 149 chemical-structures-2.2.dfsg.0.orig/src/esters/butyl_pentanoate.cml0000644000175000017500000001055410662517661025745 0ustar georgeskgeorgesk Butyl pentanoate 158.2380 158.1306798 chemical-structures-2.2.dfsg.0.orig/src/esters/propyl_pentanoate.cml0000644000175000017500000000777510662517661026146 0ustar georgeskgeorgesk Propyl pentanoate 144.2114 144.1150298 chemical-structures-2.2.dfsg.0.orig/src/esters/index.xml0000644000175000017500000003737011142231213023505 0ustar georgeskgeorgesk Esters Ester Ésters Esters Esters Esters 酯類 Ethyl acetate Acétate d'éthyle Ethyl acetate 醋酸乙酯/乙酸乙酯 ethyl_acetate Acetic acid ethyl ester Acetic acid ethyl ester 乙酸乙酯 Jerome Pansanel 2006-05-10 Butyl acetate Acétate de butyle Butyl acetate 乙酸丁酯 butyl_acetate Acetic acid n-butyl ester Acetic acid n-butyl ester 乙酸丁酯 Jerome Pansanel 2006-05-11 Butyl butanoate Butanoate de butyle Butyl butanoate 丁酸丁酯 butyl_butanoate n-Butyric acid n-butyl ester Butyl butyrate Butyrate de butyle n-Butyric acid n-butyl ester 丁酸正丁酯 Butyl butyrate 丁酸丁酯 Jerome Pansanel 2006-05-11 Butyl formate Formate de butyle Butyl formate 甲酸丁酯 butyl_formate Formic acid n-butyl ester Formic acid n-butyl ester 甲酸正丁酯 Jerome Pansanel 2006-05-11 Butyl pentanoate Pentanoate de butyle Butyl pentanoate 戊酸丁酯 butyl_pentanoate n-Valeric acid n-butyl ester n-Valeric acid n-butyl ester 戊酸正丁酯 Jerome Pansanel 2006-05-11 Butyl propanoate Propanoate de butyle Butyl propanoate 丙酸丁酯 butyl_propanoate Propionic acid n-butyl ester Butyl propionate Propionate de butyle Propionic acid n-butyl ester 丙酸正丁酯 Butyl propionate 丙酸丁酯 Jerome Pansanel 2006-05-11 Ethyl butanoate Butanoate d'éthyle Ethyl butanoate 丁酸乙酯 ethyl_butanoate n-Butyric acid ethyl ester Ethyl Butyrate Butyrate d'éthyle n-Butyric acid ethyl ester 正-丁酸乙酯 Ethyl Butyrate 丁酸乙酯 Jerome Pansanel 2006-05-11 Ethyl formate Formate d'éthyle Ethyl formate 甲酸乙酯 ethyl_formate Formic acid ethyl ester Ethyl formiate Formiate d'éthyle Formic acid ethyl ester 甲酸乙酯 Ethyl formiate 甲酸乙酯 Jerome Pansanel 2006-05-11 Ethyl pentanoate Pentanoate d'éthyle Ethyl pentanoate 戊酸乙酯 ethyl_pentanoate n-Valeric acid ethyl ester Ethyl valerate Valérate d'éthyle n-Valeric acid ethyl ester 正-戊酸乙酯 Ethyl valerate 戊酸乙酯 Jerome Pansanel 2006-05-11 Ethyl propanoate Propanoate d'éthyle Ethyl propanoate 丙酸乙酯 ethyl_propanoate Propionic acid ethyl ester Ethyl propionate Proprionate d'éthyle Propionic acid ethyl ester 丙酸乙酯 Ethyl propionate 丙酸乙酯 Jerome Pansanel 2006-05-11 Methyl acetate Acétate de méthyle Methyl acetate 乙酸甲酯 methyl_acetate Acetic acid methyl ester Acetic acid methyl ester 乙酸甲酯 Jerome Pansanel 2006-05-11 Methyl butanoate Butanoate de méthyle Methyl butanoate 丁酸甲酯 methyl_butanoate n-Butyric acid methyl ester Methyl butyrate Butyrate de méthyle n-Butyric acid methyl ester 正-丁酸甲酯 Jerome Pansanel 2006-05-11 Methyl formate Formate de méthyle Methyl formate 甲酸甲酯 methyl_formate Formic acid methyl ester Formic acid methyl ester 甲酸甲酯 Jerome Pansanel 2006-05-11 Methyl pentanoate Pentanoate de méthyle Methyl pentanoate 戊酸甲酯 methyl_pentanoate n-Valeric acid methyl ester Methyl valerate Valérate de méthyle n-Valeric acid methyl ester 正-戊酸甲酯 Methyl valerate 戊酸甲酯 Jerome Pansanel 2006-05-11 Methyl propanoate Propanoate de méthyle Methyl propanoate 丙酸甲酯 methyl_propanoate Propionic acid methyl ester Methyl propionate Propionate de méthyle Propionic acid methyl ester 丙酸甲酯 Methyl propionate 丙酸甲酯 Jerome Pansanel 2006-05-11 Pentyl acetate Acétate de pentyle Pentyl acetate 乙酸戊酯 pentyl_acetate Acetic acid pentyl ester Amyl acetate Amyl ethanoate Acétate d'amyle Ethanoate d'amyle Acetic acid pentyl ester 乙酸戊酯 Amyl acetate 乙酸戊酯 Amyl ethanoate 乙酸戊酯 Jerome Pansanel 2006-05-11 Pentyl butanoate Butanoate de pentyle Pentyl butanoate 丁酸戊酯 pentyl_butanoate n-Butyric acid pentyl ester Pentyl butyrate Amyl butyrate Butyrate de pentyle Butyrate d'amyle n-Butyric acid pentyl ester 正-丁酸戊酯 Pentyl butyrate 丁酸戊酯 Amyl butyrate 丁酸戊酯 Jerome Pansanel 2006-05-11 Pentyl formate Formate de pentyle Pentyl formate 甲酸戊酯 pentyl_formate Formic acid pentyl ester Amyl formate Formate d'amyle Formic acid pentyl ester 甲酸戊酯 Amyl formate 甲酸戊酯 Jerome Pansanel 2006-05-11 Pentyl pentanoate Pentanoate de pentyle Pentyl pentanoate 戊酸戊酯 pentyl_pentanoate n-Valeric acid pentyl ester Pentyl valerate Amyl valerate Valérate de pentyle Valérate d'amyle n-Valeric acid pentyl ester 正-戊酸戊酯 Pentyl valerate 戊酸戊酯 Amyl valerate 戊酸戊酯 Jerome Pansanel 2006-05-11 Pentyl propanoate Propanoate de pentyle Pentyl propanoate 丙酸戊酯 pentyl_propanoate Propionic acid pentyl ester Pentyl propionate Amyl propionate Proprionate de pentyle Proprionate d'amyle Propionic acid pentyl ester 丙酸戊酯 Pentyl propionate 丙酸戊酯 Amyl propionate 丙酸戊酯 Jerome Pansanel 2006-05-11 Propyl acetate Acétate de propyle Propyl acetate 乙酸丙酯 propyl_acetate Acetic acid propyl ester Acetic acid propyl ester 乙酸丙酯 Jerome Pansanel 2006-05-11 Propyl butanoate Butanoate de propyle Propyl butanoate 丁酸丙酯 propyl_butanoate n-Butyric acid propyl ester Propyl butyrate Butyrate de propyle n-Butyric acid propyl ester 正-丁酸丙酯 Propyl butyrate 丁酸丙酯 Jerome Pansanel 2006-05-11 Propyl formate Formate de propyle Propyl formate 甲酸丙酯 propyl_formate Formic acid propyl ester Formic acid propyl ester 甲酸丙酯 Jerome Pansanel 2006-05-11 Propyl pentanoate Pentanoate de propyle Propyl pentanoate 戊酸丙酯 propyl_pentanoate n-Valeric acid propyl ester Propyl valerate Valérate de propyle n-Valeric acid propyl ester 正-戊酸丙酯 Propyl valerate 戊酸丙酯 Jerome Pansanel 2006-05-11 Propyl propanoate Propanoate de propyle Propyl propanoate 丙酸丙酯 propyl_propanoate Propionic acid propyl ester Propyl propionate Propionate de propyle Propionic acid propyl ester 丙酸丙酯 Propyl propionate 丙酸丙酯 Jerome Pansanel 2006-05-11 Linolein Linoléine Linolein 亞麻油脂/三亞麻油酸甘油酯 linolein 2,3-bis[[(9Z,12Z)-Octadeca-9,12-dienoyl]oxy]propyl (9Z,12Z)-octadeca-9,12-dienoate (9Z,12Z)-Octadéca-9,12-diènoate de 2,3-bis[[(9Z,12Z)-octadéca-9,12-diènoyl]oxy]propyle 2,3-bis[[(9Z,12Z)-Octadeca-9,12-dienoyl]oxy]propyl (9Z,12Z)-octadeca-9,12-dienoate 2,3-雙[[(9Z,12Z)-十八碳-9,12-二烯醯基]氧基]丙基 (9Z,12Z-十八碳-9,12-二烯酸) Jerome Pansanel 2006-06-27 chemical-structures-2.2.dfsg.0.orig/src/esters/propyl_acetate.cml0000644000175000017500000000612110662517661025376 0ustar georgeskgeorgesk Propyl acetate 102.1317 102.0680796 101 chemical-structures-2.2.dfsg.0.orig/src/esters/methyl_pentanoate.cml0000644000175000017500000000671710662517661026116 0ustar georgeskgeorgesk Methyl pentanoate 116.1583 116.0837296 127 chemical-structures-2.2.dfsg.0.orig/src/esters/methyl_formate.cml0000644000175000017500000000425610662517661025411 0ustar georgeskgeorgesk Methyl formate 60.0520 60.0211294 -100 33 chemical-structures-2.2.dfsg.0.orig/src/esters/methyl_acetate.cml0000644000175000017500000000502710662517661025357 0ustar georgeskgeorgesk Methyl acetate 74.0785 74.0367794 -98 57 chemical-structures-2.2.dfsg.0.orig/src/esters/pentyl_formate.cml0000644000175000017500000000716510662517661025424 0ustar georgeskgeorgesk Pentyl formate 116.1583 116.0837296 -72 129 chemical-structures-2.2.dfsg.0.orig/src/esters/pentyl_butanoate.cml0000644000175000017500000001131510662517661025741 0ustar georgeskgeorgesk Pentyl butanoate 158.2380 158.1306798 -72 186 chemical-structures-2.2.dfsg.0.orig/src/esters/methyl_propanoate.cml0000644000175000017500000000562410662517661026124 0ustar georgeskgeorgesk Methyl propanoate 88.1051 88.0524295 -88 79 chemical-structures-2.2.dfsg.0.orig/src/esters/butyl_formate.cml0000644000175000017500000000612210662517661025240 0ustar georgeskgeorgesk Butyl formate 102.1317 102.0680796 106 chemical-structures-2.2.dfsg.0.orig/src/esters/ethyl_acetate.cml0000644000175000017500000000561510662517661025205 0ustar georgeskgeorgesk Ethyl acetate 88.1051 88.0524295 -84 77 chemical-structures-2.2.dfsg.0.orig/src/esters/butyl_butanoate.cml0000644000175000017500000001053010662517661025563 0ustar georgeskgeorgesk Butyl butanoate 144.2114 144.1150298 -92 164 chemical-structures-2.2.dfsg.0.orig/src/esters/CMakeLists.txt0000644000175000017500000000712211112716045024414 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "esters") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/esters/propyl_butanoate.cml0000644000175000017500000000746710662517661025770 0ustar georgeskgeorgesk Propyl butanoate 130.1849 130.0993797 143 chemical-structures-2.2.dfsg.0.orig/src/esters/pentyl_pentanoate.cml0000644000175000017500000001162310662517661026117 0ustar georgeskgeorgesk Pentyl pentanoate 172.2646 172.1463299 207 chemical-structures-2.2.dfsg.0.orig/src/esters/ethyl_pentanoate.cml0000644000175000017500000000747010662517661025736 0ustar georgeskgeorgesk Ethyl pentanoate 130.1849 130.0993797 144 chemical-structures-2.2.dfsg.0.orig/src/esters/ethyl_propanoate.cml0000644000175000017500000000640510662517661025745 0ustar georgeskgeorgesk Ethyl propanoate 102.1317 102.0680796 -73 99 chemical-structures-2.2.dfsg.0.orig/src/esters/methyl_butanoate.cml0000644000175000017500000000613010662517661025727 0ustar georgeskgeorgesk Methyl butanoate 102.1317 102.0680796 102 chemical-structures-2.2.dfsg.0.orig/src/esters/ethyl_formate.cml0000644000175000017500000000503510662517661025230 0ustar georgeskgeorgesk Ethyl formate 74.0785 74.0367794 -80 53 chemical-structures-2.2.dfsg.0.orig/src/esters/butyl_acetate.cml0000644000175000017500000000715710662517661025222 0ustar georgeskgeorgesk Butyl acetate 116.1583 116.0837296 -78 125 chemical-structures-2.2.dfsg.0.orig/src/esters/linolein.cml0000644000175000017500000005107010774671262024201 0ustar georgeskgeorgesk 2,3-Bis[[(9Z,12Z)-octadeca-9,12-dienoyl]oxy]propyl (9Z,12Z)-octadeca-9,12-dienoate 879.3844 878.7363409 chemical-structures-2.2.dfsg.0.orig/src/ketones/0000755000175000017500000000000011225622315022016 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/ketones/octan-2-one.cml0000644000175000017500000001031710662517661024552 0ustar georgeskgeorgesk Octan-2-one 128.2120 128.1201151 -16 173 chemical-structures-2.2.dfsg.0.orig/src/ketones/cyclohexanone.cml0000644000175000017500000000643410662517661025374 0ustar georgeskgeorgesk Cyclohexanone 98.1430 98.0731649 -47 155 chemical-structures-2.2.dfsg.0.orig/src/ketones/pentan-3-one.cml0000644000175000017500000000620010662517661024730 0ustar georgeskgeorgesk Pentan-3-one 86.1323 86.0731649 -42 101 chemical-structures-2.2.dfsg.0.orig/src/ketones/pyran-4-one.cml0000644000175000017500000000433610662517661024605 0ustar georgeskgeorgesk Pyran-4-one 96.0841 96.0211294 chemical-structures-2.2.dfsg.0.orig/src/ketones/pentan-2-one.cml0000644000175000017500000000620010662517661024727 0ustar georgeskgeorgesk Pentan-2-one 86.1323 86.0731649 -78 102 chemical-structures-2.2.dfsg.0.orig/src/ketones/p-benzoquinone.cml0000644000175000017500000000506210723030557025472 0ustar georgeskgeorgesk Cyclohexa-2,5-diene-1,4-dione 108.0948 108.0211294 113 chemical-structures-2.2.dfsg.0.orig/src/ketones/heptan-4-one.cml0000644000175000017500000000754710662517661024742 0ustar georgeskgeorgesk Heptan-4-one 114.1855 114.1044651 -33 144 chemical-structures-2.2.dfsg.0.orig/src/ketones/index.xml0000644000175000017500000002412711224730174023657 0ustar georgeskgeorgesk Ketones Ketone Cetonas Cétones Ketonen Ketones 酮類 Butanone Butanone Butanone 丁酮 butanone Jerome Pansanel 2006-05-10 Heptan-2-one Heptan-2-one Heptan-2-one 庚-2-酮 heptan-2-one Jerome Pansanel 2006-05-10 Heptan-3-one Heptan-3-one Heptan-3-one 庚-3-酮 heptan-3-one Jerome Pansanel 2006-05-10 Heptan-4-one Heptan-4-one Heptan-4-one 庚-4-酮 heptan-4-one Jerome Pansanel 2006-05-10 Hexan-2-one Hexan-2-one Hexan-2-one 己-2-酮 hexan-2-one Jerome Pansanel 2006-05-10 Hexan-3-one Hexan-3-one Hexan-3-one 己-3-酮 hexan-3-one Jerome Pansanel 2006-05-10 Octan-2-one Octan-2-one Octan-2-one 辛-2-酮 octan-2-one Jerome Pansanel 2006-05-10 Octan-3-one Octan-3-one Octan-3-one 辛-3-酮 octan-3-one Jerome Pansanel 2006-05-10 Octan-4-one Octan-4-one Octan-4-one 辛-4-酮 octan-4-one Jerome Pansanel 2006-05-10 Pentan-2-one Pentan-2-one Pentan-2-one 戊-2-酮 pentan-2-one Jerome Pansanel 2006-05-10 Pentan-3-one Pentan-3-one Pentan-3-one 戊-3-酮 pentan-3-one Jerome Pansanel 2006-05-10 Acetone Aceton Acétone Acetone 丙酮 acetone Propanone Dimethyl ketone Propanon Dimethylketon Propanone Diméthylcétone Propanone 丙酮 Dimethyl ketone 二甲基酮/丙酮 Jerome Pansanel 2006-05-10 p-Benzoquinone p-Benzoquinone p-Benzoquinone 對-苯醌/對苯二酮 p-benzoquinone Cyclohexa-2,5-diene-1,4-dione Cyclohexa-2,5-diène-1,4-dione Quinone Quinone Cyclohexa-2,5-diene-1,4-dione 環己-2,5-二烯-1,4-二酮 Quinone 苯醌 Jerome Pansanel 2006-06-29 o-Benzoquinone o-Benzoquinone o-Benzoquinone 鄰-苯醌/ o-benzoquinone Cyclohexa-2,4-diene-1,6-dione Cyclohexa-2,4-diène-1,6-dione o-Quinone o-Quinone Cyclohexa-2,4-diene-1,6-dione 環己-2,4-二烯-1,6-二酮 o-Quinone 鄰-苯醌/鄰苯二酮 Jerome Pansanel 2006-06-29 Cyclopentanone Cyclopentanone Cyclopentanone 環戊酮 cyclopentanone Jerome Pansanel 2006-07-31 Pyran-2-one Pyran-2-one Pyran-2-one 2-吡喃酮 pyran-2-one Jerome Pansanel 2006-07-31 Pyran-4-one Pyran-4-one Pyran-4-one 4-吡喃酮 pyran-4-one Jerome Pansanel 2006-07-31 Hexafluoroacetone Hexafluoroacétone Hexafluoroacetone 六氟丙酮 hexafluoroacetone 1,1,1,3,3,3-Hexafluoropropanone 1,1,1,3,3,3-Hexafluoropropanone 1,1,1,3,3,3-Hexafluoropropanone 1,1,1,3,3,3-六氟丙酮 Jerome Pansanel 2006-11-22 (Z)-4-Hydroxypent-3-en-2-one (Z)-4-Hydroxypent-3-en-2-one (Z)-4-Hydroxypent-3-en-2-one (Z)-4-羥基戊-3-烯-2-酮 Z-4-hydroxypent-3-en-2-one Jerome Pansanel 2006-11-22 Methyl vinyl ketone Méthyl vinyl cétone Methyl vinyl ketone 甲基乙烯基酮 methyl_vinyl_ketone But-3-en-2-one 3-Buten-2-one But-3-èn-2-one 3-Butèn-2-one But-3-en-2-one 丁烯酮 3-Buten-2-one 丁烯酮 Jerome Pansanel 2006-11-22 Cyclohex-2-en-1-one Cyclohex-2-èn-1-one Cyclohex-2-en-1-one 環己酮 cyclohex-2-en-1-one 2-Cyclohexen-1-one 2-Cyclohexèn-1-one 2-Cyclohexen-1-one 環己酮 Jerome Pansanel 2006-11-22 Cyclohexanone Cyclohexanone Cyclohexanone 環己酮 cyclohexanone Jerome Pansanel 2006-11-22 Cyclopent-2-en-1-one Cyclopent-2-èn-1-one Cyclopent-2-en-1-one 環戊-2-烯-1-酮 cyclopent-2-en-1-one 2-Cyclopenten-1-one 2-Cyclopentèn-1-one 2-Cyclopenten-1-one 環戊酮 Jerome Pansanel 2006-11-22 1,5-Dihydro-2H-pyrrol-2-one 1,5-Dihydro-2H-pyrrol-2-one 1,5-Dihydro-2H-pyrrol-2-one 1,5-二羥基-2氫-吡咯-2-酮 1_5-dihydro-2H-pyrrol-2-one 1,5-Dihydropyrrol-2-one 1,5-Dihydropyrrol-2-one 1,5-Dihydropyrrol-2-one 1,5-二羥基吡咯-2-酮 Jerome Pansanel 2009-07-06 Pyrrol-2-one Pyrrol-2-one Pyrrol-2-one 吡咯-2-酮 pyrrol-2-one Jerome Pansanel 2009-07-06 chemical-structures-2.2.dfsg.0.orig/src/ketones/Z-4-hydroxypent-3-en-2-one.cml0000644000175000017500000000531410662517661027154 0ustar georgeskgeorgesk (Z)-4-Hydroxypent-3-en-2-one 100.1158 100.0524295 chemical-structures-2.2.dfsg.0.orig/src/ketones/1_5-dihydro-2H-pyrrol-2-one.cml0000644000175000017500000000514711224730174027262 0ustar georgeskgeorgesk 1,5-Dihydro-2H-pyrrol-2-one 83.0886 83.0371138 chemical-structures-2.2.dfsg.0.orig/src/ketones/cyclopentanone.cml0000644000175000017500000000566010662517661025556 0ustar georgeskgeorgesk Cyclopentanone 84.1164 84.0575149 -51 131 chemical-structures-2.2.dfsg.0.orig/src/ketones/methyl_vinyl_ketone.cml0000644000175000017500000000503210723030557026606 0ustar georgeskgeorgesk But-3-en-2-one 70.0898 70.0418648 -7 80 chemical-structures-2.2.dfsg.0.orig/src/ketones/cyclohex-2-en-1-one.cml0000644000175000017500000000607610662517661026031 0ustar georgeskgeorgesk Cyclohex-2-en-1-one 96.1271 96.0575149 -53 170 chemical-structures-2.2.dfsg.0.orig/src/ketones/pyrrol-2-one.cml0000644000175000017500000000450411224730174024765 0ustar georgeskgeorgesk Pyrrol-2-one 81.0727 81.0214637 chemical-structures-2.2.dfsg.0.orig/src/ketones/heptan-3-one.cml0000644000175000017500000000727310662517661024735 0ustar georgeskgeorgesk Heptan-3-one 114.1855 114.1044651 148 chemical-structures-2.2.dfsg.0.orig/src/ketones/hexan-3-one.cml0000644000175000017500000000650510662517661024556 0ustar georgeskgeorgesk Hexan-3-one 100.1589 100.0888150 123 chemical-structures-2.2.dfsg.0.orig/src/ketones/pyran-2-one.cml0000644000175000017500000000434310662517661024601 0ustar georgeskgeorgesk Pyran-2-one 96.0841 96.0211294 chemical-structures-2.2.dfsg.0.orig/src/ketones/heptan-2-one.cml0000644000175000017500000000755010662517661024732 0ustar georgeskgeorgesk Heptan-2-one 114.1855 114.1044651 -35 150 chemical-structures-2.2.dfsg.0.orig/src/ketones/cyclopent-2-en-1-one.cml0000644000175000017500000000503710662517661026207 0ustar georgeskgeorgesk Cyclopent-2-en-1-one 82.1005 82.0418648 150 chemical-structures-2.2.dfsg.0.orig/src/ketones/hexan-2-one.cml0000644000175000017500000000676310662517661024563 0ustar georgeskgeorgesk Hexan-2-one 100.1589 100.0888150 -57 127 chemical-structures-2.2.dfsg.0.orig/src/ketones/CMakeLists.txt0000644000175000017500000000712311112716045024560 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "ketones") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/ketones/hexafluoroacetone.cml0000644000175000017500000000471210723030557026235 0ustar georgeskgeorgesk 1,1,1,3,3,3-Hexafluoropropanone 166.0219 165.9853339 -129 -27 chemical-structures-2.2.dfsg.0.orig/src/ketones/octan-3-one.cml0000644000175000017500000001004210662517661024546 0ustar georgeskgeorgesk Octan-3-one 128.2120 128.1201151 167 chemical-structures-2.2.dfsg.0.orig/src/ketones/octan-4-one.cml0000644000175000017500000001004410662517661024551 0ustar georgeskgeorgesk Octan-4-one 128.2120 128.1201151 166 chemical-structures-2.2.dfsg.0.orig/src/ketones/o-benzoquinone.cml0000644000175000017500000000460310723030557025471 0ustar georgeskgeorgesk Cyclohexa-2,4-diene-1,6-dione 108.0948 108.0211294 chemical-structures-2.2.dfsg.0.orig/src/ketones/butanone.cml0000644000175000017500000000540210662517661024342 0ustar georgeskgeorgesk Butanone 72.1057 72.0575149 -87 79 chemical-structures-2.2.dfsg.0.orig/src/ketones/acetone.cml0000644000175000017500000000462410723030557024142 0ustar georgeskgeorgesk Propanone 58.0791 58.0418648 -94 56 chemical-structures-2.2.dfsg.0.orig/src/styles/0000755000175000017500000000000011225622315021671 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/styles/CMakeLists.txt0000644000175000017500000000226411112716045024434 0ustar georgeskgeorgesk################################################################# # Local variable settings # ################################################################# set(LOCAL_TARGET styles) message(STATUS "Generating ${LOCAL_TARGET} Makefile") file(GLOB style_SRCS *.css) set(style_files "") add_custom_target(${LOCAL_TARGET} ALL) ################################################################# # style file handle # ################################################################# foreach(style_SRC_FILE ${style_SRCS}) get_filename_component(style_FILE ${style_SRC_FILE} NAME) add_custom_command(TARGET ${LOCAL_TARGET} COMMAND cp ${style_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${style_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(style_files ${style_files} ${style_FILE}) endforeach(style_SRC_FILE) ################################################################# # Install files # ################################################################# install(FILES ${style_files} DESTINATION ${SHARE_HOME}/styles) chemical-structures-2.2.dfsg.0.orig/src/styles/style.css0000644000175000017500000000316711225104744023553 0ustar georgeskgeorgeskbody { font-family: arial,helvetica,sans-serif; color: #336699; background: #ddddff; width: 800px; margin: auto; padding: 0px; /* Fix Opera bug */ } h2 { font-size: 16px; margin: 2px; border-bottom: 1px solid black; } h3 { font-size: 14px; margin: 2px; border-bottom: 1px solid black; } ul#directory_list { list-style: none; } ul#directory_list li { padding: 5px; margin: 2px; background: #ddddff; border: 1px dashed black; } div#header { height: 96px; margin: 4px 0px 0px 0px; width: auto; border: 1px solid black; background-image: url("../images/header_bg.png"); } div#menu { color: #ffffff; background: #336699; margin-top: 4px; border: 1px solid black; height: 1.2em; padding: 2px; } div#main { background: #ffffff; margin-top: 4px; margin-bottom: 4px; padding: 4px; border: 1px solid black; } tr { width: 100px; vertical-align: top; } div.path { float: left; } div.index { float: right; } table.data { margin-right: auto; margin-left: auto; width: 100%; } .data th { border: 1px solid black; background: #ddddff; } .data td { padding: 4px; } div#molecule div { border: 1px dashed black; margin: 5px; padding: 5px; } div#structure { width: 300px; } #menu a { color: #ffffff; } div#footer { font-size: small; } div#footer p { margin: 0; } img { margin-left: 0px; margin-right: 0px; width: auto; border: 0px; vertical-align: text-bottom; } div#structure { } div#download { } div#inchi { clear: both; } span.inchi { font-family: courier, fixed, monospace; } span.smiles { font-family: courier, fixed, monospace; } chemical-structures-2.2.dfsg.0.orig/src/aldehydes/0000755000175000017500000000000011225622315022310 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/aldehydes/butanal.cml0000644000175000017500000000540210662517661024447 0ustar georgeskgeorgesk Butanal 72.1057 72.0575149 -96 75 chemical-structures-2.2.dfsg.0.orig/src/aldehydes/index.xml0000644000175000017500000001400411142231213024127 0ustar georgeskgeorgesk Aldehydes Aldehyde Aldehídos Aldéhydes Aldehyden Aldehydes 醛類 2-Methylpropanal 2-Méthylpropanal 2-Methylpropanal 2-甲基丙醛 2-methylpropanal Isobutyraldehyde Isobutyraldehyd Aldéhyde isobutyrique Isobutyraldehyde 異丁醛 Jerome Pansanel 2006-05-10 (2R)-2-Methylbutanal (2R)-2-Méthylbutanal (2R)-2-Methylbutanal (2R)-2-甲基丁醛 2R-2-methylbutanal 2-Methylbutyraldehyde 2-Methylbutyraldehyd 2-Méthylbutyraldéhyde 2-Methylbutyraldehyde 2-甲基丁醛 Aldéhyde 2-méthylbutyrique Jerome Pansanel 2006-05-10 3-Methylbutanal 3-Méthylbutanal 3-Methylbutanal 3-甲基丁醛 3-methylbutanal Isovaleraldehyde Isovaleraldehyd Aldéhyde isovalérique Isovaleraldehyde 異戊醛 Jerome Pansanel 2006-05-10 Butanal Butanal Butanal Butanal 丁醛 butanal n-Butyraldehyde n-Butyraldehyd n-Butyraldéhyde Aldéhyde butyrique n-Butyraldehyde 正-丁醛 Jerome Pansanel 2006-05-10 Acetaldehyde Acétaldéhyde Acetaldehyde 乙醛 acetaldehyde Ethanal Ethanal Ethanal 乙醛 Jerome Pansanel 2006-05-10 Heptanal Heptanal Heptanal 庚醛 heptanal Jerome Pansanel 2006-05-10 Hexanal Hexanal Hexanal 已醛 hexanal Jerome Pansanel 2006-05-10 Formaldehyde Formaldéhyde Formaldehyd Formaldehyde 甲醛 formaldehyde Methanal Méthanal Methanal 甲醛 Jerome Pansanel 2006-05-10 Octanal Octanal Octanal 辛醛 octanal Octyl aldehyde Octylaldehyd Aldéhyde octylique Octyl aldehyde 辛醛 Jerome Pansanel 2006-05-10 Pentanal Pentanal Pentanal 戊醛 pentanal n-Valeraldehyde n-Valeraldehyd n-Valéraldéhyde Aldéhyde valérique n-Valeraldehyde 正戊醛 Jerome Pansanel 2006-05-10 Propanal Propanal Propanal 丙醛 propanal Proprionaldehyde Proprionaldehyd Proprionaldéhyde Aldéhyde proprionique Proprionaldehyde 丙醛 Jerome Pansanel 2006-05-10 Prop-2-enal Prop-2-enal Prop-2-enal 丙-2-烯醛 prop-2-enal Acrolein Acroléine Acrolein 丙烯醛 Jerome Pansanel 2006-11-21 chemical-structures-2.2.dfsg.0.orig/src/aldehydes/heptanal.cml0000644000175000017500000000752410662517661024624 0ustar georgeskgeorgesk Heptanal 114.1855 114.1044651 -43 154 chemical-structures-2.2.dfsg.0.orig/src/aldehydes/2-methylpropanal.cml0000644000175000017500000000542510662517661026224 0ustar georgeskgeorgesk 2-Methylpropanal 72.1057 72.0575149 -65 64 chemical-structures-2.2.dfsg.0.orig/src/aldehydes/hexanal.cml0000644000175000017500000000647210662517661024451 0ustar georgeskgeorgesk Hexanal 100.1589 100.0888150 130 chemical-structures-2.2.dfsg.0.orig/src/aldehydes/propanal.cml0000644000175000017500000000462610662517661024644 0ustar georgeskgeorgesk Propanal 58.0791 58.0418648 -81 48 chemical-structures-2.2.dfsg.0.orig/src/aldehydes/2R-2-methylbutanal.cml0000644000175000017500000000575110662517661026321 0ustar georgeskgeorgesk (2R)-2-Methylbutanal 86.1323 86.0731649 91 chemical-structures-2.2.dfsg.0.orig/src/aldehydes/formaldehyde.cml0000644000175000017500000000302210662517661025460 0ustar georgeskgeorgesk Formaldehyde 30.0260 30.0105647 -20 chemical-structures-2.2.dfsg.0.orig/src/aldehydes/CMakeLists.txt0000644000175000017500000000712511112716045025054 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "aldehydes") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/aldehydes/prop-2-enal.cml0000644000175000017500000000425010662517661025055 0ustar georgeskgeorgesk Prop-2-enal 56.0633 56.0262147 -87 53 chemical-structures-2.2.dfsg.0.orig/src/aldehydes/acetaldehyde.cml0000644000175000017500000000405510662517661025440 0ustar georgeskgeorgesk Acetaldehyde 44.0526 44.0262147 -125 21 chemical-structures-2.2.dfsg.0.orig/src/aldehydes/pentanal.cml0000644000175000017500000000617010662517661024626 0ustar georgeskgeorgesk Pentanal 86.1323 86.0731649 -92 102 chemical-structures-2.2.dfsg.0.orig/src/aldehydes/octanal.cml0000644000175000017500000001031410662517661024440 0ustar georgeskgeorgesk Octanal 128.2120 128.1201151 13 171 chemical-structures-2.2.dfsg.0.orig/src/aldehydes/3-methylbutanal.cml0000644000175000017500000000572310662517661026040 0ustar georgeskgeorgesk 3-Methylbutanal 86.1323 86.0731649 90 chemical-structures-2.2.dfsg.0.orig/src/heteroaromatics/0000755000175000017500000000000011225622315023537 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/heteroaromatics/picolinic_acid.cml0000644000175000017500000000545610723017777027213 0ustar georgeskgeorgesk Pyridine-2-carboxylic acid 123.1094 123.0320284 139 chemical-structures-2.2.dfsg.0.orig/src/heteroaromatics/1H-pyridine-2-thione.cml0000644000175000017500000000457310662517661027774 0ustar georgeskgeorgesk 1H-Pyridine-2-thione 111.1649 111.0142702 chemical-structures-2.2.dfsg.0.orig/src/heteroaromatics/1H-pyrazole.cml0000644000175000017500000000451710662517661026371 0ustar georgeskgeorgesk 1H-Pyrazole 68.0773 68.0374481 69 187 chemical-structures-2.2.dfsg.0.orig/src/heteroaromatics/index.xml0000644000175000017500000001543711142231213025371 0ustar georgeskgeorgesk Heteroaromatics Heteroaromaten Heteroaromáticos Heteroaromatiques Heteroaromaten Heteroaromatics 雜芳族 1H-Pyrrole 1H-Pyrrole 1H-Pyrrole 1氫-吡咯 1H-pyrrole Pyrrol Pyrrole Pyrrol 吡咯/一氮二烯伍圜 Jerome Pansanel 2006-05-10 Pyridine Pyridine Pyridine 吡啶/一氯三烯陸圜 pyridine Jerome Pansanel 2006-05-10 1,2-Oxazole 1,2-Oxazole 1,2-Oxazole 1,2-噁唑/咢唑 1_2-oxazole Oxazole Oxazole Oxazole 噁唑/咢唑 Jerome Pansanel 2006-07-31 1,2-Thiazole 1,2-Thiazole 1,2-Thiazole 1,2-噻唑 1_2-thiazole Thiazole Thiazole Thiazole 噻唑 Jerome Pansanel 2006-07-31 1,3-Oxazole 1,3-Oxazole 1,3-Thiazole 1,3-噁唑/咢唑 1_3-oxazole Isoxazole Isoxazole Isoxazole 異咢唑 Jerome Pansanel 2006-07-31 1,3-Thiazole 1,3-Thiazole 1,3-Thiazole 1,3-噻唑 1_3-thiazole Isothiazole Isothiazole Isothiazole 異噻唑 Jerome Pansanel 2006-07-31 1H-Pyrazole 1H-Pyrazole 1H-Pyrazole 1氫-吡唑 1H-pyrazole Jerome Pansanel 2006-07-31 1H-Pyridine-2-thione 1H-Pyridine-2-thione 1H-Pyridine-2-thione 1氫-吡啶-2-硫酮 1H-pyridine-2-thione Jerome Pansanel 2006-11-22 Pyridine-2-thiol Pyridine-2-thiol Pyridine-2-thiol 吡啶-2-硫醇 pyridine-2-thiol Jerome Pansanel 2006-11-22 Picolinamide Picolinamide Picolinamide 吡啶醯胺 picolinamide Pyridine-2-carboxamide Pyridine-2-carboxamide Pyridine-2-carboxamide 吡啶醯胺 Jerome Pansanel 2006-11-09 Picolinic acid Acide picolinique Picolinic acid 吡啶甲酸 picolinic_acid Pyridine-2-carboxylic acid Acide pyridine-2-carboxylique Pyridine-2-carboxylic acid 吡啶-2-羧酸 Jerome Pansanel 2006-11-09 Nicotinamide Nicotinamide Nicotinamide 菸鹼醯胺 nicotinamide Pyridine-3-carboxamide Pyridine-3-carboxamide Pyridine-3-carboxamide 菸鹼醯胺 Jerome Pansanel 2006-11-09 Nicotinic acid Acide nicotinique Nicotinic acid 菸鹼酸 nicotinic_acid Pyridine-3-carboxylic acid Acide pyridine-3-carboxylique Pyridine-3-carboxylic acid 吡啶-3-羧酸 Jerome Pansanel 2006-11-09 Isonicotinamide Isonicotinamide Isonicotinamide 異菸鹼酸 isonicotinamide Pyridine-4-carboxamide Pyridine-4-carboxamide Pyridine-4-carboxamide 異菸鹼酸 Jerome Pansanel 2006-11-09 Isonicotinic acid Acide isonicotinique Isonicotinic acid 異菸鹼酸 isonicotinic_acid Pyridine-4-carboxylic acid Acide pyridine-4-carboxylique Pyridine-4-carboxylic acid 吡啶-4-羧酸 Jerome Pansanel 2006-11-09 chemical-structures-2.2.dfsg.0.orig/src/heteroaromatics/pyridine.cml0000644000175000017500000000506710662517661026102 0ustar georgeskgeorgesk Pyridine 79.0999 79.0421992 -42 115 chemical-structures-2.2.dfsg.0.orig/src/heteroaromatics/1H-pyrrole.cml0000644000175000017500000000467610662517661026226 0ustar georgeskgeorgesk 1H-Pyrrole 67.0892 67.0421992 -23 130 chemical-structures-2.2.dfsg.0.orig/src/heteroaromatics/1_2-oxazole.cml0000644000175000017500000000404510662517661026312 0ustar georgeskgeorgesk 1,2-Oxazole 69.0620 69.0214637 95 chemical-structures-2.2.dfsg.0.orig/src/heteroaromatics/nicotinic_acid.cml0000644000175000017500000000545710723017777027222 0ustar georgeskgeorgesk Pyridine-3-carboxylic acid 123.1094 123.0320284 236 chemical-structures-2.2.dfsg.0.orig/src/heteroaromatics/CMakeLists.txt0000644000175000017500000000713311112716045026302 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "heteroaromatics") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/heteroaromatics/1_3-thiazole.cml0000644000175000017500000000405010662517661026445 0ustar georgeskgeorgesk 1,3-Thiazole 85.1276 84.9986201 117 chemical-structures-2.2.dfsg.0.orig/src/heteroaromatics/1_2-thiazole.cml0000644000175000017500000000357110662517661026453 0ustar georgeskgeorgesk 1,2-Thiazole 85.1276 84.9986201 chemical-structures-2.2.dfsg.0.orig/src/heteroaromatics/picolinamide.cml0000644000175000017500000000564010723017777026712 0ustar georgeskgeorgesk Pyridine-2-carboxamide 122.1246 122.0480128 109 chemical-structures-2.2.dfsg.0.orig/src/heteroaromatics/isonicotinamide.cml0000644000175000017500000000564010723017777027433 0ustar georgeskgeorgesk Pyridine-4-carboxamide 122.1246 122.0480128 156 chemical-structures-2.2.dfsg.0.orig/src/heteroaromatics/isonicotinic_acid.cml0000644000175000017500000000545510723017777027733 0ustar georgeskgeorgesk Pyridine-4-carboxylic acid 123.1094 123.0320284 315 chemical-structures-2.2.dfsg.0.orig/src/heteroaromatics/pyridine-2-thiol.cml0000644000175000017500000000503710662517661027353 0ustar georgeskgeorgesk Pyridine-2-thiol 111.1649 111.0142702 128 chemical-structures-2.2.dfsg.0.orig/src/heteroaromatics/nicotinamide.cml0000644000175000017500000000563610723017777026725 0ustar georgeskgeorgesk Pyridine-3-carboxamide 122.1246 122.0480128 129 chemical-structures-2.2.dfsg.0.orig/src/heteroaromatics/1_3-oxazole.cml0000644000175000017500000000404410662517661026312 0ustar georgeskgeorgesk 1,3-Oxazole 69.0620 69.0214637 69 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/0000755000175000017500000000000011225622315022630 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/haloalkanes/1-chloropentane.cml0000644000175000017500000000637710662517661026354 0ustar georgeskgeorgesk 1-Chloropentane 106.5938 106.0549280 -99 107 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/2-chloropropane.cml0000644000175000017500000000503710662517661026357 0ustar georgeskgeorgesk 2-Chloropropane 78.5407 78.0236279 -117 35 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/1_1_1_2_2_2-hexafluoroethane.cml0000644000175000017500000000430610662517661030365 0ustar georgeskgeorgesk 1,1,1,2,2,2-Hexafluoroethane 138.0118 137.9904193 -100 -78 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/dichloromethane.cml0000644000175000017500000000350610662517661026511 0ustar georgeskgeorgesk Dichloromethane 84.9326 83.9533554 -97 39 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/1_1_1-trichloroethane.cml0000644000175000017500000000430110662517661027326 0ustar georgeskgeorgesk 1,1,1-Trichloroethane 133.4042 131.9300331 -33 75 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/1-chloro-1_1_2_2_2-pentafluoroethane.cml0000644000175000017500000000357710662517661031762 0ustar georgeskgeorgesk 1-Chloro-1,1,2,2,2-pentafluoroethane 154.4664 153.9608688 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/chloroethane.cml0000644000175000017500000000425210662517661026016 0ustar georgeskgeorgesk Chloroethane 64.5141 64.0079778 -136 12 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/2-bromo-2-methylpropane.cml0000644000175000017500000000563410662517661027651 0ustar georgeskgeorgesk 2-Bromo-2-methylpropane 137.0183 135.9887623 -20 72 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/1-chlorooctane.cml0000644000175000017500000001051010662517661026153 0ustar georgeskgeorgesk 1-Chlorooctane 148.6736 148.1018782 -57 182 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/difluoromethane.cml0000644000175000017500000000350410662517661026527 0ustar georgeskgeorgesk Difluoromethane 52.0234 52.0124565 -136 -52 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/chloromethane.cml0000644000175000017500000000347610662517661026202 0ustar georgeskgeorgesk Chloromethane 50.4875 49.9923278 -97 -24 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/bromotrifluoromethane.cml0000644000175000017500000000352210662517661027770 0ustar georgeskgeorgesk Bromotrifluoromethane 148.9099 147.9135467 -168 -58 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/1_1_2_2-tetrachloroethane.cml0000644000175000017500000000431510662517661030076 0ustar georgeskgeorgesk 1,1,2,2-Tetrachloroethane 167.8493 165.8910608 -43 146 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/bromocyclohexane.cml0000644000175000017500000000665610662517661026716 0ustar georgeskgeorgesk Bromocyclohexane 163.0555 162.0044124 -56 166 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/1-chlorohexane.cml0000644000175000017500000000715310662517661026163 0ustar georgeskgeorgesk 1-Chlorohexane 120.6204 120.0705781 -94 134 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/index.xml0000644000175000017500000004063111202002412024446 0ustar georgeskgeorgesk Haloalkanes Halogenalkane Haloalcanos Halogénures d'alkyle Gehalogeneerde Alkanen Haloalkanes 鹵烷類 1,1,2,2-Tetrachloroethane 1,1,2,2-Tétrachloroéthane 1,1,2,2-Tetrachloroethane 1,1,2,2-四氯乙烷 1_1_2_2-tetrachloroethane Jerome Pansanel 2006-05-10 Bromoform Bromoforme Bromoform 溴仿 bromoform Tribromomethane Tribromométhane Tribromomethane 三溴甲烷 Jerome Pansanel 2006-05-10 Chloroform Chloroforme Chloroform 氯仿 chloroform Trichloromethane Trichlorométhane Trichloromethane 三氯甲烷 Jerome Pansanel 2006-05-10 Dichloromethane Dichlorométhane Dichloromethane 二氯甲烷 dichloromethane Jerome Pansanel 2006-05-10 Tetrachloromethane Tetrachlorométhane Tetrachloromethane 四氯甲烷 tetrachloromethane Carbon tetrachloride Tétrachlorure de carbone Carbon tetrachloride 四氯化碳 Jerome Pansanel 2006-05-10 1,3-Dichloropropane 1,3-Dichloropropane 1,3-Dichloropropane 1,3-二氯丙烷 1_3-dichloropropane Jerome Pansanel 2006-07-13 1-Chlorobutane 1-Chlorobutane 1-Chlorobutane 1-氯丁烷 1-chlorobutane n-Butyl chloride Chloryre n-butylique n-Butyl chloride 正氯丁烷 Jerome Pansanel 2006-07-13 1-Chlorodecane 1-Chlorodécane 1-Chlorodecane 1-氯癸烷 1-chlorodecane n-Decyl chloride Chlorure n-décylique n-Decyl chloride 正氯癸烷 Jerome Pansanel 2006-07-13 1-Chloroheptane 1-Chloroheptane 1-Chloroheptane 1-氯庚烷 1-chloroheptane n-Heptyl chloride Chlorure n-heptylique n-Heptyl chloride 正氯庚烷 Jerome Pansanel 2006-07-13 1-Chlorohexane 1-Chlorohexane 1-Chlorohexane 1-氯己烷 1-chlorohexane n-Hexyl chloride Chlorure n-hexylique n-Hexyl chloride 正氯己烷 Jerome Pansanel 2006-07-13 1-Chlorononane 1-Chlorononane 1-Chlorononane 1-氯壬烷 1-chlorononane n-Nonyl chloride Chlorure n-nonylique n-Nonyl chloride 正氯壬烷 Jerome Pansanel 2006-07-13 1-Chlorooctane 1-Chlorooctane 1-Chlorooctane 1-氯辛烷 1-chlorooctane n-Octyl chloride Chlorure n-octylique n-Octyl chloride 正氯辛烷 Jerome Pansanel 2006-07-13 1-Chloropentane 1-Chloropentane 1-Chloropentane 1-氯戊烷 1-chloropentane n-Amyl chloride n-Pentyl chloride Chlorure n-amylique Chlorure n-pentylique n-Amyl chloride 正氯戊烷 n-Pentyl chloride 正氯戊烷 Jerome Pansanel 2006-07-13 1-Chloropropane 1-Chloropropane 1-Chloropropane 1-氯丙烷 1-chloropropane n-Propyl chloride Chlorure n-propylique n-Propyl chloride 正氯丙烷 Jerome Pansanel 2006-07-13 2-Chloro-2-methylpropane 2-Chloro-2-méthylpropane 2-Chloro-2-methylpropane 2-氯-2-甲基丙烷 2-chloro-2-methylpropane tert-Butyl chloride Chlorure tert-butylique tert-Butyl chloride 三級氯丁烷 Jerome Pansanel 2006-07-13 (R)-Epichlorohydrin (R)-Épichlorohydrine (R)-Epichlorohydrin 環氧氯丙烷/表氯醇 R-epichlorohydrin (R)-2-(Chloromethyl)oxirane (R)-1-Chloro-2,3-epoxypropane (R)-2-(Chlorométhyl)oxirane (R)-1-Chloro-2,3-époxypropane (R)-2-(Chloromethyl)oxirane (R)-2-(氯甲基)環氧乙烷 (R)-1-Chloro-2,3-epoxypropane (R)-1-氯-2,3-環氧丙烷 Jerome Pansanel 2006-07-13 3-Chloropropene 3-Chloropropène 3-Chloropropene 3-氯丙烯 3-chloropropene Allyl chloride Chlorure allylique Allyl chloride 氯丙烯/氯化烯丙基/烯丙氯 Jerome Pansanel 2006-07-13 Chloroethane Chloroéthane Chloroethane 氯乙烷 chloroethane Ethyl chloride Chlorure éthylique Ethyl chloride 氯乙烷 Jerome Pansanel 2006-07-13 Chloromethane Chlorométhane Chloromethane 氯甲烷 chloromethane Methyl chloride Chlorure méthylique Methyl chloride 氯甲烷 Jerome Pansanel 2006-07-13 1-Bromopropane 1-Bromopropane 1-Bromopropane 1-溴丙烷 1-bromopropane n-Propyl bromide Bromure n-propylique n-Propyl bromide 正溴丙烷 Jerome Pansanel 2006-11-09 1,4-Dichlorobut-2-yne 1,4-Dichlorobut-2-yne 1,4-Dichlorobut-2-yne 1,4-二氯丁-2-炔 1_4-dichlorobut-2-yne Jerome Pansanel 2006-11-09 2-Bromopropane 2-Bromopropane 2-Bromopropane 2-溴丙烷 2-bromopropane Isopropyl bromide Bromure isopropylique Isopropyl bromide 2-溴丙烷 Jerome Pansanel 2006-11-09 2-Chloropropane 2-Chloropropane 2-Chloropropane 2-氯丙烷 2-chloropropane Isopropyl chloride Chlorure isopropylique Isopropyl chloride 2-氯丙烷 Jerome Pansanel 2006-11-09 Bromocyclohexane Bromocyclohexane Bromocyclohexane 溴環己烷 bromocyclohexane Jerome Pansanel 2006-11-09 Bromoethane Bromoéthane Bromoethane 溴乙烷 bromoethane Jerome Pansanel 2006-11-09 Bromomethane Bromométhane Bromomethane 溴甲烷 bromomethane Jerome Pansanel 2006-11-09 Bromotrifluoromethane Bromotrifluorométhane Bromotrifluoromethane 一溴三氟甲烷 bromotrifluoromethane Jerome Pansanel 2006-11-09 Chloro-(chloromethoxy)methane Chloro-(chlorométhoxy)méthane Chloro-(chloromethoxy)methane 氯-(氯甲氧基)甲烷 chloro-chloromethoxy_methane Dichloromethyl ether Ether dichlorométhylique Dichloromethyl ether 二氯甲基醚 Jerome Pansanel 2006-11-09 Chlorocyclohexane Chlorocyclohexane Chlorocyclohexane 氯環己烷 chlorocyclohexane Jerome Pansanel 2006-11-09 1,1,1,2,2,2-Hexafluoroethane 1,1,1,2,2,2-Hexafluoroéthane 1,1,1,2,2,2-Hexafluoroethane 1,1,1,2,2,2-六氟乙烷 1_1_1_2_2_2-hexafluoroethane Perfluoro ethane Perfluoro éthane Perfluoro ethane 全氟乙烷 Jerome Pansanel 2006-11-22 1,1,1,2,2-Pentafluoroethane 1,1,1,2,2-Pentafluoroéthane 1,1,1,2,2-Pentafluoroethane 1,1,1,2,2-五氟乙烷 1_1_1_2_2-pentafluoroethane Jerome Pansanel 2006-11-22 1,1,1-Trichloroethane 1,1,1-Trichloroéthane 1,1,1-Trichloroethane 三氯乙烷 1_1_1-trichloroethane Jerome Pansanel 2006-11-22 1-Chloro-1,1,2,2,2-pentafluoroethane 1-Chloro-1,1,2,2,2-pentafluoroéthane 1-Chloro-1,1,2,2,2-pentafluoroethane 1-氯-1,1,2,2,2-五氟乙烷 1-chloro-1_1_2_2_2-pentafluoroethane Jerome Pansanel 2006-11-22 2-Bromo-2-methylpropane 2-Bromo-2-methylpropane 2-Bromo-2-methylpropane 2-溴-2-甲基丙烷 2-bromo-2-methylpropane tert-Butyl bromide Bromure tert-butylique tert-Butyl bromide 三級溴丁烷 Jerome Pansanel 2006-11-22 (2S)-2-Bromobutane (2S)-2-Bromobutane (2S)-2-Bromobutane (2S)-2-溴丁烷 2S-2-bromobutane Jerome Pansanel 2006-11-22 (2S)-2-Chlorobutane (2S)-2-Chlorobutane (2S)-2-Chlorobutane (2S)-2-氯丁烷 2S-2-chlorobutane Jerome Pansanel 2006-11-22 Difluoromethane Difluorométhane Difluoromethane 二氟甲烷 difluoromethane Jerome Pansanel 2006-11-22 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/1_4-dichlorobut-2-yne.cml0000644000175000017500000000440610662517661027173 0ustar georgeskgeorgesk 1,4-Dichlorobut-2-yne 122.9806 121.9690055 166 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/2S-2-bromobutane.cml0000644000175000017500000000563610662517661026310 0ustar georgeskgeorgesk (2S)-2-Bromobutane 137.0183 135.9887623 -112 91 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/1_3-dichloropropane.cml0000644000175000017500000000504710662517661027116 0ustar georgeskgeorgesk 1,3-Dichloropropane 112.9857 111.9846556 -99 120 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/2-chloro-2-methylpropane.cml0000644000175000017500000000535410722620546030012 0ustar georgeskgeorgesk 2-Chloro-2-methylpropane 92.5673 92.0392780 -25 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/1-chloroheptane.cml0000644000175000017500000000773610662517661026346 0ustar georgeskgeorgesk 1-Chloroheptane 134.6470 134.0862282 -69 159 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/bromomethane.cml0000644000175000017500000000347210662517661026026 0ustar georgeskgeorgesk Bromomethane 94.9385 93.9418121 -94 4 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/chlorocyclohexane.cml0000644000175000017500000000665710662517661027067 0ustar georgeskgeorgesk Chlorocyclohexane 118.6045 118.0549280 -44 142 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/bromoethane.cml0000644000175000017500000000425110662517661025645 0ustar georgeskgeorgesk Bromoethane 108.9651 107.9574622 -119 38 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/1-chlorononane.cml0000644000175000017500000001126710662517661026172 0ustar georgeskgeorgesk 1-Chlorononane 162.7002 162.1175283 -39 203 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/2-bromopropane.cml0000644000175000017500000000503710662517661026207 0ustar georgeskgeorgesk 2-Bromopropane 122.9917 121.9731122 -89 59 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/1-chlorodecane.cml0000644000175000017500000001205710662517661026131 0ustar georgeskgeorgesk 1-Chlorodecane 176.7267 176.1331784 -31 223 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/chloroform.cml0000644000175000017500000000347610662517661025524 0ustar georgeskgeorgesk Chloroform 119.3776 117.9143831 -63 60 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/CMakeLists.txt0000644000175000017500000000712711112716045025376 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "haloalkanes") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/bromoform.cml0000644000175000017500000000347510662517661025353 0ustar georgeskgeorgesk Bromoform 252.7306 249.7628360 6 148 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/2S-2-chlorobutane.cml0000644000175000017500000000563710662517661026461 0ustar georgeskgeorgesk (2S)-2-Chlorobutane 92.5673 92.0392780 -140 -69 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/tetrachloromethane.cml0000644000175000017500000000351310662517661027232 0ustar georgeskgeorgesk Tetrachloromethane 153.8227 151.8754107 -23 76 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/R-epichlorohydrin.cml0000644000175000017500000000421711130373737026740 0ustar georgeskgeorgesk (R)-2-(Chloromethyl)oxirane 92.5242 92.0028925 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/1-bromopropane.cml0000644000175000017500000000504010662517661026200 0ustar georgeskgeorgesk 1-Bromopropane 122.9917 121.9731122 -110 71 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/1_1_1_2_2-pentafluoroethane.cml0000644000175000017500000000431410662517661030325 0ustar georgeskgeorgesk 1,1,1,2,2-Pentafluoroethane 120.0214 119.9998411 -103 -48 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/1-chloropropane.cml0000644000175000017500000000504110662517661026351 0ustar georgeskgeorgesk 1-Chloropropane 78.5407 78.0236279 -122 46 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/1-chlorobutane.cml0000644000175000017500000000561210662517661026167 0ustar georgeskgeorgesk 1-Chlorobutane 92.5673 92.0392780 -123 78 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/3-chloropropene.cml0000644000175000017500000000445210662517661026364 0ustar georgeskgeorgesk 3-Chloropropene 76.5248 76.0079778 -134 45 chemical-structures-2.2.dfsg.0.orig/src/haloalkanes/chloro-chloromethoxy_methane.cml0000644000175000017500000000376110662517661031240 0ustar georgeskgeorgesk Chloro-(chloromethoxy)methane 114.9586 113.9639201 chemical-structures-2.2.dfsg.0.orig/src/thioethers/0000755000175000017500000000000011225622315022524 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/thioethers/thiepin.cml0000644000175000017500000000470610662517661024703 0ustar georgeskgeorgesk Thiepin 110.1768 110.0190212 chemical-structures-2.2.dfsg.0.orig/src/thioethers/index.xml0000644000175000017500000000171611142231213024351 0ustar georgeskgeorgesk Thioethers Thioether Tioéters Thioéthers Thioethers Thioethers 硫醚類 Thiepin Thiépine Thiepin 暫譯為: 一硫柒圜 (含硫雜環) thiepin Jerome Pansanel 2006-07-31 Thiophene Thiophène Thiophene 噻吩/一硫二烯伍圜 thiophene Jerome Pansanel 2006-07-31 chemical-structures-2.2.dfsg.0.orig/src/thioethers/CMakeLists.txt0000644000175000017500000000712611112716045025271 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "thioethers") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/thioethers/thiophene.cml0000644000175000017500000000447610662517661025232 0ustar georgeskgeorgesk Thiophene 84.1396 84.0033711 -38 84 chemical-structures-2.2.dfsg.0.orig/src/thiols/0000755000175000017500000000000011225622315021650 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/thiols/R_butane-2-thiol.cml0000644000175000017500000000525410723245153025371 0ustar georgeskgeorgesk (R)-Butane-2-thiol 90.1872 85 chemical-structures-2.2.dfsg.0.orig/src/thiols/proprane-1-thiol.cml0000644000175000017500000000523110662517661025462 0ustar georgeskgeorgesk Proprane-1-thiol 76.1606 76.0346713 -113 67 chemical-structures-2.2.dfsg.0.orig/src/thiols/2-methylproprane-2-thiol.cml0000644000175000017500000000602510662517661027047 0ustar georgeskgeorgesk 2-Methylproprane-2-thiol 90.1872 90.0503213 0 64 chemical-structures-2.2.dfsg.0.orig/src/thiols/ethane-1_2-dithiol.cml0000644000175000017500000000465210662517661025644 0ustar georgeskgeorgesk Ethane-1,2-dithiol 94.1990 93.9910922 -41 145 chemical-structures-2.2.dfsg.0.orig/src/thiols/heptane-1-thiol.cml0000644000175000017500000001012610662517661025257 0ustar georgeskgeorgesk Heptane-1-thiol 132.2669 132.0972715 -43 176 chemical-structures-2.2.dfsg.0.orig/src/thiols/proprane-2-thiol.cml0000644000175000017500000000523010662517661025462 0ustar georgeskgeorgesk Proprane-2-thiol 76.1606 76.0346713 -131 57 chemical-structures-2.2.dfsg.0.orig/src/thiols/index.xml0000644000175000017500000001752011142231213023475 0ustar georgeskgeorgesk Thiols Thiole Tiols Thiols Thiolen Thiols 硫醇 2-Methylproprane-2-thiol 2-Méthylproprane-2-thiol 2-Methylpropane-2-thiol 2-甲基丙烷-2-硫醇 2-methylproprane-2-thiol 2-Methyl-2-propanethiol tert-Butyl mercaptan 2-Méthyl-2-propanethiol Mercaptan tert-butylique 2-Methyl-2-propanethiol 2-甲基-2-丙硫醇 tert-Butyl mercaptan 三級丁硫醇 Jerome Pansanel 2006-11-22 Butane-1-thiol Butane-1-thiol Butane-1-thiol 丁-1-硫醇 butane-1-thiol 1-butanethiol n-Butyl mercaptan 1-butanethiol Mercaptan n-butylique 1-butanethiol 1-丁硫醇 n-Butyl mercaptan 正-丁硫醇 Jerome Pansanel 2006-11-22 (R)-Butane-2-thiol (R)-Butane-2-thiol (R)-Butane-2-thiol (R)-丁-2-硫醇 R_butane-2-thiol (R)-2-Butanethiol sec-Butyl mercaptan (R)-2-Butanethiol Mercaptan sec-butylique (R)-2-Butanethiol (R)-2-丁硫醇 sec-Butyl mercaptan 二級丁硫醇 Jerome Pansanel 2006-11-22 Ethane-1,2-dithiol Ethane-1,2-dithiol Ethane-1,2-dithiol 乙-1,2-二硫醇 ethane-1_2-dithiol 1,2-Ethanedithiol 1,2-Dimercaptoethane 1,2-Ethanedithiol 1,2-Dimercaptoéthane 1,2-Ethanedithiol 1,2-乙二硫醇 1,2-Dimercaptoethane 1,2-乙二硫醇 Jerome Pansanel 2006-11-22 Ethanethiol Ethanethiol Ethanethiol 乙硫醇 ethanethiol Ethyl mercaptan Mercaptan éthylique Ethyl mercaptan 乙硫醇 Jerome Pansanel 2006-11-22 Heptane-1-thiol Heptane-1-thiol Heptane-1-thiol 庚-1-硫醇 heptane-1-thiol 1-Heptanethiol Heptyl mercaptan 1-Heptanethiol Mercaptan heptylique 1-Heptanethiol 1-庚硫醇 Heptyl mercaptan 庚硫醇 Jerome Pansanel 2006-11-22 Hexane-1-thiol Hexane-1-thiol Hexane-1-thiol 己-1-硫醇 hexane-1-thiol 1-Hexanethiol Hexyl mercaptan 1-Hexanethiol Mercaptan hexylique 1-Hexanethiol 1-己硫醇 Hexyl mercaptan 己硫醇 Jerome Pansanel 2006-11-22 Methanethiol Methanethiol Methanethiol 甲硫醇 methanethiol Methyl mercaptan Mercaptan méthylique Methyl mercaptan 甲硫醇 Jerome Pansanel 2006-11-22 Octane-1-thiol Octane-1-thiol Octane-1-thiol 辛-1-硫醇 octane-1-thiol 1-Octanethiol Octyl mercaptan 1-Octanethiol Mercaptan octylique 1-Octanethiol 1-辛硫醇 Octyl mercaptan 辛硫醇 Jerome Pansanel 2006-11-22 Pentane-1-thiol Pentane-1-thiol Pentane-1-thiol 戊-1-硫醇 pentane-1-thiol 1-Pentanethiol n-Amyl mercaptan 1-Pentanethiol Mercaptan n-amylique 1-Pentanethiol 1-戊硫醇 n-Amyl mercaptan 正-戊基硫醇 Jerome Pansanel 2006-11-22 Proprane-1-thiol Proprane-1-thiol Proprane-1-thiol 丙-1-硫醇 proprane-1-thiol 1-Propanethiol n-Propyl mercaptan 1-Propanethiol Mercaptan n-propylique 1-Propanethiol 1-丙硫醇 n-Propyl mercaptan 正-丙硫醇 Jerome Pansanel 2006-11-22 Proprane-2-thiol Proprane-2-thiol Proprane-2-thiol 丙-2-硫醇 proprane-2-thiol 2-Propanethiol Isopropyl mercaptan 2-Propanethiol Mercaptan isopropylique 2-Propanethiol 2-丙硫醇 Isopropyl mercaptan 異丙硫醇 Jerome Pansanel 2006-11-22 chemical-structures-2.2.dfsg.0.orig/src/thiols/methanethiol.cml0000644000175000017500000000366210662517661025050 0ustar georgeskgeorgesk Methanethiol 48.1075 48.0033711 -123 6 chemical-structures-2.2.dfsg.0.orig/src/thiols/hexane-1-thiol.cml0000644000175000017500000000734610662517661025115 0ustar georgeskgeorgesk Hexane-1-thiol 118.2404 118.0816214 -80 152 chemical-structures-2.2.dfsg.0.orig/src/thiols/butane-1-thiol.cml0000644000175000017500000000600510662517661025112 0ustar georgeskgeorgesk Butane-1-thiol 90.1872 90.0503213 -116 98 chemical-structures-2.2.dfsg.0.orig/src/thiols/octane-1-thiol.cml0000644000175000017500000001070310662517661025105 0ustar georgeskgeorgesk Octane-1-thiol 146.2935 146.1129216 -49 198 chemical-structures-2.2.dfsg.0.orig/src/thiols/ethanethiol.cml0000644000175000017500000000444010662517661024666 0ustar georgeskgeorgesk Ethanethiol 62.1340 62.0190212 -146 35 chemical-structures-2.2.dfsg.0.orig/src/thiols/CMakeLists.txt0000644000175000017500000000712211112716045024411 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "thiols") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/thiols/pentane-1-thiol.cml0000644000175000017500000000657110662517661025276 0ustar georgeskgeorgesk Pentane-1-thiol 104.2138 104.0659714 -76 125 chemical-structures-2.2.dfsg.0.orig/src/nitriles/0000755000175000017500000000000011225622315022177 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/nitriles/isobutyronitrile.cml0000644000175000017500000000524310723033311026320 0ustar georgeskgeorgesk 2-Methylpropanenitrile 69.1051 69.0578492 -72 107 chemical-structures-2.2.dfsg.0.orig/src/nitriles/butyronitrile.cml0000644000175000017500000000522510723033311025605 0ustar georgeskgeorgesk Butanenitrile 69.1051 69.0578492 -112 116 chemical-structures-2.2.dfsg.0.orig/src/nitriles/index.xml0000644000175000017500000000652511142231213024027 0ustar georgeskgeorgesk Nitriles Nitrile Nitrilos Nitriles Nitrillen Nitriles 腈類 Acetonitrile Acétonitrile Acetonitrile 乙腈/氰甲烷 acetonitrile Jerome Pansanel 2006-05-10 1,1,1-Trichloroacetonitrile 1,1,1-Trichloroacétonitrile 1,1,1-Trichloroacetonitrile 1,1,1-三氯乙腈 1_1_1-trichloroacetonitrile Cyanotrichloromethane Trichloromethyl cyanide Cyanotrichlorométhane Cyanotrichlorométhane Cyanotrichloromethane 氰三氯甲烷 Trichloromethyl cyanide 三氯甲烷氰 Jerome Pansanel 2006-11-22 Isobutyronitrile Isobutyronitrile Isobutyronitrile 異丁腈 isobutyronitrile 2-Methylpropanenitrile 2-Methylpropionitrile 2-Méthylpropanenitrile 2-Méthylpropionitrile 2-Methylpropanenitrile 2-甲基丙腈/異丁腈 2-Methylpropionitrile 2-甲基丙腈/異丁腈 Jerome Pansanel 2006-11-22 Butyronitrile Butyronitrile Butyronitrile 丁腈 butyronitrile Butanenitrile Propyl cyanide Butanenitrile 1-Cyanopropane Butanenitrile 丁腈 Propyl cyanide 丁腈/氰丙烷 Jerome Pansanel 2006-11-22 Propiononitrile Propiononitrile Propionitrile 丙腈 propionitrile Propanenitrile Propanenitrile Propanenitrile 丙腈 Ethyl cyanide Cyanoéthane Ethyl cyanide 丙腈/氰乙烷 Jerome Pansanel 2006-11-22 chemical-structures-2.2.dfsg.0.orig/src/nitriles/propionitrile.cml0000644000175000017500000000444410723033311025573 0ustar georgeskgeorgesk Propanenitrile 55.0785 55.0421992 -93 97 chemical-structures-2.2.dfsg.0.orig/src/nitriles/CMakeLists.txt0000644000175000017500000000712411112716045024742 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "nitriles") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/nitriles/acetonitrile.cml0000644000175000017500000000366210662517661025400 0ustar georgeskgeorgesk Acetonitrile 41.0519 41.0265491 -48 81 chemical-structures-2.2.dfsg.0.orig/src/nitriles/1_1_1-trichloroacetonitrile.cml0000644000175000017500000000372710662517661030126 0ustar georgeskgeorgesk 1,1,1-Trichloroacetonitrile 144.3871 142.9096320 -42 83 chemical-structures-2.2.dfsg.0.orig/src/natural_products/0000755000175000017500000000000011225622315023737 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/natural_products/D-luciferin.cml0000644000175000017500000001111311224730174026574 0ustar georgeskgeorgesk (4S)-2-(6-Hydroxy-1,3-benzothiazol-2-yl)-4,5-dihydrothiazole-4-carboxylic acid 280.3228 279.9976341 chemical-structures-2.2.dfsg.0.orig/src/natural_products/index.xml0000644000175000017500000000422111225046172025570 0ustar georgeskgeorgesk Natural products Naturstoff Sustancias naturales Substances naturelles Natuurlijke chemicaliën Natural products 天然產物/化合物 Coelenterazine Coelentérazine Coelenterazine 腔腸素 coelenterazine Renilla luciferin Luciférine de Renilla reniformis Renilla luciferin 水母螢光素 Jerome Pansanel 2009-07-06 D-Luciferin D-Luciférine D-Luciferin 螢蟲素 D-luciferin Firefly luciferin Luciférine de luciole Firefly luciferin 螢火蟲螢光素 Jerome Pansanel 2009-07-06 Norepinephrine Norépinéphrine Norepinephrine 正腎上腺素 norepinephrine Noradrenaline Noradrénaline Noradrenaline 降腎上腺素 Jerome Pansanel 2009-07-06 R-Adrenaline R-Adrénaline R-Adrenaline R-腎上腺素 R-adrenaline Jerome Pansanel 2009-07-06 chemical-structures-2.2.dfsg.0.orig/src/natural_products/R-adrenaline.cml0000644000175000017500000001071711224730174026745 0ustar georgeskgeorgesk 4-[(1R)-1-Hydroxy-2-methylaminoethyl]benzene-1,2-diol 183.2044 183.0895433 197 chemical-structures-2.2.dfsg.0.orig/src/natural_products/norepinephrine.cml0000644000175000017500000001013411224730174027462 0ustar georgeskgeorgesk 4-[(1R)-2-Amino-1-hydroxyethyl]benzene-1,2-diol 169.1778 169.0738932 218 chemical-structures-2.2.dfsg.0.orig/src/natural_products/CMakeLists.txt0000644000175000017500000000713411224730174026506 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "natural_products") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/natural_products/coelenterazine.cml0000644000175000017500000001767111224730174027461 0ustar georgeskgeorgesk 8-Benzyl-6-(4-hydroxyphenyl)-2-[(4-hydroxyphenyl)methyl]-7H-imidazo[1,2-a]pyrazin-3-one 423.4632 423.1582915 chemical-structures-2.2.dfsg.0.orig/src/index.xml0000644000175000017500000003164111225046172022205 0ustar georgeskgeorgesk Chemical Structures Chemische Strukturen Estructuras de moléculas Structures de molécules Molekulaire Structuren Chemical Structures 化學構造資料庫 Acid anhydrides Säureanhydride Anhídridos de ácido Anhydrides d'acide Carbonzuuranhydride Acid anhydrides 酸酐 acid_anhydrides Jerome Pansanel 2007-09-17 Alcohols Alkohole Alcohols Alcools Alcoholen Alcohols 醇類 alcohols Jerome Pansanel 2006-06-13 Aldehydes Aldehyde Aldehídos Aldéhydes Aldehyden Aldehydes 醛類 aldehydes Jerome Pansanel 2006-06-13 Alkanes Alkane Alcanos Alcanes Alkanen Alkanes 烷類 alkanes Jerome Pansanel 2006-06-13 Alkenes Alkene Alquenos Alcènes Alkenen Alkenes 烯類 alkenes Jerome Pansanel 2006-06-13 Alkynes Alkine Alquinos Alcynes Alkynen Alkynes 炔類 alkynes Jerome Pansanel 2006-11-03 Amides Amide Amidas Amides Amides Amides 醯胺類 amides Jerome Pansanel 2006-06-13 Amines Amine Aminas Amines Amines Amines 胺類 amines Jerome Pansanel 2006-06-13 Amino acids Aminosäuren Aminoácidos Acides aminés Aminozuren Amino acids 胺基酸 amino_acids Jerome Pansanel 2006-06-13 Aromatics Aromate Aromáticos Aromatiques Aromaten Aromatics 芳香族 aromatics Jerome Pansanel 2006-06-13 Carbamides Carbamide Carbamidas Carbamides Carbamides Carbamides 羰基胺類 carbamides Jerome Pansanel 2006-07-13 Carbohydrates Kohlenhydrate Hidratos de carbono Carbohydrates Koolhydraten Carbohydrates 碳水化合物 carbohydrates Jerome Pansanel 2006-07-13 Carboxylic acids Carbonsäuren Ácidos carboxílicos Acides carboxyliques Carbonzuren Carboxylic acids 羧酸 carboxylic_acids Jerome Pansanel 2006-06-13 Drugs Drogen Drogas Drogues Drugs Drugs 藥物 drugs Jerome Pansanel 2006-06-13 Esters Ester Ésters Esters Esters Esters 酯類 esters Jerome Pansanel 2006-06-13 Ethers Ether Éters Ethers Ethers Ethers 醚類 ethers Jerome Pansanel 2006-06-13 Fatty acids Fettsäuren Ácidos grasos Acides gras Vetzuren Fatty acids 脂肪酸 fatty_acids Jerome Pansanel 2006-06-13 Haloalkanes Halogenalkane Haloalcanos Halogénures d'alkyle Gehalogeneerde Alkanen Haloalkanes 鹵烷類 haloalkanes Jerome Pansanel 2006-06-13 Heteroaromatics Heteroaromaten Heteroaromáticos Hétéroaromatiques Heteroaromaten Heteroaromatics 雜芳族 heteroaromatics Jerome Pansanel 2006-07-31 Ketones Ketone Cetonas Cétones Ketonen Ketones 酮類 ketones Jerome Pansanel 2006-06-13 Macrocycles Makrozyklen Macrociclos Macrocycles Grote ringsystemen Macrocycles 大環類 macrocycles Jerome Pansanel 2007-05-29 Natural products Naturstoff Sustancias naturales Substances naturelles Natuurlijke chemicaliën Natural products 天然產物/化合物 natural_products Jerome Pansanel 2009-07-07 Nitriles Nitrile Nitrilos Nitriles Nitrillen Nitriles 腈類 nitriles Jerome Pansanel 2006-06-13 Nitroalkanes Nitroalkane Nitroalcanos Nitroalcanes Nitroalkanen Nitroalkanes 硝基烷類 nitroalkanes Jerome Pansanel 2006-11-20 Nucleobases Nukleobasen Nucleobases Nucléobases Nucleotiden Nucleobases 鹼基/核鹼基 nucleobases Jerome Pansanel 2006-06-13 Peptides Péptidos Peptide Peptides Peptiden Peptides 胜肽 peptides Jerome Pansanel 2009-07-07 Polycyclic alkanes Polyzyklische Alkane Alcanos policíclicos Alcanes polycycliques Polycyclische Alkanen Polycyclic alkanes 多環烷類 polycyclic_alkanes Jerome Pansanel 2006-07-31 Polycyclic aromatics Polyzyklische Aromaten Aromáticos policíclicos Aromatiques polycycliques Polycyclische Aromaten Polycyclic aromatics 多環芳香類 polycyclic_aromatics Jerome Pansanel 2006-07-31 Sulfones Sulfone Sulfonas Sulfones Sulfonen Sulfones 碸類 sulfones Jerome Pansanel 2006-11-20 Sulfoxides Sulfoxide Sulfóxidos Sulfoxydes Sulfoxides Sulfoxides 亞碸類 sulfoxides Jerome Pansanel 2006-11-20 Thioethers Thioether Tioéters Thioéthers Thioethers Thioethers 硫醚類 thioethers Jerome Pansanel 2006-07-31 Thiols Thiole Tiols Thiols Thiolen Thiols 硫醇類 thiols Jerome Pansanel 2006-11-20 Water Wasser Agua Eau Water Water 水 water Jerome Pansanel 2006-06-13 chemical-structures-2.2.dfsg.0.orig/src/aromatics/0000755000175000017500000000000011225622315022330 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/aromatics/benzonitrile.cml0000644000175000017500000000547110662517661025553 0ustar georgeskgeorgesk Benzonitrile 103.1213 103.0421992 -13 190 chemical-structures-2.2.dfsg.0.orig/src/aromatics/3-pyridin-3-ylpyridine.cml0000644000175000017500000000733410662517661027213 0ustar georgeskgeorgesk 3-Pyridin-3-ylpyridine 156.1839 156.0687483 68 291 chemical-structures-2.2.dfsg.0.orig/src/aromatics/2_4_6-trichlorophenol.cml0000644000175000017500000000553510662517661027072 0ustar georgeskgeorgesk 2,4,6-Trichlorophenol 197.4464 195.9249478 67 246 chemical-structures-2.2.dfsg.0.orig/src/aromatics/2_5-dimethylphenol.cml0000644000175000017500000000705310662517661026455 0ustar georgeskgeorgesk 2,5-Dimethylphenol 122.1644 122.0731649 76 212 chemical-structures-2.2.dfsg.0.orig/src/aromatics/2-phenylethanol.cml0000644000175000017500000000704210662517661026054 0ustar georgeskgeorgesk 2-Phenylethanol 122.1644 122.0731649 -27 219 chemical-structures-2.2.dfsg.0.orig/src/aromatics/4-chloro-2-methylphenol.cml0000644000175000017500000000631410774671262027342 0ustar georgeskgeorgesk 4-Chloro-2-methylphenol 142.5829 142.0185425 46 223 chemical-structures-2.2.dfsg.0.orig/src/aromatics/toluene.cml0000644000175000017500000000603310662517661024515 0ustar georgeskgeorgesk Toluene 92.1384 92.0626003 -93 110 chemical-structures-2.2.dfsg.0.orig/src/aromatics/4-methylbenzoic_acid.cml0000644000175000017500000000666410662517661027051 0ustar georgeskgeorgesk 4-Methylbenzoic acid 136.1479 136.0524295 180 274 chemical-structures-2.2.dfsg.0.orig/src/aromatics/1H-1_2-benzodiazepine.cml0000644000175000017500000000636610774671262026710 0ustar georgeskgeorgesk 1H-1,2-Benzodiazepine 144.1732 144.0687483 chemical-structures-2.2.dfsg.0.orig/src/aromatics/2-bromophenol.cml0000644000175000017500000000550210662517661025525 0ustar georgeskgeorgesk 2-Bromophenol 173.0073 171.9523768 5 195 chemical-structures-2.2.dfsg.0.orig/src/aromatics/2-phenylacetic_acid.cml0000644000175000017500000000667510662517661026645 0ustar georgeskgeorgesk 2-Phenylacetic acid 136.1479 136.0524295 77 265 chemical-structures-2.2.dfsg.0.orig/src/aromatics/2-chlorophenol.cml0000644000175000017500000000550510662517661025700 0ustar georgeskgeorgesk 2-Chlorophenol 128.5563 128.0028925 8 175 chemical-structures-2.2.dfsg.0.orig/src/aromatics/phenol.cml0000644000175000017500000000545510662517661024336 0ustar georgeskgeorgesk Phenol 94.1112 94.0418648 41 182 ././@LongLink0000000000000000000000000000017000000000000011563 Lustar rootrootchemical-structures-2.2.dfsg.0.orig/src/aromatics/4_bis_4-dimethylaminophenyl_methylene-2_5-cyclohexadien-1-iminium.cmlchemical-structures-2.2.dfsg.0.orig/src/aromatics/4_bis_4-dimethylaminophenyl_methylene-2_5-cyclohex0000644000175000017500000001661310774671262034054 0ustar georgeskgeorgesk 4-[Bis(4-dimethylaminophenyl)methylene]-2,5-cyclohexadien-1-iminium 344.4726 344.2126728 chemical-structures-2.2.dfsg.0.orig/src/aromatics/1_3_5-trimethylbenzene.cml0000644000175000017500000000743710662517661027247 0ustar georgeskgeorgesk 1,3,5-Trimethylbenzene 120.1916 120.0939004 -45 165 chemical-structures-2.2.dfsg.0.orig/src/aromatics/tris_4-aminophenyl_methanol.cml0000644000175000017500000001444510662517661030464 0ustar georgeskgeorgesk Tris(4-aminophenyl)methanol 305.3737 305.1528122 205 chemical-structures-2.2.dfsg.0.orig/src/aromatics/1-chloro-4-methoxybenzene.cml0000644000175000017500000000631710662517661027676 0ustar georgeskgeorgesk 1-Chloro-4-methoxybenzene 142.5829 142.0185425 -18 199 chemical-structures-2.2.dfsg.0.orig/src/aromatics/tris_4-dimethylaminophenyl_methanol.cml0000644000175000017500000002047210662517661032221 0ustar georgeskgeorgesk Tris(4-dimethylaminophenyl)methanol 389.5331 389.2467126 chemical-structures-2.2.dfsg.0.orig/src/aromatics/4-bromophenol.cml0000644000175000017500000000550410662517661025531 0ustar georgeskgeorgesk 4-Bromophenol 173.0073 171.9523768 64 236 chemical-structures-2.2.dfsg.0.orig/src/aromatics/ethoxybenzene.cml0000644000175000017500000000703410662517661025733 0ustar georgeskgeorgesk Ethoxybenzene 122.1644 122.0731649 -29 170 chemical-structures-2.2.dfsg.0.orig/src/aromatics/1_4-xylene.cml0000644000175000017500000000662410662517661024735 0ustar georgeskgeorgesk 1,4-Xylene 106.1650 106.0782503 12 138 chemical-structures-2.2.dfsg.0.orig/src/aromatics/benzamide.cml0000644000175000017500000000625610662517661025007 0ustar georgeskgeorgesk Benzamide 121.1366 121.0527638 128 289 chemical-structures-2.2.dfsg.0.orig/src/aromatics/2_4_6-trinitrotoluene.cml0000644000175000017500000000737310662517661027127 0ustar georgeskgeorgesk 2,4,6-Trinitrotoluene 227.1311 227.0178349 82 chemical-structures-2.2.dfsg.0.orig/src/aromatics/bromobenzene.cml0000644000175000017500000000527110662517661025532 0ustar georgeskgeorgesk Bromobenzene 157.0079 155.9574622 -31 156 chemical-structures-2.2.dfsg.0.orig/src/aromatics/index.xml0000644000175000017500000011227311145307406024171 0ustar georgeskgeorgesk Aromatics Aromate Aromáticos Aromatiques Aromaten Aromatics 芳香族 Aniline Anilin Aniline Aniline 苯胺 aniline Jerome Pansanel 2006-05-10 Benzene Benzol Benzène Benzene 苯 benzene Jerome Pansanel 2006-05-10 Benzoic acid Benzoesäure Acide benzoïque Benzoic acid 苯甲酸 benzoic_acid Jerome Pansanel 2006-05-10 Phenol Phénol Phenol 酚 phenol Jerome Pansanel 2006-05-10 Phenylmethanol Phénylméthanol Phenylmethanol 苯甲醇 phenylmethanol Benzyl alcohol Alcool benzylique Benzyl alcohol 芐醇/苯甲醇 Jerome Pansanel 2006-05-10 Toluene Toluol Toluène Toluene 甲苯 toluene Jerome Pansanel 2006-05-11 1,2-Xylene 1,2-Xylol 1,2-Xylène 1,2-Xylene 1,2-二甲苯 1_2-xylene o-Xylene o-Xylol o-Xylène 鄰二甲苯 Jerome Pansanel 2006-05-11 1,3-Xylene 1,3-Xylol 1,3-Xylène 1,3-Xylene 1,3-二甲苯 1_3-xylene m-Xylene m-Xylol m-Xylène 間二甲苯 Jerome Pansanel 2006-05-11 1,4-Xylene 1,4-Xylol 1,4-Xylène 1,4-Xylene 1,4-二甲苯 1_4-xylene p-Xylene p-Xylol p-Xylène 對二甲苯 Jerome Pansanel 2006-05-11 2,4,6-Trimethylaniline 2,4,6-Trimethylanilin 2,4,6-Triméthylaniline 2,4,6-Trimethylaniline 2,4,6-三甲基苯胺 2_4_6-trimethylaniline Mesidine Mesidin Mésidine Mesidine 米胺 Jerome Pansanel 2006-06-29 Benzene-1,2-diol 1,2-Dihydroxybenzol Benzène-1,2-diol Benzene-1,2-diol 1,2-苯二酚 benzene-1_2-diol Pyrocatechol Catechol Pyrocatéchol Catéchol Pyrocatechol鄰苯二酚/焦兒茶酚 Catechol 兒茶酚 Jerome Pansanel 2006-06-29 Benzene-1,3-diol 1,3-Dihydroxybenzol Benzène-1,3-diol Benzene-1,3-diol 1,3-苯二酚 benzene-1_3-diol Resorcinol Résorcinol Resorcinol 間苯二酚/樹脂酚 Jerome Pansanel 2006-06-29 Benzene-1,4-diol 1,4-Dihydroxybenzol Benzène-1,4-diol Benzene-1,4-diol 1,4-苯二酚 benzene-1_4-diol Hydroquinone Hydroquinone Hydroquinone 間苯二酚/氫醌 Jerome Pansanel 2006-06-29 (1S,2R)-1,2-Diphenylethane-1,2-diol (1S,2R)-1,2-Diphenylethan-1,2-diol (1S,2R)-1,2-Diphényléthane-1,2-diol (1S,2R)-1,2-Diphenylethane-1,2-diol (1S,2R)-1,2-二苯-1,2-乙二醇 1S_2R-1_2-diphenylethane-1_2-diol meso-Hydrobenzoin méso-Hydrobenzoïne meso-Hydrobenzoin 內消旋-氫化安息香/異氫化偶苯姻 Jerome Pansanel 2006-07-13 2,3-Dimethylphenol 2,3-Diméthylphénol 2,3-Dimethylphenol 2,3-二甲基酚 2_3-dimethylphenol 2,3-Xylenol 2,3-Xylénol 2,3-Xylenol 2,3-二甲基苯酚 Jerome Pansanel 2006-07-13 2,4,6-Trinitrotoluene 2,4,6-Trinitrotoluol 2,4,6-Trinitrotoluène 2,4,6-Trinitrotoluene 2,4,6-三硝基甲苯(TNT) 2_4_6-trinitrotoluene Jerome Pansanel 2006-07-13 2,4-Diaminotoluene 2,4-Diaminotoluol 2,4-Diaminotoluène 2,4-Diaminotoluene 2,4-二胺基甲苯 2_4-diaminotoluene Jerome Pansanel 2006-07-13 2,4-Dimethylphenol 2,4-Diméthylphénol 2,4-Dimethylphenol 2,4-二甲基酚 2_4-dimethylphenol 2,4-Xylenol 2,4-Xylénol 2,4-Xylenol 2,4-二甲基苯酚 Jerome Pansanel 2006-07-13 2,5-Dimethylphenol 2,5-Diméthylphénol 2,5-Dimethylphenol 2,5-二甲基酚 2_5-dimethylphenol 2,5-Xylenol 2,5-Xylénol 2,5-Xylenol 2,5-二甲基苯酚 Jerome Pansanel 2006-07-13 2,6-Diaminotoluene 2,6-Diaminotoluol 2,6-Diaminotoluène 2,6-Diaminotoluene 2,6-二胺基甲苯 2_6-diaminotoluene Jerome Pansanel 2006-07-13 2,6-Dimethylphenol 2,6-Diméthylphénol 2,6-Dimethylphenol 2,6-二甲基酚 2_6-dimethylphenol 2,6-Xylenol 2,6-Xylénol 2,6-Xylenol 2,6-二甲基苯酚 Jerome Pansanel 2006-07-13 2-Hydroxybenzaldehyde 2-Hydroxybenzaldehyd 2-Hydroxybenzaldéhyde 2-Hydroxybenzaldehyde 2-羥基苯甲醛 2-hydroxybenzaldehyde Salicylaldehyde Salicylaldéhyde Aldéhyde salicylique Salicylaldehyde 水楊醛/鄰羥基苯甲醛 Jerome Pansanel 2006-07-13 2-Phenylethanol 2-Phényléthanol 2-Phenylethanol 2-苯乙醇 β-苯乙醇 2-phenylethanol Phenethyl alcohol Alcool phénéthylique Phenethyl alcohol 2-苯基乙醇 β-苯基乙醇 Jerome Pansanel 2006-07-13 3,4-Dimethylphenol 3,4-Diméthylphénol 3,4-Dimethylphenol 3,4-二甲基酚 3_4-dimethylphenol 3,4-Xylenol 3,4-Xylénol 3,4-Xylenol 3,4-二甲基苯酚 Jerome Pansanel 2006-07-13 3,5-Dimethylphenol 3,5-Diméthylphénol 3,5-Dimethylphenol 3,5-二甲基酚 3_5-dimethylphenol 3,5-Xylenol 3,5-Xylénol 3,5-Xylenol 3,5-二甲基苯酚 Jerome Pansanel 2006-07-13 1,3,5-Trimethylbenzene 1,3,5-Trimethylbenzol 1,3,5-Triméthylbenzène 1,3,5-Trimethylbenzene 1,3,5-三甲基苯 1_3_5-trimethylbenzene Mesitylene Mesitylen Mésitylène Mesitylene 均三甲苯 Jerome Pansanel 2006-07-13 4-Dimethylaminobenzaldehyde 4-Diméthylaminobenzaldéhyde 4-Dimethylaminobenzaldehyde 4-二甲氨基苯甲醛 4-dimethylaminobenzaldehyde Ehrlich's reagent Ehrlich's Reagenz Réactif d'Ehrlich Ehrlich's reagent 埃利希試劑, 對二甲氨基苯甲醛 Jerome Pansanel 2006-07-13 Benzaldehyde Benzaldehyd Benzaldéhyde Benzaldehyde 苯甲醛/安息香醛 benzaldehyde Jerome Pansanel 2006-07-13 Benzene-1,2-diamine Benzene-1,2-diamin Benzène-1,2-diamine Benzene-1,2-diamine 1,2-苯二胺 benzene-1_2-diamine 鄰苯二胺 1,2-二氨基苯 Jerome Pansanel 2006-07-31 Benzene-1,3-diamine Benzene-1,3-diamin Benzène-1,3-diamine Benzene-1,3-diamine 1,3-苯二胺/間苯二胺/1,3-二胺基苯 benzene-1_3-diamine Jerome Pansanel 2006-07-31 Benzene-1,4-diamine Benzene-1,4-diamin Benzène-1,4-diamine Benzene-1,4-diamine 1,4-苯二胺 benzene-1_4-diamine 對苯二胺/1,4-二胺基苯 Jerome Pansanel 2006-07-31 Ethoxybenzene Ethoxybenzol Ethoxybenzène Ethoxybenzene 乙氧基苯 ethoxybenzene Ethyl phenyl ether Phenetole Éthyl phényl éther Phénétole Ethyl phenyl ether 乙基苯基醚 Phenetole 苯乙醚 Jerome Pansanel 2006-07-31 Tris(4-dimethylaminophenyl)methanol Tris(4-diméthylaminophényl)méthanol Tris(4-dimethylaminophenyl)methanol 三(4-二甲胺基苯)甲醇 tris_4-dimethylaminophenyl_methanol Jerome Pansanel 2006-10-15 Tris(4-aminophenyl)methanol Tris(4-aminophényl)méthanol Tris(4-aminophenyl)methanol 三(4-胺基苯)甲醇 tris_4-aminophenyl_methanol Pararosaniline base Pararosaniline base Pararosaniline base 參(對胺苯)甲醇/副玫瑰苯胺 Jerome Pansanel 2006-10-15 Triphenylmethanol Triphénylméthanol Triphenylmethanol 三苯甲醇 triphenylmethanol Triphenylcarbinol Trityl alcohol Triphénylcarbinol Alcool tritylique Triphenylcarbinol 三苯甲醇 Trityl alcohol 三苯甲醇/羥基三苯基甲烷 Jerome Pansanel 2006-10-15 4-[Bis(4-dimethylaminophenyl)methylene]-2,5-cyclohexadien-1-iminium 4-[Bis(4-diméthylaminophényl)méthylène]-2,5-cyclohexadièn-1-iminium 4-[雙(4-二甲胺基苯)次甲基]-2,5-環己烯-1-亞胺 4_bis_4-dimethylaminophenyl_methylene-2_5-cyclohexadien-1-iminium Methyl Violet 2B Méthyl Violet 2B Methyl Violet 2B 甲基紫2B Jerome Pansanel 2006-10-15 2-Bromophenol 2-Bromophénol 2-Bromophenol 2-溴酚 2-bromophenol Jerome Pansanel 2006-11-09 2-Chlorophenol 2-Chlorophénol 2-Chlorophenol 2-氯酚 2-chlorophenol Jerome Pansanel 2006-11-09 2-Phenylacetic acid Acide 2-phénylacétique 2-Phenylacetic acid 2-苯乙酸 2-phenylacetic_acid Jerome Pansanel 2006-11-09 2-Pyridin-2-ylpyridine 2-Pyridin-2-ylpyridine 2-Pyridin-2-ylpyridine 2-吡啶-2-吡咯烷 2-pyridin-2-ylpyridine 2,2'-Bipyridine 2,2'-Bipyridine 2,2'-Bipyridine 2,2'-聯吡啶 Jerome Pansanel 2006-11-09 3-Bromophenol 3-Bromophénol 3-Bromophenol 3-溴酚 3-bromophenol Jerome Pansanel 2006-11-09 3-Chlorophenol 3-Chlorophénol 3-Chlorophenol 3-氯酚 3-chlorophenol Jerome Pansanel 2006-11-09 3-Pyridin-3-ylpyridine 3-Pyridin-3-ylpyridine 3-Pyridin-3-ylpyridine 3-吡啶-3-吡咯烷 3-pyridin-3-ylpyridine 3,3'-Bipyridine 3,3'-Bipyridine 3,3'-Bipyridine 3,3'-聯吡啶 Jerome Pansanel 2006-11-09 4-Bromophenol 4-Bromophénol 4-Bromophenol 4-溴酚 4-bromophenol Jerome Pansanel 2006-11-09 4-Chlorophenol 4-Chlorophénol 4-Chlorophenol 4-氯酚 4-chlorophenol Jerome Pansanel 2006-11-09 4-Pyridin-4-ylpyridine 4-Pyridin-4-ylpyridine 4-Pyridin-4-ylpyridine 4-吡啶-4-吡咯烷 4-pyridin-4-ylpyridine 4,4'-Bipyridine 4,4'-Bipyridine 4,4'-Bipyridine 4,4'-聯吡啶 Jerome Pansanel 2006-11-09 N,N-Dimethylaniline N,N-Diméthylaniline N,N-Dimethylaniline N,N-二甲基苯胺 N_N-dimethylaniline Jerome Pansanel 2006-11-09 Anisole Anisole Anisole 苯甲醚 anisole 茴香醚/甲氧基苯 Jerome Pansanel 2006-11-09 Benzamide Benzamide Benzamide 苯甲醯胺 benzamide 安息香醯胺 Jerome Pansanel 2006-11-09 Benzoyl chloride Chlorure de benzoyle Benzoyl chloride 苯甲醯氯/氯化苯甲醯 benzoyl_chloride Jerome Pansanel 2006-11-09 Bromobenzene Bromobenzène Bromobenzene 溴苯 bromobenzene Jerome Pansanel 2006-11-09 Chlorobenzene Chlorobenzène Chlorobenzene 氯苯 chlorobenzene Jerome Pansanel 2006-11-09 Tris(4-cyanophenyl)methane Tris(4-cyanophényl)méthane Tris(4-cyanophenyl)methane 三(4-苯腈)甲烷 tris_4-cyanophenyl_methane Jerome Pansanel 2006-11-09 Tris(4-cyanophenyl)methanol Tris(4-cyanophényl)méthanol Tris(4-cyanophenyl)methanol 三(4-苯腈)甲醇 tris_4-cyanophenyl_methanol Jerome Pansanel 2006-11-09 1,3,5-Trichloro-2-methoxybenzene 1,3,5-Trichloro-2-méthoxybenzène 1,3,5-Trichloro-2-methoxybenzene 1,3,5-三氯-2-甲氧基苯 1_3_5-trichloro-2-methoxybenzene 2,4,6-Trichloranisole TCA 2,4,6-Trichloranisole TCA 2,4,6-Trichloranisole 2,4,6-三氯苯甲醚 TCA Jerome Pansanel 2006-11-24 1-Chloro-2-ethenylbenzene 1-Chloro-2-éthénylbenzène 1-Chloro-2-ethenylbenzene 1-氯-2-苯乙烯 1-chloro-2-ethenylbenzene 2-Chlorostyrene 2-Chlorostyrène 2-Chlorostyrene 鄰氯苯乙烯 Jerome Pansanel 2006-11-24 1-Chloro-2-methoxybenzene 1-Chloro-2-méthoxybenzène 1-Chloro-2-methoxybenzene 1-氯-2-甲氧基苯 1-chloro-2-methoxybenzene 2-Chloroanisole 2-Chloroanisole 2-Chloroanisole 鄰氯苯甲醚 Jerome Pansanel 2006-11-24 1-Chloro-3-methoxybenzene 1-Chloro-3-méthoxybenzène 1-Chloro-3-methoxybenzene 1-氯-3-甲氧基苯 1-chloro-3-methoxybenzene 3-Chloroanisole 3-Chloroanisole 3-Chloroanisole 間氯苯甲醚 Jerome Pansanel 2006-11-24 2-Chloro-5-methylphenol 2-Chloro-5-méthylphénol 2-Chloro-5-methylphenol 2-氯-5-甲酚 2-chloro-5-methylphenol 6-Chloro-m-cresol 6-Chloro-m-crésol 6-Chloro-m-cresol 6-氯間甲酚 Jerome Pansanel 2006-11-24 1-Chloro-4-methoxybenzene 1-Chloro-4-méthoxybenzène 1-Chloro-4-methoxybenzene 1-氯-4-甲氧基苯 1-chloro-4-methoxybenzene 4-Chloroanisole 4-Chloroanisole 4-Chloroanisole 對氯苯甲醚 Jerome Pansanel 2006-11-24 1-Phenylbutan-1-one 1-Phénylbutan-1-one 1-Phenylbutan-1-one 1-苯基-1-丁酮 1-phenylbutan-1-one n-Butyrophenone n-Butyrophénone n-Butyrophenone 丁酸酚酮 Jerome Pansanel 2006-11-24 (2,2-Dimethyl-3H-benzofuran-7-yl) N-methylcarbamate N-Méthylcarbamate de 2,2-diméthyl-3H-benzofuran-7-yle (2,2-Dimethyl-3H-benzofuran-7-yl) N-methylcarbamate 暫譯: (2,2-二甲基-3氫-苯呋喃) 氮-甲基胺甲酸酯 2_2-dimethyl-3H-benzofuran-7-yl_N-methylcarbamate Carbofuran Carbofuran Carbofuran 加保扶 Jerome Pansanel 2006-11-24 2,3,4,5,6-Pentachlorophenol 2,3,4,5,6-Pentachlorophénol 2,3,4,5,6-Pentachlorophenol 2,3,4,5,6-五氯酚 2_3_4_5_6-pentachlorophenol Jerome Pansanel 2006-11-24 2,4,6-Trichlorophenol 2,4,6-Trichlorophénol 2,4,6-Trichlorophenol 2,4,6-三氯酚 2_4_6-trichlorophenol Jerome Pansanel 2006-11-24 2-Chloro-4-nitroaniline 2-Chloro-4-nitroaniline 2-Chloro-4-nitroaniline 2-氯-4-硝基苯胺 2-chloro-4-nitroaniline Jerome Pansanel 2006-11-24 4-Bromo-5-methyl-2-propan-2-ylphenol 4-Bromo-5-méthyl-2-propan-2-ylphénol 4-Bromo-5-methyl-2-propan-2-ylphenol 4-溴-5-甲基-2-異丙基酚 4-bromo-5-methyl-2-propan-2-ylphenol Bromothymol Bromothymol Bromothymol 溴百里酚 Jerome Pansanel 2006-11-24 4-Chloro-2-methylphenol 4-Chloro-2-méthylphénol 4-Chloro-2-methylphenol 4-氯-2-甲基酚 4-chloro-2-methylphenol 4-Chloro-o-cresol 4-Chloro-o-crésol 4-Chloro-o-cresol 4-氯-鄰甲酚 Jerome Pansanel 2006-11-24 4-Chloro-3-methylphenol 4-Chloro-3-méthylphénol 4-Chloro-3-methylphenol 4-氯-3-甲基酚 4-chloro-3-methylphenol 4-Chloro-m-cresol 4-Chloro-m-crésol 4-Chloro-m-cresol 4-氯-間甲酚 Jerome Pansanel 2006-11-24 4-Chloroaniline 4-Chloroaniline 4-Chloroaniline 4-氯苯胺 4-chloroaniline Jerome Pansanel 2006-11-24 4-Methoxybenzaldehyde 4-Méthoxybenzaldéhyde 4-Methoxybenzaldehyde 4-甲氧基苯甲醛 4-methoxybenzaldehyde p-Anisaldehyde p-Anisaldéhyde Aldéhyde anisique p-Anisaldehyde 大茴香醛 Jerome Pansanel 2006-11-24 4-Methylbenzoic acid Acide 4-méthylbenzoïque 4-Methylbenzoic acid 4-甲基苯甲酸 4-methylbenzoic_acid p-Toluic acid Crithminic acid Acide p-toluique p-Toluic acid 對甲基苯甲酸 Crithminic acid Jerome Pansanel 2006-11-24 4-Octylphenol 4-Octylphénol 4-Octylphenol 4-辛基酚 4-octylphenol Jerome Pansanel 2006-11-24 5-Chloro-2-(2,4-dichlorophenoxy)phenol 5-Chloro-2-(2,4-dichlorophénoxy)phénol 5-Chloro-2-(2,4-dichlorophenoxy)phenol 5-氯-2-(2,4-二氯苯氧基)苯酚 5-chloro-2-2_4-dichlorophenoxy_phenol Triclosan Irgasan Triclosan Irgasan Triclosan 三氯沙 Irgasan Jerome Pansanel 2006-11-24 Benzonitrile Benzonitrile Benzonitrile 苯甲腈 benzonitrile Jerome Pansanel 2006-11-24 [(E)-2-Chloroethenyl]benzene [(E)-2-Chloroéthényl]benzène [(E)-2-Chloroethenyl]benzene [(E)-2-氯乙烯基]苯 E-2-chloroethenyl_benzene beta-Chlorostyrene beta-Chlorostyrène beta-Chlorostyrene β-氯苯乙烯 Jerome Pansanel 2006-11-24 [(E)-2-Phenylethenyl]benzene [(E)-2-Phényléthényl]benzène [(E)-2-Phenylethenyl]benzene [(E)-2-苯乙烯基]苯 E-2-phenylethenyl_benzene trans-Stilbene trans-1,2-Diphenylethylene trans-Stilbène trans-1,2-Diphényléthylène trans-Stilbene 反式-茋 trans-1,2-Diphenylethylene 反式-1,2-二苯乙烯 Jerome Pansanel 2006-11-24 Nitrobenzene Nitrobenzène Nitrobenzene 硝基苯 nitrobenzene Jerome Pansanel 2006-11-24 Triphenylmethane Triphénylméthane Triphenylmethane 三苯甲烷 triphenylmethane Tritane Tritane 三苯甲烷 Jerome Pansanel 2006-11-24 1H-1,2-Benzodiazepine 1H-1,2-Benzodiazépine 1H-1,2-Benzodiazepine 1氫-1,2-苯二氮平類藥物 1H-1_2-benzodiazepine Jerome Pansanel 2007-12-03 1H-1,4-Benzodiazépine 1H-1,4-Benzodiazépine 1H-1,4-Benzodiazepine 1氫-1,4-苯二氮平類藥物 1H-1_4-benzodiazepine Jerome Pansanel 2007-12-03 5-phenyl-1,3-dihydro-2H-1,4-benzodiazepin-2-one 5-phényl-1,3-dihydro-2H-1,4-benzodiazépin-2-one 5-phenyl-1,3-dihydro-2H-1,4-benzodiazepin-2-one 5-苯基-1,3-二氫-2氫-1,4-苯甲二氮平-2-酮 5-phenyl-1_3-dihydro-2H-1_4-benzodiazepin-2-one Jerome Pansanel 2007-12-03 ././@LongLink0000000000000000000000000000015000000000000011561 Lustar rootrootchemical-structures-2.2.dfsg.0.orig/src/aromatics/2_2-dimethyl-3H-benzofuran-7-yl_N-methylcarbamate.cmlchemical-structures-2.2.dfsg.0.orig/src/aromatics/2_2-dimethyl-3H-benzofuran-7-yl_N-methylcarbamate.0000644000175000017500000001172110662517661033367 0ustar georgeskgeorgesk (2,2-Dimethyl-3H-benzofuran-7-yl) N-methylcarbamate 221.2524 221.1051933 151 ././@LongLink0000000000000000000000000000014600000000000011566 Lustar rootrootchemical-structures-2.2.dfsg.0.orig/src/aromatics/5-phenyl-1_3-dihydro-2H-1_4-benzodiazepin-2-one.cmlchemical-structures-2.2.dfsg.0.orig/src/aromatics/5-phenyl-1_3-dihydro-2H-1_4-benzodiazepin-2-one.cm0000644000175000017500000001130710774671262032756 0ustar georgeskgeorgesk 5-Phenyl-1,3-dihydro-2H-1,4-benzodiazepin-2-one 236.2686 236.0949630 chemical-structures-2.2.dfsg.0.orig/src/aromatics/benzaldehyde.cml0000644000175000017500000000566110662517661025506 0ustar georgeskgeorgesk Benzaldehyde 106.1219 106.0418648 -26 179 chemical-structures-2.2.dfsg.0.orig/src/aromatics/1-phenylbutan-1-one.cml0000644000175000017500000001005410662517661026444 0ustar georgeskgeorgesk 1-Phenylbutan-1-one 148.2017 148.0888150 12 229 chemical-structures-2.2.dfsg.0.orig/src/aromatics/benzoyl_chloride.cml0000644000175000017500000000570310662517661026400 0ustar georgeskgeorgesk Benzoyl chloride 140.5670 140.0028925 -1 198 chemical-structures-2.2.dfsg.0.orig/src/aromatics/tris_4-cyanophenyl_methanol.cml0000644000175000017500000001340610662517661030466 0ustar georgeskgeorgesk Tris(4-cyanophenyl)methanol 335.3581 335.1058621 chemical-structures-2.2.dfsg.0.orig/src/aromatics/4-bromo-5-methyl-2-propan-2-ylphenol.cml0000644000175000017500000000775010721307650031404 0ustar georgeskgeorgesk 4-Bromo-5-methyl-2-propan-2-yl-phenol 229.1136 228.0149770 chemical-structures-2.2.dfsg.0.orig/src/aromatics/E-2-phenylethenyl_benzene.cml0000644000175000017500000001072410662517661027763 0ustar georgeskgeorgesk [(E)-2-Phenylethenyl]benzene 180.2451 180.0939004 123 > 300 chemical-structures-2.2.dfsg.0.orig/src/aromatics/1_2-xylene.cml0000644000175000017500000000662310662517661024732 0ustar georgeskgeorgesk 1,2-Xylene 106.1650 106.0782503 -24 144 chemical-structures-2.2.dfsg.0.orig/src/aromatics/1-chloro-2-ethenylbenzene.cml0000644000175000017500000000630510662517661027644 0ustar georgeskgeorgesk 1-Chloro-2-ethenylbenzene 138.5942 138.0236279 -63 189 chemical-structures-2.2.dfsg.0.orig/src/aromatics/4-methoxybenzaldehyde.cml0000644000175000017500000000666210662517661027267 0ustar georgeskgeorgesk 4-Methoxybenzaldehyde 136.1479 136.0524295 -1 248 chemical-structures-2.2.dfsg.0.orig/src/aromatics/5-chloro-2-2_4-dichlorophenoxy_phenol.cml0000644000175000017500000001012210662517661031766 0ustar georgeskgeorgesk 5-Chloro-2-(2,4-dichlorophenoxy)phenol 289.5418 287.9511625 57 chemical-structures-2.2.dfsg.0.orig/src/aromatics/4-dimethylaminobenzaldehyde.cml0000644000175000017500000000740210662517661030426 0ustar georgeskgeorgesk 4-Dimethylaminobenzaldehyde 149.1897 149.0840640 72 chemical-structures-2.2.dfsg.0.orig/src/aromatics/chlorobenzene.cml0000644000175000017500000000527310662517661025704 0ustar georgeskgeorgesk Chlorobenzene 112.5569 112.0079778 -45 132 chemical-structures-2.2.dfsg.0.orig/src/aromatics/4-pyridin-4-ylpyridine.cml0000644000175000017500000000733510662517661027216 0ustar georgeskgeorgesk 4-Pyridin-4-ylpyridine 156.1839 156.0687483 112 305 chemical-structures-2.2.dfsg.0.orig/src/aromatics/3_4-dimethylphenol.cml0000644000175000017500000000705010662517661026452 0ustar georgeskgeorgesk 3,4-Dimethylphenol 122.1644 122.0731649 65 227 chemical-structures-2.2.dfsg.0.orig/src/aromatics/1_3-xylene.cml0000644000175000017500000000663010662517661024731 0ustar georgeskgeorgesk 1,3-Xylene 106.1650 106.0782503 -48 138 chemical-structures-2.2.dfsg.0.orig/src/aromatics/1_3_5-trichloro-2-methoxybenzene.cml0000644000175000017500000000634510662517661031062 0ustar georgeskgeorgesk 1,3,5-Trichloro-2-methoxybenzene 211.4730 209.9405978 61 240 chemical-structures-2.2.dfsg.0.orig/src/aromatics/E-2-chloroethenyl_benzene.cml0000644000175000017500000000556010662517661027754 0ustar georgeskgeorgesk [(E)-2-Chloroethenyl]benzene 138.5942 138.0236279 chemical-structures-2.2.dfsg.0.orig/src/aromatics/benzene-1_2-diamine.cml0000644000175000017500000000627410662517661026462 0ustar georgeskgeorgesk Benzene-1,2-diamine 108.1411 108.0687483 102 257 chemical-structures-2.2.dfsg.0.orig/src/aromatics/2_4-dimethylphenol.cml0000644000175000017500000000705010662517661026451 0ustar georgeskgeorgesk 2,4-Dimethylphenol 122.1644 122.0731649 22 211 chemical-structures-2.2.dfsg.0.orig/src/aromatics/phenylmethanol.cml0000644000175000017500000000625610662517661026100 0ustar georgeskgeorgesk Phenylmethanol 108.1378 108.0575149 -15 204 chemical-structures-2.2.dfsg.0.orig/src/aromatics/2_6-dimethylphenol.cml0000644000175000017500000000706010662517661026454 0ustar georgeskgeorgesk 2,6-Dimethylphenol 122.1644 122.0731649 44 203 chemical-structures-2.2.dfsg.0.orig/src/aromatics/2_6-diaminotoluene.cml0000644000175000017500000000705310662517661026445 0ustar georgeskgeorgesk 2,6-Diaminotoluene 122.1677 122.0843983 104 289 chemical-structures-2.2.dfsg.0.orig/src/aromatics/benzene-1_3-diamine.cml0000644000175000017500000000627110662517661026460 0ustar georgeskgeorgesk Benzene-1,3-diamine 108.1411 108.0687483 63 283 chemical-structures-2.2.dfsg.0.orig/src/aromatics/tris_4-cyanophenyl_methane.cml0000644000175000017500000001320510662517661030275 0ustar georgeskgeorgesk Tris(4-cyanophenyl)methane 319.3587 319.1109474 chemical-structures-2.2.dfsg.0.orig/src/aromatics/N_N-dimethylaniline.cml0000644000175000017500000000724610662517661026700 0ustar georgeskgeorgesk N,N-Dimethylaniline 121.1796 121.0891494 2 193 chemical-structures-2.2.dfsg.0.orig/src/aromatics/3_5-dimethylphenol.cml0000644000175000017500000000705110662517661026454 0ustar georgeskgeorgesk 3,5-Dimethylphenol 122.1644 122.0731649 64 222 chemical-structures-2.2.dfsg.0.orig/src/aromatics/benzene-1_2-diol.cml0000644000175000017500000000570010662517661025774 0ustar georgeskgeorgesk Benzene-1,2-diol 110.1106 110.0367794 103 245 chemical-structures-2.2.dfsg.0.orig/src/aromatics/CMakeLists.txt0000644000175000017500000000712511112716045025074 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "aromatics") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/aromatics/4-chloro-3-methylphenol.cml0000644000175000017500000000631110662517661027336 0ustar georgeskgeorgesk 4-Chloro-3-methylphenol 142.5829 142.0185425 66 235 chemical-structures-2.2.dfsg.0.orig/src/aromatics/2-chloro-5-methylphenol.cml0000644000175000017500000000631110662517661027336 0ustar georgeskgeorgesk 2-Chloro-5-methylphenol 142.5829 142.0185425 46 196 chemical-structures-2.2.dfsg.0.orig/src/aromatics/benzoic_acid.cml0000644000175000017500000000610010662517661025446 0ustar georgeskgeorgesk Benzoic acid 122.1213 122.0367794 123 249 chemical-structures-2.2.dfsg.0.orig/src/aromatics/1H-1_4-benzodiazepine.cml0000644000175000017500000000636510774671262026711 0ustar georgeskgeorgesk 1H-1,4-Benzodiazepine 144.1732 144.0687483 chemical-structures-2.2.dfsg.0.orig/src/aromatics/3-chlorophenol.cml0000644000175000017500000000550610662517661025702 0ustar georgeskgeorgesk 3-Chlorophenol 128.5563 128.0028925 32 214 chemical-structures-2.2.dfsg.0.orig/src/aromatics/benzene-1_4-diamine.cml0000644000175000017500000000627610662517661026466 0ustar georgeskgeorgesk Benzene-1,4-diamine 108.1411 108.0687483 140 267 chemical-structures-2.2.dfsg.0.orig/src/aromatics/4-chlorophenol.cml0000644000175000017500000000550610662517661025703 0ustar georgeskgeorgesk 4-Chlorophenol 128.5563 128.0028925 43 220 chemical-structures-2.2.dfsg.0.orig/src/aromatics/triphenylmethane.cml0000644000175000017500000001311310721307650026406 0ustar georgeskgeorgesk Triphenylmethane 244.3303 244.1252005 92 > 350 chemical-structures-2.2.dfsg.0.orig/src/aromatics/3-bromophenol.cml0000644000175000017500000000550410662517661025530 0ustar georgeskgeorgesk 2-Bromophenol 173.0073 171.9523768 31 236 chemical-structures-2.2.dfsg.0.orig/src/aromatics/1S_2R-1_2-diphenylethane-1_2-diol.cml0000644000175000017500000001145010662517661030551 0ustar georgeskgeorgesk (1S,2R)-1,2-Diphenylethane-1,2-diol 214.2598 214.0993797 138 chemical-structures-2.2.dfsg.0.orig/src/aromatics/2_3_4_5_6-pentachlorophenol.cml0000644000175000017500000000555310662517661030051 0ustar georgeskgeorgesk 2,3,4,5,6-Pentachlorophenol 266.3365 263.8470031 174 310 chemical-structures-2.2.dfsg.0.orig/src/aromatics/2_3-dimethylphenol.cml0000644000175000017500000000705010662517661026450 0ustar georgeskgeorgesk 2,3-Dimethylphenol 122.1644 122.0731649 73 217 chemical-structures-2.2.dfsg.0.orig/src/aromatics/4-octylphenol.cml0000644000175000017500000001305210662517661025542 0ustar georgeskgeorgesk 4-Octylphenol 206.3239 206.1670653 43 chemical-structures-2.2.dfsg.0.orig/src/aromatics/2-hydroxybenzaldehyde.cml0000644000175000017500000000610210662517661027263 0ustar georgeskgeorgesk 2-Hydroxybenzaldehyde 122.1213 122.0367794 -4 197 chemical-structures-2.2.dfsg.0.orig/src/aromatics/2-pyridin-2-ylpyridine.cml0000644000175000017500000000733310662517661027210 0ustar georgeskgeorgesk 2-Pyridin-2-ylpyridine 156.1839 156.0687483 70 272 chemical-structures-2.2.dfsg.0.orig/src/aromatics/2_4-diaminotoluene.cml0000644000175000017500000000705410662517661026444 0ustar georgeskgeorgesk 2,4-Diaminotoluene 122.1677 122.0843983 99 284 chemical-structures-2.2.dfsg.0.orig/src/aromatics/benzene-1_4-diol.cml0000644000175000017500000000567710662517661026013 0ustar georgeskgeorgesk Benzene-1,4-diol 110.1106 110.0367794 172 286 chemical-structures-2.2.dfsg.0.orig/src/aromatics/1-chloro-2-methoxybenzene.cml0000644000175000017500000000632110662517661027667 0ustar georgeskgeorgesk 1-Chloro-2-methoxybenzene 142.5829 142.0185425 -27 196 chemical-structures-2.2.dfsg.0.orig/src/aromatics/nitrobenzene.cml0000644000175000017500000000570210662517661025546 0ustar georgeskgeorgesk Nitrobenzene 123.1094 123.0320284 5 210 chemical-structures-2.2.dfsg.0.orig/src/aromatics/benzene-1_3-diol.cml0000644000175000017500000000567710662517661026012 0ustar georgeskgeorgesk Benzene-1,3-diol 110.1106 110.0367794 110 281 chemical-structures-2.2.dfsg.0.orig/src/aromatics/aniline.cml0000644000175000017500000000565310662517661024470 0ustar georgeskgeorgesk Aniline 93.1265 93.0578492 -6 184 chemical-structures-2.2.dfsg.0.orig/src/aromatics/1-chloro-3-methoxybenzene.cml0000644000175000017500000000604210662517661027670 0ustar georgeskgeorgesk 1-Chloro-3-methoxybenzene 142.5829 142.0185425 193 chemical-structures-2.2.dfsg.0.orig/src/aromatics/anisole.cml0000644000175000017500000000624210662517661024476 0ustar georgeskgeorgesk Anisole 108.1378 108.0575149 -37 154 chemical-structures-2.2.dfsg.0.orig/src/aromatics/2-chloro-4-nitroaniline.cml0000644000175000017500000000605610662517661027326 0ustar georgeskgeorgesk 2-Chloro-4-nitroaniline 172.5691 172.0039551 108 chemical-structures-2.2.dfsg.0.orig/src/aromatics/4-chloroaniline.cml0000644000175000017500000000570210662517661026033 0ustar georgeskgeorgesk 4-Chloroaniline 127.5715 127.0188769 70 232 chemical-structures-2.2.dfsg.0.orig/src/aromatics/triphenylmethanol.cml0000644000175000017500000001331010662517661026604 0ustar georgeskgeorgesk Triphenylmethanol 260.3297 260.1201151 161 360 chemical-structures-2.2.dfsg.0.orig/src/aromatics/benzene.cml0000644000175000017500000000525010662517661024470 0ustar georgeskgeorgesk Benzene 78.1118 78.0469502 5 80 chemical-structures-2.2.dfsg.0.orig/src/aromatics/2_4_6-trimethylaniline.cml0000644000175000017500000001004010774671262027225 0ustar georgeskgeorgesk 2,4,6-Trimethylaniline 135.2062 135.1047994 -4 233 chemical-structures-2.2.dfsg.0.orig/src/peptides/0000755000175000017500000000000011225622315022163 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/peptides/aspartame.cml0000644000175000017500000001411011224730174024634 0ustar georgeskgeorgesk (3S)-3-Amino-4-[[(1S)-1-benzyl-2-methoxy-2-oxoethyl]amino]-4-oxobutanoic acid 294.3031 294.1215717 249 chemical-structures-2.2.dfsg.0.orig/src/peptides/index.xml0000644000175000017500000000165711225046172024026 0ustar georgeskgeorgesk Peptides Péptidos Peptide Peptides Peptiden Peptides 胜肽 Aspartame Aspartame Aspartame 阿斯巴甜 (雙肽甜味料) aspartame L-Aspartyl-L-phenylalanine methyl ester Ester méthylique de L-aspartyl-L-phénylalanine L-Aspartyl-L-phenylalanine methyl ester 天門冬醯-L-苯丙胺酸甲酯 Jerome Pansanel 2009-07-06 chemical-structures-2.2.dfsg.0.orig/src/peptides/CMakeLists.txt0000644000175000017500000000712411224730174024731 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "peptides") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/acid_anhydrides/0000755000175000017500000000000011225622315023460 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/acid_anhydrides/3-methylfuran-2_5-dione.cml0000644000175000017500000000532010673461003030333 0ustar georgeskgeorgesk 3-Methylfuran-2,5-dione 112.0835 112.0160440 7 213 chemical-structures-2.2.dfsg.0.orig/src/acid_anhydrides/furan-2_5-dione.cml0000644000175000017500000000452010673461003026751 0ustar georgeskgeorgesk Furan-2,5-dione 98.0569 98.0003939 54 200 chemical-structures-2.2.dfsg.0.orig/src/acid_anhydrides/index.xml0000644000175000017500000000310011142231213025272 0ustar georgeskgeorgesk Acid anhydrides Säureanhydride Anhídridos de ácido Anhydrides d'acide Carbonzuuranhydride Acid anhydrides 酸酐 3-Methylfuran-2,5-dione 3-Méthylfuran-2,5-dione 3-Methylfuran-2,5-dione 3-甲基夫喃-2,5-二酮 3-methylfuran-2_5-dione Citraconic anhydride 2-Methylmaleic anhydride Anhydride citraconique Anhydride 2-méthylmaléique Citraconic anhydride 檸康酐 Jerome Pansanel 2007-09-17 Furan-2,5-dione Furan-2,5-dione Furan-2,5-dione 呋喃-2,5-二酮 furan-2_5-dione Maleic anhydride Anhydride maléique Maleic anhydride 順丁烯二酸酐 Jerome Pansanel 2007-09-17 chemical-structures-2.2.dfsg.0.orig/src/acid_anhydrides/CMakeLists.txt0000644000175000017500000000713311112716045026223 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "acid_anhydrides") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/amino_acids/0000755000175000017500000000000011225622315022614 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/amino_acids/D-alanine.cml0000644000175000017500000000525710721554445025122 0ustar georgeskgeorgesk (2R)-2-Aminopropanoic acid 89.0932 89.0476785 314 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/D-glutamine.cml0000644000175000017500000000705710721555302025471 0ustar georgeskgeorgesk (2R)-2-Amino-4-carbamoylbutanoic acid 146.1445 146.0691422 185 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/D-glutamic_acid.cml0000644000175000017500000000664310721554445026300 0ustar georgeskgeorgesk (2R)-2-Aminopentanedioic acid 147.1293 147.0531578 205 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/L-tryptophan.cml0000644000175000017500000001100010724003164025700 0ustar georgeskgeorgesk (2S)-2-Amino-3-(1H-indol-3-yl)propanoic acid 204.2252 204.0898776 283 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/D-proline.cml0000644000175000017500000000633010721554445025154 0ustar georgeskgeorgesk (2R)-Pyrrolidine-2-carboxylic acid 115.1305 115.0633285 223 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/D-serine.cml0000644000175000017500000000547510721555302024773 0ustar georgeskgeorgesk (2R)-2-Amino-3-hydroxypropanoic acid 105.0926 105.0425931 222 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/D-tyrosine.cml0000644000175000017500000001014210721554445025354 0ustar georgeskgeorgesk (2R)-2-Amino-3-(4-hydroxyphenyl)propanoic acid 181.1885 181.0738932 > 300 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/L-alanine.cml0000644000175000017500000000526010721554445025124 0ustar georgeskgeorgesk (2S)-2-Aminopropanoic acid 89.0932 89.0476785 314 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/L-histidine.cml0000644000175000017500000000664410721554445025504 0ustar georgeskgeorgesk (2S)-2-Amino-3-(3H-imidazol-4-yl)propanoic acid 155.1546 155.0694765 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/D-aspartic_acid.cml0000644000175000017500000000602310721554445026271 0ustar georgeskgeorgesk (2R)-2-Aminobutanedioic acid 133.1027 133.0375077 > 300 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/D-arginine.cml0000644000175000017500000001015210721544676025302 0ustar georgeskgeorgesk (2R)-2-Amino-5-(diaminomethylideneamino)pentanoic acid 174.2010 174.1116757 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/index.xml0000644000175000017500000005534010727223757024471 0ustar georgeskgeorgesk Amino acids Aminosäuren Aminoácidos Acides aminés Aminozuren D-Alanine D-Alanin D-Alanine D-alanine (2R)-2-Aminopropanoic acid (2R)-2-Aminopropansäure Acide (2R)-2-aminopropanoïque Jerome Pansanel 2006-05-10 D-Arginine D-Arginin D-Arginine D-arginine (2R)-2-Amino-5-(diaminomethylideneamino)pentanoic acid (2R)-2-Amino-5-(diaminomethylideneamino)pentansäure Acide (2R)-2-amino-5-(diaminométhylidèneamino)pentanoïque Jerome Pansanel 2006-05-10 D-Asparagine D-Asparagin D-Asparagine D-asparagine (2R)-2-Amino-3-carbamoylpropanoic acid (2R)-2-Amino-3-carbamoylpropansäure Acide (2R)-2-amino-3-carbamoylpropanoïque Jerome Pansanel 2006-05-10 D-Aspartic acid D-Asparaginsäure Acide D-aspartique D-aspartic_acid (2R)-2-Aminobutanedioic acid (2R)-2-Aminobutandisäure Acide (2R)-2-aminobutanedioïque Jerome Pansanel 2006-05-10 D-Cysteine D-Cystein D-Cystéine D-cysteine (2S)-2-Amino-3-sulfanylpropanoic acid (2S)-2-Amino-3-sulfanylpropansäure Acide (2S)-2-amino-3-sulfanylpropanoïque Jerome Pansanel 2006-05-10 D-Glutamic acid D-Glutaminsäure Acide D-glutamique D-glutamic_acid (2R)-2-Aminopentanedioic acid (2R)-2-Aminopentandisäure Acide (2S)-2-aminopentanedioïque Jerome Pansanel 2006-05-10 D-Glutamine D-Glutamin D-Glutamine D-glutamine (2R)-2-Amino-4-carbamoylbutanoic acid (2R)-2-Amino-4-carbamoylbutansäure Acide (2R)-2-amino-4-carbamoylbutanoïque Jerome Pansanel 2006-05-10 D-Histidine D-Histidin D-Histidine D-histidine (2R)-2-Amino-3-(3H-imidazol-4-yl)propanoic acid (2R)-2-Amino-3-(3H-imidazol-4-yl)propansäure Acide (2R)-2-amino-3-(3H-imidazol-4-yl)propanoïque Jerome Pansanel 2006-05-10 D-Isoleucine D-Isoleucin D-Isoleucine D-isoleucine (2R,3R)-2-Amino-3-methylpentanoic acid (2R,3R)-2-Amino-3-methylpentansäure Acide (2R,3R)-2-amino-3-méthylpentanoïque Jerome Pansanel 2006-05-10 D-Leucine D-Leucin D-Leucine D-leucine (2R)-2-Amino-4-methylpentanoic acid (2R)-2-Amino-4-methylpentansäure Acide (2R)-2-amino-4-méthylpentanoïque Jerome Pansanel 2006-05-10 D-Lysine D-Lysin D-Lysine D-lysine (2R)-2,6-Diaminohexanoic acid (2R)-2,6-Diaminohexansäure Acide (2R)-2,6-diaminohexanoïque Jerome Pansanel 2006-05-10 D-Methionine D-Methionin D-Méthionine D-methionine (2R)-2-Amino-4-methylsulfanylbutanoic acid (2R)-2-Amino-4-methylsulfanylbutansäure Acide (2R)-2-amino-4-méthylsulfanylbutanoïque Jerome Pansanel 2006-05-10 D-Phenylalanine D-Phenylalanin D-Phénylalanine D-phenylalanine (2R)-2-Amino-3-phenylpropanoic acid (2R)-2-Amino-3-phenylpropansäure Acide (2R)-2-amino-3-phénylpropanoïque Jerome Pansanel 2006-05-10 D-Proline D-Prolin D-Proline D-proline (2R)-Pyrrolidine-2-carboxylic acid (2R)-Pyrrolidine-2-carbonsäure Acide (2R)-pyrrolidine-2-carboxylique Jerome Pansanel 2006-05-10 D-Serine D-Serin D-Sérine D-serine (2R)-2-Amino-3-hydroxypropanoic acid (2R)-2-Amino-3-hydroxypropansäure Acide (2R)-2-amino-3-hydroxypropanoïque Jerome Pansanel 2006-05-10 D-Threonine D-Threonin D-Thréonine D-threonine (2R,3S)-2-Amino-3-hydroxybutanoic acid (2R,3S)-2-Amino-3-hydroxybutansäure Acide (2R,3S)-2-amino-3-hydroxybutanoïque Jerome Pansanel 2006-05-10 D-Tryptophan D-Tryptophan D-Tryptophane D-tryptophan (2R)-2-Amino-3-(1H-indol-3-yl)propanoic acid (2R)-2-Amino-3-(1H-indol-3-yl)propansäure Acide (2R)-2-amino-3-(1H-indol-3-yl)propanoïque Jerome Pansanel 2006-05-10 D-Tyrosine D-Tyrosin D-Tyrosine D-tyrosine (2R)-2-Amino-3-(4-hydroxyphenyl)propanoic acid (2R)-2-Amino-3-(4-hydroxyphenyl)propansäure Acide (2R)-2-amino-3-(4-hydroxyphényl)propanoïque Jerome Pansanel 2006-05-10 D-Valine D-Valin D-Valine D-valine (2R)-2-Amino-3-methylbutanoic acid (2R)-2-Amino-3-methylbutansäure Acide (2R)-2-amino-3-méthylbutanoïque Jerome Pansanel 2006-05-10 Glycine Glycin Glycine glycine 2-Aminoacetic acid 2-Aminoessigsäure Acide 2-aminoacétique Gly G Jerome Pansanel 2006-05-10 L-Alanine L-Alanin L-Alanine L-alanine (2S)-2-Aminopropanoic acid (2S)-2-Aminopropansäure Acide (2S)-2-aminopropanoïque Ala A Jerome Pansanel 2006-05-10 L-Arginine L-Arginin L-Arginine L-arginine (2S)-2-Amino-5-(diaminomethylideneamino)pentanoic acid (2S)-2-Amino-5-(diaminomethylideneamino)pentansäure Acide (2S)-2-amino-5-(diaminométhylidèneamino)pentanoïque Arg R Jerome Pansanel 2006-05-10 L-Asparagine L-Asparagin L-Asparagine L-asparagine (2S)-2-Amino-3-carbamoylpropanoic acid (2S)-2-Amino-3-carbamoylpropansäure Acide (2S)-2-amino-3-carbamoylpropanoïque Asn N Jerome Pansanel 2006-05-10 L-Aspartic acid L-Asparaginsäure Acide L-aspartique L-aspartic_acid (2S)-2-Aminobutanedioic acid (2S)-2-Aminobutansäure Acide (2S)-2-aminobutanedioïque Asp D Jerome Pansanel 2006-05-10 L-Cysteine L-Cysteine L-Cystéine L-cysteine (2R)-2-Amino-3-sulfanylpropanoic acid (2R)-2-Amino-3-sulfanylpropansäure Acide (2R)-2-amino-3-sulfanylpropanoïque Cys C Jerome Pansanel 2006-05-10 L-Glutamic acid L-Glutaminsäure Acide L-glutamique L-glutamic_acid (2S)-2-Aminopentanedioic acid (2S)-2-Aminopentandisäure Acide (2S)-2-aminopentanedioïque Glu E Jerome Pansanel 2006-05-10 L-Glutamine L-Glutamin L-Glutamine L-glutamine (2S)-2-Amino-4-carbamoylbutanoic acid (2S)-2-Amino-4-carbamoylbutansäure Acide (2S)-2-amino-4-carbamoylbutanoïque Gln Q Jerome Pansanel 2006-05-10 L-Histidine L-Histidin L-Histidine L-histidine (2S)-2-Amino-3-(3H-imidazol-4-yl)propanoic acid (2S)-2-Amino-3-(3H-imidazol-4-yl)propansäure Acide (2S)-2-amino-3-(3H-imidazol-4-yl)propanoïque His H Jerome Pansanel 2006-05-10 L-Isoleucine L-Isoleucin L-Isoleucine L-isoleucine (2S,3S)-2-Amino-3-methylpentanoic acid (2S,3S)-2-Amino-3-methylpentansäure Acide (2S,3S)-2-amino-3-méthylpentanoïque Ile I Jerome Pansanel 2006-05-10 L-Leucine L-Leucin L-Leucine L-leucine (2S)-2-Amino-4-methylpentanoic acid (2S)-2-Amino-4-methylpentansäure Acide (2S)-2-amino-4-méthylpentanoïque Leu L Jerome Pansanel 2006-05-10 L-Lysine L-Lysin L-Lysine L-lysine (2S)-2,6-Diaminohexanoic acid (2S)-2,6-Diaminohexansäure Acide (2S)-2,6-diaminohexanoïque Lys K Jerome Pansanel 2006-05-10 L-Methionine L-Methionin L-Methionine L-methionine (2S)-2-Amino-4-methylsulfanylbutanoic acid (2S)-2-Amino-4-methylsulfanylbutansäure Acide (2S)-2-amino-4-méthylsulfanylbutanoïque Met M Jerome Pansanel 2006-05-10 L-Phenylalanine L-Phenylalanin L-Phenylalanine L-phenylalanine (2S)-2-Amino-3-phenylpropanoic acid (2S)-2-Amino-3-phenylpropansäure Acide (2S)-2-amino-3-phénylpropanoïque Phe F Jerome Pansanel 2006-05-10 L-Proline L-Prolin L-Proline L-proline (2S)-Pyrrolidine-2-carboxylic acid (2S)-Pyrrolidine-2-carbonsäure Acide (2S)-pyrrolidine-2-carboxylique Pro P Jerome Pansanel 2006-05-10 L-Serine L-Serin L-Sérine L-serine (2S)-2-Amino-3-hydroxypropanoic acid (2S)-2-Amino-3-hydroxypropansäure Acide (2S)-2-amino-3-hydroxypropanoïque Ser S Jerome Pansanel 2006-05-10 L-Threonine L-Threonin L-Thréonine L-threonine (2S,3R)-2-Amino-3-hydroxybutanoic acid (2S,3R)-2-Amino-3-hydroxybutansäure Acide (2S,3R)-2-amino-3-hydroxybutanoïque Thr T Jerome Pansanel 2006-05-10 L-Tryptophan L-Tryptophan L-Tryptophane L-tryptophan (2S)-2-Amino-3-(1H-indol-3-yl)propanoic acid (2S)-2-Amino-3-(1H-indol-3-yl)propansäure Acide (2S)-2-amino-3-(1H-indol-3-yl)propanoïque Trp W Jerome Pansanel 2006-05-10 L-Tyrosine L-Tyrosin L-Tyrosine L-tyrosine (2S)-2-Amino-3-(4-hydroxyphenyl)propanoic acid (2S)-2-Amino-3-(4-hydroxyphenyl)propansäure Acide (2S)-2-amino-3-(4-hydroxyphényl)propanoïque Tyr Y Jerome Pansanel 2006-05-10 L-Valine L-Valin L-Valine L-valine (2S)-2-Amino-3-methylbutanoic acid (2S)-2-Amino-3-methylbutansäure Acide (2S)-2-amino-3-méthylbutanoïque Val V Jerome Pansanel 2006-05-10 D-allo-Threonine D-allo-Threonin D-allo-Thréonine D-allo-threonine (2R,3R)-2-Amino-3-hydroxybutanoic acid (2R,3R)-2-Amino-3-hydroxybutansäure Acide (2R,3R)-2-amino-3-hydroxybutanoïque Jerome Pansanel 2006-06-26 L-allo-Isoleucine L-allo-Isoleucin L-allo-Isoleucine L-allo-isoleucine (2S,3R)-2-Amino-3-methylpentanoic acid (2S,3R)-2-Amino-3-methylpentansäure Acide (2S,3R)-2-amino-3-méthylpentanoïque Jerome Pansanel 2006-06-26 L-4-Nitrophenylalanine L-4-Nitrophénylalanine L-4-nitrophenylalanine (S)-2-Amino-3-(4-nitrophenyl)propanoic acid Acide (S)-2-Amino-3-(4-nitrophényl)propanoïque Jerome Pansanel 2007-12-03 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/D-asparagine.cml0000644000175000017500000000627510721555302025617 0ustar georgeskgeorgesk (2R)-2-Amino-3-carbamoylpropanoic acid 132.1179 132.0534921 280 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/L-arginine.cml0000644000175000017500000001016110721554445025305 0ustar georgeskgeorgesk (2S)-2-Amino-5-(diaminomethylideneamino)pentanoic acid 174.2010 174.1116757 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/D-lysine.cml0000644000175000017500000001000310721554445024777 0ustar georgeskgeorgesk (2R)-2,6-Diaminohexanoic acid 146.1876 146.1055277 215 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/L-lysine.cml0000644000175000017500000000777210721554445025032 0ustar georgeskgeorgesk (2S)-2,6-Diaminohexanoic acid 146.1876 146.1055277 215 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/L-isoleucine.cml0000644000175000017500000000743410721554445025661 0ustar georgeskgeorgesk (2S,3S)-2-Amino-3-methylpentanoic acid 131.1729 131.0946287 291 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/glycine.cml0000644000175000017500000000444110721554445024756 0ustar georgeskgeorgesk 2-Aminoacetic acid 75.0666 75.0320284 240 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/D-isoleucine.cml0000644000175000017500000000744510721554445025653 0ustar georgeskgeorgesk (2R,3R)-2-Amino-3-methylpentanoic acid 131.1729 131.0946287 290 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/D-tryptophan.cml0000644000175000017500000001100710724003164025677 0ustar georgeskgeorgesk (2R)-2-Amino-3-(1H-indol-3-yl)propanoic acid 204.2252 204.0898776 283 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/D-leucine.cml0000644000175000017500000000740110721555302025121 0ustar georgeskgeorgesk (2R)-2-Amino-4-methylpentanoic acid 131.1729 131.0946287 > 300 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/L-leucine.cml0000644000175000017500000000741210721555302025133 0ustar georgeskgeorgesk (2S)-2-Amino-4-methylpentanoic acid 131.1729 131.0946287 > 300 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/L-aspartic_acid.cml0000644000175000017500000000602510721554445026303 0ustar georgeskgeorgesk (2S)-2-Aminobutanedioic acid 133.1027 133.0375077 > 300 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/L-threonine.cml0000644000175000017500000000627010721554445025512 0ustar georgeskgeorgesk (2S,3R)-2-Amino-3-hydroxybutanoic acid 119.1192 119.0582432 272 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/L-glutamic_acid.cml0000644000175000017500000000664010721554445026305 0ustar georgeskgeorgesk (2S)-2-Aminopentanedioic acid 147.1293 147.0531578 205 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/D-allo-threonine.cml0000644000175000017500000000627010721555302026420 0ustar georgeskgeorgesk (2R,3R)-2-Amino-3-hydroxybutanoic acid 119.1192 119.0582432 276 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/L-glutamine.cml0000644000175000017500000000705610721555302025500 0ustar georgeskgeorgesk (2S)-2-Amino-4-carbamoylbutanoic acid 146.1445 146.0691422 185 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/L-proline.cml0000644000175000017500000000632710721554445025172 0ustar georgeskgeorgesk (2S)-Pyrrolidine-2-carboxylic acid 115.1305 115.0633285 223 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/L-allo-isoleucine.cml0000644000175000017500000000743710721554445026611 0ustar georgeskgeorgesk (2S,3R)-2-Amino-3-methylpentanoic acid 131.1729 131.0946287 290 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/L-4-nitrophenylalanine.cml0000644000175000017500000001000410724755521027552 0ustar georgeskgeorgesk (S)-2-Amino-3-(4-nitrophenyl)propanoic acid 210.1867 210.0640568 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/L-valine.cml0000644000175000017500000000664310721555302024772 0ustar georgeskgeorgesk (2S)-2-Amino-3-methylbutanoic acid 117.1463 117.0789786 > 295 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/D-histidine.cml0000644000175000017500000000664510721554445025475 0ustar georgeskgeorgesk (2R)-2-Amino-3-(3H-imidazol-4-yl)propanoic acid 155.1546 155.0694765 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/L-cysteine.cml0000644000175000017500000000545610721555302025340 0ustar georgeskgeorgesk (2R)-2-Amino-3-sulfanylpropanoic acid 121.1582 121.0197495 230 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/L-tyrosine.cml0000644000175000017500000001010610721554445025364 0ustar georgeskgeorgesk (2S)-2-Amino-3-(4-hydroxyphenyl)propanoic acid 181.1885 181.0738932 > 300 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/CMakeLists.txt0000644000175000017500000000712711112716045025362 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "amino_acids") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/amino_acids/D-phenylalanine.cml0000644000175000017500000000771010721555302026327 0ustar georgeskgeorgesk (2R)-2-Amino-3-phenylpropanoic acid 165.1891 165.0789786 266 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/L-phenylalanine.cml0000644000175000017500000000770010721555302026336 0ustar georgeskgeorgesk (2S)-2-Amino-3-phenylpropanoic acid 165.1891 165.0789786 266 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/D-cysteine.cml0000644000175000017500000000545010721555302025322 0ustar georgeskgeorgesk (2S)-2-Amino-3-sulfanylpropanoic acid 121.1582 121.0197495 230 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/D-threonine.cml0000644000175000017500000000626510721554445025506 0ustar georgeskgeorgesk (2R,3S)-2-Amino-3-hydroxybutanoic acid 119.1192 119.0582432 272 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/L-methionine.cml0000644000175000017500000000654610721555302025655 0ustar georgeskgeorgesk (2S)-2-Amino-4-methylsulfanylbutanoic acid 149.2113 149.0510496 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/L-asparagine.cml0000644000175000017500000000627110721555302025623 0ustar georgeskgeorgesk (2S)-2-Amino-3-carbamoylpropanoic acid 132.1179 132.0534921 280 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/D-methionine.cml0000644000175000017500000000655210721555302025642 0ustar georgeskgeorgesk (2R)-2-Amino-4-methylsulfanylbutanoic acid 149.2113 149.0510496 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/L-serine.cml0000644000175000017500000000550110721555302024771 0ustar georgeskgeorgesk (2S)-2-Amino-3-hydroxypropanoic acid 105.0926 105.0425931 222 chemical-structures-2.2.dfsg.0.orig/src/amino_acids/D-valine.cml0000644000175000017500000000664710721555302024766 0ustar georgeskgeorgesk (2R)-2-Amino-3-methylbutanoic acid 117.1463 117.0789786 295 chemical-structures-2.2.dfsg.0.orig/src/images/0000755000175000017500000000000011225622315021613 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/images/favicon.ico0000644000175000017500000000427610774671262023762 0ustar georgeskgeorgesk ( @   # ' 7$)))+++S8444]>;;;zQ)UNG^/d2[[[f3g4f_Xh5j9k9k:l;m<dddn=qBtFvI|Pttt}Q/^UUVY]3f`ijlpqsyz}£Ħħŧɯ˱ͳʹӽ­Ƴʹppppppppppe:  :eppppppppppppppppppR  RpppppppppppppppppppppppppppR pHZklW7 RpppppppppJppG 2ppAJpppppppR pN#pph Rpppppp p+1Vpp_ ppppp=`ppppBpppR?ppppd@Rpp_pp\9pebpp%3pe:0gp26fp: -Qgl[Kp    )////////////////////////////))////////////////////////////) >pppppppppppppppppppppppppppp>!pppppppppppN2#$<^pppppppppp!Cnppppppppo8DcjP&TppppppppnCe>ppppppppI?ppppY6pppppppp>ep!pppppppp.[pppppppppppppp!ppS4pppppppmppppppppppppp4Sppp'Opppppp"ippppppppppppO'pppppappppp3Xppp;=pppppappppppS appppU?pppppppa SpppppppM OppppLFcj,5pppO MpppppppppS4pppp]A(*Eipp4Spppppppppppp'>nppppppppn>'pppppppppppppppS!>OaaO>!SppppppppppppppppppeC!  !Ceppppppppppchemical-structures-2.2.dfsg.0.orig/src/images/header_bg.png0000644000175000017500000000020310627064724024225 0ustar georgeskgeorgeskPNG  IHDR`Sߏ! pHYs  tIME  )a*"IDATc?P i3l㴙C8\I IENDB`chemical-structures-2.2.dfsg.0.orig/src/images/CMakeLists.txt0000644000175000017500000000227211112716045024355 0ustar georgeskgeorgesk################################################################# # Local variable settings # ################################################################# set(LOCAL_TARGET images) message(STATUS "Generating ${LOCAL_TARGET} Makefile") file(GLOB image_SRCS *.png *.ico) set(image_files "") add_custom_target(${LOCAL_TARGET} ALL) ################################################################# # Image file handle # ################################################################# foreach(image_SRC_FILE ${image_SRCS}) get_filename_component(image_FILE ${image_SRC_FILE} NAME) add_custom_command(TARGET ${LOCAL_TARGET} COMMAND cp ${image_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${image_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(image_files ${image_files} ${image_FILE}) endforeach(image_SRC_FILE) ################################################################# # Install files # ################################################################# install(FILES ${image_files} DESTINATION ${SHARE_HOME}/images) chemical-structures-2.2.dfsg.0.orig/src/images/header.png0000644000175000017500000007755010627064724023600 0ustar georgeskgeorgeskPNG  IHDRX`Nb pHYs  tIME  g IDATx}wxW>wޯzlYe;'SIK٥oYvX:KX`7,JH!8qlǽʲ-Y~$78n;Ǐ33gޙs~-i   0Ѐ _  85JK_ӀA 06b8UUEQA!z=4M4UUeYT*Rd2Y*Ng"Xf"B?o Yƀ.$MNNNOOq0 ðaXQSirT*viq< X[[KO?MAgѢE^:"4 B Hӻvp8TqdY0 Aݎh"H4M=z̲l<rn::;;xCPkk+A`СA 0pe044t6כf3 M.+֎t:][[d$Ijhhiz۶m\siH XVEQ\.WMM$EQ(|>A DhoDQ|'GFFt85k֘L&#a``I |>_MM|ccc333(ʲ<99p8,?~$IMt)AMMM$IVigy)Mim(bD0,7(cѢE P(422B,044433j*,c8P]]-B{{LMM>28~݉f``x<(J>( p]wy^xh3DPxك:*?Oݹ[ ͱcǎu zE%If###@$ɓ'O~YC뫪-vbHdtd28t:Q!԰,l0lll;$IRM07E^aIVjD罣>oJdm ـ3DQed2ԩS(<_,s\6mkkCQ4444455mܸÇ{^EK,cccǏf(ZVب( $IbFn`&RH$R.GGGnȈ$I$ɲ,˲(j.Gȕw&dD  wXL ǵKǢOG;;o=2AW}kxK}㳩ba"0a!sS%F~p 0fEJHX,iYQM*R A 4]]]MQ Á@@$arEQzn 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qEUUmeew|FF媹s7jj:-z{²:]ޱDiiŨ|eeӼy[v:9v;Ơf@iiE{{/`&`0\.}$ILEiqb11bFyiɓPVJ|{L7>{RuЗ.+Q:eR>0gΞ XtVnn5GP^>&_\qE|pWٳ/8牶F  `(LQ l Ngp.K̔H(F4@(] 1|ojiX,J% N ƨ|}ڴq`AAE(G^p޺ղiӊA+ 1&S(x-}fېdZb˘Q E3LBa\bcǶqCTҫWN׷lYA$wڜ16]]ݎ tPX o?^PD(7w^Q!5$}yPxHW ܄ PlXz}|\\.֭/i)<)*ʩlRdU۷B+V֋?߲eݧ .qjuUU[yp³g-+{d=ʕ[(,O># da0l6{RJrvlBD|V?svF,Y]J0d$''$3qasM&GMwxؖZprʢA]'wg ֊3׮Yf~0޶Z΍?yO>9Ѥ};} x Zn+׮ʋϟ qql6{qH7eJJJ !IqaðI0 A@lCwċ'E"q͚n\.Y#G-WLQt4Z 8}[\h+.6~hמ4$I\A$(b2l6D":{Qͷwܭu:D"Zt>_02pcceSIIQΜUWwXdg?_9gΔȖj'$M`0;aw8$pxz}o@Db|,#dgeEvP0Lv4-;Idׯ+Y=|҃f9aˎ۲og6qY㣷;_]{P Ç= muu_{'N*-=V8Zի8%%Zm:{mߤnhtB!Hp9^gi vOlQ f2>ړWxł?{{=K[zĪTrL*5(M*J{jk ShIi &Zӌ{fǂ;wO[6cP@an93 O3.>D^R2Au&A!o5t]V}f΄k OXLlIENDB`chemical-structures-2.2.dfsg.0.orig/src/fatty_acids/0000755000175000017500000000000011225622315022640 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/fatty_acids/octanoic_acid.cml0000644000175000017500000001053010662517661026126 0ustar georgeskgeorgesk Octanoic acid 144.2114 144.1150298 16 237 chemical-structures-2.2.dfsg.0.orig/src/fatty_acids/oleic_acid.cml0000644000175000017500000001711310722312703025411 0ustar georgeskgeorgesk (Z)-Octadec-9-enoic acid 282.4614 282.2558803 13 chemical-structures-2.2.dfsg.0.orig/src/fatty_acids/lauric_acid.cml0000644000175000017500000001317410722312703025600 0ustar georgeskgeorgesk Dodecanoic acid 200.3178 200.1776300 45 chemical-structures-2.2.dfsg.0.orig/src/fatty_acids/cervonic_acid.cml0000644000175000017500000001745710722312703026141 0ustar georgeskgeorgesk (4Z,7Z,10Z,13Z,16Z,19Z)-Docosa-4,7,10,13,16,19-hexaenoic acid 328.4883 328.2402303 chemical-structures-2.2.dfsg.0.orig/src/fatty_acids/stearic_acid.cml0000644000175000017500000001773310722312703025760 0ustar georgeskgeorgesk Octadecanoic acid 284.4772 284.2715304 68 361 chemical-structures-2.2.dfsg.0.orig/src/fatty_acids/heptanoic_acid.cml0000644000175000017500000000775010662517661026313 0ustar georgeskgeorgesk Heptanoic acid 130.1849 130.0993797 -10 223 chemical-structures-2.2.dfsg.0.orig/src/fatty_acids/linolenic_acid.cml0000644000175000017500000001576110722312703026301 0ustar georgeskgeorgesk (9Z,12Z,15Z)-Octadeca-9,12,15-trienoic acid 278.4296 278.2245802 chemical-structures-2.2.dfsg.0.orig/src/fatty_acids/hexanoic_acid.cml0000644000175000017500000000716410662517661026136 0ustar georgeskgeorgesk Hexanoic acid 116.1583 116.0837296 -4 202 chemical-structures-2.2.dfsg.0.orig/src/fatty_acids/index.xml0000644000175000017500000002206311142231213024463 0ustar georgeskgeorgesk Fatty acids Fettsäuren Ácidos grasos Acides gras Vetzuren Fatty acids 脂肪酸 Cervonic acid Acide cervonique Cervonic acid 二十二碳六烯酸 (22:6) cervonic_acid (4Z,7Z,10Z,13Z,16Z,19Z)-Docosa-4,7,10,13,16,19-hexaenoic acid Acide (4Z,7Z,10Z,13Z,16Z,19Z)-docosa-4,7,10,13,16,19-hexaenoïque (4Z,7Z,10Z,13Z,16Z,19Z)-Docosa-4,7,10,13,16,19-hexaenoic acid (4Z,7Z,10Z,13Z,16Z,19Z)-二十二碳-4,7,10,13,16,19-六烯酸 (22:6) Jerome Pansanel 2006-05-10 (5Z,8Z,11Z,14Z,17Z)-Icosa-5,8,11,14,17-pentaenoic acid Acide (5Z,8Z,11Z,14Z,17Z)-icosa-5,8,11,14,17-pentaènoïque (5Z,8Z,11Z,14Z,17Z)-Icosa-5,8,11,14,17-pentaenoic acid 二十碳五烯酸 (20:5) 5Z_8Z_11Z_14Z_17Z-icosa-5_8_11_14_17-pentaenoic_acid Jerome Pansanel 2006-05-10 Arachidonic acid Acide arachidonique Arachidonic acid 花生油酸/二十碳四烯酸 (20:4) arachidonic_acid (5Z,8Z,11Z,14Z)-Icosa-5,8,11,14-tetraenoic acid Acide (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tétraènoïque (5Z,8Z,11Z,14Z)-Icosa-5,8,11,14-tetraenoic acid (5Z,8Z,11Z,14Z)-二十碳-5,8,11,14-四烯酸 (20:4) Jerome Pansanel 2006-05-10 (6Z,9Z,12Z)-Octadeca-6,9,12-trienoic acid Acide (6Z,9Z,12Z)-octadeca-6,9,12-triènoïque (6Z,9Z,12Z)-Octadeca-6,9,12-trienoic acid 次亞麻油酸/十八碳三烯酸 (18:3) 6Z_9Z_12Z-octadeca-6_9_12-trienoic_acid Jerome Pansanel 2006-05-10 Linolenic acid Acide linolénique Linolenic acid 次亞麻油酸 (18:3) linolenic_acid (9Z,12Z,15Z)-Octadeca-9,12,15-trienoic acid Acide (9Z,12Z,15Z)-octadéca-9,12,15-triènoïque (9Z,12Z,15Z)-Octadeca-9,12,15-trienoic acid (9Z,12Z,15Z)-十八碳-9,12,15-三烯酸 (18:3) 蘇子油酸/十八碳三烯酸 Jerome Pansanel 2006-05-10 Stearic acid Acide stéarique Stearic acid 硬脂酸 (18:0) stearic_acid Octadecanoic acid Acide octadécanoïque Octadecanoic acid 十八酸 (18:0) Jerome Pansanel 2006-05-10 Oleic acid Acide oléique Oleic acid 油酸 (18:1) oleic_acid (Z)-Octadec-9-enoic acid Acide (Z)-octadéc-9-ènoïque (Z)-Octadec-9-enoic acid (Z)-十八-9-烯酸 (18:1) Jerome Pansanel 2006-05-10 Pentanoic acid Acide pentanoïque Pentanoic acid 戊酸 (5:0) pentanoic_acid Valeric acid Valerianic acid Acide valérique Acide valérianique Valeric acid 纈草酸 (5:0) Valerianic acid 吉草酸/穿心排草酸戊酸 Jerome Pansanel 2006-05-11 Hexanoic acid Acide hexanoïque Hexanoic acid 已酸 (6:0) hexanoic_acid Caproic acid Acide caproïque Caproic acid 羊油酸 (6:0) Jerome Pansanel 2006-05-11 Heptanoic acid Acide heptanoïque Heptanoic acid 庚酸 (7:0) heptanoic_acid Enanthic acid Acide énanthique Enanthic acid 毒水芹酸 (7:0) Jerome Pansanel 2006-05-11 Octanoic acid Acide octanoïque Octanoic acid 辛酸 (8:0) octanoic_acid Caprylic acid Acide caprylique Caprylic acid 辛酸 (8:0) Jerome Pansanel 2006-05-11 Decanoic acid Acide décanoïque Decanoic acid 癸酸 (10:0) decanoic_acid Caprinic acid Capric acid Acide caprinique Acide caprique Caprinic acid 羊脂酸 (10:0) Jerome Pansanel 2006-05-11 Lauric acid Acide laurique Lauric acid 月桂酸 (12:0) lauric_acid Dodecanoic acid Acide dodécanoïque Dodecanoic acid 十二酸 (12:0) Jerome Pansanel 2006-05-11 Myristic acid Acide myristique Myristic acid 肉豆蔻酸 (14:0) myristic_acid Tetradecanoic acid Acide tétradécanoïque Tetradecanoic acid 十四酸 (14:0) Jerome Pansanel 2006-05-11 Palmitic acid Acide palmitique Palmitic acid 棕櫚酸/軟脂酸 (16:0) palmitic_acid Hexadecanoic acid Acide hexadécanoïque Hexadecanoic acid 十六酸 (16;0) Jerome Pansanel 2006-05-11 Linoleic acid Acide linoléique Linoleic acid 亞麻油酸 (18:2) linoleic_acid (9Z,12Z)-Octadeca-9,12-dienoic acid Acide (9Z,12Z)-octadéca-9,12-diènoïque (9Z,12Z)-Octadeca-9,12-dienoic acid (9Z,12Z)-十八碳-9,12-二烯酸 (18:2) Jerome Pansanel 2006-05-10 chemical-structures-2.2.dfsg.0.orig/src/fatty_acids/linoleic_acid.cml0000644000175000017500000001705010722312703026114 0ustar georgeskgeorgesk (9Z,12Z)-Octadeca-9,12-dienoic acid 280.4455 280.2402303 -5 229 chemical-structures-2.2.dfsg.0.orig/src/fatty_acids/myristic_acid.cml0000644000175000017500000001454710722312703026171 0ustar georgeskgeorgesk Tetradecanoic acid 228.3709 228.2089301 53 ././@LongLink0000000000000000000000000000015500000000000011566 Lustar rootrootchemical-structures-2.2.dfsg.0.orig/src/fatty_acids/5Z_8Z_11Z_14Z_17Z-icosa-5_8_11_14_17-pentaenoic_acid.cmlchemical-structures-2.2.dfsg.0.orig/src/fatty_acids/5Z_8Z_11Z_14Z_17Z-icosa-5_8_11_14_17-pentaenoic_0000644000175000017500000001645110662517661032301 0ustar georgeskgeorgesk (5Z,8Z,11Z,14Z,17Z)-Icosa-5,8,11,14,17-pentaenoic acid 302.4510 302.2245802 chemical-structures-2.2.dfsg.0.orig/src/fatty_acids/palmitic_acid.cml0000644000175000017500000001637210722312703026126 0ustar georgeskgeorgesk Hexadecanoic acid 256.4241 256.2402303 62 271 chemical-structures-2.2.dfsg.0.orig/src/fatty_acids/decanoic_acid.cml0000644000175000017500000001210010662517661026067 0ustar georgeskgeorgesk Decanoic acid 172.2646 172.1463299 31 269 chemical-structures-2.2.dfsg.0.orig/src/fatty_acids/arachidonic_acid.cml0000644000175000017500000001754710722312703026575 0ustar georgeskgeorgesk (5Z,8Z,11Z,14Z)-Icosa-5,8,11,14-tetraenoic acid 304.4669 304.2402303 -49 170 chemical-structures-2.2.dfsg.0.orig/src/fatty_acids/CMakeLists.txt0000644000175000017500000000712711112716045025406 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "fatty_acids") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/fatty_acids/6Z_9Z_12Z-octadeca-6_9_12-trienoic_acid.cml0000644000175000017500000001577110662517661032130 0ustar georgeskgeorgesk (6Z,9Z,12Z)-Octadeca-6,9,12-trienoic acid 278.4296 278.2245802 chemical-structures-2.2.dfsg.0.orig/src/fatty_acids/pentanoic_acid.cml0000644000175000017500000000640610662517661026316 0ustar georgeskgeorgesk Pentanoic acid 102.1317 102.0680796 -19 185 chemical-structures-2.2.dfsg.0.orig/src/amides/0000755000175000017500000000000011225622315021610 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/amides/1-bromopyrrolidine-2_5-dione.cml0000644000175000017500000000513010662517661027533 0ustar georgeskgeorgesk 1-Bromopyrrolidine-2,5-dione 177.9841 176.9425404 173 chemical-structures-2.2.dfsg.0.orig/src/amides/acetamide.cml0000644000175000017500000000444410662517661024242 0ustar georgeskgeorgesk Acetamide 59.0672 59.0371138 80 221 chemical-structures-2.2.dfsg.0.orig/src/amides/index.xml0000644000175000017500000000524411142231213023435 0ustar georgeskgeorgesk Amides Amide Amidas Amides Amides Amides 醯胺 N,N-Dimethylformamide N,N-Dimethylformamid N,N-Diméthylformamide N,N-Dimethylformamide N,N-二甲基甲醯胺 N_N-dimethylformamide DMF DMF DMF DMF 二甲基甲醯胺 Jerome Pansanel 2006-05-10 Oxamide Oxamid Oxamide Oxamide 草醯胺 oxamide Jerome Pansanel 2006-07-31 1-Bromopyrrolidine-2,5-dione 1-Bromopyrrolidine-2,5-dione 1-Bromopyrrolidine-2,5-dione 1-溴吡咯烷-2,5-二酮 1-bromopyrrolidine-2_5-dione Jerome Pansanel 2006-07-31 Acetamide Acétamide Acetamide 乙醯胺 acetamide Jerome Pansanel 2006-11-09 Ethyl carbamate Carbamate d'éthyle Ethyl carbamate 胺甲酸乙酯 ethyl_carbamate Urethane Uréthane Urethane 胺甲酸乙酯 Jerome Pansanel 2006-11-22 N,N-Dimethylacetamide N,N-Diméthylacétamide N,N-Dimethylacetamide N,N-二甲基乙醯胺 N_N-dimethylacetamide Jerome Pansanel 2006-11-22 chemical-structures-2.2.dfsg.0.orig/src/amides/ethyl_carbamate.cml0000644000175000017500000000543510662517661025453 0ustar georgeskgeorgesk Ethyl carbamate 89.0932 89.0476785 49 183 chemical-structures-2.2.dfsg.0.orig/src/amides/N_N-dimethylacetamide.cml0000644000175000017500000000601610662517661026447 0ustar georgeskgeorgesk N,N-Dimethylacetamide 87.1204 87.0684139 -20 165 chemical-structures-2.2.dfsg.0.orig/src/amides/oxamide.cml0000644000175000017500000000437210662517661023754 0ustar georgeskgeorgesk Oxamide 88.0654 88.0272774 > 300 chemical-structures-2.2.dfsg.0.orig/src/amides/CMakeLists.txt0000644000175000017500000000712211112716045024351 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "amides") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/amides/N_N-dimethylformamide.cml0000644000175000017500000000524710662517661026503 0ustar georgeskgeorgesk N,N-Dimethylformamide 73.0938 73.0527638 -61 153 chemical-structures-2.2.dfsg.0.orig/src/carbamides/0000755000175000017500000000000011225622315022440 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/carbamides/index.xml0000644000175000017500000000125011142231213024256 0ustar georgeskgeorgesk Carbamides Carbamides Carbamidas Carbamides Carbamides Carbamides 羰基胺類 Urea Harnstoff Urée Urea 尿素 urea Jerome Pansanel 2006-07-13 chemical-structures-2.2.dfsg.0.orig/src/carbamides/CMakeLists.txt0000644000175000017500000000712611112716045025205 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "carbamides") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/carbamides/urea.cml0000644000175000017500000000376310662517661024115 0ustar georgeskgeorgesk Urea 60.0553 60.0323628 135 chemical-structures-2.2.dfsg.0.orig/src/CMakeLists.txt0000644000175000017500000000577511225104744023125 0ustar georgeskgeorgeskmessage(STATUS "Generating src Makefile") set(level "0") add_custom_target(index ALL) set(index_files "") set(main_index_files "") ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Main index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(main_index_files ${main_index_files} "${CMAKE_CURRENT_BINARY_DIR}/name_index_${lang}.html") set(main_index_files ${main_index_files} "${CMAKE_CURRENT_BINARY_DIR}/formula_index_${lang}.html") endforeach(lang) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET index COMMAND ${PYTHON_EXECUTABLE} ${MAKEINDEXFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) add_custom_command(TARGET clean_xhtml COMMAND rm *.html WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}) install(FILES ${main_index_files} DESTINATION ${SHARE_HOME}) ################################################################# # Add subdirectories # ################################################################# add_subdirectory(acid_anhydrides) add_subdirectory(alcohols) add_subdirectory(aldehydes) add_subdirectory(alkanes) add_subdirectory(alkenes) add_subdirectory(alkynes) add_subdirectory(amides) add_subdirectory(amines) add_subdirectory(amino_acids) add_subdirectory(aromatics) add_subdirectory(carbamides) add_subdirectory(carbohydrates) add_subdirectory(carboxylic_acids) add_subdirectory(drugs) add_subdirectory(esters) add_subdirectory(ethers) add_subdirectory(fatty_acids) add_subdirectory(haloalkanes) add_subdirectory(heteroaromatics) add_subdirectory(htdocs) add_subdirectory(images) add_subdirectory(jmol) add_subdirectory(ketones) add_subdirectory(macrocycles) add_subdirectory(natural_products) add_subdirectory(nitriles) add_subdirectory(nitroalkanes) add_subdirectory(nucleobases) add_subdirectory(peptides) add_subdirectory(polycyclic_alkanes) add_subdirectory(polycyclic_aromatics) add_subdirectory(styles) add_subdirectory(sulfones) add_subdirectory(sulfoxides) add_subdirectory(thioethers) add_subdirectory(thiols) add_subdirectory(water) chemical-structures-2.2.dfsg.0.orig/src/nucleobases/0000755000175000017500000000000011225622315022651 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/nucleobases/thymine.cml0000644000175000017500000000567710722620721025042 0ustar georgeskgeorgesk 5-Methyl-1H-pyrimidine-2,4-dione 126.1133 126.0429274 > 300 chemical-structures-2.2.dfsg.0.orig/src/nucleobases/index.xml0000644000175000017500000000642311142231213024476 0ustar georgeskgeorgesk Nucleobases Nukleobasen Nucleobases Bases nucléiques Nucleotiden Nucleobases 鹼基/核鹼基 Uracil Uracil Uracile Uracil 尿嘧啶 uracil 1H-Pyrimidine-2,4-dione 1H-Pyrimidine-2,4-dione 1H-Pyrimidine-2,4-dione 1氫-嘧啶-2, 4-二酮 U Jerome Pansanel 2006-09-28 Guanine Guanin Guanina Guanine Guanine 鳥嘌呤 guanine 2-Amino-3,7-dihydropurin-6-one 2-Amino-3,7-dihydropurin-6-one 2-Amino-3,7-dihydropurin-6-one 2-胺基-3, 7-二氫嘌呤-6-酮 G Jerome Pansanel 2006-09-28 Cytosine Cytosin Cytosina Cytosine Cytosine 胞嘧啶 cytosine 4-Amino-3H-pyrimidin-2-one 4-Amino-3H-pyrimidin-2-one C 4-Amino-3H-pyrimidin-2-one 4-胺基-3氫-嘧啶-2-酮 Jerome Pansanel 2006-09-28 Thymine Thymine Thymine Thymine 胸嘧啶 thymine 5-Methyl-1H-pyrimidine-2,4-dione 5-Methyl-1H-pyrimidine-2,4-dione 5-Methyl-1H-pyrimidine-2,4-dione 5-甲基-1氫-嘧啶-2, 4-二酮 T Jerome Pansanel 2006-09-28 Adenine Adenin Adenina Adénine Adenine 腺嘌呤 adenine 7H-Purin-6-amine 7H-Purin-6-amine 7H-Purin-6-amine 7氫-嘌呤-6-胺 A Jerome Pansanel 2006-09-28 chemical-structures-2.2.dfsg.0.orig/src/nucleobases/guanine.cml0000644000175000017500000000615210722620721025000 0ustar georgeskgeorgesk 2-Amino-3,7-dihydropurin-6-one 151.1261 151.0494098 > 300 chemical-structures-2.2.dfsg.0.orig/src/nucleobases/cytosine.cml0000644000175000017500000000527410722620721025213 0ustar georgeskgeorgesk 4-Amino-3H-pyrimidin-2-one 111.1020 111.0432618 > 300 chemical-structures-2.2.dfsg.0.orig/src/nucleobases/uracil.cml0000644000175000017500000000507610722620721024635 0ustar georgeskgeorgesk 1H-Pyrimidine-2,4-dione 112.0868 112.0272774 > 300 chemical-structures-2.2.dfsg.0.orig/src/nucleobases/adenine.cml0000644000175000017500000000570710722620721024762 0ustar georgeskgeorgesk 7H-Purin-6-amine 135.1267 135.0544952 > 300 chemical-structures-2.2.dfsg.0.orig/src/nucleobases/CMakeLists.txt0000644000175000017500000000712711112716045025417 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "nucleobases") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/nitroalkanes/0000755000175000017500000000000011225622315023040 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/nitroalkanes/nitroethane.cml0000644000175000017500000000464610662517661026102 0ustar georgeskgeorgesk Nitroethane 75.0666 75.0320284 -90 114 chemical-structures-2.2.dfsg.0.orig/src/nitroalkanes/index.xml0000644000175000017500000000172111142231213024661 0ustar georgeskgeorgesk Nitroalkanes Nitroalkan Nitroalcanos Nitroalcanes Nitroalkanen Nitroalkanes 硝基烷類 Nitroethane Nitroéthane Nitroethane 硝乙烷 nitroethane Jerome Pansanel 2006-11-22 Nitromethane Nitrométhane Nitromethane 硝甲烷 nitromethane Jerome Pansanel 2006-11-22 chemical-structures-2.2.dfsg.0.orig/src/nitroalkanes/CMakeLists.txt0000644000175000017500000000713011112716045025600 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "nitroalkanes") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/nitroalkanes/nitromethane.cml0000644000175000017500000000407010662517661026246 0ustar georgeskgeorgesk Nitromethane 61.0400 61.0163783 -29 101 chemical-structures-2.2.dfsg.0.orig/src/water/0000755000175000017500000000000011225622315021470 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/water/water.cml0000644000175000017500000000306510723245415023317 0ustar georgeskgeorgesk Oxidane 18.0153 18.0105647 0 100 chemical-structures-2.2.dfsg.0.orig/src/water/index.xml0000644000175000017500000000146711142231213023320 0ustar georgeskgeorgesk Water Wasser Agua Eau Water Water 水 Water Wasser Eau Water 水 water Oxidane Oxidan Oxidane Oxidane 氧烷 Jerome Pansanel 2006-05-10 chemical-structures-2.2.dfsg.0.orig/src/water/CMakeLists.txt0000644000175000017500000000712111112716045024230 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "water") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/ethers/0000755000175000017500000000000011225622315021640 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/ethers/furan.cml0000644000175000017500000000421210662517661023462 0ustar georgeskgeorgesk Furan 68.0740 68.0262147 31 chemical-structures-2.2.dfsg.0.orig/src/ethers/ethylmethylether.cml0000644000175000017500000000446410722031472025744 0ustar georgeskgeorgesk Methoxyethane 60.0950 60.0575149 chemical-structures-2.2.dfsg.0.orig/src/ethers/diisopropylether.cml0000644000175000017500000000740010722031472025742 0ustar georgeskgeorgesk 2-Propane-2-yloxypropane 102.1748 102.1044651 -85 69 chemical-structures-2.2.dfsg.0.orig/src/ethers/1_4_7_10_13_16-hexaoxacyclooctadecane.cml0000644000175000017500000001427410662517661030776 0ustar georgeskgeorgesk 1,4,7,10,13,16-Hexaoxacyclooctadecane 264.3154 264.1572885 38 chemical-structures-2.2.dfsg.0.orig/src/ethers/di-tert-butylether.cml0000644000175000017500000001022110722031472026065 0ustar georgeskgeorgesk 2-Methyl-2-tert-butoxypropane 130.2279 130.1357652 chemical-structures-2.2.dfsg.0.orig/src/ethers/R-2-ethoxybutane.cml0000644000175000017500000000710710662517661025432 0ustar georgeskgeorgesk (R)-2-Ethoxybutane 102.1748 102.1044651 81 chemical-structures-2.2.dfsg.0.orig/src/ethers/index.xml0000644000175000017500000002053411224730174023477 0ustar georgeskgeorgesk Ethers Ether Éters Ethers Ethers Ethers 醚類 1,4-Dioxane 1,4-Dioxane 1,4-Dioxane 1,4-二氧六環/二氧陸圜/二氧化二伸乙基 1_4-dioxane Jerome Pansanel 2006-05-10 Dipropylether Dipropyléther Dipropylether 二丙醚 dipropylether 1-Propoxypropane n-Propylether 1-Propoxypropane n-Propyléther 1-Propoxypropane 1-丙氧丙烷/二丙醚 n-Propylether 正-二丙醚 Jerome Pansanel 2006-05-10 Di-tert-butylether Di-tert-butyléther Di-tert-butylether 二-第三丁醚 di-tert-butylether 2-Methyl-2-tert-butoxypropane 2-Méthyl-2-tert-butoxypropane 2-Methyl-2-tert-butoxypropane 2-甲基-2-第三丁基醚 Jerome Pansanel 2006-05-10 Dibutylether Dibutyléther Dibutylether 二丁醚 dibutylether 1-Butoxybutane 1-Butoxybutane 1-Butoxybutane 1-丁基醚 Jerome Pansanel 2006-06-26 Diisopropylether Diisopropyléther Diisopropylether 二異丙醚 diisopropylether 2-Propan-2-yloxypropane 2-Propan-2-yloxypropane 2-Propan-2-yloxypropane 二異丙醚 Jerome Pansanel 2006-05-10 Diethylether Diéthyléther Diethylether 二乙醚 diethylether Ethoxyethane Ether Ethoxyéthane Ether Ethoxyethane 二乙醚 Ether 醚 Jerome Pansanel 2006-05-10 Furan Furane Furan 呋喃 furan Jerome Pansanel 2006-05-10 Ethylmethylether Ethylméthyléther Ethylmethylether 甲乙醚 ethylmethylether Methoxyethane Méthoxyéthane Methoxyethane 甲乙醚 Jerome Pansanel 2006-05-10 Dimethylether Diméthyléther Dimethylether 二甲醚 dimethylether Methoxymethane Méthoxyméthane Methoxymethane 二甲醚 Jerome Pansanel 2006-05-10 Tetrahydrofuran Tétrahydrofurane Tetrahydrofuran 四氫呋喃 (縮寫為 THF) tetrahydrofuran Oxacyclopentane Oxolane Oxacyclopentane Oxolane Oxacyclopentane 四氫呋喃/氧雜環戊烷 Oxolane 四氫呋喃/氧雜環戊烷 Jerome Pansanel 2006-05-10 2,3-Dimethyloxepin 2,3-Diméthyloxépine 2,3-Dimethyloxepin 暫譯為: 2,3-二甲基一氧柒圜/二甲基七員環醚 2_3-dimethyloxepin Jerome Pansanel 2006-07-13 2,7-Dimethyloxepin 2,7-Diméthyloxépine 2,7-Dimethyloxepin 暫譯為: 2,7-二甲基一氧柒圜/二甲基七員環醚 2_7-dimethyloxepin Jerome Pansanel 2006-07-13 Oxepin Oxépine Oxepin 暫譯為: 一氧柒圜/七員環醚 oxepin Jerome Pansanel 2006-07-31 (R)-2-Ethoxybutane (R)-2-Ethoxybutane (R)-2-Ethoxybutane (R)-2-乙氧基丁烷 R-2-ethoxybutane Jerome Pansanel 2006-11-09 1,4,7,10,13,16-Hexaoxacyclooctadecane 1,4,7,10,13,16-Hexaoxacyclooctadécane 1,4,7,10,13,16-Hexaoxacyclooctadecane 1,4,7,10,13,16-六氧環十八烷 1_4_7_10_13_16-hexaoxacyclooctadecane 18-Crown-6 ether Ether 18-couronne-6 18-Crown-6 ether 冠狀環醚 18-Crown-6 (18 員環, 6 個氧) Jerome Pansanel 2006-11-22 2-(2-Hydroxyethoxy)ethanol 2-(2-Hydroxyéthoxy)éthanol 2-(2-Hydroxyethoxy)ethanol 2-(2-羥基乙氧基)乙醇 2-2-hydroxyethoxy_ethanol Diethylene glycol Diéthylène glycol Diethylene glycol 二乙二醇/二甘醇 Jerome Pansanel 2006-11-22 Tetrahydropyran Tétrahydropyrane Tetrahydropyran 四氫吡喃 tetrahydropyran Oxane Oxacyclohexane Oxane Oxacyclohexane Oxane 暫譯: 氧烷 Oxacyclohexane 暫譯: 氧環己烷 Jerome Pansanel 2009-07-06 chemical-structures-2.2.dfsg.0.orig/src/ethers/diethylether.cml0000644000175000017500000000600310722031472025025 0ustar georgeskgeorgesk Ethoxyethane 74.1216 74.0731649 -116 35 chemical-structures-2.2.dfsg.0.orig/src/ethers/dimethylether.cml0000644000175000017500000000444110722031472025206 0ustar georgeskgeorgesk Methoxymethane 46.0684 46.0418648 -141 -25 chemical-structures-2.2.dfsg.0.orig/src/ethers/dibutylether.cml0000644000175000017500000001071310722031472025042 0ustar georgeskgeorgesk 1-Butoxybutane 130.2279 130.1357652 -98 142 chemical-structures-2.2.dfsg.0.orig/src/ethers/1_4-dioxane.cml0000644000175000017500000000565210662517661024370 0ustar georgeskgeorgesk 1,4-Dioxane 88.1051 88.0524295 11 101 chemical-structures-2.2.dfsg.0.orig/src/ethers/2_3-dimethyloxepin.cml0000644000175000017500000000630710662517661026001 0ustar georgeskgeorgesk 2,3-Dimethyloxepin 122.1644 122.0731649 chemical-structures-2.2.dfsg.0.orig/src/ethers/dipropylether.cml0000644000175000017500000000736210722031472025236 0ustar georgeskgeorgesk 1-Propoxypropane 102.1748 102.1044651 -123 89 chemical-structures-2.2.dfsg.0.orig/src/ethers/CMakeLists.txt0000644000175000017500000000712211112716045024401 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "ethers") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/ethers/2_7-dimethyloxepin.cml0000644000175000017500000000631010662517661025777 0ustar georgeskgeorgesk 2,7-Dimethyloxepin 122.1644 122.0731649 chemical-structures-2.2.dfsg.0.orig/src/ethers/tetrahydrofuran.cml0000644000175000017500000000546410722031472025566 0ustar georgeskgeorgesk Oxacyclopentane 72.1057 72.0575149 -108 65 chemical-structures-2.2.dfsg.0.orig/src/ethers/oxepin.cml0000644000175000017500000000470210662517661023655 0ustar georgeskgeorgesk Oxepin 94.1112 94.0418648 chemical-structures-2.2.dfsg.0.orig/src/ethers/tetrahydropyran.cml0000644000175000017500000000622411224730174025602 0ustar georgeskgeorgesk Oxane 86.1323 86.0731649 -48 88 chemical-structures-2.2.dfsg.0.orig/src/ethers/2-2-hydroxyethoxy_ethanol.cml0000644000175000017500000000642410662517661027335 0ustar georgeskgeorgesk 2-(2-Hydroxyethoxy)ethanol 106.1204 106.0629942 -10 245 chemical-structures-2.2.dfsg.0.orig/src/sulfones/0000755000175000017500000000000011225622315022204 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/sulfones/p-toluenesulfonic_acid.cml0000644000175000017500000000712410723242616027344 0ustar georgeskgeorgesk 4-Methylbenzenesulfonic acid 172.2016 172.0194151 104 140 chemical-structures-2.2.dfsg.0.orig/src/sulfones/index.xml0000644000175000017500000000347211142231213024032 0ustar georgeskgeorgesk Sulfones Sulfone Sulfonas Sulfones Sulfonen Sulfones 碸 p-Toluenesulfonic acid Acide p-toluènesulfonique p-Toluenesulfonic acid 對-甲苯磺酸 p-toluenesulfonic_acid 4-Methylbenzenesulfonic acid Acide 4-méthylbenzènesulfonique 4-Methylbenzenesulfonic acid 4-甲基苯磺酸 PTSA Jerome Pansanel 2006-11-22 Benzenesulfonic acid Acide benzènesulfonique Benzenesulfonic acid 苯磺酸 benzenesulfonic_acid Jerome Pansanel 2006-11-22 Methanesulfonic acid Acide méthanesulfonique Methanesulfonic acid 甲磺酸 methanesulfonic_acid Methylsulfonic acid Acide méthylsulfonique Methylsulfonic acid 甲磺酸 MSA Jerome Pansanel 2006-11-22 chemical-structures-2.2.dfsg.0.orig/src/sulfones/CMakeLists.txt0000644000175000017500000000712411112716045024747 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "sulfones") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/sulfones/benzenesulfonic_acid.cml0000644000175000017500000000603610662517661027072 0ustar georgeskgeorgesk Benzenesulfonic acid 158.1750 158.0037651 47 chemical-structures-2.2.dfsg.0.orig/src/sulfones/methanesulfonic_acid.cml0000644000175000017500000000421710662517661027064 0ustar georgeskgeorgesk Methanesulfonic acid 96.1057 95.9881150 20 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/0000755000175000017500000000000011225622315024562 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/tetralin.cml0000644000175000017500000000766610662517661027133 0ustar georgeskgeorgesk Tetralin 132.2023 132.0939004 -36 208 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/anthracene.cml0000644000175000017500000000760610662517661027413 0ustar georgeskgeorgesk Anthracene 178.2292 178.0782503 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/caffeine.cml0000644000175000017500000001007110723241547027024 0ustar georgeskgeorgesk 1,3,7-Trimethylpurine-2,6-dione 194.1906 194.0803756 235 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/7H-purine.cml0000644000175000017500000000527210662517661027056 0ustar georgeskgeorgesk 7H-Purine 120.1121 120.0435961 216 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/quinazoline.cml0000644000175000017500000000632310662517661027634 0ustar georgeskgeorgesk Quinazoline 130.1466 130.0530982 48 243 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/quinoline.cml0000644000175000017500000000651210662517661027301 0ustar georgeskgeorgesk Quinoline 129.1586 129.0578492 -15 237 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/index.xml0000644000175000017500000003304311202002412026377 0ustar georgeskgeorgesk Polycyclic aromatics Polyzyklische Aromaten Aromáticos policíclicos Aromatiques polycycliques Polycyclische Aromaten Polycyclic aromatics 多環芳香類 1,10-Phenanthroline 1,10-Phénanthroline 1,10-Phenanthroline 1,10二氮雜菲 1_10-phenanthroline Jerome Pansanel 2006-07-31 1,8-Naphthyridine 1,8-Naphthyridine 1,8-Naphthyridine 1,8-萘啶 1_8-naphthyridine 1,8-Diazanaphthalene 1,8-Diazanaphthalène 1,8-Diazanaphthalene Jerome Pansanel 2006-07-31 1H-Indene 1H-Indène 1H-Indene 1氫-茚 1H-indene Jerome Pansanel 2006-07-31 1H-Indole 1H-Indole 1H-Indole 1氫-吲哚 1H-indole Jerome Pansanel 2006-07-31 N-(2-Hydroxyethyl)phthalimide N-(2-Hydroxyéthyl)phthalimide N-(2-Hydroxyethyl)phthalimide N-(2-羥乙基)鄰苯二甲醯亞胺 N-2-hydroxyethylphthalimide 2-(2-Hydroxyethyl)isoindole-1,3-dione 2-Phthalimidoethanol 2-(2-Hydroxyéthyl)isoindole-1,3-dione 2-Phthalimidoéthanol 2-(2-Hydroxyethyl)isoindole-1,3-dione 2-(2-羥乙基)異吲哚-1,3-二酮 2-Phthalimidoethanol 酞醯亞胺基乙醇 Jerome Pansanel 2006-07-31 2H-Chromene 2H-Chromène 2H-Chromene 2氫-克唏 2H-chromene 2H-1-Benzopyran 2H-1-Benzopyran 2H-1-Benzopyran 2氫-1-苯并呱喃 Jerome Pansanel 2006-07-31 4H-Chromene 4H-Chromène 4H-Chromene 4氫-克唏 4H-chromene 4H-1-Benzopyran 4H-1-Benzopyran 4H-1-Benzopyran 4氫-1-苯并呱喃 Jerome Pansanel 2006-07-31 7H-Purine 7H-Purine 7H-Purine 7氫-嘌呤 7H-purine Jerome Pansanel 2006-07-31 9H-Carbazole 9H-Carbazole 9H-Carbazole 9氫-咔唑 9H-carbazole Jerome Pansanel 2006-07-31 9H-Fluorene 9H-Fluorène 9H-Fluorene 9氫-茀 9H-fluorene Jerome Pansanel 2006-07-31 9H-Xanthene 9H-Xanthène 9H-Xanthene 9氫-二苯并喃 9H-xanthene Jerome Pansanel 2006-07-31 Acridine Acridine Acridine 吖啶/一氮蒽 acridine Jerome Pansanel 2006-07-31 Anthracene Anthracène Anthracene 蔥 anthracene Jerome Pansanel 2006-07-31 Benzofuran Benzofurane Benzofuran 苯并夫喃 benzofuran Jerome Pansanel 2006-07-31 Benzothiophene Benzothiophène Benzothiophene 苯并噻吩 benzothiophene Jerome Pansanel 2006-07-31 Coumarin Coumarine Coumarin 香豆素/薰草素 coumarin Chromen-2-one Chromèn-2-one Chromen-2-one 克唏-2-酮 Jerome Pansanel 2006-07-31 Chromone Chromone Chromone 色酮 chromone Chromen-4-one 1-Benzopyran-4-one Chromèn-4-one 1-Benzopyran-4-one Chromen-4-one 克唏-4-酮 1-Benzopyran-4-one 1-苯并夫喃-4-酮 Jerome Pansanel 2006-07-31 Cinnoline Cinnoline Cinnoline 辛啉 cinnoline Jerome Pansanel 2006-07-31 Phthalimide Phthalimide Phthalimide 鄰苯二甲醯亞胺 phthalimide Isoindole-1,3-dione 1,3-Dihydro-1,3-dioxoisoindole Isoindole-1,3-dione 1,3-Dihydro-1,3-dioxoisoindole Isoindole-1,3-dione 異吲哚-1,3-二酮 1,3-Dihydro-1,3-dioxoisoindole 1,3-二氫-1,3-二氧異吲哚 Jerome Pansanel 2006-07-31 Isoquinoline Isoquinoline Isoquinoline 異構喹啉 isoquinoline Jerome Pansanel 2006-07-31 Naphthalene Naphthalène Naphthalene 萘 naphthalene Jerome Pansanel 2006-07-31 Phenanthrene Phénanthrène Phenanthrene 菲 phenanthrene Jerome Pansanel 2006-07-31 Quinazoline Quinazoline Quinazoline 喹唑啉 quinazoline Jerome Pansanel 2006-07-31 Quinoline Quinoline Quinoline 喹啉 quinoline Jerome Pansanel 2006-07-31 Tetralin Tétraline Tetralin 四氫萘 tetralin Jerome Pansanel 2006-07-31 2-Benzofuranyl methyl ketone 2-Benzofuranyl méthyl cétone 2-Benzofuranyl methyl ketone 2-苯并夫喃基甲基酮 2-Benzofuranyl_methyl_ketone 1-(1-Benzofuran-2-yl)ethanone 2-Acetylbenzofuran 1-(1-Benzofuran-2-yl)éthanone 2-Acétobenzofurane 1-(1-Benzofuran-2-yl)ethanone 2-Acetylbenzofuran Jerome Pansanel 2006-10-15 Acenaphthenequinone Acénaphthènequinone Acenaphthenequinone 乙烷萘醌 acenaphthenequinone Acenaphthene-1,2-dione Acénaphthène-1,2-dione Acenaphthene-1,2-dione 苊-1,2-二酮 Jerome Pansanel 2006-11-09 Acenaphthene Acénaphthène Acenaphthene 苊 acenaphthene Jerome Pansanel 2006-11-09 Acenaphthylene Acénaphthylène Acenaphthylene 苊烯 acenaphthylene Acenaphthalene Acénaphthalène Acenaphthalene 苊烯 Jerome Pansanel 2006-11-09 Caffeine Cafféine Caffeine 咖啡因/咖啡鹼 caffeine 1,3,7-Trimethylpurine-2,6-dione 1,3,7-Trimethylxanthine 1,3,7-Triméthylpurine-2,6-dione 1,3,7-Triméthylxanthine 1,3,7-Trimethylpurine-2,6-dione 1,3,7-三甲基嘌呤-2,6-二酮 1,3,7-Trimethylxanthine 1,3,7-三甲基黃嘌呤 Jerome Pansanel 2006-11-21 D-Warfarin D-Warfarine D-Warfarin D-殺鼠靈 D-warfarin 2-hydroxy-3-[(1R)-3-oxo-1-phenylbutyl]chromen-4-one 2-hydroxy-3-[(1R)-3-oxo-1-phénylbutyl]chromèn-4-one 2-hydroxy-3-[(1R)-3-oxo-1-phenylbutyl]chromen-4-one 2-羥-3-[(1R)-3-氧基-1-苯丁基]克唏-4-酮 Jerome Pansanel 2006-11-21 Uric acid Acide urique Uric acid 尿酸 uric_acid 7,9-dihydro-3H-purine-2,6,8-trione 2,6,8-Trihydroxypurine 7,9-dihydro-3H-purine-2,6,8-trione 2,6,8-Trihydroxypurine 7,9-dihydro-3H-purine-2,6,8-trione 7,9-二氫-3H-嘌呤-2,6,8-三酮 2,6,8-Trihydroxypurine 2,6,8-三羥基嘌呤 Jerome Pansanel 2006-11-21 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/acridine.cml0000644000175000017500000001015310662517661027050 0ustar georgeskgeorgesk Acridine 179.2173 179.0734993 111 345 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/9H-carbazole.cml0000644000175000017500000000775310662517661027526 0ustar georgeskgeorgesk 9H-Carbazole 167.2066 167.0734993 247 355 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/N-2-hydroxyethylphthalimide.cml0000644000175000017500000000771610723241547032617 0ustar georgeskgeorgesk 2-(2-Hydroxyethyl)isoindole-1,3-dione 191.1834 191.0582432 129 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/D-warfarin.cml0000644000175000017500000001346310723241547027266 0ustar georgeskgeorgesk 2-Hydroxy-3-[(1R)-3-oxo-1-phenylbutyl]chromen-4-one 308.3279 308.1048590 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/2-Benzofuranyl_methyl_ketone.cml0000644000175000017500000000710010723241547033027 0ustar georgeskgeorgesk 1-(1-Benzofuran-2-yl)ethanone 160.1693 160.0524295 71 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/9H-fluorene.cml0000644000175000017500000001014310662517661027366 0ustar georgeskgeorgesk 9H-Fluorene 166.2185 166.0782503 116 294 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/9H-xanthene.cml0000644000175000017500000001035010662517661027361 0ustar georgeskgeorgesk 9H-Xanthene 182.2179 182.0731649 100 311 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/naphthalene.cml0000644000175000017500000000667210662517661027574 0ustar georgeskgeorgesk Naphthalene 128.1705 128.0626003 80 218 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/benzothiophene.cml0000644000175000017500000000613410662517661030317 0ustar georgeskgeorgesk Benzothiophene 134.1982 134.0190212 32 221 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/coumarin.cml0000644000175000017500000000652110723241547027106 0ustar georgeskgeorgesk Chromen-2-one 146.1427 146.0367794 71 302 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/chromone.cml0000644000175000017500000000623610723241547027106 0ustar georgeskgeorgesk Chromen-4-one 146.1427 146.0367794 47 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/phenanthrene.cml0000644000175000017500000001034111130373737027743 0ustar georgeskgeorgesk Phenanthrene 178.2292 178.0782503 101 340 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/uric_acid.cml0000644000175000017500000000616210723241547027214 0ustar georgeskgeorgesk 7,9-Dihydro-3H-purine-2,6,8-trione 168.1103 168.0283400 > 300 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/cinnoline.cml0000644000175000017500000000556310662517661027261 0ustar georgeskgeorgesk Cinnoline 130.1466 130.0530982 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/CMakeLists.txt0000644000175000017500000000714011112716045027323 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "polycyclic_aromatics") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/benzofuran.cml0000644000175000017500000000564610662517661027456 0ustar georgeskgeorgesk Benzofuran 118.1326 118.0418648 174 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/phthalimide.cml0000644000175000017500000000611010723241547027553 0ustar georgeskgeorgesk Isoindole-1,3-dione 147.1308 147.0320284 238 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/1_10-phenanthroline.cml0000644000175000017500000001000210662517661030737 0ustar georgeskgeorgesk 1,10-Phenanthroline 180.2053 180.0687483 117 > 300 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/1_8-naphthyridine.cml0000644000175000017500000000560410662517661030532 0ustar georgeskgeorgesk 1,8-Naphthyridine 130.1466 130.0530982 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/2H-chromene.cml0000644000175000017500000000615510662517661027350 0ustar georgeskgeorgesk 2H-Chromene 132.1592 132.0575149 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/1H-indene.cml0000644000175000017500000000650310662517661027006 0ustar georgeskgeorgesk 1H-Indene 116.1598 116.0626003 -2 183 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/acenaphthenequinone.cml0000644000175000017500000000713510723241547031315 0ustar georgeskgeorgesk Acenaphthene-1,2-dione 182.1748 182.0367794 259 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/acenaphthene.cml0000644000175000017500000000775010662517661027726 0ustar georgeskgeorgesk Acenaphthene 154.2078 154.0782503 93 279 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/1H-indole.cml0000644000175000017500000000631510662517661027017 0ustar georgeskgeorgesk 1H-Indole 117.1479 117.0578492 52 254 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/acenaphthylene.cml0000644000175000017500000000735710662517661030276 0ustar georgeskgeorgesk Acenaphthylene 152.1919 152.0626003 90 280 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/4H-chromene.cml0000644000175000017500000000616110662517661027347 0ustar georgeskgeorgesk 4H-Chromene 132.1592 132.0575149 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_aromatics/isoquinoline.cml0000644000175000017500000000623710662517661030020 0ustar georgeskgeorgesk Isoquinoline 129.1586 129.0578492 26 chemical-structures-2.2.dfsg.0.orig/src/carbohydrates/0000755000175000017500000000000011225622315023200 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/carbohydrates/d-ribose.cml0000644000175000017500000000646410700715641025415 0ustar georgeskgeorgesk (2R,3R,4R)-2,3,4,5-Tetrahydroxypentanal 150.1299 150.0528234 chemical-structures-2.2.dfsg.0.orig/src/carbohydrates/d-erythrulose.cml0000644000175000017500000000547610700715641026521 0ustar georgeskgeorgesk (3R)-1,3,4-Trihydroxybutan-2-one 120.1039 120.0422587 chemical-structures-2.2.dfsg.0.orig/src/carbohydrates/d-talose.cml0000644000175000017500000000745710700715641025424 0ustar georgeskgeorgesk (2S,3S,4S,5R)-2,3,4,5,6-Pentahydroxyhexanal 180.1559 180.0633881 chemical-structures-2.2.dfsg.0.orig/src/carbohydrates/index.xml0000644000175000017500000003124011142231213025020 0ustar georgeskgeorgesk Carbohydrates Kohlenhydrate Hidratos de carbono Carbohydrates Koolhydraten Carbohydrates 碳水化合物 D-Allose D-Allose D-Allose D-阿洛糖 d-allose D-allo-Hexose D-allo-Hexose D-別己糖 這是種六碳醛糖 (aldohexose) Jerome Pansanel 2007-10-02 D-Altrose D-Altrose D-Altrose 阿卓糖 d-altrose D-altro-Hexose D-altro-Hexose 這是種六碳醛糖 (aldohexose) Jerome Pansanel 2007-10-02 D-Arabinose D-Arabinose D-Arabinose 阿拉伯糖/樹膠糖 d-arabinose D-arabino-Pentose D-arabino-Pentose 這是種五碳醛糖 (aldopentose) Jerome Pansanel 2007-10-02 D-Erythrose D-Erythrose D-Erythrose D-赤藻糖 d-erythrose D-erythro-Tetrose D-érythro-Tétrose D-erythro-Tetrose 赤藻糖/原藻醛糖/丁糖/四碳糖 這是種四碳醛糖 (aldotetrose) Jerome Pansanel 2007-10-02 D-Erythrulose D-Érythrulose D-Erythrulose 赤藻酮糖 d-erythrulose D-glycero-2-Tetrulose D-glycéro-2-Tétrulose D-glycero-2-Tetrulose 這是種四碳酮糖 (ketotetrose) Jerome Pansanel 2007-10-02 D-Fructose D-Fructose D-Fructose D-果糖 d-fructose D-arabino-2-Hexulose D-Levulose Fruit Sugar D-arabino-2-Hexulose D-Levulose D-arabino-2-Hexulose D-Levulose D-左旋糖 Fruit Sugar 果糖 這是種六碳酮糖 (ketohexose) Jerome Pansanel 2007-10-02 D-Galactose D-Galactose D-Galactose D-半乳糖 d-galactose D-galacto-Hexose D-galacto-Hexose D-galacto-Hexose 這是種六碳醛糖 (aldohexose) Jerome Pansanel 2007-10-02 D-Glucose D-Glucose D-Glucose D-葡萄糖 d-glucose D-gluco-Hexose Dextrose D-gluco-Hexose Dextrose D-gluco-Hexose Dextrose 右旋糖 這是種六碳醛糖 (aldohexose) Jerome Pansanel 2007-10-02 D-Glyceraldehyde D-Glycéraldéhyde D-Glyceraldehyde D-甘油醛 d-glyceraldehyde D-glycero-Triose D-Glycerose D-glycéro-Triose D-Glycérose D-glycero-Triose D-Glycerose D-甘油糖 這是種三碳醛糖 (aldotriose) Jerome Pansanel 2007-10-02 D-Gulose D-Gulose D-Gulose 古洛糖 d-gulose D-gulo-Hexose D-gulo-Hexose D-gulo-Hexose 這是種六碳醛糖 (aldohexose) Jerome Pansanel 2007-10-02 D-Idose D-Idose D-Idose 艾杜糖 d-idose D-ido-Hexose D-ido-Hexose D-ido-Hexose 這是種六碳醛糖 (aldohexose) Jerome Pansanel 2007-10-02 Dihydroxyacetone Dihydroxyacétone Dihydroxyacetone 二羥丙酮 dihydroxyacetone Glycerone Glycérone Glycerone 這是種三碳酮糖 (ketotriose) DHA Jerome Pansanel 2007-10-02 D-Lyxose D-Lyxose D-Lyxose D-來蘇糖 d-lyxose D-lyxo-Pentose D-lyxo-Pentose D-lyxo-Pentose 這是種五碳醛糖 (aldopentose) Jerome Pansanel 2007-10-02 D-Mannose D-Mannose D-Mannose D-甘露糖 d-mannose D-manno-Hexose D-manno-Hexose D-manno-Hexose 這是種六碳醛糖 (aldohexose) Jerome Pansanel 2007-10-02 D-Psicose D-Psicose D-Psicose D-阿洛酮糖 d-psicose D-ribo-2-Hexulose D-Allulose D-ribo-2-Hexulose D-Allulose D-ribo-2-Hexulose 這是種六碳酮糖 (ketohexose) Jerome Pansanel 2007-10-02 D-Ribose D-Ribose D-Ribose 核糖 d-ribose D-ribo-Pentose D-ribo-Pentose D-ribo-Pentose 這是種五碳醛糖 (aldopentose) Jerome Pansanel 2007-10-02 D-Ribulose D-Ribulose D-Ribulose 核酮糖 d-ribulose D-erythro-2-Pentulose D-érythro-2-Pentulose D-erythro-2-Pentulose 這是種五碳酮糖 (ketopentose) Jerome Pansanel 2007-10-02 D-Sorbose D-Sorbose D-Sorbose 山梨糖/花椒糖 d-sorbose D-xylo-2-Hexulose D-xylo-2-Hexulose D-xylo-2-Hexulose 這是種六碳酮糖 (ketohexose) Jerome Pansanel 2007-10-02 D-Tagatose D-Tagatose D-Tagatose 塔格糖 d-tagatose D-lyxo-2-Hexulose D-lyxo-2-Hexulose D-lyxo-2-Hexulose 這是種六碳酮糖 (ketohexose) Jerome Pansanel 2007-10-02 D-Talose D-Talose D-Talose 塔羅糖/太洛糖 d-talose D-talo-Hexose D-talo-Hexose D-talo-Hexose D-5右羥己糖 這是種六碳醛糖 (aldohexose) Jerome Pansanel 2007-10-02 D-Threose D-Thréose D-Threose D-蘇糖/異赤藻糖 d-threose D-threo-Tetrose D-thréo-Tétrose D-threo-Tetrose 這是種四碳醛糖 (aldotetrose) Jerome Pansanel 2007-10-02 D-Xylose D-Xylose D-Xylose 木糖 d-xylose D-xylo-Pentose Wood Sugar D-xylo-Pentose D-xylo-Pentose Wood Sugar 木糖 這是種五碳醛糖 (aldopentose) Jerome Pansanel 2007-10-02 D-Xylulose D-Xylulose D-Xylulose 木酮糖 d-xylulose D-threo-2-Pentulose D-thréo-2-Pentulose D-threo-2-Pentulose 這是種五碳酮糖 (ketopentose) Jerome Pansanel 2007-10-02 chemical-structures-2.2.dfsg.0.orig/src/carbohydrates/d-xylose.cml0000644000175000017500000000646410700715641025455 0ustar georgeskgeorgesk (2R,3S,4R)-2,3,4,5-Tetrahydroxypentanal 150.1299 150.0528234 chemical-structures-2.2.dfsg.0.orig/src/carbohydrates/d-allose.cml0000644000175000017500000000773210700715641025410 0ustar georgeskgeorgesk (2R,3R,4R,5R)-2,3,4,5,6-Pentahydroxyhexanal 180.1559 180.0633881 144 chemical-structures-2.2.dfsg.0.orig/src/carbohydrates/d-tagatose.cml0000644000175000017500000000746610700715641025744 0ustar georgeskgeorgesk (3S,4S,5R)-1,3,4,5,6-Pentahydroxyhexan-2-one 180.1559 180.0633881 chemical-structures-2.2.dfsg.0.orig/src/carbohydrates/d-altrose.cml0000644000175000017500000000745010700715641025577 0ustar georgeskgeorgesk (2S,3R,4R,5R)-2,3,4,5,6-Pentahydroxyhexanal 180.1559 180.0633881 chemical-structures-2.2.dfsg.0.orig/src/carbohydrates/d-galactose.cml0000644000175000017500000000745510700715641026075 0ustar georgeskgeorgesk (2R,3S,4S,5R)-2,3,4,5,6-Pentahydroxyhexanal 180.1559 180.0633881 chemical-structures-2.2.dfsg.0.orig/src/carbohydrates/dihydroxyacetone.cml0000644000175000017500000000475510700715641027274 0ustar georgeskgeorgesk 1,3-Dihydroxypropan-2-one 90.0779 90.0316941 78 chemical-structures-2.2.dfsg.0.orig/src/carbohydrates/d-erythrose.cml0000644000175000017500000000550010700715641026144 0ustar georgeskgeorgesk (2R,3R)-2,3,4-Trihydroxybutanal 120.1039 120.0422587 chemical-structures-2.2.dfsg.0.orig/src/carbohydrates/d-idose.cml0000644000175000017500000000746110700715641025233 0ustar georgeskgeorgesk (2S,3R,4S,5R)-2,3,4,5,6-Pentahydroxyhexanal 180.1559 180.0633881 chemical-structures-2.2.dfsg.0.orig/src/carbohydrates/d-gulose.cml0000644000175000017500000000745210700715641025426 0ustar georgeskgeorgesk (2R,3R,4S,5R)-2,3,4,5,6-Pentahydroxyhexanal 180.1559 180.0633881 chemical-structures-2.2.dfsg.0.orig/src/carbohydrates/d-mannose.cml0000644000175000017500000000746010700715641025567 0ustar georgeskgeorgesk (2S,3S,4R,5R)-2,3,4,5,6-Pentahydroxyhexanal 180.1559 180.0633881 chemical-structures-2.2.dfsg.0.orig/src/carbohydrates/d-threose.cml0000644000175000017500000000547510700715641025604 0ustar georgeskgeorgesk (2S,3R)-2,3,4-Trihydroxybutanal 120.1039 120.0422587 chemical-structures-2.2.dfsg.0.orig/src/carbohydrates/d-psicose.cml0000644000175000017500000000746410700715641025600 0ustar georgeskgeorgesk (3R,4R,5R)-1,3,4,5,6-Pentahydroxyhexan-2-one 180.1559 180.0633881 chemical-structures-2.2.dfsg.0.orig/src/carbohydrates/d-sorbose.cml0000644000175000017500000000745710700715641025611 0ustar georgeskgeorgesk (3R,4S,5R)-1,3,4,5,6-Pentahydroxyhexan-2-one 180.1559 180.0633881 chemical-structures-2.2.dfsg.0.orig/src/carbohydrates/d-ribulose.cml0000644000175000017500000000646510700715641025757 0ustar georgeskgeorgesk (3R,4R)-1,3,4,5-Tetrahydroxypentan-2-one 150.1299 150.0528234 chemical-structures-2.2.dfsg.0.orig/src/carbohydrates/CMakeLists.txt0000644000175000017500000000713111225106077025744 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "carbohydrates") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/carbohydrates/d-glucose.cml0000644000175000017500000000745510700715641025574 0ustar georgeskgeorgesk (2R,3S,4R,5R)-2,3,4,5,6-Pentahydroxyhexanal 180.1559 180.0633881 chemical-structures-2.2.dfsg.0.orig/src/carbohydrates/d-xylulose.cml0000644000175000017500000000646510700715641026017 0ustar georgeskgeorgesk (3S,4R)-1,3,4,5-Tetrahydroxypentan-2-one 150.1299 150.0528234 chemical-structures-2.2.dfsg.0.orig/src/carbohydrates/d-glyceraldehyde.cml0000644000175000017500000000451410700715641027111 0ustar georgeskgeorgesk (2R)-2,3-Dihydroxypropanal 90.0779 90.0316941 chemical-structures-2.2.dfsg.0.orig/src/carbohydrates/d-arabinose.cml0000644000175000017500000000647110700715641026073 0ustar georgeskgeorgesk (2S,3R,4R)-2,3,4,5-Tetrahydroxypentanal 150.1299 150.0528234 chemical-structures-2.2.dfsg.0.orig/src/carbohydrates/d-fructose.cml0000644000175000017500000000747110700715641025763 0ustar georgeskgeorgesk (3S,4R,5R)-1,3,4,5,6-Pentahydroxyhexan-2-one 180.1559 180.0633881 chemical-structures-2.2.dfsg.0.orig/src/carbohydrates/d-lyxose.cml0000644000175000017500000000647110700715641025453 0ustar georgeskgeorgesk (2S,3S,4R)-2,3,4,5-Tetrahydroxypentanal 150.1299 150.0528234 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_alkanes/0000755000175000017500000000000011225622315024216 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/polycyclic_alkanes/cis-decahydronaphthalene.cml0000644000175000017500000001126210662517661031656 0ustar georgeskgeorgesk cis-Decahydronaphthalene 138.2499 138.1408506 -43 194 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_alkanes/abietic_acid.cml0000644000175000017500000001676010662517661027320 0ustar georgeskgeorgesk Abietic acid 302.4510 302.2245802 173 ././@LongLink0000000000000000000000000000015200000000000011563 Lustar rootrootchemical-structures-2.2.dfsg.0.orig/src/polycyclic_alkanes/hexadecahydro-1H-cyclopenta_a_phenanthrene.cmlchemical-structures-2.2.dfsg.0.orig/src/polycyclic_alkanes/hexadecahydro-1H-cyclopenta_a_phenanthren0000644000175000017500000001511210662517661034263 0ustar georgeskgeorgesk 2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17-Hexadecahydro-1H-cyclopenta[a]phenanthrene 232.4042 232.2191009 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_alkanes/index.xml0000644000175000017500000001161011142231213026035 0ustar georgeskgeorgesk Polycyclic alkanes Polyzyklische Alkane Alcanos policíclicos Alcanes polycycliques Polycyclische Alkanen Polycyclic alkanes 多環烷類 cis-Decahydronaphthalene cis-Décahydronaphthalène cis-Decahydronaphthalene 順十氫萘/順十氫化萘 cis-decahydronaphthalene cis-Decalin cis-Décaline cis-Decalin 順十氫萘/順十氫化萘 Jerome Pansanel 2006-07-31 trans-Decahydronaphthalene trans-Décahydronaphthalène trans-Decahydronaphthalene 反十氫萘/反十氫化萘 trans-decahydronaphthalene trans-Decalin trans-Décaline trans-Decalin 反十氫萘/反十氫化萘 Jerome Pansanel 2006-07-31 Hexadecahydro-1H-cyclopenta[a]phenanthrene Hexadecahydro-1H-cyclopenta[a]phenanthrène Hexadecahydro-1H-cyclopenta[a]phenanthrene 16氫-1氫-環戊烷并[a]菲 hexadecahydro-1H-cyclopenta_a_phenanthrene Jerome Pansanel 2006-07-31 Abietic acid Abietinsäure Acide abiétique Abietic acid 松脂酸 abietic_acid Sylvic acid Abietinic acid Sylvinsäure Acide sylvitique Acide abiétinique Sylvic acid 松香酸 Abietinic acid 松脂酸 Jerome Pansanel 2006-11-09 (1R)-Camphor (1R)-Camphor (1R)-Camphor (1R)-樟腦 1R-camphor (1R,4S)-1,7,7-Trimethylnorbornan-2-one D-Camphor (1R,4S)-1,7,7-Triméthylnorbornan-2-one D-Camphor (1R,4S)-1,7,7-Trimethylnorbornan-2-one (1R,4S)-1,7,7-三甲基降樟腦 D-Camphor D-樟腦 Jerome Pansanel 2006-11-22 (1R)-Camphene (1R)-Camphène (1R)-Camphene 莰烯/松精油/樟腦精 1R-camphene (1R,4S)-2,2-Dimethyl-3-methylidenenorbornane D-Camphene (1R,4S)-2,2-Diméthyl-3-méthylidènenorbornane D-Camphène (1R,4S)-2,2-Dimethyl-3-methylidenenorbornane (1R,4S)-2,2-二甲基-3-亞甲基降莰烷 D-Camphene 莰烯 Jerome Pansanel 2006-11-22 Cubane Cubane Cubane 立方體烷 cubane Jerome Pansanel 2006-11-22 Norbornane Norbornane Norbornane 降莰烷 norbornane Bicyclo[2.2.1]heptane Bicyclo[2.2.1]heptane Bicyclo[2.2.1]heptane 雙環[2.2.1]庚烷 Jerome Pansanel 2007-12-03 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_alkanes/1R-camphene.cml0000644000175000017500000001075410723044250026760 0ustar georgeskgeorgesk (1R,4S)-2,2-Dimethyl-3-methylidenenorbornane 136.2340 136.1252005 37 159 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_alkanes/norbornane.cml0000644000175000017500000000663410724756115027100 0ustar georgeskgeorgesk Bicyclo[2.2.1]heptane 96.1702 96.0939004 86 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_alkanes/cubane.cml0000644000175000017500000000576610662517661026201 0ustar georgeskgeorgesk Cubane 104.1491 104.0626003 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_alkanes/trans-decahydronaphthalene.cml0000644000175000017500000001126510662517661032232 0ustar georgeskgeorgesk trans-Decahydronaphthalene 138.2499 138.1408506 -31 186 chemical-structures-2.2.dfsg.0.orig/src/polycyclic_alkanes/CMakeLists.txt0000644000175000017500000000713611112716045026764 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "polycyclic_alkanes") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/polycyclic_alkanes/1R-camphor.cml0000644000175000017500000001066410723044250026631 0ustar georgeskgeorgesk (1R,4S)-1,7,7-Trimethylnorbornan-2-one 152.2334 152.1201151 180 chemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/0000755000175000017500000000000011225622315023650 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/4-aminobutanoic_acid.cml0000644000175000017500000000623011224730174030321 0ustar georgeskgeorgesk 4-Aminobutanoic acid 103.1198 103.0633285 201 chemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/2_2_2-trichloroacetic_acid.cml0000644000175000017500000000432710662517661031325 0ustar georgeskgeorgesk 2,2,2-Trichloroacetic acid 163.3871 161.9042123 56 196 chemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/L-ascorbic_acid.cml0000644000175000017500000000717310721776211027320 0ustar georgeskgeorgesk (2R)-2-[(1S)-1,2-Dihydroxyethyl]-4,5-dihydroxyfuran-3-one 176.1241 176.0320880 193 chemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/2_2-dichloroacetic_acid.cml0000644000175000017500000000432110662517661030674 0ustar georgeskgeorgesk 2,2-Dichloroacetic acid 128.9421 127.9431847 10 194 chemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/E-2-methylbut-2-enedioic_acid.cml0000644000175000017500000000561410673462010031605 0ustar georgeskgeorgesk (E)-2-Methylbut-2-enedioic acid 130.0987 130.0266087 202 chemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/index.xml0000644000175000017500000003364611224730174025517 0ustar georgeskgeorgesk Carboxylic acids Carbonsäuren Ácidos carboxílicos Acides carboxyliques Carbonzuren Carboxylic acids 羧酸 2,2,2-Trifluoroacetic acid 2,2,2-Trifluoroessigsäure Acide 2,2,2-Trifluoroacétique 2,2,2-Trifluoroacetic acid 2,2,2-三氟乙酸 2_2_2-trifluoroacetic_acid Perfluoroacetic acid Perfluoroessig säure Acide perfluoroacétique Perfluoroacetic acid Jerome Pansanel 2006-05-10 Citric acid Zitronsaüre Acide citrique Citric acid 檸檬酸 citric_acid 2-Hydroxypropane-1,2,3-tricarboxylic acid 2-Hydroxypropan-1,2,3-tricarbonsäure Acide 2-hydroxypropan-1,2,3-tricarboxylique 2-Hydroxypropane-1,2,3-tricarboxylic acid 2-羥基丙-1,2,3-三酸 Jerome Pansanel 2006-05-10 L-Ascorbic acid L-Ascorbinsäure Acide L-ascorbique L-Ascorbic acid L-抗壞血酸 L-ascorbic_acid (2R)-2-[(1S)-1,2-Dihydroxyethyl]-4,5-dihydroxyfuran-3-one (2R)-2-[(1S)-1,2-Dihydroxyethyl]-4,5-dihydroxyfuran-3-on (2R)-2-[(1S)-1,2-Dihydroxyethyl]-4,5-dihydroxyfuran-3-one (2R)-2-[(1S)-1,2-Dihydroxyethyl]-4,5-dihydroxyfuran-3-one (2R)-2-[(1S)-1,2-二羥乙基]-4,5-二羥基夫喃-3-酮 抗壞血酸又叫維他命 C (vitamin C) Jerome Pansanel 2006-05-10 D-Malic acid D-Äpfelsäure Acide D-malique D-Malic acid 蘋果酸 D-malic_acid (R)-2-Hydroxybutanedioic acid (R)-2-Hydroxysuccinic acid (R)-2-Hydroxysuccinicsäure (R)-2-Hydroxybutandicarbonsäure Acide (R)-2-hydroxybutanedioïque Acide (R)-2-hydroxysuccinique (R)-2-Hydroxybutanedioic acid (R)-2-羥基丁二酸 (R)-2-Hydroxysuccinic acid (R)-2-羥基琥珀酸 Jerome Pansanel 2006-05-10 D-Lactic acid D-Milchsäure Acide D-lactique D-Lactic acid D-乳酸 D-lactic_acid (R)-2-Hydroxypropanoic acid (R)-2-Hydroxypropansäure Acide (R)-2-hydroxypropanoïque (R)-2-Hydroxypropanoic acid (R)-2-羥基丙酸 Jerome Pansanel 2006-05-10 L-Tartaric acid L-Weinsäure Acide L-tartrique L-Tartaric acid L-酒石酸 L-tartaric_acid (2R,3R)-2,3-Dihydroxybutanedioic acid (2R,3R)-2,3-Dihydroxybutandicarbonsäure Acide (2R,3R)-2,3-Dihydroxybutanedioïque (2R,3R)-2,3-Dihydroxybutanedioic acid (2R,3R)-2,3-二羥基丁二酸 Jerome Pansanel 2006-05-10 L-Malic acid L-Äpfelsäure Acide L-malique L-Malic acid L-蘋果酸 L-malic_acid (S)-2-Hydroxybutanedioic acid (S)-2-Hydroxybutanedicarbonsäure Acide (S)-2-hydroxybutanedioïque (S)-2-Hydroxybutanedioic acid (S)-2-羥基丁二酸 Jerome Pansanel 2006-05-10 L-Lactic acid L-Milchsäure Acide L-lactique L-Lactic acid L-乳酸 L-lactic_acid (S)-2-Hydroxypropanoic acid (S)-2-Hydroxypropansäure Acide (S)-2-hydroxypropanoïque (S)-2-Hydroxypropanoic acid (S)-2-羥基丙酸 Jerome Pansanel 2006-05-10 (2S,3S)-2,3-Dihydroxybutanedioic acid (2S,3S)-2,3-Dihydroxybutandicarbonsäure Acide (2S,3S)-2,3-dihydroxybutanedioïque (2S,3S)-2,3-Dihydroxybutanedioic acid (2S,3S)-2,3-二羥基丁二酸 D-tartaric_acid D-Tartaric acid D-Weinsäure Acide D-tartrique D-Tartaric acid D-酒石酸 Jerome Pansanel 2006-05-10 Acetic acid Essigsäure Acide acétique Acetic acid 醋酸 acetic_acid Ethanoic acid Acide éthanoïque Ethanoic acid 乙酸 Jerome Pansanel 2006-05-10 Butanedioic acid Butandisäure Acide butanedioïque Butanedioic acid 丁二酸 butanedioic_acid Succinic acid Bernsteinsäure Acide succinique Succinic acid 琥珀酸 Jerome Pansanel 2006-05-10 Butanoic acid Butansäure Acide butanoïque Butanoic acid 丁酸 butanoic_acid n-Butyric acid Buttersäure Acide n-butyrique n-Butyric acid 正酪酸 Jerome Pansanel 2006-05-10 Formic acid Ameisensäure Acide formique Formic acid 蟻酸 formic_acid Methanoic acid Acide méthanoïque Methanoic acid 甲酸 Jerome Pansanel 2006-05-10 Isobutyric acid Isobuttersäure Acide isobutyrique Isobutyric acid 異丁酸 isobutyric_acid Jerome Pansanel 2006-05-10 Oxalic acid Oxalsäure Acide oxalique Oxalic acid 草酸/乙二酸 oxalic_acid Jerome Pansanel 2006-05-10 Propanoic acid Acide propanoïque Propansäure Propanoic acid 丙酸 propanoic_acid Propionic acid Acide propionique Propionic acid 丙酸 Jerome Pansanel 2006-05-10 2,2,2-Trichloroacetic acid Acide 2,2,2-trichloroacétique 2,2,2-Trichloroacetic acid 2,2,2-三氯乙酸 (縮寫為 TCA) 2_2_2-trichloroacetic_acid Jerome Pansanel 2006-11-24 2,2-Dichloroacetic acid Acide 2,2-dichloroacétique 2,2-Dichloroacetic acid 2,2-二氯乙酸 2_2-dichloroacetic_acid Jerome Pansanel 2006-11-24 (E)-2-Methylbut-2-enedioic acid Acide (E)-2-méthylbut-2-ènedioïque (E)-2-Methylbut-2-enedioic acid (E)-2-甲基丁-2-烯二酸 E-2-methylbut-2-enedioic_acid Mesaconic acid Acide mésaconique Mesaconic acid 中康酸 Jerome Pansanel 2007-09-17 (E)-Butenedioic acid Acide (E)-butènedioïque (E)-Butenedioic acid (E)-丁烯二酸 E-butenedioic_acid Fumaric acid Acide fumarique Fumaric acid 富馬酸/延胡索酸 boletic acid 反丁烯二酸 Jerome Pansanel 2007-09-17 (Z)-2-Methylbut-2-enedioic acid Acide (Z)-2-méthylbut-2-ènedioïque (Z)-2-Methylbut-2-enedioic acid (Z)-2-甲基丁-2-烯二酸 Z-2-methylbut-2-enedioic_acid Citraconic acid Acide Citraconique Citraconic acid 檸康酸/甲基順丁烯二酸 Jerome Pansanel 2007-09-17 (Z)-Butenedioic acid Acide (Z)-butènedioïque (Z)-Butenedioic acid (Z)-丁烯二酸 Z-butenedioic_acid Maleic acid Toxilic acid Acide maléique Acide toxilique Maleic acid 馬來酸 Toxilic acid 順丁烯二酸 Jerome Pansanel 2007-09-17 4-Aminobutanoic acid Acide 4-aminobutanoïque 4-Aminobutanoic acid 4-胺基丁酸 4-aminobutanoic_acid 4-Aminobutyric acid gamma-Aminobutyric acid Acide 4-aminobutyrique Acide gamma-aminobutyrique 4-Aminobutyric acid 4-胺基丁酸 gamma-Aminobutyric acid 伽馬-胺基丁酸 (簡稱為 GABA) Jerome Pansanel 2009-07-06 chemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/Z-butenedioic_acid.cml0000644000175000017500000000500510673462010030026 0ustar georgeskgeorgesk (Z)-Butenedioic acid 116.0722 116.0109586 138 chemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/L-malic_acid.cml0000644000175000017500000000610110721776211026606 0ustar georgeskgeorgesk (S)-2-Hydroxybutanedioic acid 134.0874 134.0215233 131 203 chemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/formic_acid.cml0000644000175000017500000000347710662517661026632 0ustar georgeskgeorgesk Formic acid 46.0254 46.0054793 8 100 chemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/Z-2-methylbut-2-enedioic_acid.cml0000644000175000017500000000560710673462010031634 0ustar georgeskgeorgesk (Z)-2-Methylbut-2-enedioic acid 130.0987 130.0266087 91 chemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/L-tartaric_acid.cml0000644000175000017500000000604610721776211027342 0ustar georgeskgeorgesk (2R,3R)-2,3-Dihydroxybutanedioic acid 150.0868 150.0164379 173 chemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/L-lactic_acid.cml0000644000175000017500000000454610721776211026773 0ustar georgeskgeorgesk (S)-2-Hydroxypropanoic acid 90.0779 90.0316941 chemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/D-lactic_acid.cml0000644000175000017500000000454510721776211026762 0ustar georgeskgeorgesk (R)-2-Hydroxypropanoic acid 90.0779 90.0316941 chemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/propanoic_acid.cml0000644000175000017500000000504610662517661027337 0ustar georgeskgeorgesk Propanoic acid 74.0785 74.0367794 -23 141 chemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/D-tartaric_acid.cml0000644000175000017500000000604710721776211027333 0ustar georgeskgeorgesk (2S,3S)-2,3-Dihydroxybutanedioic acid 150.0868 150.0164379 173 chemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/CMakeLists.txt0000644000175000017500000000713411112716045026414 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "carboxylic_acids") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/butanoic_acid.cml0000644000175000017500000000562410662517661027153 0ustar georgeskgeorgesk Butanoic acid 88.1051 88.0524295 -6 163 chemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/butanedioic_acid.cml0000644000175000017500000000564310662517661027636 0ustar georgeskgeorgesk Butanedioic acid 118.0880 118.0266087 187 235 chemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/oxalic_acid.cml0000644000175000017500000000400410662517661026615 0ustar georgeskgeorgesk Oxalic acid 90.0349 89.9953085 189 chemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/2_2_2-trifluoroacetic_acid.cml0000644000175000017500000000432310662517661031341 0ustar georgeskgeorgesk 2,2,2-Trifluoroacetic acid 114.0233 113.9928639 -15 72 chemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/citric_acid.cml0000644000175000017500000000723110721776211026612 0ustar georgeskgeorgesk 2-Hydroxypropane-1,2,3-tricarboxylic acid 192.1235 192.0270026 153 chemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/acetic_acid.cml0000644000175000017500000000425510662517661026576 0ustar georgeskgeorgesk Acetic acid 60.0520 60.0211294 16 117 chemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/isobutyric_acid.cml0000644000175000017500000000563010662517661027540 0ustar georgeskgeorgesk Isobutyric acid 88.1051 88.0524295 -47 154 chemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/E-butenedioic_acid.cml0000644000175000017500000000500210673462010027776 0ustar georgeskgeorgesk (E)-Butenedioic acid 116.0722 116.0109586 300 chemical-structures-2.2.dfsg.0.orig/src/carboxylic_acids/D-malic_acid.cml0000644000175000017500000000610410721776211026601 0ustar georgeskgeorgesk (R)-2-Hydroxybutanedioic acid 134.0874 134.0215233 131 203 chemical-structures-2.2.dfsg.0.orig/src/sulfoxides/0000755000175000017500000000000011225622315022533 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/sulfoxides/index.xml0000644000175000017500000000166011202002412024350 0ustar georgeskgeorgesk Sulfoxides Sulfoxide Sulfóxidos Sulfoxydes Sulfoxides Sulfoxides 亞碸類 Dimethyl sulfoxide Diméthylsulfoxyde Dimethyl sulfoxide 二甲亞碸 dimethyl_sulfoxide Methylsulfinylmethane Méthylsulfinylméthane Methylsulfinylmethane 甲基亞磺醯基甲烷 DMSO Jerome Pansanel 2006-11-22 chemical-structures-2.2.dfsg.0.orig/src/sulfoxides/CMakeLists.txt0000644000175000017500000000712611112716045025300 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "sulfoxides") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/sulfoxides/dimethyl_sulfoxide.cml0000644000175000017500000000466010723243342027140 0ustar georgeskgeorgesk Methylsulfinylmethane 78.1334 78.0139358 18 189 chemical-structures-2.2.dfsg.0.orig/src/alkynes/0000755000175000017500000000000011225622315022014 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/alkynes/but-2-yne.cml0000644000175000017500000000461310662517661024252 0ustar georgeskgeorgesk But-2-yne 54.0904 54.0469502 -32 27 chemical-structures-2.2.dfsg.0.orig/src/alkynes/index.xml0000644000175000017500000000412311142231213023634 0ustar georgeskgeorgesk Alkynes Alkine Alquinos Alcynes Alkynen Alkynes 炔類 Acetylene Acetylen Acétylène Acetylene 乙炔 acetylene Ethyne Ethyne Ethyne 乙炔 Jerome Pansanel 2006-11-09 But-1-yne But-1-yn But-1-yne But-1-yne 丁-1-炔 but-1-yne 1-Butyne 1-Butin 1-Butyne 1-Butyne 1-丁炔 Jerome Pansanel 2006-11-09 But-2-yne But-2-yn But-2-yne But-2-yne 丁-2-炔 but-2-yne 2-Butyne 2-Butin 2-Butyne 2-Butyne 2-丁炔 Jerome Pansanel 2006-11-09 Propyne Propyn Propyne Propyne 丙炔 propyne Jerome Pansanel 2006-11-09 chemical-structures-2.2.dfsg.0.orig/src/alkynes/propyne.cml0000644000175000017500000000404110662517661024217 0ustar georgeskgeorgesk Propyne 40.0639 40.0313001 -102 -23 chemical-structures-2.2.dfsg.0.orig/src/alkynes/CMakeLists.txt0000644000175000017500000000712311112716045024556 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "alkynes") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/alkynes/acetylene.cml0000644000175000017500000000327110662517661024500 0ustar georgeskgeorgesk Acetylene 26.0373 26.0156501 -84 -81 chemical-structures-2.2.dfsg.0.orig/src/alkynes/but-1-yne.cml0000644000175000017500000000461610662517661024254 0ustar georgeskgeorgesk But-1-yne 54.0904 54.0469502 -126 8 chemical-structures-2.2.dfsg.0.orig/src/alkanes/0000755000175000017500000000000011225622315021764 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/alkanes/cyclodecane.cml0000644000175000017500000001126210662517661024747 0ustar georgeskgeorgesk Cyclodecane 140.2658 140.1565006 201 chemical-structures-2.2.dfsg.0.orig/src/alkanes/methane.cml0000644000175000017500000000344510662517661024123 0ustar georgeskgeorgesk Methane 16.0425 16.0313001 -183 -161 chemical-structures-2.2.dfsg.0.orig/src/alkanes/4S-2_4-dimethylhexane.cml0000644000175000017500000001030110662517661026345 0ustar georgeskgeorgesk (4S)-2,4-Dimethylhexane 114.2285 114.1408506 108 chemical-structures-2.2.dfsg.0.orig/src/alkanes/3R-3-ethyl-2_5-dimethylhexane.cml0000644000175000017500000001136410662517661027641 0ustar georgeskgeorgesk (3R)-3-Ethyl-2,5-dimethylhexane 142.2817 142.1721507 chemical-structures-2.2.dfsg.0.orig/src/alkanes/tridecane.cml0000644000175000017500000001416010662517661024434 0ustar georgeskgeorgesk Tridecane 184.3614 184.2191009 -5 235 chemical-structures-2.2.dfsg.0.orig/src/alkanes/pentane.cml0000644000175000017500000000635110662517661024133 0ustar georgeskgeorgesk Pentane 72.1488 72.0939004 -130 36 chemical-structures-2.2.dfsg.0.orig/src/alkanes/hexane.cml0000644000175000017500000000713210662517661023747 0ustar georgeskgeorgesk Hexane 86.1754 86.1095504 -95 68 chemical-structures-2.2.dfsg.0.orig/src/alkanes/2-methylbutane.cml0000644000175000017500000000611410662517661025336 0ustar georgeskgeorgesk 2-Methylbutane 72.1488 72.0939004 30 chemical-structures-2.2.dfsg.0.orig/src/alkanes/cyclohexane.cml0000644000175000017500000000662310662517661025005 0ustar georgeskgeorgesk Cyclohexane 84.1595 84.0939004 5 80 chemical-structures-2.2.dfsg.0.orig/src/alkanes/nonane.cml0000644000175000017500000001125710662517661023760 0ustar georgeskgeorgesk Nonane 128.2551 128.1565006 -53 150 chemical-structures-2.2.dfsg.0.orig/src/alkanes/propane.cml0000644000175000017500000000501010662517661024134 0ustar georgeskgeorgesk Propane 44.0956 44.0626003 -188 -42 chemical-structures-2.2.dfsg.0.orig/src/alkanes/3-ethylpentane.cml0000644000175000017500000000720210662517661025335 0ustar georgeskgeorgesk 3-Ethylpentane 100.2019 100.1252005 chemical-structures-2.2.dfsg.0.orig/src/alkanes/octane.cml0000644000175000017500000001050010662517661023741 0ustar georgeskgeorgesk Octane 114.2285 114.1408506 -57 126 chemical-structures-2.2.dfsg.0.orig/src/alkanes/index.xml0000644000175000017500000003706011142231213023612 0ustar georgeskgeorgesk Alkanes Alkane Alcanos Alcanes Alkanen Alkanes 烷類 (1R,2S)-1,2-Dimethylcyclopentane (1R,2S)-1,2-Dimethylcyclopentan (1R,2S)-1,2-Diméthylcyclopentane (1R,2S)-1,2-Dimethylcyclopentane (1R,2S)-1,2-二甲基環戊烷 1R_2S-1_2-dimethylcyclopentane Jerome Pansanel 2006-05-10 (1R,3S)-1,3-Dimethylcyclopentane (1R,3S)-1,3-Dimethylcyclopentan (1R,3S)-1,3-Diméthylcyclopentane (1R,3S)-1,3-Dimethylcyclopentane (1R,3S)-1,3-二甲基環戊烷 1R_3S-1_3-dimethylcyclopentane Jerome Pansanel 2006-05-10 2,3,4-Trimethylpentane 2,3,4-Trimethylpentan 2,3,4-Triméthylpentane 2,3,4-Trimethylpentane 2,3,4-三甲基戊烷 2_3_4-trimethylpentane Jerome Pansanel 2006-05-10 2,3-Dimethylbutane 2,3-Dimethylbutan 2,3-Diméthylbutane 2,3-Dimethylbutane 2,3-二甲基丁烷 2_3-dimethylbutane Jerome Pansanel 2006-05-10 2-Methylbutane 2-Methylbutan 2-Méthylbutane 2-Methylbutane 2-甲基丁烷 2-methylbutane Jerome Pansanel 2006-05-10 2-Methylheptane 2-Methylheptan 2-Méthylheptane 2-Methylheptane 2-甲基庚烷 2-methylheptane Jerome Pansanel 2006-05-10 2-Methylhexane 2-Methylhexan 2-Méthylhexane 2-Methylhexane 2-甲基己烷 2-methylhexane Jerome Pansanel 2006-05-10 2-Methylpentane 2-Methylpentan 2-Méthylpentane 2-Methylpentane 2-甲基戊烷 2-methylpentane Jerome Pansanel 2006-05-10 2-Methylpropane 2-Methylpropan 2-Methylpropan 2-Methylpropane 2-甲基丙烷 2-methylpropane Isobutane Isobutan Isobutane Isobutane 異丁烷 Jerome Pansanel 2006-05-10 3-Ethylhexane 3-Ethylhexan 3-Ethylhexane 3-Ethylhexane 3-乙基己烷 3-ethylhexane Jerome Pansanel 2006-05-10 3-Ethylpentane 3-Ethylpentan 3-Ethylpentane 3-Ethylpentane 3-乙基戊烷 3-ethylpentane Jerome Pansanel 2006-05-10 3-Methylpentane 3-Methylpentan 3-Méthylpentane 3-Methylpentane 3-甲基戊烷 3-methylpentane Jerome Pansanel 2006-05-10 (3R,4S)-3,4-Dimethylhexane (3R,4S)-3,4-Dimethylhexan (3R,4S)-3,4-Diméthylhexane (3R,4S)-3,4-Dimethylhexane (3R,4S)-3,4-二甲基己烷 3R_4S-3_4-dimethylhexane Jerome Pansanel 2006-05-10 (3S)-2,3-Dimethylpentane (3S)-2,3-Dimethylpentan (3S)-2,3-Diméthylpentane (3S)-2,3-Dimethylpentane (3S)-2,3-二甲基戊烷 3S-2_3-dimethylpentane Jerome Pansanel 2006-05-10 (3S)-3-Methylheptane (3S)-3-Methylheptan (3S)-3-Méthylheptane (3S)-3-Methylheptane (3S)-3-甲基庚烷 3S-3-methylheptane Jerome Pansanel 2006-05-10 (4S)-2,4-Dimethylhexane (4S)-2,4-Dimethylhexan (4S)-2,4-Diméthylhexane (4S)-2,4-Dimethylhexane (4S)-2,4-二甲基己烷 4S-2_4-dimethylhexane Jerome Pansanel 2006-05-10 Butane Butan Butane Butane 丁烷 butane Jerome Pansanel 2006-05-10 Cyclodecane Cyclodecan Cyclodécane Cyclodecane 環癸烷 cyclodecane Jerome Pansanel 2006-05-10 Cycloheptane Cycloheptan Cycloheptane Cycloheptane 環庚烷 cycloheptane Jerome Pansanel 2006-05-10 Cyclononane Cyclononan Cyclononane Cyclononane 環壬烷 cyclononane Jerome Pansanel 2006-05-10 Cyclooctane Cyclooctan Cyclooctane Cyclooctane 環辛烷 cyclooctane Jerome Pansanel 2006-05-10 Cyclopentane Cyclopentan Cyclopentane Cyclopentane 環戊烷 cyclopentane Jerome Pansanel 2006-05-10 Cyclohexane Cyclohexan Cyclohexane Cyclohexane 環己烷 cyclohexane Jerome Pansanel 2006-05-10 Decane Decan Décane Decane 癸烷 decane Jerome Pansanel 2006-05-10 Dodecane Dodecan Dodécane Dodecane 十二烷 dodecane Jerome Pansanel 2006-05-10 Eicosane Eicosan Eicosane Eicosane 二十烷 eicosane Jerome Pansanel 2006-05-10 Ethane Ethan Ethane Ethane 乙烷 ethane Jerome Pansanel 2006-05-10 Heptane Heptan Heptane Heptane 庚烷 heptane Jerome Pansanel 2006-05-10 Hexadecane Hexadecan Hexadécane Hexadecane 十六烷 hexadecane Jerome Pansanel 2006-05-10 Hexane Hexan Hexane Hexane 己烷 hexane Jerome Pansanel 2006-05-10 Methane Methan Methane Methane 甲烷 methane Jerome Pansanel 2006-05-10 Methylcyclohexane Methylcyclohexan Méthylcyclohexane Methylcyclohexane 甲環己烷 methylcyclohexane Jerome Pansanel 2006-05-10 Methylcyclopentane Methylcyclopentan Méthylcyclopentane Methylcyclopentane 甲環戊烷 methylcyclopentane Jerome Pansanel 2006-05-10 Nonane Nonan Nonane Nonane 壬烷 nonane Jerome Pansanel 2006-05-10 Octane Octan Octane Octane 辛烷 octane Jerome Pansanel 2006-05-10 Pentane Pentan Pentane Pentane 戊烷 pentane Jerome Pansanel 2006-05-10 Propane Propan Propane Propane 丙烷 propane Jerome Pansanel 2006-05-10 Tetracosane Tetracosan Tétracosane Tetracosane 二十四烷 tetracosane Jerome Pansanel 2006-05-10 Undecane Undecan Undécane Undecane 十一烷 undecane Jerome Pansanel 2006-05-10 (3R)-3-Ethyl-2,5-dimethylhexane (3R)-3-Ethyl-2,5-dimethylhexan (3R)-3-Ethyl-2,5-diméthylhexane (3R)-3-Ethyl-2,5-dimethylhexane (3R)-3-乙基-2,5-二甲基己烷 3R-3-ethyl-2_5-dimethylhexane Jerome Pansanel 2006-07-13 Pentadecane Pentadecan Pentadécane Pentadecane 十五烷 pentadecane Jerome Pansanel 2006-07-13 Tetradecane Tetradecan Tétradécane Tetradecane 十四烷 tetradecane Jerome Pansanel 2006-07-13 Tridecane Tridecan Tridécane Tridecane 十三烷 tridecane Jerome Pansanel 2006-07-13 (1S,2S)-1-Ethyl-2-methylcyclopentane (1S,2S)-1-Ethyl-2-methylcyclopentan (1S,2S)-1-Ethyl-2-méthylcyclopentane (1S,2S)-1-Ethyl-2-methylcyclopentane (1S,2S)-1-乙基-2-甲基環戊烷 1S_2S-1-ethyl-2-methylcyclopentane Jerome Pansanel 2006-10-15 chemical-structures-2.2.dfsg.0.orig/src/alkanes/1R_3S-1_3-dimethylcyclopentane.cml0000644000175000017500000000722110662517661030127 0ustar georgeskgeorgesk (1R,3S)-1,3-Dimethylcyclopentane 98.1861 98.1095504 91 chemical-structures-2.2.dfsg.0.orig/src/alkanes/dodecane.cml0000644000175000017500000001342010662517661024236 0ustar georgeskgeorgesk Dodecane 170.3348 170.2034508 -10 216 chemical-structures-2.2.dfsg.0.orig/src/alkanes/butane.cml0000644000175000017500000000557010662517661023761 0ustar georgeskgeorgesk Butane 58.1222 58.0782503 -138 -1 chemical-structures-2.2.dfsg.0.orig/src/alkanes/hexadecane.cml0000644000175000017500000001633510662517661024571 0ustar georgeskgeorgesk Hexadecane 226.4412 226.2660511 18 287 chemical-structures-2.2.dfsg.0.orig/src/alkanes/3-ethylhexane.cml0000644000175000017500000000776110662517661025165 0ustar georgeskgeorgesk 3-Ethylhexane 114.2285 114.1408506 chemical-structures-2.2.dfsg.0.orig/src/alkanes/tetracosane.cml0000644000175000017500000002420710662517661025011 0ustar georgeskgeorgesk Tetracosane 338.6538 338.3912516 50 391 chemical-structures-2.2.dfsg.0.orig/src/alkanes/decane.cml0000644000175000017500000001204710662517661023717 0ustar georgeskgeorgesk Decane 142.2817 142.1721507 -30 174 chemical-structures-2.2.dfsg.0.orig/src/alkanes/3-methylpentane.cml0000644000175000017500000000670410662517661025520 0ustar georgeskgeorgesk 3-Methylpentane 86.1754 86.1095504 63 chemical-structures-2.2.dfsg.0.orig/src/alkanes/2-methylheptane.cml0000644000175000017500000001025210662517661025502 0ustar georgeskgeorgesk 2-Methylheptane 114.2285 114.1408506 116 chemical-structures-2.2.dfsg.0.orig/src/alkanes/cycloheptane.cml0000644000175000017500000000741210662517661025156 0ustar georgeskgeorgesk Cycloheptane 98.1861 98.1095504 -12 118 chemical-structures-2.2.dfsg.0.orig/src/alkanes/tetradecane.cml0000644000175000017500000001474710662517661024770 0ustar georgeskgeorgesk Tetradecane 198.3880 198.2347510 6 253 chemical-structures-2.2.dfsg.0.orig/src/alkanes/2-methylpentane.cml0000644000175000017500000000716010662517661025514 0ustar georgeskgeorgesk 2-Methylpentane 86.1754 86.1095504 -154 61 chemical-structures-2.2.dfsg.0.orig/src/alkanes/3S-2_3-dimethylpentane.cml0000644000175000017500000000751510662517661026542 0ustar georgeskgeorgesk (3S)-2,3-Dimethylpentane 100.2019 100.1252005 89 chemical-structures-2.2.dfsg.0.orig/src/alkanes/2_3_4-trimethylpentane.cml0000644000175000017500000001052710662517661026701 0ustar georgeskgeorgesk 2,3,4-Trimethylpentane 114.2285 114.1408506 -110 113 chemical-structures-2.2.dfsg.0.orig/src/alkanes/ethane.cml0000644000175000017500000000422310662517661023741 0ustar georgeskgeorgesk Ethane 30.0690 30.0469502 -172 -88 chemical-structures-2.2.dfsg.0.orig/src/alkanes/2_3-dimethylbutane.cml0000644000175000017500000000716210662517661026101 0ustar georgeskgeorgesk 2,3-Dimethylbutane 86.1754 86.1095504 -129 58 chemical-structures-2.2.dfsg.0.orig/src/alkanes/3R_4S-3_4-dimethylhexane.cml0000644000175000017500000001030310662517661026714 0ustar georgeskgeorgesk (3R,4S)-3,4-Dimethylhexane 114.2285 114.1408506 118 chemical-structures-2.2.dfsg.0.orig/src/alkanes/2-methylpropane.cml0000644000175000017500000000561310662517661025527 0ustar georgeskgeorgesk 2-Methylpropane 58.1222 58.0782503 -160 -12 chemical-structures-2.2.dfsg.0.orig/src/alkanes/CMakeLists.txt0000644000175000017500000000712311112716045024526 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "alkanes") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/alkanes/eicosane.cml0000644000175000017500000002125310662517661024265 0ustar georgeskgeorgesk Eicosane 282.5475 282.3286513 36 343 chemical-structures-2.2.dfsg.0.orig/src/alkanes/cyclononane.cml0000644000175000017500000001021610662517661025004 0ustar georgeskgeorgesk Cyclononane 126.2392 126.1408506 chemical-structures-2.2.dfsg.0.orig/src/alkanes/cyclooctane.cml0000644000175000017500000000771710662517661025013 0ustar georgeskgeorgesk Cyclooctane 112.2126 112.1252005 150 chemical-structures-2.2.dfsg.0.orig/src/alkanes/1S_2S-1-ethyl-2-methylcyclopentane.cml0000644000175000017500000000752310662517661030657 0ustar georgeskgeorgesk (1S,2S)-1-Ethyl-2-methylcyclopentane 112.2126 112.1252005 chemical-structures-2.2.dfsg.0.orig/src/alkanes/undecane.cml0000644000175000017500000001263610662517661024266 0ustar georgeskgeorgesk Undecane 156.3083 156.1878008 -26 195 chemical-structures-2.2.dfsg.0.orig/src/alkanes/3S-3-methylheptane.cml0000644000175000017500000001027310662517661025771 0ustar georgeskgeorgesk (3S)-3-Methylheptane 114.2285 114.1408506 118 chemical-structures-2.2.dfsg.0.orig/src/alkanes/heptane.cml0000644000175000017500000000771710662517661024134 0ustar georgeskgeorgesk Heptane 100.2019 100.1252005 -91 98 chemical-structures-2.2.dfsg.0.orig/src/alkanes/pentadecane.cml0000644000175000017500000001553510662517661024754 0ustar georgeskgeorgesk Pentadecane 212.4146 212.2504010 10 270 chemical-structures-2.2.dfsg.0.orig/src/alkanes/2-methylhexane.cml0000644000175000017500000000774410662517661025342 0ustar georgeskgeorgesk 2-Methylhexane 100.2019 100.1252005 -118 90 chemical-structures-2.2.dfsg.0.orig/src/alkanes/cyclopentane.cml0000644000175000017500000000605010662517661025161 0ustar georgeskgeorgesk Cyclopentane 70.1329 70.0782503 -94 50 chemical-structures-2.2.dfsg.0.orig/src/alkanes/1R_2S-1_2-dimethylcyclopentane.cml0000644000175000017500000000674410662517661030136 0ustar georgeskgeorgesk (1R,2S)-1,2-Dimethylcyclopentane 98.1861 98.1095504 chemical-structures-2.2.dfsg.0.orig/src/alkanes/methylcyclopentane.cml0000644000175000017500000000664710662517661026420 0ustar georgeskgeorgesk Methylcyclopentane 84.1595 84.0939004 -142 72 chemical-structures-2.2.dfsg.0.orig/src/alkanes/methylcyclohexane.cml0000644000175000017500000000742610662517661026232 0ustar georgeskgeorgesk Methylcyclohexane 98.1861 98.1095504 -126 100 chemical-structures-2.2.dfsg.0.orig/src/alkenes/0000755000175000017500000000000011225622315021770 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/alkenes/Z-oct-2-ene.cml0000644000175000017500000000764710662517661024416 0ustar georgeskgeorgesk (Z)-Oct-2-ene 112.2126 112.1252005 126 chemical-structures-2.2.dfsg.0.orig/src/alkenes/cycloocta-1_3_5_7-tetraene.cml0000644000175000017500000000635210662517661027325 0ustar georgeskgeorgesk Cycloocta-1,3,5,7-tetraene 104.1491 104.0626003 -27 142 chemical-structures-2.2.dfsg.0.orig/src/alkenes/Z-cyclooctene.cml0000644000175000017500000000762510662517661025230 0ustar georgeskgeorgesk (Z)-Cyclooctene 110.1968 110.1095504 -16 145 chemical-structures-2.2.dfsg.0.orig/src/alkenes/Z-hex-3-ene.cml0000644000175000017500000000630710662517661024406 0ustar georgeskgeorgesk (Z)-Hex-3-ene 84.1595 84.0939004 67 chemical-structures-2.2.dfsg.0.orig/src/alkenes/E-oct-2-ene.cml0000644000175000017500000000764710662517661024371 0ustar georgeskgeorgesk (E)-Oct-2-ene 112.2126 112.1252005 123 chemical-structures-2.2.dfsg.0.orig/src/alkenes/cycloocta-1_3-diene.cml0000644000175000017500000000725710662517661026135 0ustar georgeskgeorgesk Cycloocta-1,3-diene 108.1809 108.0939004 -55 143 chemical-structures-2.2.dfsg.0.orig/src/alkenes/cyclohexene.cml0000644000175000017500000000624610662517661025016 0ustar georgeskgeorgesk Cyclohexene 82.1436 82.0782503 -104 82 chemical-structures-2.2.dfsg.0.orig/src/alkenes/cyclohepta-1_4-diene.cml0000644000175000017500000000572210662517661026304 0ustar georgeskgeorgesk Cyclohepta-1,4-diene 94.1543 94.0782503 chemical-structures-2.2.dfsg.0.orig/src/alkenes/Z-hept-2-ene.cml0000644000175000017500000000707710662517661024566 0ustar georgeskgeorgesk (Z)-Hept-2-ene 98.1861 98.1095504 98 chemical-structures-2.2.dfsg.0.orig/src/alkenes/index.xml0000644000175000017500000004036311142231213023616 0ustar georgeskgeorgesk Alkenes Alkene Alquenos Alcènes Alkenen Alkenes 烯類 But-1-ene But-1-en But-1-ène But-1-ene 丁-1-烯 but-1-ene Jerome Pansanel 2006-05-10 (Z)-But-2-ene (Z)-But-2-en (Z)-But-2-ène (Z)-But-2-ene (Z)-丁-2-烯 Z-but-2-ene Jerome Pansanel 2006-05-10 (Z)-Cycloheptene (Z)-Cyclohepten (Z)-Cycloheptène (Z)-Cycloheptene (Z)-環庚烯 Z-cycloheptene Jerome Pansanel 2006-05-10 Cyclohexene Cyclohexen Cyclohexène Cyclohexene 環己烯 cyclohexene Jerome Pansanel 2006-05-10 (Z)-Cyclooctene (Z)-Cycloocten (Z)-Cyclooctène (Z)-Cyclooctene (Z)-環辛烯 Z-cyclooctene Jerome Pansanel 2006-05-10 Cyclopentene Cyclopenten Cyclopentene Cyclopentene 環戊烯 cyclopentene Jerome Pansanel 2006-05-10 (Z)-Hept-2-ene (Z)-Hept-2-en (Z)-Hept-2-ène (Z)-Hept-2-ene (Z)-庚-2-烯 Z-hept-2-ene Jerome Pansanel 2006-05-10 (Z)-Hept-3-ene (Z)-Hept-3-en (Z)-Hept-3-ène (Z)-Hept-3-ene (Z)-庚-3-烯 Z-hept-3-ene Jerome Pansanel 2006-05-10 (Z)-Hex-2-ene (Z)-Hex-2-en (Z)-Hex-2-ène (Z)-Hex-2-ene (Z)-己-2-烯 Z-hex-2-ene Jerome Pansanel 2006-05-10 (Z)-Hex-3-ene (Z)-Hex-3-en (Z)-Hex-3-ène (Z)-Hex-3-ene (Z)-己-3-烯 Z-hex-3-ene Jerome Pansanel 2006-05-10 (Z)-Oct-2-ene (Z)-Oct-2-en (Z)-Oct-2-ène (Z)-Oct-2-ene (Z)-辛-2-烯 Z-oct-2-ene Jerome Pansanel 2006-05-10 (Z)-Oct-3-ene (Z)-Oct-3-en (Z)-Oct-3-ène (Z)-Oct-3-ene (Z)-辛-3-烯 Z-oct-3-ene Jerome Pansanel 2006-05-10 (Z)-Oct-4-ene (Z)-Oct-4-en (Z)-Oct-4-ène (Z)-Oct-4-ene (Z)-辛-4-烯 Z-oct-4-ene Jerome Pansanel 2006-05-10 (Z)-Pent-2-ene (Z)-Pent-2-en (Z)-Pent-2-ène (Z)-Pent-2-ene (Z)-戊-2-烯 Z-pent-2-ene Jerome Pansanel 2006-05-10 Ethene Ethen Ethène Ethene 乙烯 ethene Ethylene Ethylen Ethylène Ethylene 乙烯 Jerome Pansanel 2006-05-10 Hept-1-ene Hept-1-en Hept-1-ène Hept-1-ene 庚-1-烯 hept-1-ene Jerome Pansanel 2006-05-10 Hex-1-ene Hex-1-en Hex-1-ène Hex-1-ene 己-1-烯 hex-1-ene Jerome Pansanel 2006-05-10 Oct-1-ene Oct-1-en Oct-1-ène Oct-1-ene 辛-1-烯 oct-1-ene Jerome Pansanel 2006-05-10 Pent-1-ene Pent-1-en Pent-1-ène Pent-1-ene 戊-1-烯 pent-1-ene Jerome Pansanel 2006-05-10 Propene Propen Propène Propene 丙烯 propene Jerome Pansanel 2006-05-10 (E)-But-2-ene (E)-But-2-en (E)-But-2-ène (E)-But-2-ene (E)-丁-2-烯 E-but-2-ene Jerome Pansanel 2006-05-10 (E)-Hept-2-ene (E)-Hept-2-en (E)-Hept-2-ène (E)-Hept-2-ene (E)-庚-2-烯 E-hept-2-ene Jerome Pansanel 2006-05-10 (E)-Hept-3-ene (E)-Hept-3-en (E)-Hept-3-ène (E)-Hept-3-ene (E)-庚-3-烯 E-hept-3-ene Jerome Pansanel 2006-05-10 (E)-Hex-2-ene (E)-Hex-2-en (E)-Hex-2-ène (E)-Hex-2-ene (E)-己-2-烯 E-hex-2-ene Jerome Pansanel 2006-05-10 (E)-Hex-3-ene (E)-Hex-3-en (E)-Hex-3-ène E-hex-3-ene Jerome Pansanel 2006-05-10 (E)-Oct-2-ene (E)-Oct-2-en (E)-Oct-2-ène (E)-Hex-3-ene (E)-己-3-烯 E-oct-2-ene Jerome Pansanel 2006-05-10 (E)-Oct-3-ene (E)-Oct-3-en (E)-Oct-3-ène (E)-Oct-3-ene (E)-辛-3-烯 E-oct-3-ene Jerome Pansanel 2006-05-10 (E)-Oct-4-ene (E)-Oct-4-en (E)-Oct-4-ène (E)-Oct-4-ene (E)-辛-4-烯 E-oct-4-ene Jerome Pansanel 2006-05-10 (E)-Pent-2-ene (E)-Pent-2-en (E)-Pent-2-ène (E)-Pent-2-ene (E)-戊-2-烯 E-pent-2-ene Jerome Pansanel 2006-05-10 2-Methylbuta-1,3-diene 2-Methylbuta-1,3-dien 2-Méthylbuta-1,3-diène 2-Methylbuta-1,3-diene 2-甲基-1,3-丁二烯 2-methylbuta-1_3-diene Isoprene Isopentadiene Isoprène Isopentadiène Isopren Isoprene 異戊二烯 Jerome Pansanel 2006-05-11 (3E)-Penta-1,3-diene (3E)-Penta-1,3-dien (3E)-Penta-1,3-diène (3E)-Penta-1,3-diene (3E)-戊-1,3-二烯 3E-penta-1_3-diene trans-Piperylene trans-Pipérylène Jerome Pansanel 2006-05-11 (3Z)-Penta-1,3-diene (3Z)-Penta-1,3-dien (3Z)-Penta-1,3-diène (3Z)-Penta-1,3-diene ((3Z)-戊-1,3-二烯 3Z-penta-1_3-diene cis-Piperylene cis-Pipérylène cis-Piperylene 順-戊二烯 Jerome Pansanel 2006-05-11 2-Methylbut-2-ene 2-Methylbut-2-en 2-Methylbut-2-ène 2-Methylbut-2-ene 2-甲基-2-丁烯 2-methylbut-2-ene Jerome Pansanel 2006-07-13 (3Z)-3-ethylhepta-1,3-diene (3Z)-3-ethylhepta-1,3-dien (3Z)-3-ethylhepta-1,3-diène (3Z)-3-ethylhepta-1,3-diene (3Z)-3-乙基-1,3-庚二烯 3Z_3-ethylhepta-1_3-diene Jerome Pansanel 2006-10-15 Cyclohepta-1,3,5-triene Cyclohepta-1,3,5-trien Cyclohepta-1,3,5-triène Cyclohepta-1,3,5-triene 環庚-1,3,5-三烯 cyclohepta-1_3_5-triene Tropilidene Tropilidène Tropilidene 環庚三烯 Jerome Pansanel 2006-11-21 Cyclohepta-1,3-diene Cyclohepta-1,3-dien Cyclohepta-1,3-diène Cyclohepta-1,3-diene 環庚-1,3-二烯 cyclohepta-1_3-diene Jerome Pansanel 2006-11-21 Cyclohepta-1,4-diene Cyclohepta-1,4-dien Cyclohepta-1,4-diène Cyclohepta-1,4-diene 環庚-1,4-二烯 cyclohepta-1_4-diene Jerome Pansanel 2006-11-21 Cyclohexa-1,3-diene Cyclohexa-1,3-dien Cyclohexa-1,3-diène Cyclohexa-1,3-diene 環己-1,3-二烯 cyclohexa-1_3-diene Jerome Pansanel 2006-11-21 Cyclohexa-1,4-diene Cyclohexa-1,4-dien Cyclohexa-1,4-diène Cyclohexa-1,4-diene 環己-1,4-二烯 cyclohexa-1_4-diene Jerome Pansanel 2006-11-21 Cycloocta-1,3,5,7-tetraene Cycloocta-1,3,5,7-tetraen Cycloocta-1,3,5,7-tétraène Cycloocta-1,3,5,7-tetraene 環辛-1,3,5,7-四烯 cycloocta-1_3_5_7-tetraene [8]Annulene [8]Annulène [8]Annulene Jerome Pansanel 2006-11-21 Cycloocta-1,3,5-triene Cycloocta-1,3,5-trien Cycloocta-1,3,5-triène Cycloocta-1,3,5-triene 環辛-1,3,5-三烯 cycloocta-1_3_5-triene Jerome Pansanel 2006-11-21 Cycloocta-1,3-diene Cycloocta-1,3-dien Cycloocta-1,3-diène Cycloocta-1,3-diene 環辛-1,3-二烯 cycloocta-1_3-diene Jerome Pansanel 2006-11-21 Cyclopenta-1,3-diene Cyclopenta-1,3-dien Cyclopenta-1,3-diène Cyclopenta-1,3-diene 環戊-1,3-二烯 cyclopenta-1_3-diene Jerome Pansanel 2006-11-21 chemical-structures-2.2.dfsg.0.orig/src/alkenes/E-hex-2-ene.cml0000644000175000017500000000656510662517661024366 0ustar georgeskgeorgesk (E)-Hex-2-ene 84.1595 84.0939004 -98 68 chemical-structures-2.2.dfsg.0.orig/src/alkenes/Z-but-2-ene.cml0000644000175000017500000000522010662517661024404 0ustar georgeskgeorgesk (Z)-But-2-ene 56.1063 56.0626003 -139 4 chemical-structures-2.2.dfsg.0.orig/src/alkenes/cyclopenta-1_3-diene.cml0000644000175000017500000000511210662517661026302 0ustar georgeskgeorgesk Cyclopenta-1,3-diene 66.1011 66.0469502 -97 40 chemical-structures-2.2.dfsg.0.orig/src/alkenes/Z-cycloheptene.cml0000644000175000017500000000656210662517661025402 0ustar georgeskgeorgesk (Z)-Cycloheptene 96.1702 96.0939004 113 chemical-structures-2.2.dfsg.0.orig/src/alkenes/3Z-penta-1_3-diene.cml0000644000175000017500000000516010662517661025545 0ustar georgeskgeorgesk (3Z)-Penta-1,3-diene 68.1170 68.0626003 43 chemical-structures-2.2.dfsg.0.orig/src/alkenes/2-methylbuta-1_3-diene.cml0000644000175000017500000000543410662517661026465 0ustar georgeskgeorgesk 2-Methylbuta-1,3-diene 68.1170 68.0626003 -146 34 chemical-structures-2.2.dfsg.0.orig/src/alkenes/E-oct-3-ene.cml0000644000175000017500000000765110662517661024365 0ustar georgeskgeorgesk (E)-Oct-3-ene 112.2126 112.1252005 122 chemical-structures-2.2.dfsg.0.orig/src/alkenes/E-hept-2-ene.cml0000644000175000017500000000707210662517661024534 0ustar georgeskgeorgesk (E)-Hept-2-ene 98.1861 98.1095504 98 chemical-structures-2.2.dfsg.0.orig/src/alkenes/E-hex-3-ene.cml0000644000175000017500000000630610662517661024360 0ustar georgeskgeorgesk (E)-Hex-3-ene 84.1595 84.0939004 67 chemical-structures-2.2.dfsg.0.orig/src/alkenes/oct-1-ene.cml0000644000175000017500000001010710662517661024167 0ustar georgeskgeorgesk Oct-1-ene 112.2126 112.1252005 -101 123 chemical-structures-2.2.dfsg.0.orig/src/alkenes/cyclohepta-1_3_5-triene.cml0000644000175000017500000000610310662517661026723 0ustar georgeskgeorgesk Cyclohepta-1,3,5-triene 92.1384 92.0626003 -80 116 chemical-structures-2.2.dfsg.0.orig/src/alkenes/2-methylbut-2-ene.cml0000644000175000017500000000600310662517661025557 0ustar georgeskgeorgesk 2-Methylbut-2-ene 70.1329 70.0782503 -134 36 chemical-structures-2.2.dfsg.0.orig/src/alkenes/Z-oct-4-ene.cml0000644000175000017500000000766110662517661024414 0ustar georgeskgeorgesk (Z)-Oct-4-ene 112.2126 112.1252005 122 chemical-structures-2.2.dfsg.0.orig/src/alkenes/3Z_3-ethylhepta-1_3-diene.cml0000644000175000017500000000763310662517661027036 0ustar georgeskgeorgesk (3Z)-3-Ethylhepta-1_3-diene 124.2233 124.1252005 chemical-structures-2.2.dfsg.0.orig/src/alkenes/hept-1-ene.cml0000644000175000017500000000733310662517661024351 0ustar georgeskgeorgesk Hept-1-ene 98.1861 98.1095504 -119 94 chemical-structures-2.2.dfsg.0.orig/src/alkenes/cyclohepta-1_3-diene.cml0000644000175000017500000000620710662517661026302 0ustar georgeskgeorgesk Cyclohepta-1,3-diene 94.1543 94.0782503 120 chemical-structures-2.2.dfsg.0.orig/src/alkenes/propene.cml0000644000175000017500000000442610662517661024156 0ustar georgeskgeorgesk Propene 42.0797 42.0469502 -185 -48 chemical-structures-2.2.dfsg.0.orig/src/alkenes/Z-hept-3-ene.cml0000644000175000017500000000707610662517661024566 0ustar georgeskgeorgesk (Z)-Hept-3-ene 98.1861 98.1095504 96 chemical-structures-2.2.dfsg.0.orig/src/alkenes/CMakeLists.txt0000644000175000017500000000712311112716045024532 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "alkenes") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/alkenes/cyclohexa-1_4-diene.cml0000644000175000017500000000567510662517661026137 0ustar georgeskgeorgesk Cyclohexa-1,4-diene 80.1277 80.0626003 -49 87 chemical-structures-2.2.dfsg.0.orig/src/alkenes/E-but-2-ene.cml0000644000175000017500000000522010662517661024357 0ustar georgeskgeorgesk (E)-But-2-ene 56.1063 56.0626003 -105 1 chemical-structures-2.2.dfsg.0.orig/src/alkenes/Z-hex-2-ene.cml0000644000175000017500000000631010662517661024377 0ustar georgeskgeorgesk (Z)-Hex-2-ene 84.1595 84.0939004 69 chemical-structures-2.2.dfsg.0.orig/src/alkenes/but-1-ene.cml0000644000175000017500000000520510662517661024177 0ustar georgeskgeorgesk But-1-ene 56.1063 56.0626003 -185 -6 chemical-structures-2.2.dfsg.0.orig/src/alkenes/E-oct-4-ene.cml0000644000175000017500000000765110662517661024366 0ustar georgeskgeorgesk (E)-Oct-4-ene 112.2126 112.1252005 122 chemical-structures-2.2.dfsg.0.orig/src/alkenes/E-pent-2-ene.cml0000644000175000017500000000601110662517661024532 0ustar georgeskgeorgesk (E)-Pent-2-ene 70.1329 70.0782503 -140 36 chemical-structures-2.2.dfsg.0.orig/src/alkenes/cyclopentene.cml0000644000175000017500000000546410662517661025201 0ustar georgeskgeorgesk Cyclopentene 68.1170 68.0626003 -135 45 chemical-structures-2.2.dfsg.0.orig/src/alkenes/Z-oct-3-ene.cml0000644000175000017500000000766210662517661024414 0ustar georgeskgeorgesk (Z)-Oct-3-ene 112.2126 112.1252005 123 chemical-structures-2.2.dfsg.0.orig/src/alkenes/pent-1-ene.cml0000644000175000017500000000551310662517661024355 0ustar georgeskgeorgesk Pent-1-ene 70.1329 70.0782503 30 chemical-structures-2.2.dfsg.0.orig/src/alkenes/cyclohexa-1_3-diene.cml0000644000175000017500000000542010662517661026122 0ustar georgeskgeorgesk Cyclohexa-1,3-diene 80.1277 80.0626003 80 chemical-structures-2.2.dfsg.0.orig/src/alkenes/hex-1-ene.cml0000644000175000017500000000626710662517661024202 0ustar georgeskgeorgesk Hex-1-ene 84.1595 84.0939004 63 chemical-structures-2.2.dfsg.0.orig/src/alkenes/ethene.cml0000644000175000017500000000364510662517661023760 0ustar georgeskgeorgesk Ethene 28.0532 28.0313001 -169 -104 chemical-structures-2.2.dfsg.0.orig/src/alkenes/cycloocta-1_3_5-triene.cml0000644000175000017500000000615010662517661026552 0ustar georgeskgeorgesk Cycloocta-1,3,5-triene 106.1650 106.0782503 chemical-structures-2.2.dfsg.0.orig/src/alkenes/Z-pent-2-ene.cml0000644000175000017500000000600610662517661024563 0ustar georgeskgeorgesk (Z)-Pent-2-ene 70.1329 70.0782503 -180 37 chemical-structures-2.2.dfsg.0.orig/src/alkenes/E-hept-3-ene.cml0000644000175000017500000000735510662517661024541 0ustar georgeskgeorgesk (E)-Hept-3-ene 98.1861 98.1095504 -137 95 chemical-structures-2.2.dfsg.0.orig/src/alkenes/3E-penta-1_3-diene.cml0000644000175000017500000000543410662517661025524 0ustar georgeskgeorgesk (3E)-Penta-1,3-diene 68.1170 68.0626003 -87 42 chemical-structures-2.2.dfsg.0.orig/src/amines/0000755000175000017500000000000011225622315021622 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/amines/1S_2S-1_2-diaminocyclohexane.cml0000644000175000017500000000741710723245757027414 0ustar georgeskgeorgesk (1S,2S)-Cyclohexane-1,2-diamine 114.1888 114.1156985 42 chemical-structures-2.2.dfsg.0.orig/src/amines/pyrrolidine.cml0000644000175000017500000000537210662517661024701 0ustar georgeskgeorgesk Pyrrolidine 71.1210 71.0734993 87 chemical-structures-2.2.dfsg.0.orig/src/amines/ethylamine.cml0000644000175000017500000000463010723245757024476 0ustar georgeskgeorgesk Ethanamine 45.0837 45.0578492 -81 16 chemical-structures-2.2.dfsg.0.orig/src/amines/1-aminooctane.cml0000644000175000017500000001107210723245757024770 0ustar georgeskgeorgesk Octan-1-amine 129.2432 129.1517496 -4 176 chemical-structures-2.2.dfsg.0.orig/src/amines/aminocyclohexane.cml0000644000175000017500000000722610723245757025671 0ustar georgeskgeorgesk Cyclohexanamine 99.1741 99.1047994 -18 134 chemical-structures-2.2.dfsg.0.orig/src/amines/1-aminopentane.cml0000644000175000017500000000675410723245757025164 0ustar georgeskgeorgesk Pentan-1-amine 87.1634 87.1047994 -52 104 chemical-structures-2.2.dfsg.0.orig/src/amines/1_5-diaminopentane.cml0000644000175000017500000000734510723245757025722 0ustar georgeskgeorgesk Pentane-1,5-diamine 102.1781 102.1156985 9 179 chemical-structures-2.2.dfsg.0.orig/src/amines/1H-azepine.cml0000644000175000017500000000511210662517661024232 0ustar georgeskgeorgesk 1H-Azepine 93.1265 93.0578492 chemical-structures-2.2.dfsg.0.orig/src/amines/1-aminononane.cml0000644000175000017500000001165510723245757025004 0ustar georgeskgeorgesk Nonan-1-amine 143.2697 143.1673997 -1 201 chemical-structures-2.2.dfsg.0.orig/src/amines/1-aminopropane.cml0000644000175000017500000000541610723245757025170 0ustar georgeskgeorgesk Propan-1-amine 59.1103 59.0734993 -83 48 chemical-structures-2.2.dfsg.0.orig/src/amines/index.xml0000644000175000017500000005052511142231213023451 0ustar georgeskgeorgesk Amines Amines Aminas Amines Amines Amines 胺類 Ammonia Ammoniak Ammoniaque Ammonia 氨 ammonia Azane Azane Azane 氮烷 Jerome Pansanel 2006-05-10 Morpholine Morpholin Morpholine Morpholine 嗎啉/嗎福林/1,4-氧氮陸圜 morpholine Jerome Pansanel 2006-05-10 Triethylamine Triethylamin Triéthylamine Triethylamine 三乙胺 triethylamine N,N-Diethylethanamine N,N-Diethylethanamin N,N-Diéthyléthanamine N,N-Diethylethanamine N,N-二乙基乙胺 Jerome Pansanel 2006-05-10 Trimethylamine Trimethylamin Triméthylamine Trimethylamine 三甲胺 trimethylamine N,N-Dimethylethanamine N,N-Dimethylethanamin N,N-Diméthyléthanamine N,N-Dimethylethanamine N,N-二甲基乙胺 Jerome Pansanel 2006-05-10 Piperazine Piperazin Pipérazine Piperazine 比倍拉淨/1，4-二氮陸圜 piperazine Jerome Pansanel 2006-05-10 Piperidine Piperidin Pipéridine Piperidine 六氫吡啶/一氮陸圜 piperidine Jerome Pansanel 2006-05-10 Pyrrolidine Pyrrolidin Pyrrolidine Pyrrolidine 吡咯啶 pyrrolidine Azacyclopentane Tetrahydropyrrole Azacyclopentane Tétrahydropyrrole Tetrahydropyrrole 四氫吡咯 Jerome Pansanel 2006-06-26 1-Aminobutane 1-Aminobutan 1-Aminobutane 1-Aminobutane 1-胺丁烷/1-丁胺 1-aminobutane Butan-1-amine n-Butylamine Butan-1-amin n-Butylamin Butan-1-amine n-Butylamine Butan-1-amine 丁-1-胺 n-Butylamine 正-丁胺 Jerome Pansanel 2006-07-13 1-Aminodecane 1-Aminodecan 1-Aminodécane 1-Aminodecane 1-胺癸烷/癸胺 1-aminodecane Decan-1-amine n-Decylamine Decan-1-amin n-Decylamin Décan-1-amine n-Décylamine Decan-1-amine 癸-1-胺 n-Decylamine 正-癸胺 Jerome Pansanel 2006-07-13 Ethylamine Ethylamin Ethylamine Ethylamine 乙胺 ethylamine Ethanamine Ethanamin Ethanamine Ethanamine 乙胺 Jerome Pansanel 2006-07-13 1-Aminoheptane 1-Aminoheptan 1-Aminoheptane 1-Aminoheptane 1-庚胺 1-aminoheptane Heptan-1-amine n-Heptylamine Heptan-1-amin n-Heptylamin Heptan-1-amine n-Heptylamine Heptan-1-amine 庚-1-胺 n-Heptylamine 正-庚胺 Jerome Pansanel 2006-07-13 1-Aminohexane 1-Aminohexan 1-Aminohexane 1-Aminohexane 1-己胺 1-aminohexane Hexan-1-amine n-Hexylamine Hexan-1-amin n-Hexylamin Hexan-1-amine n-Hexylamine Hexan-1-amine 己-1-胺 n-Hexylamine 正-己胺 Jerome Pansanel 2006-07-13 Methylamine Methylamin Méthylamine Methylamine 甲胺 methylamine Methanamine Methanamin Méthanamine Methanamine 甲胺 Jerome Pansanel 2006-07-13 1-Aminononane 1-Aminononan 1-Aminononane 1-Aminononane 1-壬胺 1-aminononane Nonan-1-amine n-Nonylamine Nonan-1-amin n-Nonylamine Nonan-1-amine n-Nonylamine Nonan-1-amine 壬-1-胺 n-Nonylamine 正-壬胺 Jerome Pansanel 2006-07-13 1-Aminooctane 1-Aminooctan 1-Aminooctane 1-Aminooctane 1-辛胺 1-aminooctane Octan-1-amine n-Octylamine Octan-1-amin n-Octylamin Octan-1-amine n-Octylamine Octan-1-amine 辛-1-胺 n-Octylamine 正-辛胺 Jerome Pansanel 2006-07-13 1-Aminopentane 1-Aminopentan 1-Aminopentane 1-Aminopentane 1-胺戊烷/1-戊胺 1-aminopentane Pentan-1-amine n-Pentylamine n-Amylamine Pentan-1-amin n-Pentylamin Pentan-1-amine n-Pentylamine n-Amylamine Pentan-1-amine 戊-1-胺 n-Pentylamine 正-戊胺 Jerome Pansanel 2006-07-13 1-Aminopropane 1-Aminopropane 1-Aminopropane 1-Aminopropane 1-丙胺 1-aminopropane Propan-1-amine n-Propylamine Propan-1-amin n-Propylamin Propan-1-amine n-Propylamine Propan-1-amine 丙-1-胺 n-Propylamine 正-丙胺 Jerome Pansanel 2006-07-13 2-Aminopropane 2-Aminopropane 2-Aminopropane 2-Aminopropane 2-丙胺 2-aminopropane Propan-2-amine Isopropylamine Propan-2-amin Isopropylamin Propan-2-amine Isopropylamine Propan-2-amine 丙-2-胺 Isopropylamine 異丙胺 Jerome Pansanel 2006-07-13 Azepane Azepan Azépane Azepane 氮雜環庚烷 azepane Jerome Pansanel 2006-07-31 1H-Azepine 1H-Azepin 1H-Azépine 1H-Azepine 1H-氮雜環庚三烯/氮呯 1H-azepine Jerome Pansanel 2006-07-31 Triethylenediamine Triethylenediamin Triéthylènediamine Triethylenediamine 三伸乙二胺/三亞乙基二胺 triethylenediamine 1,4-Diazabicyclo[2.2.2]octane 1,4-Diazabicyclo[2.2.2]octan 1,4-Diazabicyclo[2.2.2]octane 1,4-Diazabicyclo[2.2.2]octane 1,4-二氮雜二環[2.2.2]辛烷 TED Jerome Pansanel 2006-11-22 (1R,2S)-1,2-Diaminocyclohexane (1R,2S)-1,2-Diaminocyclohexan (1R,2S)-1,2-Diaminocyclohexane (1R,2S)-1,2-Diaminocyclohexane (1R,2S)-1,2-環己二胺 1R_2S-1_2-diaminocyclohexane (1R,2S)-Cyclohexane-1,2-diamine (1R,2S)-Cyclohexane-1,2-diamin (1R,2S)-Cyclohexane-1,2-diamine (1R,2S)-Cyclohexane-1,2-diamine (1R,2S)-環己-1,2-二胺 Jerome Pansanel 2006-11-22 (1S,2S)-1,2-Diaminocyclohexane (1S,2S)-1,2-Diaminocyclohexan (1S,2S)-1,2-Diaminocyclohexane (1S,2S)-1,2-Diaminocyclohexane (1S,2S)-1,2-環己二胺 1S_2S-1_2-diaminocyclohexane (1S,2S)-Cyclohexane-1,2-diamine (1S,2S)-Cyclohexane-1,2-diamin (1S,2S)-Cyclohexane-1,2-diamine (1S,2S)-Cyclohexane-1,2-diamine (1S,2S)-環己-1,2-二胺 Jerome Pansanel 2006-11-22 tert-Butylamine tert-Butylamin tert-Butylamine tert-Butylamine 三級丁胺 tert-butylamine 2-Methylpropan-2-amine 2-Amino-2-methylpropane 2-Methylpropan-2-amin 2-Amino-2-methylpropan 2-Méthylpropan-2-amine 2-amino-2-méthylpropane 2-Methylpropan-2-amine 2-甲基-2-丙胺- 2-Amino-2-methylpropane 2-胺-2-甲基丙烷 Jerome Pansanel 2006-11-22 (S)-sec-Butylamine (S)-sec-Butylamin (S)-sec-Butylamine (S)-sec-Butylamine (S)-二級丁胺 S-sec-butylamine (S)-Butan-2-amine (S)-2-Aminobutane (S)-Butan-2-amin (S)-2-Aminobutan (S)-Butan-2-amine (S)-2-Aminobutane (S)-Butan-2-amine (S)-丁-2-胺 (S)-2-Aminobutane (S)-2-丁胺 Jerome Pansanel 2006-11-22 Aminocyclohexane Aminocyclohexane Aminocyclohexane Aminocyclohexane 環己胺 aminocyclohexane Cyclohexanamine Cyclohexylamine Cyclohexanamin Cyclohexylamin Cyclohexanamine Cyclohexylamine Cyclohexanamine 環己胺 Cyclohexylamine 環己胺 Jerome Pansanel 2006-11-22 Aminocyclopentane Aminocyclopentan Aminocyclopentane Aminocyclopentane 環戊胺 aminocyclopentane Cyclopentanamine Cyclopentylamine Cyclopentanamin Cyclopentylamin Cyclopentanamine Cyclopentylamine Cyclopentanamine 環戊胺 Cyclopentylamine 環戊胺 Jerome Pansanel 2006-11-22 Diethylamine Diethylamin Diéthylamine Diethylamine 二乙胺 diethylamine N-Ethylethanamine N-Ethylethanamin N-Ethyléthanamine N-Ethylethanamine N-乙基乙胺 Jerome Pansanel 2006-11-22 Dimethylamine Dimethylamin Diméthylamine Dimethylamine 二甲胺 dimethylamine N-Methylmethanamine N-Methylmethanamin N-Méthylméthanamine N-Methylmethanamine N-甲基甲胺 DMA Jerome Pansanel 2006-11-22 N,N,N',N'-Tetramethylethane-1,2-diamine N,N,N',N'-Tetramethylethane-1,2-diamin N,N,N',N'-Tetramethylethane-1,2-diamine N,N,N',N'-Tetramethylethane-1,2-diamine N,N,N',N'-四甲基-1,2-乙二胺 N_N_N2_N2-tetramethylethane-1_2-diamine N,N,N',N'-Tetramethylethylenediamine N,N,N',N'-Tetramethylethylenediamin N,N,N',N'-Tétraméthyléthylènediamine N,N,N',N'-Tetramethylethylenediamine N,N,N',N'-四甲基乙二胺 TEMED Jerome Pansanel 2006-11-22 1,5-Diaminopentane 1,5-Diaminopentane 1,5-Diaminopentane 1,5-Diaminopentane 1,5-戊二胺 1_5-diaminopentane Pentane-1,5-diamine Cadaverine Pentane-1,5-diamin Cadaverin Pentane-1,5-diamine Cadavérine Pentane-1,5-diamine 戊烷-1,5-二胺 Cadaverine 屍胺 Jerome Pansanel 2006-11-22 chemical-structures-2.2.dfsg.0.orig/src/amines/piperazine.cml0000644000175000017500000000624310662517661024505 0ustar georgeskgeorgesk Piperazine 86.1356 86.0843983 110 145 chemical-structures-2.2.dfsg.0.orig/src/amines/methylamine.cml0000644000175000017500000000405210723245757024651 0ustar georgeskgeorgesk Methanamine 31.0571 31.0421992 -93 -6 chemical-structures-2.2.dfsg.0.orig/src/amines/1-aminobutane.cml0000644000175000017500000000617310723245757025003 0ustar georgeskgeorgesk Butan-1-amine 73.1368 73.0891494 -49 78 chemical-structures-2.2.dfsg.0.orig/src/amines/aminocyclopentane.cml0000644000175000017500000000645510723245757026056 0ustar georgeskgeorgesk Cyclopentanamine 85.1475 85.0891494 -86 107 chemical-structures-2.2.dfsg.0.orig/src/amines/1-aminoheptane.cml0000644000175000017500000001031710723245757025144 0ustar georgeskgeorgesk Heptan-1-amine 115.2166 115.1360995 -21 155 chemical-structures-2.2.dfsg.0.orig/src/amines/ammonia.cml0000644000175000017500000000325210723245757023757 0ustar georgeskgeorgesk Azane 17.0305 17.0265491 -78 -33 chemical-structures-2.2.dfsg.0.orig/src/amines/CMakeLists.txt0000644000175000017500000000712211112716045024363 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "amines") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/amines/N_N_N2_N2-tetramethylethane-1_2-diamine.cml0000644000175000017500000001020610662517661031411 0ustar georgeskgeorgesk N,N,N',N'-Tetramethylethane-1,2-diamine 116.2046 116.1313485 -55 121 chemical-structures-2.2.dfsg.0.orig/src/amines/2-aminopropane.cml0000644000175000017500000000541710723245757025172 0ustar georgeskgeorgesk Propan-2-amine 59.1103 59.0734993 -99 33 chemical-structures-2.2.dfsg.0.orig/src/amines/triethylamine.cml0000644000175000017500000000755610723245757025227 0ustar georgeskgeorgesk N,N-Diethylethanamine 101.1900 101.1204495 -115 89 chemical-structures-2.2.dfsg.0.orig/src/amines/1-aminodecane.cml0000644000175000017500000001244110723245757024737 0ustar georgeskgeorgesk Decan-1-amine 157.2963 157.1830497 15 218 chemical-structures-2.2.dfsg.0.orig/src/amines/dimethylamine.cml0000644000175000017500000000464310723245757025174 0ustar georgeskgeorgesk N-Methylmethanamine 45.0837 45.0578492 -93 7 chemical-structures-2.2.dfsg.0.orig/src/amines/trimethylamine.cml0000644000175000017500000000543510723245757025376 0ustar georgeskgeorgesk N,N-Dimethylmethanamine 59.1103 59.0734993 -117 3 chemical-structures-2.2.dfsg.0.orig/src/amines/tert-butylamine.cml0000644000175000017500000000621310723245757025463 0ustar georgeskgeorgesk 2-Methylpropan-2-amine 73.1368 73.0891494 -67 45 chemical-structures-2.2.dfsg.0.orig/src/amines/azepane.cml0000644000175000017500000000644410662517661023765 0ustar georgeskgeorgesk Azepane 99.1741 99.1047994 chemical-structures-2.2.dfsg.0.orig/src/amines/triethylenediamine.cml0000644000175000017500000000705010723245757026221 0ustar georgeskgeorgesk 1,4-Diazabicyclo[2.2.2]octane 112.1729 112.1000484 157 chemical-structures-2.2.dfsg.0.orig/src/amines/1R_2S-1_2-diaminocyclohexane.cml0000644000175000017500000000713310723245757027406 0ustar georgeskgeorgesk (1R,2S)-Cyclohexane-1,2-diamine 114.1888 114.1156985 chemical-structures-2.2.dfsg.0.orig/src/amines/diethylamine.cml0000644000175000017500000000620510723245757025013 0ustar georgeskgeorgesk N-Ethylethanamine 73.1368 73.0891494 -49 55 chemical-structures-2.2.dfsg.0.orig/src/amines/piperidine.cml0000644000175000017500000000643110662517661024466 0ustar georgeskgeorgesk Piperidine 85.1475 85.0891494 -13 106 chemical-structures-2.2.dfsg.0.orig/src/amines/1-aminohexane.cml0000644000175000017500000000753310723245757024776 0ustar georgeskgeorgesk Hexan-1-amine 101.1900 101.1204495 -20 131 chemical-structures-2.2.dfsg.0.orig/src/amines/S-sec-butylamine.cml0000644000175000017500000000622110723245757025456 0ustar georgeskgeorgesk (2S)-Butan-2-amine 73.1368 73.0891494 -104 63 chemical-structures-2.2.dfsg.0.orig/src/amines/morpholine.cml0000644000175000017500000000605010662517661024507 0ustar georgeskgeorgesk Morpholine 87.1204 87.0684139 -6 129 chemical-structures-2.2.dfsg.0.orig/src/jmol/0000755000175000017500000000000011543322650021311 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/jmol/Jmol.js0000644000175000017500000014564011225617132022561 0ustar georgeskgeorgesk/* Jmol 11.7 script library Jmol.js 15:32 06.12.2008 Bob Hanson checkbox heirarchy -- see http://chemapps.stolaf.edu/jmol/docs/examples-11/check.htm based on: * * Copyright (C) 2004-2005 Miguel, Jmol Development, www.jmol.org * * Contact: hansonr@stolaf.edu * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Lesser General Public * License as published by the Free Software Foundation; either * version 2.1 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public * License along with this library; if not, write to the Free Software * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA * 02111-1307 USA. */ // for documentation see www.jmol.org/jslibrary try{if(typeof(_jmol)!="undefined")exit() // place "?NOAPPLET" on your command line to check applet control action with a textarea // place "?JMOLJAR=xxxxx" to use a specific jar file // bob hanson -- jmolResize(w,h) -- resizes absolutely or by percent (w or h 0.5 means 50%) // angel herraez -- update of jmolResize(w,h,targetSuffix) so it is not tied to first applet // bob hanson -- jmolEvaluate -- evaluates molecular math 8:37 AM 2/23/2007 // bob hanson -- jmolScriptMessage -- returns all "scriptStatus" messages 8:37 AM 2/23/2007 // bob hanson -- jmolScriptEcho -- returns all "scriptEcho" messages 8:37 AM 2/23/2007 // bob hanson -- jmolScriptWait -- 11:31 AM 5/2/2006 // bob hanson -- remove trailing separatorHTML in radio groups -- 12:18 PM 5/6/2006 // bob hanson -- adds support for dynamic DOM script nodes 7:04 AM 5/19/2006 // bob hanson -- adds try/catch for wiki - multiple code passes 7:05 AM 5/19/2006 // bob hanson -- auto-initiates to defaultdir/defaultjar -- change as desired. // bob hanson -- adding save/restore orientation w/ and w/o delay 11:49 AM 5/25/2006 // bob hanson -- adding AjaxJS service 11:16 AM 6/3/2006 // bob hanson -- fix for iframes not available for finding applet // bob hanson -- added applet fake ?NOAPPLET URL flag // bob hanson -- added jmolSetCallback(calbackName, funcName) 3:32 PM 6/13/2006 // used PRIOR to jmolApplet() or jmolAppletInline() // added 4th array element in jmolRadioGroup -- title // added and id around link, checkbox, radio, menu // fixing AJAX loads for MSIE/Opera-Mozilla incompatibility // -- renamed Jmol-11.js from Jmol-new.js; JmolApplet.jar from JmolAppletProto.jar // renamed Jmol.js for Jmol 11 distribution // -- modified jmolRestoreOrientation() to be immediate, no 1-second delay // bob hanson -- jmolScriptWait always returns a string -- 11:23 AM 9/16/2006 // bh -- jmolCommandInput() // bh -- jmolSetTranslation(TF) -- forces translation even if there might be message callback issues // bh -- minor fixes suggested by Angel // bh -- adds jmolSetSyncId() and jmolGetSyncId() // bh 3/2008 -- adds jmolAppendInlineScript() and jmolAppendInlineArray() // bh 3/2008 -- fixes IE7 bug in relation to jmolLoadInlineArray() // bh 6/2008 -- adds jmolSetAppletWindow() // Angel H. 6/2008 -- added html " var t = "" if (labelHtml.toLowerCase().indexOf("")>=0) { t += eospan eospan = ""; } t += "" +eospan; if (_jmol.debugAlert) alert(t); return _jmolDocumentWrite(t); } function jmolStartNewRadioGroup() { ++_jmol.radioGroupCount; } function jmolRadioGroup(arrayOfRadioButtons, separatorHtml, groupName, id, title) { /* array: [radio1,radio2,radio3...] where radioN = ["script","label",isSelected,"id","title"] */ _jmolInitCheck(); var type = typeof arrayOfRadioButtons; if (type != "object" || type == null || ! arrayOfRadioButtons.length) { alert("invalid arrayOfRadioButtons"); return; } if (separatorHtml == undefined || separatorHtml == null) separatorHtml = "  "; var len = arrayOfRadioButtons.length; jmolStartNewRadioGroup(); if (!groupName) groupName = "jmolRadioGroup" + (_jmol.radioGroupCount - 1); var t = ""; for (var i = 0; i < len; ++i) { if (i == len - 1) separatorHtml = ""; var radio = arrayOfRadioButtons[i]; type = typeof radio; if (type == "object") { t += _jmolRadio(radio[0], radio[1], radio[2], separatorHtml, groupName, (radio.length > 3 ? radio[3]: (id ? id : groupName)+"_"+i), (radio.length > 4 ? radio[4] : 0), title); } else { t += _jmolRadio(radio, null, null, separatorHtml, groupName, (id ? id : groupName)+"_"+i, title); } } t+="" if (_jmol.debugAlert) alert(t); return _jmolDocumentWrite(t); } function jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, id, title) { _jmolInitCheck(); if (_jmol.radioGroupCount == 0) ++_jmol.radioGroupCount; var t = _jmolRadio(script, labelHtml, isChecked, separatorHtml, groupName, (id ? id : groupName + "_" + _jmol.radioCount), title ? title : 0); if (_jmol.debugAlert) alert(t); return _jmolDocumentWrite(t); } function jmolLink(script, label, id, title) { _jmolInitCheck(); if (id == undefined || id == null) id = "jmolLink" + _jmol.linkCount; if (label == undefined || label == null) label = script.substring(0, 32); ++_jmol.linkCount; var scriptIndex = _jmolAddScript(script); var t = "" + label + ""; if (_jmol.debugAlert) alert(t); return _jmolDocumentWrite(t); } function jmolCommandInput(label, size, id, title) { _jmolInitCheck(); if (id == undefined || id == null) id = "jmolCmd" + _jmol.cmdCount; if (label == undefined || label == null) label = "Execute"; if (size == undefined || isNaN(size)) size = 60; ++_jmol.cmdCount; var t = ""; if (_jmol.debugAlert) alert(t); return _jmolDocumentWrite(t); } function jmolMenu(arrayOfMenuItems, size, id, title) { _jmolInitCheck(); if (id == undefined || id == null) id = "jmolMenu" + _jmol.menuCount; ++_jmol.menuCount; var type = typeof arrayOfMenuItems; if (type != null && type == "object" && arrayOfMenuItems.length) { var len = arrayOfMenuItems.length; if (typeof size != "number" || size == 1) size = null; else if (size < 0) size = len; var sizeText = size ? " size='" + size + "' " : ""; var t = "" if (labelHtml.toLowerCase().indexOf("")>=0) { t += eospan eospan = ""; } t += "" +eospan + separatorHtml; return t; } function _jmolFindApplet(target) { // first look for the target in the current window var applet = _jmolFindAppletInWindow(_jmol.appletWindow != null ? _jmol.appletWindow : window, target); // THEN look for the target in child frames if (applet == undefined) applet = _jmolSearchFrames(window, target); // FINALLY look for the target in sibling frames if (applet == undefined) applet = _jmolSearchFrames(top, target); // look starting in top frame return applet; } function _jmolGetApplet(targetSuffix){ var target = "jmolApplet" + (targetSuffix ? targetSuffix : "0"); var applet = _jmolFindApplet(target); if (applet) return applet if(!_jmol.alerted)alert("could not find applet " + target); _jmol.alerted = true; return null } function _jmolSearchFrames(win, target) { var applet; var frames = win.frames; if (frames && frames.length) { // look in all the frames below this window try{ for (var i = 0; i < frames.length; ++i) { applet = _jmolSearchFrames(frames[i], target); if (applet) return applet; } }catch(e) { if (_jmol.debugAlert) alert("Jmol.js _jmolSearchFrames cannot access " + win.name + ".frame[" + i + "] consider using jmolSetAppletWindow()") } } return applet = _jmolFindAppletInWindow(win, target) } function _jmolFindAppletInWindow(win, target) { var doc = win.document; // getElementById fails on MacOSX Safari & Mozilla if (_jmol.useHtml4Object || _jmol.useIEObject) return doc.getElementById(target); else if (doc.applets) return doc.applets[target]; else return doc[target]; } function _jmolAddScript(script) { if (! script) return 0; var index = _jmol.scripts.length; _jmol.scripts[index] = script; return index; } function _jmolClick(scriptIndex, targetSuffix, elementClicked) { _jmol.element = elementClicked; jmolScript(_jmol.scripts[scriptIndex], targetSuffix); } function _jmolMenuSelected(menuObject, targetSuffix) { var scriptIndex = menuObject.value; if (scriptIndex != undefined) { jmolScript(_jmol.scripts[scriptIndex], targetSuffix); return; } var len = menuObject.length; if (typeof len == "number") { for (var i = 0; i < len; ++i) { if (menuObject[i].selected) { _jmolClick(menuObject[i].value, targetSuffix); return; } } } alert("?Que? menu selected bug #8734"); } _jmol.checkboxMasters = {}; _jmol.checkboxItems = {}; function jmolSetCheckboxGroup(chkMaster,chkBox) { var id = chkMaster; if(typeof(id)=="number")id = "jmolCheckbox" + id; chkMaster = document.getElementById(id); if (!chkMaster)alert("jmolSetCheckboxGroup: master checkbox not found: " + id); var m = _jmol.checkboxMasters[id] = {}; m.chkMaster = chkMaster; m.chkGroup = {}; for (var i = 1; i < arguments.length; i++){ var id = arguments[i]; if(typeof(id)=="number")id = "jmolCheckbox" + id; checkboxItem = document.getElementById(id); if (!checkboxItem)alert("jmolSetCheckboxGroup: group checkbox not found: " + id); m.chkGroup[id] = checkboxItem; _jmol.checkboxItems[id] = m; } } function _jmolNotifyMaster(m){ //called when a group item is checked var allOn = true; var allOff = true; for (var chkBox in m.chkGroup){ if(m.chkGroup[chkBox].checked) allOff = false; else allOn = false; } if (allOn)m.chkMaster.checked = true; if (allOff)m.chkMaster.checked = false; if ((allOn || allOff) && _jmol.checkboxItems[m.chkMaster.id]) _jmolNotifyMaster(_jmol.checkboxItems[m.chkMaster.id]) } function _jmolNotifyGroup(m, isOn){ //called when a master item is checked for (var chkBox in m.chkGroup){ var item = m.chkGroup[chkBox] item.checked = isOn; if (_jmol.checkboxMasters[item.id]) _jmolNotifyGroup(_jmol.checkboxMasters[item.id], isOn) } } function _jmolCbClick(ckbox, whenChecked, whenUnchecked, targetSuffix) { _jmol.control = ckbox _jmolClick(ckbox.checked ? whenChecked : whenUnchecked, targetSuffix); if(_jmol.checkboxMasters[ckbox.id]) _jmolNotifyGroup(_jmol.checkboxMasters[ckbox.id], ckbox.checked) if(_jmol.checkboxItems[ckbox.id]) _jmolNotifyMaster(_jmol.checkboxItems[ckbox.id]) } function _jmolCbOver(ckbox, whenChecked, whenUnchecked) { window.status = _jmol.scripts[ckbox.checked ? whenUnchecked : whenChecked]; } function _jmolMouseOver(scriptIndex) { window.status = _jmol.scripts[scriptIndex]; } function _jmolMouseOut() { window.status = " "; return true; } function _jmolSetCodebase(codebase) { _jmol.codebase = codebase ? codebase : "."; if (_jmol.debugAlert) alert("jmolCodebase=" + _jmol.codebase); } function _jmolOnloadResetForms() { // must be evaluated ONLY once _jmol.previousOnloadHandler = window.onload; window.onload = function() { with (_jmol) { if (buttonCount+checkboxCount+menuCount+radioCount+radioGroupCount > 0) { var forms = document.forms; for (var i = forms.length; --i >= 0; ) forms[i].reset(); } if (previousOnloadHandler) previousOnloadHandler(); } } } //////////////////////////////////// /////extensions for getProperty///// //////////////////////////////////// function _jmolEvalJSON(s,key){ s=s+"" if(!s)return [] if(s.charAt(0)!="{"){ if(s.indexOf(" | ")>=0)s=s.replace(/\ \|\ /g, "\n") return s } var A = eval("("+s+")") if(!A)return if(key && A[key])A=A[key] return A } function _jmolEnumerateObject(A,key){ var sout="" if(typeof(A) == "string" && A!="null"){ sout+="\n"+key+"=\""+A+"\"" }else if(!isNaN(A)||A==null){ sout+="\n"+key+"="+(A+""==""?"null":A) }else if(A.length){ sout+=key+"=[]" for(var i=0;ib[0]?-1:0) } function _jmolSortMessages(A){ if(!A || typeof(A)!="object")return [] var B = [] for(var i=A.length-1;i>=0;i--)for(var j=0;j=0;) for(var j=0;j< Ret[i].length;j++) s+=Ret[i][j]+"\n" return s } function jmolScriptWaitOutput(script, targetSuffix) { if(!targetSuffix)targetSuffix="0" var ret = "" try{ if (script) { _jmolCheckBrowser(); var applet=_jmolGetApplet(targetSuffix); if (applet) ret += applet.scriptWaitOutput(script); } }catch(e){ } return ret; } function jmolEvaluate(molecularMath, targetSuffix) { //carries out molecular math on a model if(!targetSuffix)targetSuffix="0" var result = "" + jmolGetPropertyAsJavaObject("evaluate", molecularMath, targetSuffix); var s = result.replace(/\-*\d+/,"") if (s == "" && !isNaN(parseInt(result)))return parseInt(result); var s = result.replace(/\-*\d*\.\d*/,"") if (s == "" && !isNaN(parseFloat(result)))return parseFloat(result); return result; } function jmolScriptEcho(script, targetSuffix) { // returns a newline-separated list of all echos from a script if(!targetSuffix)targetSuffix="0" var Ret=jmolScriptWaitAsArray(script, targetSuffix) var s = "" for(var i=Ret.length;--i>=0;) for(var j=Ret[i].length;--j>=0;) if (Ret[i][j][1] == "scriptEcho")s+=Ret[i][j][3]+"\n" return s.replace(/ \| /g, "\n") } function jmolScriptMessage(script, targetSuffix) { // returns a newline-separated list of all messages from a script, ending with "script completed\n" if(!targetSuffix)targetSuffix="0" var Ret=jmolScriptWaitAsArray(script, targetSuffix) var s = "" for(var i=Ret.length;--i>=0;) for(var j=Ret[i].length;--j>=0;) if (Ret[i][j][1] == "scriptStatus")s+=Ret[i][j][3]+"\n" return s.replace(/ \| /g, "\n") } function jmolScriptWaitAsArray(script, targetSuffix) { var ret = "" try{ jmolGetStatus("scriptEcho,scriptMessage,scriptStatus,scriptError",targetSuffix) if (script) { _jmolCheckBrowser(); var applet=_jmolGetApplet(targetSuffix); if (applet) ret += applet.scriptWait(script); ret = _jmolEvalJSON(ret,"jmolStatus") if(typeof ret == "object") return ret } }catch(e){ } return [[ret]] } //////////// save/restore orientation ///////////// function jmolSaveOrientation(id, targetSuffix) { if(!targetSuffix)targetSuffix="0" return _jmol["savedOrientation"+id] = jmolGetPropertyAsArray("orientationInfo","info",targetSuffix).moveTo } function jmolRestoreOrientation(id, targetSuffix) { if(!targetSuffix)targetSuffix="0" var s=_jmol["savedOrientation"+id] if (!s || s == "")return s=s.replace(/1\.0/,"0") return jmolScriptWait(s,targetSuffix) } function jmolRestoreOrientationDelayed(id, delay, targetSuffix) { if(arguments.length < 2)delay=1; if(!targetSuffix)targetSuffix="0" var s=_jmol["savedOrientation"+id] if (!s || s == "")return s=s.replace(/1\.0/,delay) return jmolScriptWait(s,targetSuffix) } //////////// add parameter ///////////// /* * for adding callbacks or other parameters. Use: jmolSetDocument(0) var s= jmolApplet(....) s = jmolAppletAddParam(s,"messageCallback", "myFunctionName") document.write(s) jmolSetDocument(document) // if you want to then write buttons and such normally */ function jmolAppletAddParam(appletCode,name,value){ if(value == "")return appletCode return appletCode.replace(/\\n=0){ jmolApplet = function(w){ var s="" +"
" +"Applet would be here" +"

" +"

" return _jmolDocumentWrite(s) } _jmolFindApplet = function(){return jmolApplet0} jmolApplet0 = { script: function(script){document.getElementById("fakeApplet").value="\njmolScript:\n"+script} ,scriptWait: function(script){document.getElementById("fakeApplet").value="\njmolScriptWait:\n"+script} ,loadInline: function(data,script){document.getElementById("fakeApplet").value="\njmolLoadInline data:\n"+data+"\n\nscript:\n"+script} } } /////////////////////////////////////////// //new 9:49 AM 3/6/2007: updated 13 Jun 2009 /* Resizes absolutely (pixels) or by percent of window (w or h 0.5 means 50%). targetSuffix is optional and defaults to zero (first applet in page). Both w and h are optional, but needed if you want to use targetSuffix. h defaults to w w defaults to 100% of window If either w or h is between 0 and 1, then it is taken as percent/100. If either w or h is greater than 1, then it is taken as a size (pixels). */ function jmolResize(w,h,targetSuffix) { _jmol.alerted = true; var percentW = (!w ? 100 : w <= 1 && w > 0 ? w * 100 : 0) var percentH = (!h ? percentW : h <= 1 && h > 0 ? h * 100 : 0) if (_jmol.browser=="msie") { var width=document.body.clientWidth; var height=document.body.clientHeight; } else { var netscapeScrollWidth=15; var width=window.innerWidth - netscapeScrollWidth; var height=window.innerHeight-netscapeScrollWidth; } var applet = _jmolGetApplet(targetSuffix); if(!applet)return; applet.style.width = (percentW ? width * percentW/100 : w)+"px" applet.style.height = (percentH ? height * percentH/100 : (h ? h : w))+"px" //title=width + " " + height + " " + (new Date()) } chemical-structures-2.2.dfsg.0.orig/src/jmol/README.txt0000644000175000017500000001320111225617132023003 0ustar georgeskgeorgesk============================================================================== === Jmol === ============================================================================== Jmol is an open-source molecule viewer and editor written in Java. Full information is available at http://www.jmol.org/ Usage questions and comments should be posted to jmol-users@lists.sourceforge.net Development questions, suggestions and comments should be posted to jmol-developers@lists.sf.net List of files included: ------------------- - README.txt This file. - COPYRIGHT.txt Copyright informations. - LICENSE.txt GNU LGPL (terms of license for use and distribution of Jmol). - Jmol.jar Executable file for the Jmol application (a program written in Java). This works as any other program: opens in its own window, can be resized or minimized, admits drag-and-drop, has a top menu bar, can open and save files, etc. It can be run from the command line (particulary, using the shell or batch files described below), but if Java is properly configured in your system, it's usually enough to double-click on this file. - jmol (Some kind of batch file to start Jmol application) - jmol.bat A batch file to start Jmol application under Windows. - jmol.mac (Some kind of batch file to start Jmol application) - jmol.sh A shell script to start Jmol application under Unix-like systems, like Linux, BSD, Solaris and Cygwin for Windows. - JmolApplet.jar The applet, i.e. a version of the program that will only run when embedded in a web page. This is an all-in-one (or monolithic) file, kept mainly for compatibility with old pages that call it explicitly. Current recommended procedure is to use the split version (JmolApplet0.jar etc., described below). In particular, Jmol.js uses the split version. You may wish to use this if you want to keep your website simple or you just want to upload a single jar file whenever new versions are released. However, this will load Jmol somewhat slower than the split versions, as all the program components must get loaded onto a user's machine before any structure is displayed. To invoke JmolApplet.jar from Jmol.js, either: a) put it in the folder containing the HTML page requiring it and do not use jmolInitialize() or b) identify it explicitly in jmolInitialize(), for example: jmolInitialize("folder-containing-jar-files", "JmolApplet.jar") - JmolAppletSigned.jar An equivalent version of the applet, but this is a "signed" or "trusted" applet (a term in Java security language). This means it must be authorized by the web page visitor for it to run, but then it will have less security restrictions for file access. For example, it can access files on any part of the user's computer or from any other web server. Typically users get a message asking if they want to accept the "certificate" or if they "trust" the applet, but this security feature is not always enabled. If you decide to use JmolAppletSigned.jar you should keep this in mind. Other than reading files, Jmol does not currently utilize other capabilities of signed applets, such as accessing the System clipboard or writing files. Use only if you know what you are doing and have considered the security issues. To invoke JmolAppletSigned.jar from Jmol.js, use: jmolInitialize("folder-containing-jar-files", "JmolAppletSigned.jar") - Jmol.js The utilities library, written in JavaScript language, that assists in the preparation of web pages that use Jmol applet, without the need to know and write detailed JmolApplet code. This library uses by default the split version of the applet (either unsigned or signed). Fully documented at http://jmol.org/jslibrary/ - JmolApplet0.jar and JmolApplet0(severalSuffixes).jar The applet is divided up into several pieces according to their function, so that if a page does not require a component, that component is not downloaded from the server. It is still recommended that you put all JmolApplet0*.jar files on your server, even if your page does not use the capabilities provided by some of the files, because the pop-up menu and Jmol console both allow users to access parts of Jmol you might not have considered. The set of these files is equivalent to the single JmolApplet.jar. This split version is the one that will be used by default if you use Jmol.js. For that, use the simplest form of jmolInitialize(), just indicating the folder containing the set of jar files: jmolInitialize("folder-containing-jar-files") for example, jmolInitialize(".") (if jar files are in the same folder as the web page) jmolInitialize("../jmol") (if jar files are in a parallel folder, named 'jmol') - JmolAppletSigned0.jar and JmolAppletSigned0(severalSuffixes).jar The signed version of the split applet. This version allows the user to access files anywhere on the computer and from any location on the web. Typically, users get a message asking if they want to accept the certificate for **each** of the (currently 16) loadable jar files. For this reason, this version may not be of general use. The set of these files is equivalent to the single JmolAppletSigned.jar. To use this with Jmol.js, use either: a) jmolInitialize("folder-containing-jar-files", true) or b) jmolInitialize("folder-containing-jar-files", "JmolAppletSigned0.jar") --------------------------- Given the descriptions, you will realize that the distribution package contains 4 full copies of the applet (signed or unsigned, split or not). --------------------------- chemical-structures-2.2.dfsg.0.orig/src/jmol/CHANGES.txt0000644000175000017500000050760011225617132023131 0ustar georgeskgeorgesk# Developers: to add a description of changes you have made, # add it on a line starting with # below the "version=..." line version=11.6.25 # bug fix: select model=1 does not work (since 11.6.RC17!) # bug fix: dipole offsetside not working for molecular dipole (EVER!) # bug fix: 2 pixels off in y for labels. Don't know why I thought that was necessary in Text.java::setBoxXY. # bug fix: dipoles cannot be colored by name # bug fix: dipole settings not accessible via wildcards # bug fix: gzipped gzip file not read properly. (Jmol-FAH files) # bug fix: Crystallographic Information File not recognized. # ----------------------------------------------------------------------------- #version=11.6.24 # bug fix: Application setAppletContext null pointer # bug fix: point + integer wrong result # bug fix: biomolecules for new PDB format # bug fix: isosurface cavity colorscheme not applied # bug fix: isosurface cavity colorscheme "sets" error # bug fix: selected connected(hbond) not working. # ----------------------------------------------------------------------------- #version=11.6.23 # bug fix: {atomExpression}.fxyz does not return factional value, just 0.0 # bug fix: Hall lattice operation (SHELX only) could place atoms in unexpected unit cell # bug fix: unitCell normalization error could miss some atoms in multi-unit cell visualizations # bug fix: calculate hbonds can fail when group does not have O or OXT atoms # bug fix: data "append" does not set model the way load "append" does # bug fix: application frame arrows do not work after loading multiple models # bug fix: isosurface incorrectly setting number of grid points for MEP surface map # ----------------------------------------------------------------------------- #version=11.6.22 # bug fix: minimization callback does not report dE # bug fix: minimization does not interrupt or stop in applet # bug fix: rotate quaternion with NaN values not ignored # bug fix: applet console not closed when web page destroyed # bug fix: autoBond option in Preference menu was not writing to properties file in $HOME/.jmol # bug fix: load file:///xxx.xxx (file:/// with file in root path) causes unrecoverable exception # bug fix: signed applet JmolAppletSigned0.jar does not include minimizer in internal jar index # bug fix: rotate -x n rotates wrong direction # bug fix: Jaguar reader vibrations not correct # ----------------------------------------------------------------------------- #version=11.6.21 # bug fix: reading multiple files from a ZIP file collection, Jmol was forcing autobond # even when bonds were defined # bug fix: (application) animation tooltips incorrect # bug fix: V3000 reader chokes on CHG=n and does not recognize MASS=n # bug fix: MOL files within ZIP files do not respect bonding. # (not fully fixed, but fixed when reading single MOL files from ZIP files) # ----------------------------------------------------------------------------- #version=11.6.20 # bug fix: automatic adjustment for 5D (spherical) orbitals, especially for Spartan Smol reader # bug fix: try/catch needed around rendering # bug fix: animation/spin while script is rendering can cause Exception # bug fix: MO rendering with antialiasDisplay information font incorrect # bug fix: draw arrow/vector slightly overshoots end point # ----------------------------------------------------------------------------- #version=11.6.19 # bug fix: isosurface/mo FRONTONLY not operative # bug fix: MO calculations skips d2+ orbital due to integer division. # bug fix: (application) measurement tool bar icon not toggling # bug fix: "color MO" if executed twice can crash Jmol # ----------------------------------------------------------------------------- #version=11.6.18 # bug fix: line raster not completing lines # bug fix: (Application) meaurement table not updating properly # bug fix: subtle MarchingSquares calculation error produces incorrect contours for mapped plane # bug fix: isosurface TRIANGLES not turning off when isosurface cleared # bug fix: remapping colors of translucent isosurface can have incorrect colors # bug fix: isosurface sphere 1.0 map molecular not working # bug fix: MO calculation with selected atoms can fail # bug fix: Jmol in other applications not initialized the same way can cause null pointer exception loading file with symmetry # ----------------------------------------------------------------------------- #version=11.6.17 # bug fix: Spartan reader reads MOs improperly when only a partials set of MOs is included in the file # bug fix: Some Spartan files not reading: Compound Document not properly finding root directory block # ----------------------------------------------------------------------------- #version=11.6.16 # bug fix: PDB load filter broken for ANISOU # bug fix: isosurface plane improperly coloring nonmapped planes # bug fix: Mopac graphf UHF files not read properly for beta orbitals, or can't read file # ----------------------------------------------------------------------------- #version=11.6.15 # bug fix: set picking draw can lose focus during drag operation # bug fix: {*}.formalCharge = 1 after {*}.formalCharge = -1 sets formal charge to -7 and exception # bug fix: write command does not report full path to file written # bug fix: Menu File|Open does not honor "start in" directory # ----------------------------------------------------------------------------- #version=11.6.14 # bug fix: @~xxx({xxxx}) compiler bug # bug fix: structure helix ({xx:yy}) compiler bug # bug fix: user menu write povray/vrml/maya missing quotation marks in command # ----------------------------------------------------------------------------- #version=11.6.13 # bug fix: user menu ...Text menus not translated # ----------------------------------------------------------------------------- #version=11.6.12 # bug fix: protein-protein hydrogen bonds not calculated across biopolymer boundaries # bug fix: quaternion straightness update # ----------------------------------------------------------------------------- #version=11.6.11 # aargh -- forgot to upload file for 11.6.10 # ----------------------------------------------------------------------------- #version=11.6.10 # bug fix: vibrationperiod set to 0 if vibration off when state saved # ----------------------------------------------------------------------------- #version=11.6.9 # bug fix: application -i option still gives message from "set xxxx" # bug fix: some quaternions cannot be created from a 3x3, namely: # q = quaternion({1 2 -2}, {2 1 2}) = {0.57735026 0.57735026 0.0 0.57735026} (xyzw format) # bug fix: ignoreError -- need not get error string # bug fix: write image does not set mustRender # bug fix: set debugscript and set loglevel do not act in script immediately # bug fix: translations of Console not implemented correctly # bug fix: translation not disabled when messageCallback is present # bug fix: script error messages not updating when language changed # bug fix: MO scale # bug fix: measure allConnected broken # ----------------------------------------------------------------------------- #version=11.6.8 # bug fix: write .... @{...} fails # bug fix: write .... @{...} can fail # bug fix: write image CLIPBOARD broken # bug fix: select {*.ca} (phi < select(y; {*.ca}; y.resno = _x.resno + 1).phi) fails when atomExpression is ({}) # bug fix: applet compilation error not sent in termination message # bug fix: build javax package does not include Matrix4d.class, AxisAngle4d.class # bug fix: compilation of myfunc({1 2 3}) fails # bug fix: hover watcher occasional uncaught exception # ----------------------------------------------------------------------------- #version=11.6.7 # bug fix: quaternion straightness update # bug fix: applet improperly reporting status of "quiet" commands # bug fix: stereo not in state # bug fix: stereoDegrees parameter not reported correctly # ----------------------------------------------------------------------------- #version=11.6.6 # bug fix: negative number in range involving ^ still fails # bug fix: translucency of mapped isosurfaces not saved in state # bug fix: Dialog look and feel for Mac # ----------------------------------------------------------------------------- #version=11.6.5 # bug fix: negative number in range involving ^ fails: select 10^P -17^P # bug fix: goto xxx with trailing white space fails to find xxx # bug fix: goto with a # comment in the script prior to the target line fails # bug fix: two //xxx comments in a row breaks script # code: superfast JVXL compression/decompression # bug fix: straightness absolute value -- values 0 (not straight) to 1 (straight) # load =1crn;calculate straightness;color "bwr" range 0 1;color straightness # # bug fix: isosurface APBS dx file reader broken (since 4/2007) # menu: "Minimize" GT # ----------------------------------------------------------------------------- #version=11.6.4 # bug fix: UFF.txt not included in build # bug fix: function definitions occurring before prior script commands are executed. # bug fix: message @{xxxx} in function not picking up function context variables # bug fix: Some browsers do NOT strip \n from tags, necessitating changes in loadInLine() # bug fix: "valence" not "valency" in data property_valence # bug fix: initializeBspf(); missing in setTrajectory() # ----------------------------------------------------------------------------- #version=11.6.3 # bug fix: set antialiastranslucent false not functional # bug fix: text color near black with antialiasdisplay becomes white # bug fix: text antialiasing of near-black text looks very bad when antialiased # ----------------------------------------------------------------------------- #version=11.6.2 # bug fix: forcefield file UFF.prm --> UFF.txt # bug fix: better Escape method for strings # bug fix: connect auto not registered in state # bug fix: draw point translucent only draws ring # bug fix: load string inline with multiple models fails # # code: FindBugs fixes for Eval, DrawRenderer, Isosurface, ForceFieldUFF # code: ScriptWindow public: sendConsoleEcho,sendConsoleMessage,notifyScriptStart,notifyScriptTermination # ----------------------------------------------------------------------------- #version=11.6.1 # bug fix: set labelToggle malfunctioning # bug fix: missing default background for toggled labels # bug fix: color {oxygen} translucent blue # bug fix: color translucent 1 blue 1-8 integer settings off by one # bug fix: background color +/-1 adjustment removed # bug fix: spardir within /M... directory # bug fix: (minor) "set echo xxx display" equivalent to "set echo xxx displayed" missing # bug fix: (minor) "set echo xxx hide" equivalent to "set echo xxx hidden" missing # ----------------------------------------------------------------------------- #version=11.6 # bug fix: GIF encoder color / class not found issues # bug fix: very thin cylinder does not appear at all viewing angles # bug fix: load "/xxx" with unsigned remote applet loads local file instead of remote root directory # bug fix: sulfur/sulphur always spelt as in IUPAC Red Book # bug fix: display of aromaticSingle bond for NEW bond results in dotted bond. # translation: English language variants no longer ignored # ----------------------------------------------------------------------------- #version=11.6.RC18 # bug fix: fileName not reset after ZAP # bug fix: set echo none; color echo green null pointer exception # bug fix: .x not recognized # bug fix: set xxxCallback "" does not clear callback ("none" was required unnecessarily) # bug fix: cartoons ending in helix or strand draw single dot for final amino acid # ----------------------------------------------------------------------------- #version=11.6.RC17 # bug fix: draw scale not saved in state for arc or xy arrow # bug fix: drag/drop not enabled on consoles # bug fix: Jmol state command "calculate surfaceDistance WITHIN ({...})" not passing compiler # bug fix: Swing antialiasDisplay broken due to setTransparentBackground debugging # bug fix: trajectories not enabled # code: if (true...)/ if (false...) code cleanup # bug fix: select model=_modelNumber didn't differentiate between 2.10 and 2.1 # bug fix: select model=0.0 caused infinite loop # ----------------------------------------------------------------------------- #version=11.6.RC16 # bug fix: mol2 PDB format better handling of chains and derived element types # bug fix: save image button/menu interface broken in 11.6.RC15 # ----------------------------------------------------------------------------- #version=11.6.RC15 # new feature: MOL2 reader is PDB-enabled. # new feature: data() and DATA expanded to allow fixed-column entry # bug fix: data property_partialcharge does not update atomic partialCharge data itself for MEP # but instead just creates a data type "property_partialcharge" # bug fix: CML reader failst to load primitive lattice parameters when no symmetry # note: CML reader only reads the first structure of a file # bug fix: CML reader not assigning atom labels # bug fix: CML files not properly loading symmetry # bug fix: O- formal charge radius MUCH too large; N+ MUCH too small. -- REMOVED # code: thread control for Java Swing in applet context # thread creating Swing objects MUST be event thread # -- using SwingUtilities.invokeAndWait() from the commandWatcher thread # new feature: load menu items for signed applet # new feature: save menu items for signed applet # bug fix: applet -- setting a jmolScript callback prevents menu updates # new feature: minimize menu item # new feature: signed applet allows "load ?" and includes previewer # bug fix: H-M spacegroup designations specifying nonstandard Hall symbols by default # new feature: signed applet/application load ?xxx uses load dialog # webexport help updated to reflect ability to handle files opened with "load append" # ----------------------------------------------------------------------------- #version=11.6.RC14 # new feature: signed applet may write file, images, scripts, variables to disk. User dialog is required. # new feature: write GIF # code: allows for getJpeg(quality,asString) option to return byte array instead of base64. # bug fix: xxx.split()[3].replace does not do selection first # bug fix: ramachandran and quaternion derivative not indicating structure due to dropping last atom # ----------------------------------------------------------------------------- #version=11.6.RC13 # bug fix: set historyLevel recording full scripts, not individual commands # bug fix: y-offset for echo text and images # bug fix/new feature: HIDE/DiSPLAY/DELETE/COLOR $*xxx* extended to ECHO # bug fix: findbugs input stream closure # translation: add GT.escapeHTML and stricter checking for special characters in file names # used by web export. # ----------------------------------------------------------------------------- #version=11.6.RC12 # bug fix: getProperty("atominfo",{atom expression}) not working for "atominfo[0].xxx # bug fix: getProperty("modelinfo",{atom expression}) not working # new feature: set atomPicking TRUE/FALSE # new feature: set bondPicking TRUE/FALSE # bug fix: draw pointgroup when principalPlane == null # bug fix: findbugs corrections in minimize.forcefield, modelset.AtomCollection, shapespecial.DrawRenderer # new feature: applet parameter jmolSetCallback("maximumSize", nnn) -- sets maximum size of applet when resizing to this value # cml reader fix for not applying symmetry to first model # translation: added GT._ calls for HTML templates and JS in WebExport # ----------------------------------------------------------------------------- #version=11.6.RC11 # bug fix: echo IMAGE and antialiasdisplay # bug fix: super/subscripts with antialiasdisplay # translation: menu items in console # bug fix: web export / language # bug fix: draw pointgroup C2 2 not distinguished from draw pointgroup C2 1 # bug fix: d2 point groups cause null pointer exception due to missing principal axis # bug fix: {*}.x = .... broken # ----------------------------------------------------------------------------- #version=11.6.RC10 # bug fix -- set picking spin, also compatibility of set picking spin and doing measurements # bug fix -- draw pointgroup, write pointgroup draw # ----------------------------------------------------------------------------- #version=11.6.RC9 # code: more efficient return of point group information and calculation # new feature: getProperty PointGroupInfo # bug fix: show pointgroup draw null pointer exception # bug fix: print $planeA - capital letters in a draw name disallow finding it. # ----------------------------------------------------------------------------- #version=11.6.RC8 # bug fix: ramachandran / ramachandran r navigation problem # code: Minor refactoring and pruning. # --- Core applet now 715K (JmolApplet0.jar + _Core, _Jars, _Main, _Popup, and _Viewer) # code: Pre-Jmol.js button controls removed, saving about 10K # new feature: script APPLET appletName "some script" # --allows direct inter-applet communication independent of set SYNC # --appletName can be * (all applets), > (other applets), . (this applet), # or an applet name such as "jmolApplet0" or just the extension "0" # or a quoted set of applet names separated by commas. # --for *, the current applet always reports LAST # new feature: x = script("some script", "appletName") # --same as above # --in addition, allows retrieval of information from another applet # for example: # # x = script("print getProperty(\"modelInfo.modelCount\")","B") # # gets the number of models loaded in applet jmolAppletB. # # x = script("show orientation moveto","jmolApplet2") # # gets the current orientation of applet jmolApplet2. # # xList = script("print getProperty(\"appletInfo.fullName\").split(\"__\")[1] + \":\" + script(\"show rotation\").trim()","*") # # gets a new-line-separated list of rotational quaternions for all applets with applet names. # # # new feature: print getProperty("modelInfo.models[3].file") syntax # ----------------------------------------------------------------------------- #version=11.6.RC7 # new feature: draw ramachandran includes planes connecting atoms. # bug fix: refresh for hover # bug fix: state definition for lcaoCartoons, isosurface with IDs containing spaces # new feature: $*xx* double wild cards # new feature: generally for objects (draw,pmesh,isosurface,etc.) use DISPLAY/HIDE rather than ON/OFF # so as to be consistent with other objects. (OFF was not deleting these) # new feature: support for application transparent background -- "-b" command switch (testing only) # and setAppletContext "-b" switch as well. # bug fix: structure helix|sheet|turn|none {atomExpression} was undocumented and had state issues # new feature: HIDE $xxx # new feature: DISPLAY $xxx # new feature: DELETE $xxx # bug fix: adaptation for malformed PDB files (HEADER with nothing following it) # bug fix: more language localization in webexport # new feature: applet message regarding help and command entry # ----------------------------------------------------------------------------- #version=11.6.RC6 # code: better navigation refreshing # bug fix: oops, 11.6.RC5 is totally broken due to missing refreshes # bug fix: language localization in webexport # ----------------------------------------------------------------------------- #version=11.6.RC5 # bug fix: set fontscaling with multiple echo texts/images at the same xyz location only scaling the first item # bug fix: set echo xxxx 30 40 # bug fix: WAY more streamlined refreshing # bug fix: createImage(), not getImage() in order to allow dynamic file change # bug fix: halo size for antialiased display # Addition of translation tags to webexport # bug fix: write IMAGE broken for 11.6.RC2+ # bug fix: unnecessary refreshes removed from moveto/zoom with time 0 # new feature: background IMAGE "filename" # code: viewer refactoring to simplify/remove private methods and synchronization # ----------------------------------------------------------------------------- #version=11.6.RC4 # bug fix: select @m throws an error # code: refactoring shapespecial into shapespecial and shapesurface # code: refactoring modelset.CellInfo into symmetry.SymmetryInfo # code: realignment of applet JAR files # -- new _ShapeSurface.jar, which now includes org.jmol.jvxl/** # -- removal of _Jvxl.jar # -- refactoring reduces preliminary applet Jar file loading to 720K (if English) # -- should provide faster loading of simple models and more efficient loading of more complex ones # -- basic minimum load involves just JmolApplet0.jar + _Core, _Jars, _Main, _Popup, and _Viewer # ----------------------------------------------------------------------------- #version=11.6.RC3 # bug fix: minor error in pointgroup; dimension tied to radius # new feature: set dotDensity [-3 to 3] # new feature: draw pointGroup [type] [index] SCALE [x] # where [type] is one of Cs, Ci, Cn, or Sn, where n is an integer or the character "n" # ----------------------------------------------------------------------------- #version=11.6.RC2 # bug fix: image background transparency # new feature: set pointGroupDistanceTolerance (default 0.2 angstroms) # new feature: set pointGroupLinearTolerance (default 8 degrees) # bug fix: Cs pointgroup not found # bug fix: set echo DEPTH/IMAGE # bug fix: workaround for Java 1.6.0_10 diallowing popup menu # new feature: in Java 1.6.0_10, right-click activates the console, and the # console has a menubar menu item "Jmol" that is the pop-up menu. # new feature: applet console has "help" menu item, which includes several hundred items. # ----------------------------------------------------------------------------- #version=11.6.RC1 # bug fix: D3h point group # bug fix: LOAD "..." nn loading of model numbers for PDB files should read real model number, not sequentially. # new feature: write/show pointgroup gives counts and tab-separated listing; # new feature: write pointgroup draw delivers draw commands # new feature: better draw pointgroup # new feature: no saving of point group -- just recalculated each time # bug fix: measures were messed up # new feature: echo myecho IMAGE "filename" # -- reads a JPG, GIF, or PNG image and displays it the # same as text is displayed. # new feature: echo myecho DEPTH xx # -- sets the depth in percent (0% far back, 100% front) for the placement of the image # -- note that images can be placed in 3D, just as for text. # -- setting "background echo xxx" then specifies the color # that is to be designated as the background color (the color that should be omitted). # -- using "background echo none" specifies that the first pixel # of the image specifies the color that should be omitted. # bug fix: 11.5.52 may have lost "true" as a keyword # new feature: pointgroups with vibration vectors # bug fix: more testing with pointgroups # new feature: spacefill/dots/geosurface/cartoon/trace/etc. ONLY # -- show only this rendering type # -- same as restrict not selected; spacefill ON # bug fix: application rubberband selecting inappropriately selects atoms not visible # new feature: wildcard at beginning for draw/pmesh/isosurface/etc. *xxx on/off/delete allowed # bug fix: in draw pointGroup -- height of cylinder was too small # bug fix: longstanding exception: isosurface fullylit --> isosurface backlit --> isosurface frontlit # ----------------------------------------------------------------------------- #version=11.5.52 # new feature: calculate pointGroup # new feature: draw pointGroup # new feature: write pointGroup # including x = script("write pointGroup") # new feature: webexport now compresses data files over 512 MB # new feature: calculate pointGroup -- preliminary only -- untested # ----------------------------------------------------------------------------- #version=11.5.51 # bug fix: 11.5.49 and 11.5.50 broken for ".max" # new feature: PRELIMINARY aniso_beta for cif files -- has not been checked for correct Ortep type -- set to 0 for now # new feature: application select button reinstated # new feature: application pick button reinstated # new feature: application measure button tied to picking style # new feature: application [>|] button # bug fix: ramachandran/quaternion "reset" not decoupled from model decouple # code: model orientation saved with model. # bug fix: set axesOrientationRasmol finally correctly implemented # new feature: axes labels change subtly for set axesMolecular and setAxesOrientationRasmol # bug fix: JmolViewer interface deprecated "rotateTo..." methods changed to "rotate..." # because that's what they really do. # bug fix: set defaults jmol/rasmol must do reset(). # new feature: webexport now cleans up scratch files on deletion of instances and program exit. # ----------------------------------------------------------------------------- #version=11.5.50 # bug fix: vibration thread not closing down for applet destroy when applet is off-screen # bug fix: was reading server path for local path from history in Webexport # bug fix: $ptx[2] notation broken in 11.5.49 # code: various cleaning/simplifying # code: way cleaner quaternion derivative calculation code # ----------------------------------------------------------------------------- #version=11.5.49 # bug fix: strange "scripted: ?" message with measurements removed # bug fix: extra values in measure reporting, and wrong format # bug fix: 11.5.48 is broken for scripts with array definitions such as # p = array(); p[pt] = .... # code: simplification/unification of statement length checking AFTER allowing for variable substitution # code: removal of unnecessary/inflexible compilation step involving color parameters # code: major refactoring/simplification of Token # code: refactoring/simplification of Compiler # code: compiler flags for allowed number of parameters removed (not consistent with Jmol math) # (defaultON and noArgs remain) # new feature: dipole/draw/ellipsoid/isosurface/pmesh/mo/lcaocartoon ID keyword optional # but without ID, one is restricted to words that are simple text and not Jmol entities. # with ID, the next quantity can be anything. # new feature: $"xxx" quotations or $@{...} allows variable definition of object id reference # new feature: draw {point} PLANE [plane def, including xy, yz, x, etc.] # ----------------------------------------------------------------------------- #version=11.5.48 # new feature: mol file bond type 8 as partial # code: compiler error reporting improved # bug fix: PDB site definition does not ignore empty site definitions # bug fix: DEFINE can cause compiling error, e.g. "[2MO]" in 1tmo # bug fix: quaternion derivative DRAW arrows placed on residue i+1 instead of residue i # bug fix: connect aromatic auto; select connected([bond type],...) # bug fix: queue thread termination when applets are off screen # bug fix : sheetsmoothing not consistent among structures in multi-chain systems # bug fix: messages not sent to messageCallback # code: simpler matrix-->quaternion code # bug fix: 11.5.47 shows oddly sized arrow for very first rendering # bug fix: quaternion frame "n" after rotationSelected does not reset NH hydrogen positions # new feature: // at beginning of a line marks comments # ----------------------------------------------------------------------------- #version=11.5.47 # bug fix: Removed stray semicolons from header script comments in webexport templates. They # were causing WYSIWG web editors to corrupt the code scripts. # bug fix: 11.5.46 broke standard "spin x 30" (b) # new feature: draw ARC {pt1} {pt2} {ptref} {theta0, nDegrees, fractionalOffset} # new feature: draw ARROW ARC {pt1} {pt2} {ptref} {theta0, nDegrees, fractionalOffset} # # draws a circular arc or arrow around an axis defined by {pt1} and {pt2} # using {ptref} as a starting point (looking down the axis, angles # are measured in a clockwise manner, starting with the projected position # of {ptref} in a plane perpendicular to the axis. This is similar (but opposite) # to the way dihedral angles are indicated. # theta0 is the the offset angle from 0 # nDegrees is the number of degrees of arc to draw # fractionalOffset is the fraction of the distance from {pt1} to {pt2} for the # plane containing the arc. # # new feature: draw RAMACHANDRAN # draws phi and psi angles in the form of draw ARROW ARC # new feature: write RAMACHANDRAN draw # ----------------------------------------------------------------------------- #version=11.5.46 # bug fix: remove the skipping of semicolons if parentheses or braces have been closed. (11.5.43 bug) # bug fix: set picking on broken in 11.5.39 # # new feature: measure {atomExpression or point} {atomExpression or point} ... # measurements to POINTS, including using the mouse (set drawPicking on) # will persist and can be saved in the state (11.5.38 did not allow this) # for example: # measure {0 0 0} {atomno=3} {atomno=5} # measure $point2 {atomno=3} $line[1] # # new feature: rotate branch {atom1} {atom2} ... # new feature: select within(branch, {atom1}, {atom2}) # new feature: Jmol math within("branch", {atom1}, {atom2}) # code: refactoring of getAtomsWithin() and getAtomBits() # # bug fix: array size limited # new feature: quaternion({atom expression}) -- returns calculated # frame based on quaternionFrame setting. # bug fix: drawhover not in state # bug fix: ramachandran for systems including nucleic acids when quaternionFrame = 'n' # new feature: isosurface functionXY can be used for mapping. # new feature: spacegroup/symmetry for CML files with tags # # bug fix: 11.5.39 could break isosurface/pmesh save/write state in certain cases. # bug fix: Popin.png in WebExport replaced, was too large, causing dialog box to default to too big on small screens. # bug fix: zap 2.1 for quaternion frame causes exception # bug fix: quaternion r derivative2 nonfunctional in 11.5.45 # bug fix: isosurface functionXY not working # bug fix for 11.5.45: application not returning echos and status messages to console # ----------------------------------------------------------------------------- #version=11.5.45 # new feature: show rotation aka show orientation rotation # new feature: show translation aka show orientation translation # code: mouse manager refactoring # bug fix: picking off structure did not clear picking for set picking spin # bug fix: jmolScriptWait() improperly reporting to applet console # bug fix: too many messages to applet console # # Note: planes, axisAngles, and quaternions are all saved as Token.point4f # axisAngle() and quaternion() are both processed to quaternion format # {x y z w} where w = cos(theta/2) and {x y z} = sin(theta/2)*unitNormal # quaternions are always fixed so that cos(theta/2) > 0 -- that is, so that # the reported theta (q %-2) is in the range [0, 180] # This is important. One can also get a directed theta based on a # specified axis using q % {x y z w}. w is ignored; x y z is the # axis to dot with the quaternion normal in order to switch the # sign of theta if that value is negative. # # new feature: show atom(s) # new feature: show group(s) # new feature: show selected # new feature: draw {point} {plane} # new feature: draw vector {point} {plane} # new feature: draw arrow {point} {plane} # new feature: q = axisAngle({x y z}, theta) # new feature: q = axisAngle(x, y, z, theta) # new feature: q = axisAngle("{x y x theta}") # new feature: q = quaternion("{x y z w}") # new feature: rotate @{quaternion(....)} # new feature: rotate @{axisAngle(....)} # new feature: rotate quaternion {x y z w} # new feature: rotate axisAngle {x y z theta} # new feature: {point1} == {point2} if distance < 0.000001 # new feature: {quaternion} == {quaternion2} if distance < 0.000001 # new feature: float1 == float2 if |float1 - float2| < 0.000001 # code: refactoring and simplification of rotate/spin # code: threads named # bug fix: hover will find atom in hidden frame. # bug fix: ellipsoid translucency not saved in state. # bug fix: local assignment var x = array() followed by x[n] = ... does not work # bug fix: f(x[i],x[j]) selects only x[j], not both x[i] and x[j] # bug fix: quaternion frame "n" recognizes file-based H atoms on N for frame definition # ----------------------------------------------------------------------------- #version=11.5.44 # bug fix: Java exception with write(quaternion) instead of write("quaternion") # bug fix: set picking spin did not enable draw spin/picking # bug fix: _applet variable not initializing properly # bug fix: math calculation .xyz, .color averages broken in 11.5.42 # bug fix: select @x broken in 11.5.43 # bug fix: integer addition not remaining integer # ----------------------------------------------------------------------------- #version=11.5.43 # bug fix -- if last helix is last atom, SHOW STRUCTURE fails to identify it. # # new feature/feature change: # # selectX is no longer necessary. Simply use # # select {atomExpression} (property expression) # # with no "x." An implied variable "_x" can be used explicitly: # # select {*} (straightness < 0.995) # does not round # select {*.ca} (atomY < atomX) # select {*.ca} (phi < select(y; {*.ca}; y.resno = _x.resno + 1).phi) # # new feature: quaterion % point4f --- "thetaDirected" -- # point4f is {x, y, z, w} (w ignored), where {x y z} is a # preferred direction. # Returns a point4f angle-Axis equivalent with x, y, z the normal for the quaternion # rotation and w = theta for the rotation, where the normal and theta are chosen # to be directed with a positive dot product between the input {x y z} # vector and the output {x y z}. # # thus, because the negative angle switches the normal: # # print quaternion({1 0 0}, -20) % 1 ==> {-1 0 0}; %1 ==> 20 # # but % {1 0 0 0} forces the angle associated with {1 0 0} to be reported # # print quaternion({1 0 0}, -20) % {1 0 0 0} ==> {1 0 0 20} # # bug fix: POV-RAY output of quadrilaterals. # new feature: Ramachandran "r" --- includes third (Z) axis quaternion r difference2 X component equivalent # bug fix: quaternion definition with dot-product check not effective -- removed # bug fix: quaternion construction from matrix error # # new feature: _applet boolean # # new feature: extended quaternion math # # q = quaternion({x y z}, angleDegrees) # q = quaternion(q0, q1, q2,q3) # q = {qx, qy, qz, qw} # # returning component values: # # q.x, q.y, q.z, q.w # # note that the Point4f equivalent stores w LAST, even though it is "q0" # because the Java Quat4f() and Point4f() both do that as well. We're just # being consistent with other Java use. # # Modulus operator for extended information retrieval: # # (q%0) -- q0 (w) # (q%1) -- q1 (x) # (q%2) -- q2 (y) # (q%3) -- q3 (z) # (q%-1) -- the vector {q1, q2, q3} # (q%-2) -- theta # (q%-3) -- equivalent rotational frame X-axis # (q%-4) -- equivalent rotational frame Y-axis # (q%-5) -- equivalent rotational frame Z-axis # (q%{x y z}) -- rotational transform of a point or vector based on a quaternion # # thus, for example, (q%{1 0 0}) is the same as (q%-3) # # (!q) -- quaternion inverse # # # Quaternion right division (difference "dq"): # # q2 / q1 = q2 * (!q1) # # Quaternion left division (relative difference n): # # q2 \ q1 = (!q1) * q2 # # Examples: # # q = quaternion({1 1 1},120) # print "" + (q%{1 0 0}) + " " + (q%{0 1 0}) + " " + (q%{0 0 1}) # # {0 1.0 0} {0 0 1.0} {1.0 0 0} # # new feature: Numerical left division (integer divide) # # 3.6 \ 2 = 1 # 3.6 \ 1.3 = 2 # # new feature: sqrt(x) # # bug fix: load trajectory for cases with different atom counts. # # experimental: "straightness" defined as 1 - 2 * acos(normal(dq[i]%-1) dot normal(dq[i+1])) / PI # giving a measure proportional to the difference in local helical axis angle # and ranging from -1 (opposite direction) to 1 (same direction) for proteins # -- a work in progress. See # # load =1d66 # calculate straightness;color straightness # ----------------------------------------------------------------------------- #version=11.5.42 # code: modified Jmol encoded PDB data output # bug fix: color of NaN float values changed from "center of color scheme" to GRAY # bug fix: connect "_1" was inadvertently dropped in 11.5.26. # bug fix: state script fails to save data for atoms created using the quaternion command # bug fix: axes/boundbox/unitcell dotted not working since 11.5.6 # bug fix: spin thread not stopped for applet destroy() # bug fix: quaternion derivative for i/i+1 assigned to i+1 instead of i; now assigned to i # bug fix: quaternion calculation using published algorithms was giving inverted quaternions # # new feature: set PICKLABEL "xxx" -- allows customized pick reports # # for example: set pickLabel "%n x = %x, y = %y, z = %z" # # new feature: "quaternion derivative" --> "quaternion difference", which is more # appropriate, we think, with "absolute" and "relative" qualifiers: # # quaternion absolute difference # in the molecular frame # quaternion relative difference # in the (local) frame of first quaternion: # # dq_absolute = q2 * q1_inverse # dq_relative = q1_inverse * q2 # # absolute involves un-doing q1's rotation (making it the reference frame), then applying q2. # relative involves applying q2 (maintaining the original reference frame), then undoing q1. # # new feature: quaternion [w|x|y|z|a|r] [difference][2] [draw] # new feature: draw quaternion [w|x|y|z|a|r] [difference][2] # new feature: write quaternion [w|x|y|z|a|r] [difference][2] [draw] # and with that: write("quaternion" [,"w"|"x"|"y"|"z"|"a"|"r"][,"difference"|"difference2"][,"draw"]) # # new feature: set quaternionFrame "N" -- for solid state NMR PISEMA 15N chemical shift frame # using alpha = 0 and beta = 17 degrees. # # new feature: select whatever; quaternion draw # draws x,y,z and n vectors for a quaternion center # # new feature: straightness, defined as: # # straightness = 2*|n(dq1).dot(n(dq2))| - 1 # # where q1 and q2 are quaternions defined generally as: # # q = frame{ vA, (vC x vA), vC } # # using quaternionFrame "p", which I define as # # protein: # # vA = C--CA # vB = C--N[i+1] # # purine: # # vA = N9--C4 # vB = N9--C8 # # pyrimidine: # # vA = N1--C2 # vB = N1--C6 # # Differences dq1 and dq2 are absolute quaternion differences # on the two sides of a residue: # # dq1 === q[i] * q[i-1]_inverse # dq2 === q[i+1] * q[i]_inverse # # and n(dq) = the normal vector associated with this quaternion. # Range is from -1 to 1 # # applications (note that CALCULATE must be invoked first): # # calculate straightness # must be invoked first; # color straightness; # select straightness < 0.70; # rounds to nearest hundredth # selectX {*} x.straightness < 0.995 # does not round # # new feature: "%T" label format for straightness # ----------------------------------------------------------------------------- #version=11.5.41 # new feature: xyz reader reads partial charge in 5th field # bug fix: carbohydrate popup menu script incorrect # new feature: "load" of Jmol state scripts works same as "script" command # (file recognized as SPT type and read as a script instead) # bug fix: Jmol Embedded scripts containing script comments /* */ # new feature: getproperty menu current # bug fix: 11.5.40 cannot read most state scripts. # ----------------------------------------------------------------------------- #version=11.5.40 # (with corrected 40_dev draw scale) # new feature: new command: # # selectX {atomExpression} booleanEvaluation # # same as select() function, but simpler to implement # # new feature: full math on individual atom properties using # a new function: # # select(x;{atomexpression};booleanEvaluation) # # for example: # # x = select(x;{*};x.distance({atomno=3}) / 3 > x.distance({atomno=2})) # x = select(x;{*.ca};x.phi < select(y; {*.ca}; y.resno = x.resno + 1).phi) # # bug fix: H1 and H3 in DNA are NOT backbone # new feature: quaternion derivative2 (2nd derivative) and quaternion e derivative [experimental] # new feature: draw Vector [x y] or [x y %] {x' y' z'} # new feature: draw [x y] or [x y %] can be incorporated into lines, curves, arrows # bug fix: set picking center should not zoom -- just too annoying # new feature: set echo myecho [x y] and set echo myecho [x y %] # new feature: axes position [x y] and axes position [x y %] # sets the axes to the x y screen position or percent indicated. # bug fix: echos with active script and a model designation # and multiple models select even if not displayed because it is not their model # that is displayed. # bug fix: missing echocallback, scriptcallback, measurecallback "set"able variables # bug fix: "set picking identify" should be equivalent to "set picking ident" # bug fix: popup menu had stereo reversed # # new feature: signed applet shows frank "Jmol-S" which is NOT removable. # possibly to come: signed applet will send confirmation first time it reads a local file? # bug fix: reading .mmol (biological unit) files such as # http://pqs.ebi.ac.uk/pqs-doc/macmol/1j7n_1.mmol # new feature: frank appears RED in signed applet, and popup about menu identifies the applet as signed. # code: better handling of twin script manager threads # new feature: /*SPLIT*/ in a command string allows it to be processed by # the two independent processors. (just to isolate javascript from load commands # for the signed applet # ----------------------------------------------------------------------------- #version=11.5.39 # new feature: --threaded option for command processor uses # a watcher thread to monitor a Vector, allowing the signed applet to open any file # the signed applet uses this automatically unless there is a # jmolSetCallback("useCommandThread", "false") # which overrides the default behavior and disallows reading of files from # JavaScript. # # NOTE a limitation: scripts intended for the signed applet that # contain both load/script commands or the load() function # CANNOT be combined with the JAVASCRIPT command. This is because # in that environment, the JAVASCRIPT command must run on the browser's # JavaScript thread, and the load command -- if crossing server boundaries -- # must NOT run on that thread. I have configured the ScriptManager to # detect the presence of the word "javascript" followed by a space (exactly that case) # and if found, use the JavaScript thread instead of the applet thread. # # Because it might be useful to combine LOAD and JAVASCRIPT (for the equivalent of a # "file loaded" callback (but see set LoadStructCallback), if a script contains # the phrase /*SPLIT*/ in upper case, exactly like that, it will be split and then run # correctly as two independent scripts. # # new feature: _signedApplet boolean is available: # # print _signedApplet # if(_signedApplet); # javascript alert("you are using the signed applet"); # end if; # # bug fix: JmolSimpleViewer caused null pointer exception -- needed setAppletContext() # bug fix: model-based drawing in multiple-model mode using an # array of points to load causes null pointer exception: # load cyclohexane_movie.xyz;pts = {C5}.split();print pts;draw @{pts.xyz.sub({1 0 0})} "X" # bug fix: quaternion derivative multiplication order # bug fix: 3D echo text not centering properly with set ECHO myEcho CENTER # bug fix: select _Xx; select unknown # bug fix: better reporting of script commands and comments # new feature: reading COMPND and HEADER records of PDB file # new features for Protein Explorer: # new feature: set messageStyleChime # -- No atoms selected! # -- atoms selected! # -- atom picking: # Atom: xxx Group: xxx Chain: xxx Model: xxx Coordinates: x y z # -- script # -- Chime script completed. # new features: # show info # show residue(s) # show chain(s) # show sequence # show orientation moveto # just the moveTo; no comments # set pdbGetHeader TRUE # to get the header when loading (for Protein Explorer) # new feature: jmolSetCallback("evalCallback", "someFunction") # -- overrides _jmol.noEval # -- canNOT be set using "set evalCallback" # -- was necessary for Protein Explorer javascript callbacks # ----------------------------------------------------------------------------- #version=11.5.38 # bug fix: lcaoCartoon naming for multiple centers # bug fix: pm rounding to integer value # bug fix: scaling of draw object for multimodel environment can cause null pointer exception # bug fix: scaling of VECTOR was from center, not origin # bug fix: select n-m:c chain selection inappropriately case sensitive # bug fix: draw ARROW {atom center} {xyz} draws arrow the wrong way # bug fix: draw CIRCLE for multiple models # bug fix: application -- "make crystal..." menu item does nothing -- removed # bug fix: zap of quaternion also zaps model inappropriately # bug fix: zap to one model assigns -1 to currentModelIndex instead of 0 # new feature: draw CIRCLE [FILL | MESH NOFILL] more intuitive open/filling syntax # new feature: draw VECTOR {atom center} {dx dy dz} # new feature: draw with mixed types processes them in order # (11.4 does {x,y,z}, then $xxx, then {atomExpression}, then @{{atoms}.split()}) # new feature: draw .... ">xxx" first character of title ">" forces title to # last point, not first # new feature: set quaternionFrame "c" "p" "q" # - "c" -- CA-C and CA-N, as per Andy Hanson # - "q" -- peptide plane CA-C and N'-CA' as per J.R.Quine # - "p" -- peptide plane CA-C and C-N' # new feature: random(a), random(a,b) where a is lower bound and b is upper bound # new feature: cross(a,b) # new feature: sin(x), cos(x) # new feature: set pdbSequential (default FALSE) for custom PDB files # -- bypasses inter-group bonding check when creating polymers # new feature: set drawPicking now enables measuring among atoms and DRAW points # -- not saved -- just transient measurements (see 11.5.46) # new feature: CIF reading of B factors for thermal ellipsoids # new feature: [draw|pmesh|isosurface] xxx* [on|off|delete] # -- turns on, turns off, or deletes all objects of the type starting with "xxx" # code: refactoring of biopolyer resolver # ----------------------------------------------------------------------------- #version=11.5.37 # code: faster ellipsoid rendering with precalc radius factors # bug fix: spacefill ADPMIN/ADPMAX using probability ellipsoids # and ellipsoid size setting (Note -- ellipsoid command # must be run once prior to setting spacefill # bug fix: reading output from "set showscript 1" # bug fix: ellipsoids for Uiso atoms uses simple r = sqrt(value) # bug fix: ellipsoids for applied symmetry causes odd shapes (s8.cif) # bug fix: security for no mayscript may cause problem with measure callback # bug fix: rocket positions after translateselected # ----------------------------------------------------------------------------- #version=11.5.36 # bug fix: frame titles not positioning correctly for antialiased display # bug fix: quaternions created with extraneous atom lines # bug fix: select symop not behaving intuitively # code: meshrenderer debug line not removed # new feature: (popup menu) Biomolecules submenu added within title menu # ----------------------------------------------------------------------------- #version=11.5.35 # bug fix: proper thermal ellipsoid probability measures # code: better garbage collection in relation to JmolAdapter class # bug fix: load FILTER not saved in state # bug fix: application -- undo/redo buttons not disabling # new feature: ZAP clears undo stack # ----------------------------------------------------------------------------- #version=11.5.34 # bug fix: biomolecule really works this time! # ----------------------------------------------------------------------------- #version=11.5.33 # bug fix: modelLoader was assigning too much array space for chains # new feature: more load FILTER options: # # #i a specific BIOMT transformation # !#i not a specific BIOMT transformation # [XXX] a specific group ID # ![XXX] not a specific group ID (e.g. ![HOH]) # *.XX an atom name, such as .CA # !.XX not a specific atom name # *:X a chain ID # !:X not a specific chain ID # # Between types, or involving NOT, options are AND'd together # Within a type not involving NOT, options are OR'd together # Within a type, a single ! implies all are NOT # Within a type, a single * implies all are ANY # new feature: load [file info] FILTER "BIOMOLECULE n;NOSYMMETRY" # FILTER "BIOMOLECULE 1" by default now reads the symmetry; # use load FILTER "BIOMOLECULE 1;NOSYMMETRY" to not read symmetry # # bug fix: ellipsoids for navigation mode and perspective depth # bug fix: PDB biomolecule for many-BIOMT system # ----------------------------------------------------------------------------- #version=11.5.32 # bug fix: load FILTER "BIOMOLECULE 1;APPLY SYMMETRY" does not read second line of chain list # bug fix: added connections do not save properly in state # # application only: command undo disabled automatically if saving takes more than one second # flag is "set undo TRUE/FALSE" # # new feature: load [file info] FILTER "[filter string]" # new feature: load [file info] FILTER "BIOMOLECULE n" # new feature: load [file info] FILTER "[filter string];BIOMOLECULE n" # # The first format loads only those atoms matching a specific filter or set of # filter terms -- only a crude filter here, only for PDB and mmCIF files: # # *.XX an atom name, such as .CA # *:X a chain ID # # multiple matches are allowed -- implied AND: # # load "1sva.pdb" FILTER "*.CA" # # the match IS CASE SENSITIVE; * IS required # # also, "BIOMOLECULE 1" automatically selects for the chains listed for biomolecule 1 # in REMARK 350, and APPLY SYMMETRY applies the symmetry as described in those REMARKS # # new feature: isosurface ELLIPSOID id # AXES {ix iy iz} {jx jy jz} {kx ky kz} # CENTER {x y z} # SCALE n.m # COLOR [translucent [x.y] |opaque] [color] # ON|OFF # # id is a REQUIRED field. AXES is required if a new ellipsoid is being defined # these axes must be perpendicular # all other parameters are optional # # bug fix: isosurface ELLIPSOID was disabled # bug fix: Vector4f in Sphere3D causes applet failure, as it includes # an implicit Vector4d call # bug fix: stronger wireframe for antialiased display and generator (POV-ray) # default change: ellipsoids ball only, no axes # code: better ellipsoid fill method # default change: ellipsoids ball only, no axes # Hungarian translation # ----------------------------------------------------------------------------- #version=11.5.31 # bug fix: set picking measure distance not doing callback (from 11.5.23) # bug fix: picking echos not working with set antialiasdisplay # default change: ellipsoids are so fast now, can use default "set ellipsoidBall true" # bug fix: set ellipsoidAxisDiameter [int] sets the diameter in milliAngstroms # bug fix: sequence range for missing sequence numbers returns 0 # # code: fast ellipsoid ball+fill - axis idea; no luck with POV-ray fill # code: ellipsoid equation/axes conversion in Sphere3D; # code: POV-Ray ellipsoid generation # code: better ellipsoid ball rendering using Shade3D.calcIntensity() # code: 2-fold improvement in rendering ellipsoids by not using getNormix() # code: 4-fold improvement in rendering ellipsoids by using Miguel's no-mesh idea # code: 2-fold improvement in rendering ellipsoids by using 40x40x40 shade cache # code: overall 20-fold improvement in rendering over mesh/normix; # code: full POV-ray support for ellipsoids # code: proper partial derivative normalization of ellipsoid shading # code: refactoring of static quadric surface methods into their own class # ----------------------------------------------------------------------------- #version=11.5.30 # bug fix: measurement labels for angles do not appear in slab mode (goes WAY back before 10.0) # bug fix: U_iso_or_equiv fields not read in CIF # bug fix: (application) writeTip GT string not defined. # bug fix: (forwared compatibility) invalid state setting (due to later version) now ignored. # bug fix: state for draw arrow in multimodel context delivers wrong coordinates # # new feature: ellipsoid ball rendering tied to "set wireframerotation" option # new feature: set ellipsoidAxisDiameter x.y # # code: better ellipsoid arc rendering using Hermite fill # code: CifReader cleanup # ----------------------------------------------------------------------------- #version=11.5.29 # new features for ellipsoid rendering: # # set ellipsoidAxes [true] # set ellipsoidArcs [true] # set ellipsoidFill [false] # set ellipsoidDots [false] # set ellipsoidBall [false] # set ellipsoidDotCount [200] # # [dots|stars|spacefill] ADPMIN [percent] # [dots|stars|spacefill] ADPMAX [percent] # # /* general logic: # * # * # * 1) octant and DOTS are incompatible; octant preferred over dots # * 2) If not BALL, ARCS, or DOTS, the rendering defaults to AXES # * 3) If DOTS, then turn off ARCS and FILL # * # * note that FILL serves to provide a cut-out for BALL and a # * filling for ARCS # */ # ----------------------------------------------------------------------------- #version=11.5.28 # bug fix: state "set measures angstroms" does not include "select *" # bug fix: labels can change size in returning from antialiasdisplay=true to antialiasdisplay=false # ELLIPSOID command -- with symmetry and crude footballs, including PDB files # note that for now PDB file reading of ANISOU requires using {x y z} in load # command, but you can use {1 1 0} to load ANISOU without applying symmetry # # Italian translation # ----------------------------------------------------------------------------- #version=11.5.27 # bug fix: data CLEAR command nonfunctional # bug fix: "....".trim("xyz") function not properly trimming ANY x,y,z # bug fix: draw OFFSET not working properly # bug fix: PovRAY output of draw objects -- cylinder end caps not considered # bug fix: draw width 0.05 {...} {...} -- line does not properly render # bug fix: data "model"...end "model" saves state without first line if first line is empty # bug fix: "show data types" putting comma in wrong location # new feature: DATA "data2d_xxxxx"..... end "data2d_xxxxx" # new feature: isosurface FunctionXY "data2d_xxxxx" {origin} {ni x 0 0} {nj 0 y 0} {nk 0 0 z} # allows setting isosurface Z values using a block of data (ni rows by nj columns) # new feature: isosurface FunctionXY "data2d_xyz_xxxx" {origin} {ni x 0 0} {nj 0 y 0} {nk 0 0 z} # allows setting isosurface values using a block of x y z data, all points for which should be # on the surface. # new feature: GamessUK reader # new feature: reset VARIABLES (replaces "reset ALL") # ----------------------------------------------------------------------------- #version=11.5.26 # bug fix: draw adds extra circle in 11.5.25 # bug fix: minimization out-of-plane energy calculation error # bug fix: better initial minimization parameters # bug fix: (applet) script termination callback should not be sent to message queue # bug fix: hover appears when a load script leaves an atom very close to (0,0) in the window # bug fix: draw width -1 or draw mesh nofill with very short cylinders creates odd jumpy effect # bug fix: draw CIRCLE for multiple model sets # # # new feature: draw CYLINDER # # Korean translation # ----------------------------------------------------------------------------- #version=11.5.25 # new feature: draw CIRCLE # # A circle is a 2D object that behaves like a halo, always appearing circular # # draw circle {molecule=1} mesh nofill # around specified atoms # draw diameter 2.0 circle {atomno=3} mesh nofill # 2.0 angstroms; scales # draw diameter 100 circle {_O}[1] mesh nofill # 100 pixels (doesn't scale) # draw circle {*} fill # a solid plane in the shape of a circle # ----------------------------------------------------------------------------- #version=11.5.24 # new feature: minimization CONSTRAINTS {xx} {xx} [{xx} [{xx}]] x.y # new feature: minimization FIX {atom expression} # # multiple constraints can be present; one per line input # minimization CLEAR releases constraints and fixed atoms # also, minimize ENERGY saves a detailed listing, which can be # displayed using one of the two following commands: # # new feature: show minimization # new feature: x = getProperty("minimizationInfo") # # to dump the info to a file: # minimize # var x = getProperty("minimizationInfo") # write VAR x "myfile.out" # # new feature: isosurface MAXSET n # removes larger fragment sets # new feature: isosurface DOWNSAMPLE n # down-factors the number of points in a CUBE file by a factor of n # ----------------------------------------------------------------------------- #version=11.5.23 # new feature: minimize ENERGY # no stepping # new feature: minimize STEPS n # new feature: minimize CRITERION x.y # new feature: minimize CLEAR # flushes logged info and saved atom info # # new feature: echoCallback # new feature: measureCallback # new feature: minimizationCallback # new feature: scriptCallback # new feature: save/restore coordinates # new feature: getProperty minimizationInfo # # code: more efficient minimize calculation setup; better logging # code: "notify" methods in JmolStatusListener consolidated # code: Tokens organized # # ----------------------------------------------------------------------------- #version=11.5.22 # bug fix: UFF torsion calculation incorrect # bug fix: UFF.prm not properly recognizing sp2 N in N-oxides # bug fix: minimizer for compounds containing isotopes D and T # # code: eval/compiler error processing update # ----------------------------------------------------------------------------- #version=11.5.21 # new feature: minimize command -- mostly untested # # set minimizationSteps 100 # set minimizationRefresh true # set minimizationCriterion 0.001 # set loglevel 4 # for a very minimal report # set loglevel 5 # for a summary report # set loglevel 6 # for a detailed report # minimize # minimize stop # minimize cancel # # # for example: # # load caffeine.xyz # minimizationSteps = 80 # minimizationRefresh = true # set loglevel 4 # select connected(2) or connected(3) or oxygen and connected(1) # connect aromatic modify # calculate aromatic # set measurementunits pm # measure {_O}[1] {_O}[2] # color measure red # minimize # # new feature: set loglevel 6 allows a "debugHigh" setting # # bug fix: load unitcell {a b c alpha beta gamma} not working (since 11.5.8) # ----------------------------------------------------------------------------- #version=11.5.20 # bug fix: zap file > 2 multiple models do not properly delete # ----------------------------------------------------------------------------- #version=11.5.19 # bug fix: null surfaceGenerator causes MO exception # bug fix: isosurface reading/writing JVXL files having insideout keyword # ----------------------------------------------------------------------------- #version=11.5.18 # bug fix: zap x.y additional work -- connections, isosurfaces # bug fix: zap x.y not correcting Eval variables # bug fix: isosurface user VolumeData not properly loading # ----------------------------------------------------------------------------- #version=11.5.17 # new feature: delete {atom expression} NEEDS TESTING # bug fix: zap x.y for dots # bug fix: zap {atom expression} for not including all atoms in a model in the selection # ----------------------------------------------------------------------------- #version=11.5.16 # new feature: zap {atom expression} # zaps models associated with given atoms. # use "show models" to see what models are present, then zap them with their # file.model number: # # zap 1.1,2.1 # these two models deleted # zap atomIndex=0 # ALL ATOMS IN FIRST MODEL deleted # # Note that file.model numbers do not change after this. # So if initially there were two files loaded # # zap 1.1 # # removes the first model and leaves the second as "2.1" # # NEEDS THOROUGH TESTING, particularly in regard to saving/restoring the state # bug fix: atomChooser not updated for zap # bug fix: isosurface model keyword does not carry on to saved state # bug fix: lcaocartoons do not color properly or get restored from state properly # bug fix: popup menu selection of groups and symmetry operations does not work # menu: internationalization of "Monomer" and "Shapely" # bug fix: mol2 reader cannot read files with single-line comments # ----------------------------------------------------------------------------- #version=11.5.15 # bug fix: CAChe CSF reader not reading partial charges # bug fix: WebExport with http:// files fails to save file # bug fix: WebExport with local . directory fails to save JmolApplet.jar and Jmol.js # code: refactoring of jmol.app.webexport: adding html subdirectory # bug fix: state saving with rotateSelected spinning spins entire model # bug fix: getproperty("chaininfo") for non-biological model causes null pointer exception # ----------------------------------------------------------------------------- #version=11.5.14 # bug fix: rotateSelected INTERNAL not adjusting for internal rotation center # bug fix: .max/.min not allowed in context: "select resno=@{{visible}.resno.max}" # bug fix: Parser: "3xxx" read as 3 instead of 0; "3.5xxx" read as 3.5 instead of NaN # application menu: Write state moved to main export menu; Export PDF to image writing # new feature: MODEL/ENDMDL records in write PDB (still no TER records) # bug fix: write PDB format incorrectly writes atoms with 4-length names # bug fix: Spartan SMOL directory reader doesn't assign bonds # new feature: Spartan archive reader now reads aromatic bonding # ----------------------------------------------------------------------------- #version=11.5.13 BROKEN FOR XYZ READER # bug fix: Parser: "3xxx" read as 3 instead of 0; "3.5xxx" read as 3.5 instead of NaN # application menu: Write state moved to main export menu; Export PDF to image writing # new feature: MODEL/ENDMDL records in write PDB (still no TER records) # bug fix: write PDB format incorrectly writes atoms with 4-length names # bug fix: Spartan SMOL directory reader doesn't assign bonds # new feature: Spartan archive reader now reads aromatic bonding # ----------------------------------------------------------------------------- #version=11.5.12 # new feature: four optional defaults for Van der Waals radii: # # set defaultVDW jmol # set defaultVDW rasmol # set defaultVDW babel # set defaultVDW user # # To set the user variety, first set one of the other sets as a basis # Then add a DATA statement to include the specific elements you want to give # new radii to: # # set defaultVDW babel; # DATA "element_vdw" 6 1.7 END "element_vdw"; # DATA "element_vdw" 6 1.7; 7 1.8 END "element_vdw"; # separate using semicolons or new lines # # For full state compatibility, these commands should be given prior to # model loading, as they affect all calculations involving Van der Waals # radii -- except default zoom. # # Now select the user set: # # set defaultVDW user # spacefill on # # To delete all user entries: # # reset VDW # # If user vdw radii are currently set, then this resets the defaults to Jmol. # # new feature: show vdw shows a listing of the currently set VDW radii # # new feature: integration of star, halo, and spacefill code so all behave the same. # # stars 1.0 # set to a specific angstrom radius # spacefill 100% # percent of CURRENT vdw set # stars 100%Jmol # percent of Jmol standard # stars 50%Babel # percent of Babel standard # spacefill 5%Rasmol # percent of Rasmol standard # spacefill 30%User # percent of User-defined values (or CURRENT if not defined) # spacefill +1.2 # angstroms added to current vdw scheme # halos 50%Jmol # -- halos also have an added bit to make sure they are visible # spacefill 250 # RasMol 250 units/Angstrom units still # spacefill -20 # neg numbers same as percentages: 20% here, using current vdw set # stars @{x+0.1} # math OK # spacefill @x% # make sure x comes out integer, otherwise % is ignored # # note that dots do not have a %Jmol option: # # dots 30 # syntax already assumes percent for dots using an integer # # # # see src/org/jmol/_documents/vdw_comparison.xls # ----------------------------------------------------------------------------- #version=11.5.11 # bug fix: save/restore of atom data incorrect when user has set propertyAtomNumberField or propertyDataField # bug fix: functions, save/restore state were disabled by bug in 1.5.8 # bug fix: command "test()" where test() is a user-defined function causes array-out-of-bounds error # bug fix: undocumented .vdw atom property was equivalent to .valence # bug fix: GAMESS reading of F orbital order incorrect # new feature: settable Van der Waals radius using {carbon}.vanderwaals = 1.7 # or using DATA "property_vanderwaals" # new feature: DATA "property_x i j" .... END "property_x i j" # overrides default propertyAtomNumberField (i) and propertyDataField (j) # new feature: State save of property_xxx now in easily readable Jmol Data Format # ----------------------------------------------------------------------------- #version=11.5.10 # NOTE: REMOVED FROM SERVICE -- see 11.5.11 # bug fix: ISOSURFACE LIST command requires current isosurface # bug fix: JVXL writing does not properly save pocket cavities or minsets # bug fix: DATA command assigning property to last atom in structure fails # ----------------------------------------------------------------------------- #version=11.5.9 # NOTE: REMOVED FROM SERVICE -- see 11.5.11 # bug fix: Gaussian reader not considering possibility of cartesian D and spherical F # bug fix: ADF reader not reading coordinates for newer ADF output # ----------------------------------------------------------------------------- #version=11.5.8 # NOTE: REMOVED FROM SERVICE -- see 11.5.11 # bug fix: lines starting with @{ redefine "{" # bug fix: echo offsets do not correct for window position # bug fix: menu reports too many chains # new feature: menu includes all standard color scheme options # new feature: inline math @{x+3} extended to all commands # new feature: .sub(), .add(), .mul(), .div() extended to all operand types # ----------------------------------------------------------------------------- #version=11.5.7 # bug fix: explicit "SELECT NONE" must be given for label defaults to be set # bug fix: menu select element missing SELECT command # bug fix: for delayed font scaling animation using the font command and antialias display # ----------------------------------------------------------------------------- #version=11.5.6 # bug fix: HETATM atoms not automatically bonded to nearby ATOM atoms # bug fix: setParameterValue("perspectiveDepth",perspectiveDepth); # bug fix: sets offset based on imageFontScaling, not overall font scaling # bug fix: multiline labels not positioned properly with offset 0 0 # bug fix: labels not scaling properly # new feature: label "scaleReference" if > 5.0 is taken to be a reference zoom setting # saying "make the font size X at a zoom of Y" # bug fix: labels not scaling properly when in script with file load # bug fix: labels not appearing in contrast when given same color as background # bug fix: fixes applet memory leak in relation to consoles # ----------------------------------------------------------------------------- #version=11.5.5 # bug fix: fixes applet memory leak due to # platform objects/delay threads not being destroyed # new feature -- syncCallback -- intercepts messages that would otherwise go to applets for syncing # when syncCallback is set to a JavaScript function name, that function # intercepts the sync message and can pass it on (by returning it), # consume it (by returning an empty string ""), or modify it as desired. # this allows, for example, monitoring of orientation information so that # zoom sliders and such can accurately portray their values # ----------------------------------------------------------------------------- #version=11.5.4 # bug fixes -- font scaling # new feature: Spartan input files read as Odyssey format # # new feature: set delayMaximumMs sets the maximum delay that scripts will use, primarily for testing scripts # new feature: set fontScaling TRUE/FALSE # new feature: font [type] [size] [face] [weight] [scaleReference (Angstroms per pixel)] # atom labels and 3D echos then scale properly. # note that the current zoom affects the label size. # bug fix: image writing does not scale fonts properly. # bug fix: antialias of images not functionally independent of antialias for display # bug fix: label offset doubled for multiline labels with left/right/center alignment not specified # bug fix: default label offsets mangled by default Front/Group # new feature: getProperty("appletInfo") includes a key "registry" for which # the value is the static Hashtable htRegistry # //note that the following JavaScript retrieves the registry: # var registry = jmolGetPropertyAsJavaObject("appletInfo").get("registry") # // and the following code then retrieves an array of applets: # var AppletNames = registry.keySet().toArray() # // and the following sends commands to an applet in the registry: # registry.get(AppletNames[0]).script("background white") # new feature: reading of Spartan spinput files (uses Odyssey reader) # bug fix: PDB files with missing amino acid carbonyl O cause exception # ----------------------------------------------------------------------------- #version=11.5.3 # bug fix: check if the file is CIF before PDB # bug fix: color hbonds translucent # bug fix: state: calculate hbonds not saved # bug fix: state: calculate surfaceDistance WITHIN (({....})) # missing outermost parentheses # bug fix: state: selection state "end function" missing semicolon # bug fix: isosurface lcaoCartoon "pz" translucent not setting both lobes translucent # bug fix: color isosurface when isosurface is an lcaoCartoon only colors one lobe # bug fix: save state for "color SelectionHalos" # ----------------------------------------------------------------------------- #version=11.5.2 # Translation update: Estonian # new feature: "getProperty FILECONTENTS ." in the context of # a zip directory defaultDirectory # new feature: zip file reading extended to write FILE # # bug fix: unclosed InputStream readers in zip file accessing # # new feature: allows zip files to be designated as default directoriesusing # set defaultDirectory "myfile.zip" # and then using a filename # bug fix: unclosed readers in Pmesh, FileManager, Jvxl # new feature: pmesh BINARY "filename" # BINARY keyword is optional, but recommended for efficiency # # * 4 bytes: P M \1 \0 # * 1 byte: \0 for bigEndian # * 3 bytes: reserved # * 4 bytes: (int) vertexCount # * 4 bytes: (int) polygonCount # * 64 bytes: reserved # * ------------------------------ # * float[vertexCount*3]vertices {x,y,z} # * [polygonCount] polygons # * --each polygon-- # * 4 bytes: (int)nVertices (1,2,3, or 4) # * [4 bytes * nVertices] int[nVertices] # * # * note that there is NO redundant extra vertex in this format # # see little-endian example at http://chemapps.stolaf.edu/jmol/docs/misc/pmesh.bin # and http://chemapps.stolaf.edu/jmol/docs/misc/pmesh.bin.txt # ----------------------------------------------------------------------------- #version=11.5.1 # bug fix: quaternion for nucleic acids # code: inefficiencies in Quaternion code # new feature: within(structure,atom_expression) # for proteins, just the helix or turn or sheet containing those atoms; # for nucleic acids, just the chain # bug fix: wing vectors for biopolymers # not containing O improperly drawn for sheets # and, in the case of set traceAlpha TRUE (the default), helixes # bug fix: translateSelected/rotateSelected does not move cartoons # bug fix: tainted occupancy not saved in state # bug fix: biopolymers have wrong wing vectors (from 11.3.62) # bug fix: restore of state does not reset user-defined atom properties # code: refactoring Atom and AtomCollection # ----------------------------------------------------------------------------- #version=11.3.66 # bug fix: CIF reader not skipping loops with load of a specific model of a model set # bug fix: explicit format LOAD "XXX::whatever" extended to XML variants # code: adapter/readers/more/JmolDataReader.java removed. # code: adapter/smarter/Resolver.java cleaned up in relation to XML and DOM options # ----------------------------------------------------------------------------- #version=11.3.65 # full run of monster_script.spt # bug fix: pmesh test1 "inline" "1 {2. 0. 0.} 0" disallowed, but that should be OK # bug fix: isosurface gridpoints "ch3cl_map.jvxl" -- gridpoints for jvxl files that are already mapped # bug fix: isosurface lcaoCartoon "type" {atomExpression} # files: JUnitTest for scripts -- # monster script in run directory tests scripts now uses # files at http://chemapps.stolaf.edu # all monster scripts made the same # tests/scripts/check_performance removed. # # bug fix: better checking of scripts involving full run of all scripts # bug fix: defaultDirectory for Jmol application not usable for http:// protocols # bug fix: load "files" not properly loading zip files or files involving default directory # ----------------------------------------------------------------------------- #version=11.3.64 # bug fix: version integer missing sometimes # bug fix: isosurface with trajectories # interesting that if 1.1 and 1.2 are trajectories you can do # frame 1.2; isosurface select(*/1.1) sasurface # this creates an isosurface for model 1.2 that uses the atomic coordinates of model 1.1! # # bug fix: isosurface MEP mapped to plane not exactly reproduced in JVXL # bug fix: isosurface COLOR RANGE by itself does nothing -- changed to use full range # new feature: isosurface COLOR RANGE ALL added as an equivalent to COLOR RANGE with no numbers # ----------------------------------------------------------------------------- #version=11.3.63 # -- all functionality in new.htm, new2.htm, and new0.htm tested -- # bug fix: draw/isosurface/etc. on/off/delete should operate on all objects # bug fix: display within(plane...) # bug fix: select site=n broken # bug fix: quaternion/ramachandran/model can show up together if user issues FRAME ALL # bug fix: frame 1.2 when file 1 only has one model displaying all files # bug fix: quaternion x reports wrong frame number # bug fix: selectionHalo status and color not in state # bug fix: color selectionHalos none # bug fix: polyhedra .... translucent 0.3 green # bug fix: moveto alternative format missing necessary 0 rotationRadius requirement # moveTo ...... {atomExpression} 0 [zoomOrZoomFactor] # where [zoomOrZoomFactor] is n, +n, -n, *n, /n, or 0 (to indicate fill screen) # bug fix: subsets not properly handling restrict # bug fix: models with turns crash jmol if not first model loaded # bug fix: quaternion command by itself not switching to most recent quaternion # bug fix: background color off when not white and ends in "FF" # bug fix: print {atomSet}.color -- .color returning bounding box! # bug fix: multiframe draw with labels different for each frame not properly saved in state # bug fix: within upgrade for boundbox: within(boundbox), within(boundbox,atomExpression) # ----------------------------------------------------------------------------- #version=11.3.62 # bug fix: calculate hbonds for trajectories # code: distinction between file-derived or connected hbonds and calculated hydrogen bonds # bug fix: calculate hbonds broken in 11.3.58 (missing model field in BioPolymer) # bug fix: Jmol not putting structures in for all models in a PDB file # bug fix: calculate polymers (never documented) not necessary -- calculate structure suffices # bug fix: calculate structure updated for ignoring jmolDataFrames and using currently selected atoms # webexport help instructions fix to be consistent for local testing. # ----------------------------------------------------------------------------- #version=11.3.61 # bug fix: multifile cartoons improperly rendering in all frames # bug fix: dipoleScale not saved in state # bug fix: quaternions broken in 11.3.58 # code: Closest class deleted # code: Quaternion class moved to modelsetbio # code: dipoles moved to shapespecial # bug fix: select 1.5 in trajectory context should switch to that set of coordinates # bug fix: draw not colored # bug fix: mousewheel too low power # bug fix: select */4 when "4" is inappropriate returns all instead of none # bug fix: memory leak in applet due to mouse/hoverwatcher listeners # bug fix: applets not self-destroying when window containing them close # bug fix: rotate commands not sent to other applets when set syncScript if OFF # ----------------------------------------------------------------------------- #version=11.3.60 # bug fix: more work on trajectories in a multimodel context # bug fix: quick fix for disabling popup menu under Java 7 where permissions are not granted # bug fix: load trajectory extended to multifile context # in which case "select 1.3", if file 1 is a trajectory, not only # selects that file, but also sets the trajectory to 1.3. # So a "select" of a trajectory also affects the display. # This makes "select" in a trajectory context similar to "display" # but doesn't require listing of all the models. # ----------------------------------------------------------------------------- #version=11.3.59 # bug fix: load append not saved in state properly # code: trajectory command (never documented) removed # bug fix: draw ... nofill mesh properties not processed # bug fix: draw DIAMETER N not properly functioning for curves or arrows # new feature: draw DIAMETER X.Y allows setting diameter of points, lines, curves, and arrows to Angstroms # bug fix: 11.3.58 can't set bond diameters # bug fix: with set syncMouse, target applet sets syncMouse off inappropriately # ----------------------------------------------------------------------------- #version=11.3.58 # bug fix: set mouseSync with sync * ON disabling sync but not reenabling it # bug fix: spin on missing in final state function. # bug fix: select within (3.3, {-1 1 1}) does not work with negative integer coordinate # bug fix: trajectories were not fully implemented # code: refactoring of ModelSet and related classes for trajectories # code: trajectories implemented as independent models # code: debug comments in AppletRegistry # new feature: trajectory command no longer necessary -- deprecated (was in 11.2) # ----------------------------------------------------------------------------- #version=11.3.57 # bug fix: revised sync commands # new feature: set syncScript; set syncMouse # sync ON; set syncMouse false; set syncScript false Tracks orientation only # sync ON; set syncMouse true; set syncScript false Sends mouse events only # sync ON; set syncMouse false; set syncScript true Sends script commands only # sync ON; set syncMouse true; set syncScript true Sends both mouse events and script commands # # bug fix: "load trajectory" broken # ----------------------------------------------------------------------------- #version=11.3.56 # bug fix: isosurface map of properties lost in 11.3.54 # new feature: set c? -- displays all Jmol parameters starting with "c" or "_c" # set _? -- displays all read-only variables (starting with "_") # new feature: formatted gOpenMol formatted plt volume data reader. # new Jmol.js for 11.4 # ----------------------------------------------------------------------------- #version=11.3.55 # bug fix: axes/unitcell improperly slabbing on internal slab # bug fix: XOR returning OR when not a bitset # bug fix: unary minus for planes and points # FEATURE CHANGE: slab REFERENCE removed -- no longer necessary # new feature: set wireframeRotation # code: simplified Logger.debugging flag # bug fix: slab/depth planes not properly constructed # new feature: _slabPlane, _depthPlane variables # code: MUCH simpler slab plane code # bug fix: applet.loadInline(String[] models) messes up # this involves the fact that Safari will deliver null pointer when it # mistakenly matches a String[] signature to a String, or vice-versa. # The solution is to use # # applet.loadInlineString(String model, String script, boolean isAppend) # # and # # applet.loadInlineArray(String[] model_or_models, String script, boolean isAppend) # # explicitly # code: refactoring loadInline and interfaces WrappedApplet and JmolAppletInterface # bug fix: scroll wheel with synchronization does not track properly # ----------------------------------------------------------------------------- #version=11.3.54 # bug fix: JVXL writing/reading of simple plane writes precision color flag # new feature: (isosurface) reading of XPLOR ascii electron density map data # bug fix: reinstating "insideout" isosurface option # bug fix: JVXL writing of lobe, sphere, ellipsoid, hydrogenOrbital # bug fix: loadInline not properly autobonding -- causes null pointer error # bug fix: data ... end model instead of end "model" causes null pointer exception # ----------------------------------------------------------------------------- #version=11.3.53 # bug fix: symop=0NNN not returning all atoms with translation NNN # code: optimization of algorithm used for load RANGE # modification for load RANGE -x.x (within x.x Angstroms of symop=1555) to be within x.x of the # box containing symop=1555, not the atoms themselves. # code: cleanup of readers. # bug fix: no special atom checks for PDB symmetry files # bug fix: HallInfo --- Hall term miscalculation OUCH! -- mistken commenting out of code in 11.1.28 March, 29, 2007. revision 7243 # bug fix: set measures 0.1 --- solid line does not move. # bug fix: completion of set parameter clean up # ----------------------------------------------------------------------------- #version=11.3.52 # bug fix: set of many more (but not all) parameters can accept mathematical expressions # bug fix; set strandCount not properly handled # new feature: set strandCountForStrands # new feature: set strandCountForMeshRibbon # note --- set strandCount sets BOTH, but now each is independent # bug fix: quaternion not including chain designation # bug fix: default connections include proper PDB CONECT records # new feature: connect PDB # just does PDB CONECT connections # new feature: connect PDB AUTO # PDB CONECT and autobonding # ----------------------------------------------------------------------------- #version=11.3.51 # bug fix: write FILE not handling binary file formats properly # bug fix: PDB CONECT records not creating bonds for ALL models # bug fix: load =xxxx broken in 11.3.50 # bug fix: amino not a subset of protein # bug fix: proteins with just C CA N not recognized as such # code: minor refactoring in org/jmol/util # code: minor refactoring in org/jmol/jvxl # code: minor refactoring in org/jmol/adapter # ----------------------------------------------------------------------------- #version=11.3.50 # new feature: MOL isotope column read; interpreted for D, T, 11C, 13C, 15N (for now) # bug fix: WebExport not properly accessing files in more complicated situations (pmesh, isosurface, multiple files, etc.) # bug fix: WebExport not allowing variety of local location options # bug fix: return command not allowed in simple context # bug fix: setting perspective model resets unit cell on # bug fix: debug comment in TransformManager # bug fix: hideNotSelected not in state. # ----------------------------------------------------------------------------- #version=11.3.49 # bug fix: set perspectiveDepth off broken in 11.3.48 # bug fix: set scaleAngstromsPerInch not turning off perspectiveDepth # bug fix: scaleAngstromsPerInch not in state # bug fix: _firstFrame/_lastFrame variables mess up state # bug fix: calculate surfaceDistance broken for 11.3.48 # new feature: direct reading of MAC Spartan06 directories. # ----------------------------------------------------------------------------- #version=11.3.48 # # new feature: script "myfile.zip|xxx.spt" # # bug fix: scale3D not working # # new feature: load "myfile.zip|CH3CL.MOL" # loads a given named model from within a zip file. # # new feature: load "myfile.zip|myfile2.zip|CH3CL.MOL" # loads a given named model from within a zip file within a zip file. # # these selections override any manifest that might be in a ZIP file. # new feature: print getProperty("fileContents","zipFileName", "subfile", "subFile",...) # getProperty now allows drilling down through a ZIP file. If no subfile is shown, # then the directory listing is given: # # print getProperty("fileContents", "data/test.zip") # # CH3CL.MOL # CH3CL~1.MOL # CH3F~1.MOL # CH3OH~1.MOL # CH4~1.MOL # BENZEN~1.ZIP # ENALSP~1.ZIP # WATERV~1.ZIP # JmolManifest # # print getProperty("fileContents", "data/test.zip", "BENZEN~1.ZIP") # # benzenevib.spardir/ # benzenevib.spardir/_locked # benzenevib.spardir/_spartandir # benzenevib.spardir/Document # benzenevib.spardir/M0001/ # benzenevib.spardir/M0001/_spartan # benzenevib.spardir/M0001/archive # ... # benzenevib.spardir/SpreadSheet/ # benzenevib.spardir/SpreadSheet/SheetData # print getProperty("fileContents", "data/test.zip", "BENZEN~1.ZIP","benzenevib.spardir/M0001/") # # benzenevib.spardir/M0001/ # benzenevib.spardir/M0001/_spartan # benzenevib.spardir/M0001/archive # benzenevib.spardir/M0001/Calculations # benzenevib.spardir/M0001/Commands # benzenevib.spardir/M0001/Geometry # benzenevib.spardir/M0001/input # benzenevib.spardir/M0001/log # benzenevib.spardir/M0001/Molecule # benzenevib.spardir/M0001/output # benzenevib.spardir/M0001/parchive # benzenevib.spardir/M0001/proparc # benzenevib.spardir/M0001/ret_code # benzenevib.spardir/M0001/voutput # # print getProperty("fileContents", "data/test.zip", "BENZEN~1.ZIP","benzenevib.spardir/M0001/Commands") # # # Verbose Mode: 1 # # version: MacSPARTAN '06 129 129 x86/Darwin # # rootKeys: 'OPT' 'HF' '3-21G(*)' '' '' # # new Keys: 'OPT HF 3-21G(*) FREQ ' # # ...etc.... # # new feature: load "myfile.zip" MANIFEST "...." # new feature: JmolManifest in a zip file directs which files to load and in what order # JmolManifest is simply a list of files, one per line. # # Rules include: # # 1) blank lines and lines beginning with # are ignored. # 2) file names are case-sensitive and must be complete, with full path within the ZIP file # 3) files must be on separate lines or separated by vertical bar | marks; no whitespace around names # 4) files may be ZIP files themselves. # 5) some comments are special: # IGNORE_ERRORS --- process the file and do not stop if some files are not valid model files # IGNORE_MANIFEST --- (on the load command line) indicates that the internal ZIP file manifest should be ignored # EXCEPT_FILES --- process all files EXCEPT those given # # new feature: show spacegroup "X,Y,Z;-X,Y,Z;..." finds space group associated with specific operations # bug fix: multimodel files could have connected atoms between different models. # bug fix: application animation frame button reset always goes to frame 1 # new feature: load xxx.zip n # where n is the desired file, starting with 1 # new feature: Spartan06 file format reader # new feature: ZIP file reading for multiple models # bug fix: antialiasDisplay changes during spinning (or any rendering) causes null pointer error # ----------------------------------------------------------------------------- #version=11.3.47 # coding efficiencies in atom iterators # vast speed up of smoothed isosurface map properties # deprecated: calculate surface (equates to surfaceDistance WITHIN) # deprecated: calculate surface {...} (equates to surfaceDistance FROM) # new feature: calculate surfaceDistance FROM {atomExpression} # new feature: calculate surfaceDistance WITHIN {atomExpression} # ----------------------------------------------------------------------------- #version=11.3.46 # new feature: calculate surface {atomExpression} # new feature: set isosurfacePropertySmoothing # default TRUE # smooths the coloring for isosurface ... map property ... # bug fix: "isosurface select() map property xxxx" array out of bounds error # bug fix: color bonds CPK not working # new feature: calculate polymers # allows recalculation of polymers after connections are made/broken # bug fix: tRNA, rRNA with abnormal distances do not connect biopolymers # bug fix: Jmol math getProperty() doesn't pass parameter in some cases # code: refactoring,optimizing Escape.toJSON() and Escape.toReadable() # bug fix: isosurface CAP not turned off prior to map sasurface # bug fix: adjustable boundbox in multimodel context not specific to model of selected atoms # bug fix: Jmol math (x[2])[3] indistinguishable from x[2][3] # ----------------------------------------------------------------------------- #version=11.3.45 # bug fix: new boundbox command with small numbers of atoms # bug fix: state not saved for coloring elements # bug fix: state not properly representing deleted bonds # bug fix: setColix not clearing shading in certain cases # new feature: Jmol math {atomset}.boundbox returns list of center, vector, corner0, corner1 for this set of atoms # code: ModelSet.BoxInfo abstraction/refactoring # ----------------------------------------------------------------------------- #version=11.3.44 # new feature: Jmol math getProperty() function # allows FULL math access to ALL getProperty types # # syntax: getProperty(propertyType, qualifier, item, item, item,...) # # examples: # # print getProperty("modelInfo") # print getProperty("boundboxInfo") # print getProperty("boundboxInfo", "center") # print getProperty("boundboxInfo", "vector") # print getProperty("atomInfo",{atomno=3}) # print getproperty("bondInfo",{*},2,"atom1") # print getProperty() # displays list of possibilities # print getproperty("polymerinfo",{*},"models",2,"polymers",1,"monomers",39,"atomIndex2") # # For many property types, the qualifier is an atom set # If the atom set is not given, those properties default to {visible} # For "stateInfo", the qualifier is string: "fileState", "modelState", etc. # Items may be integers or string-based keys # Integer items follow the rules of Jmol math selectors: # 1 first item, 0 last item, -1 next to last item, etc. # code: set instead of = in measures and labels state # bug fix: POVRAY and other buttons aren't enabled when there are no atoms but instead draw objects and isosurfaces # bug fix: new label fonts not loaded when labels resized # bug fix: nuisance "render mesh error" console report # new feature: boundbox {atomExpression} [on|off] # sets the bound box around the specified atom expression # default ON/OFF is to NOT change current setting # new feature: boundbox {point or expression} {vector to corner} [on|off] # sets the bound box to be centered with a given size based on a vector to a corner # new feature: boundbox corners {point or expression} {point or expression} [on|off] # sets the bound box to encompass the two corner points # strangely enough this allows setting the boundbox to a 2D or 1D box # new feature: show boundbox gives valid boundbox commands and volume # bug fix for bioshapes visible outside of current visible frame set # bug fix for selecting atoms of atomsets using [-n] or [0] # isosurface POINTSPERANGSTROM synonym for RESOLUTION # also reported in show isosurface # bug fix: more natural mouse SHIFT-RIGHT behavior. # new feature: isosurface CAP [plane definition] # caps the isosurface at the designated plane. # Specifically for molecular/solvent-type isosurface. # [plane definition] can be {x y z w} or any combination of # three {x y z} points, draw point references, or atom expressions # ----------------------------------------------------------------------------- #version=11.3.43 # bug fix: select statement comparisons of negative decimal properties to "-1" (not "-1.0") causes none found # new feature: Back to "SET" for state definitions of Jmol parameters. # bug fix: Strings too long in state can cause Eclipse "infinite loop" bug # # solution is a new feature: # new feature: "\" at the end of a line marks a continuation of that line # bug fix: assigning a negative value to a dataAtomNumberField value caused BitSet.set() exception # bug fix: Jmol parameter setting syntax too loose # The following statement was allowed: # pickCallback = myfunction # OK, so that might look good, but it evaluates to # # pickCallback = "" # # since the VARIABLE myfunction has not been defined. # # Solution: Don't allow the syntax # # [jmolParameter] = [Token.identifier] # # the following is OK: # # [jmolParameter] = "some string" # # the following is preferred: # # SET [jmolParameter] [value] # # bug fix: antialias with translucent but antialiasTranslucent = false; labels, text, echos, hover, picking, out of alignment # bug fix: negative formal charges # new feature: set drawPicking TRUE # then reports picking of draw objects as a JavaScript array: # [ "draw","[drawID]",[modelIndex],[vertexIndex],[x],[y],[z] ] # this goes to the pickCallback function as the second parameter, # with the first parameter (normally the atomIndex) being -2. # bug fix: write coord mol not working # new feature: connect (...) (...) aromatic auto # similar to calculate aromatic, except it's isolated to this set of connections; implicit modifyOnly # can be used in place of # select *; calculate aromatic # # code: refactoring of BondCollection.makeConnections # # bug fix: connect (..) (..) # with implicit "single" causes state to use "partial 0" # new feature: shadows can be activated again via noShadows parameter in .pov file # ----------------------------------------------------------------------------- #version=11.3.42 # bug fix: new frame title and state # new feature: set echo [echoID] MODEL [model number] # bug fix: select by itself not working; oy. Since at least 11.0 # bug fix: ramachandran/quaternion fix for assignment of structure # bug fix: isosurfaces not taking their default name properly # new feature: frame title "this a title for THIS frame only" # bug fix: small fix for povray cap at back side # bug fix: overly long titles now again substringed in the popup menu. # bug fix: memory leak in merge -- models[i].modelSet causes modelSet to not finalize. # bug fix: quaternion # bug fix: set xxxCallback not allowed # new feature: **** Jmol Embedded Script **** recognized in /* ... */ comments and /** ... **/ super-comment blocks # if found, ONLY this text is processed and all other text in the file is ignored. # ----------------------------------------------------------------------------- #version=11.3.41 # bug fix: math operations with bond bitsets; % and + operating on arrays # bug fix: _set variable definition removed # new feature: .type math function # new feature: Jmol math allows direct string replacement in select atom expressions: # x = "atomno=3" # select @x # or select @{x} # select @{x + 3} # selects atomno=33 # x = array("atomno<10","atomno>20") # select @x # OR of the list elements # select @{x[2]} # just element 2 of x (atomno>20) # select @x[2] # same as {@x}[2] # new feature: set atom properties using an array instead of a DATA statement: # (was introduced in 11.3.29, but not fully articulated) # {*}.x = array(2,3,4,5,6); # {atomno<=3}.color = array("red","green","blue") # {*}.property_mydata = array(1.0,5.5,4.4,3.3); # {atomno < 4}.xyz = array({3 4 5},{4 5 6},{5 6 7}) # if the array is shorter than the number of atoms selected, then # only that number of atoms are affected # new feature: set atom properties from space-separated string: # {atomno < 5}.property_mydata = "1.0 5.5 4.4 3.3"; # ----------------------------------------------------------------------------- #version=11.3.40 # new feature: Ramachandran/Model commands switch between plot and model # -- one Ramachandran plot per model # -- axes labels and special hover label for Ramachandran plots # -- Ramachandran saved in state # bug fix: Overlapping CPK at a slab now correct for up to 10.000 clipped atoms. # bug fix: @{} for within(1.0,point,@{....}) # new feature: set xxxx where xxxx is not a Jmol variable causes ERROR # code: privatized Token to avoid null value problem in Eval.statementAsString() # POV-Ray clipping coding minor tweak # POV-Ray fix for number formatting width > 999 # new feature: model-based parallel array calculations: # x = {atomno=3}.split() # a list, one element for each model # draw @{x.xyz.sub({1 0 0})} # a set of points, one per model # new feature: point3f in array(): # xlist = array({1,2,3}, {1,1,0});print xlist[1]+{1 0 0}; # bug fix: draw @{x - {1 0 0}} # bug fix: antialias with set picking draw # bug fix: draw object text not selective for frame # new feature: draw object title line number corresponds to model number for multi-model draw objects # new feature: matte finish for isosurfaces # remark: matte finish replaced by adaptable translucent finish (see below) # bug fix: noninteger MO occupancies # bug fix: antialias labels not fully bitmapped # bug fix: RPN processor too limited in nesting level # bug fix: MO processing for Gaussian and PSI3 errors # new feature: MoldenReader (Matthew Zwier ) # new feature: MO calculations for spherical orbital basis (Matthew Zwier ) # bug fix: slabbed atoms are now capped in povray output. # Note: In CPK mode atoms overlap, but are capped at the same height. # there is a priority in Jmol, but not yet clear to me which. The current priority # in povray is based on the signed distance from the slab to the atom center. # bug fix: povray output of translucent objects now have reduced glare, for # clarity of the representation and better compatibility with the Jmol viewer. # ----------------------------------------------------------------------------- #version=11.3.39 # bug fix: antialias causing image to be partial size. # bug fix: hover state not properly showing specific-atom hover labels. # new feature: write FILE (text-files only) #new feature webexport: automatic usage of a different path to the applet for local files to allow testing # only works for Pop-In template at present. Required updates to JmolPopin.js and templates. #webexport instruction updated to reflect new feature. # bug fix: antialias adjustments for hover text and background box # bug fix: antialias fix for text color same as background and in front of translucent surface appearing transparent # bug fix: antialias fix for applet # webexport instruction updates. # bug fix: webexport scriptbutton template had erroneous script names. # ----------------------------------------------------------------------------- #version=11.3.38 # bug fix: antialiasing with translucent/POV-ray # new feature: set antialiasTranslucent TRUE/FALSE # along with antialiasDisplay and antialiasImages # determines the extent of antialiasing. Requires # antialiasDisplay or antialiasimages TRUE. # ----------------------------------------------------------------------------- #version=11.3.37 # new feature: @{mathExpression} for echos, select, etc. where @x can be used. # select atomno=@{x*2}; # xlist = array("red", "green", "blue"); # n = 2; # color atoms @{xlist[n]}; # new feature: {atomExpression}.color = "red" (or "[xff0000]" or {255,0,0} # new feature: helixes as barrels in cartoons or rockets using # rocketBarrels = true # bug fix: -- adds antialiasing for translucent objects # bug fix: error in state for connect DELETE # bug fix: 0-diameter atoms displayed as single pixels when perspectiveDepth = false # ----------------------------------------------------------------------------- #version=11.3.36 # antialias better dots # bug fix: inline loading not working # POV-Ray dialog update # set antialiasDisplay T/F (false by default) # set antialiasImages T/F (true by default) # ----------------------------------------------------------------------------- #version=11.3.35 # POV-Ray slab/depth # POV-Ray text -- ALL text (echos, labels, axes, etc.) # POV-Ray cleaner for Molecular Orbitals # bug fix: getproperty atominfo returning string to Integer() # PDB remediated atom name upgrade -- NEEDS CAREFUL CHECKING # ----------------------------------------------------------------------------- #version=11.3.34 # write povray [width] [height] filename # POV-Ray for mapped isosurfaces # POV-Ray embeds Jmol script # POV-Ray .pov files created by Jmol can be loaded as scripts # code: cleaning of JmolConstants specialAtomNames # code: cleaning of TextFormat.simpleReplace # bug fix: select [SET] or [2MO] or [DB'] # bug fix: app -c flag errors not going to Logger.Error # bug fix: no partial charges! # bug fix: 11.3.14+ does not write colormapped JVXL files # bug fix: Using isosurface within 1.0 @pt1 where pt1 is a draw point save state cannot be restored # ----------------------------------------------------------------------------- #version=11.3.33 # code: PovRay tweaks -- multiple bonds # code: PovRay output uses BufferedWriter # adds support for "xx'" atom designations in PDB and variable names # bug fix: insertion codes stored incorrectly in 11.3.32 # new feature: inline scripting allows math # # script INLINE "select " + site_list[2] # new feature: site_ support for PDB and CIF # # loading of PDB and CIF files containing site information # automatically defines variables site_xxx and defines selections site_xxx and site_n # where xxx is the site identifier and n is the site number. # These settings are reset each time a file is loaded. # They do not carry over from one file to the next. # adds "OP1" and "OP2" as backbone designators (new PDB designation) # _PovrayExporter adds draw, halos, stars, dipoles, vectors, polyhedra, # backbone, cartoons, meshRibbon, ribbon, rockets, strands, trace, # dots, geosurface, molecular orbitals, LCAO cartoons, pmesh, # single-color isosurfaces # Web Export Dialog changes: new intro tab, new minilog at bottom, instructions converted to # buttons which open the info in the standard Jmol Help Dialog. # bug fix: rockets color incorrect for head groups # ----------------------------------------------------------------------------- #version=11.3.32 # bug fix: vibration disabled in 11.3.31 # bug fix: zoomto cancels slabbing # bug fix: zoomto (atomExpression) 0 # zooms to 2x # new feature: getproperty stateinfo TYPE # where TYPE is one of: # # colorState # dataState # fileState # frameState # modelState # perspectiveState # selectionState # variableState # windowState # # bug fix: backbone not in state # code(I): Mmset merged into ModelSet; # Viewer accesses ModelSet methods directly # ModelManager streamlined substantially # # This basically removes two full layers of abstraction. # All the atoms, bonds, and models are now in ModelSet. # # code(II): ModelSet extends ModelCollection extends BondCollection extends AtomCollection # # bug fix: dipoles moved back into shape from shapespecial # bug fix: semi missing in show orientation message, second part (zyz text) # bug fix: select 0 selects all instead of PDB group 0 # bug fix: write t.xxx # ----------------------------------------------------------------------------- #version=11.3.31 # bug fix: calculate aromatic for N and O refined # new feature: valence -- sum of bond orders # print {atomno=3}.valence # {atomno=1}.valence = 3 # select (carbon and valence != 4) # new feature: settable atom properties (preliminary): # .x, .y. .z, .xyz, # .fx, .fy, .fz, .fxyz, # .vx, .vy, .vz, .vxyz, # .formalcharge, .occupancy, .partialcharge # .temperature, .valence # for example: # a = {atomno=30} # a.xyz = {1.0, 2.0, 2.3} # a.temperature = 3.0 # a.formalcharge = 2 # new feature: set atom properties using {xxxx}.x = # # {atomno=3}.x = 3 # {(*)[2]}.xyz = {1 2 3} # for(var i = 1; i < 3; i = i + 1); {(*)[i]}.x = 5;end for; # {atomno=3}.property_whatever = 2.0 # new feature: set atom properties using an array instead of a DATA statement: # {*}.property_mydata = array(1.0,5.5,4.4,3.3); # {*}.property_mydata = "3 4 5 6 7 8"; # {atomno < 4}.xyz = array({3 4 5},{4 5 6},{5 6 7}) # code optimization for within() and setAtomBits() # more export generator classes # bug fix: unitcell missing some lines when axes turned off # ----------------------------------------------------------------------------- #version=11.3.30 # new feature: adds H/Br/Cl/I/C logic to aromatic bond assignments # new feature: adds Oxygen/Sulfur logic to aromatic bond assignments # new feature: adds Nitrogen logic to aromatic bond assignments # bug fix: menu for UNITCELL # new feature: PovrayExporter (pim schravendijk ) # ----------------------------------------------------------------------------- #version=11.3.29 # new feature: aromaticSingle and aromaticDouble bond order options # new feature: "smartaromatic" bonds # turned off with "smartAromatic = false" # new feature: calculate aromatic # calculates reasonable aromatic double/single alternation. # new feature: reset aromatic # sets all aromaticDouble and aromaticSingle back to aromatic # new feature: select ISAROMATIC # selects aromatic atoms # new feature: MOL reader recognizes bond types 4,5,6,7 # new feature: isosurface/mo "squared" # new feature: fully generalized bond order "partial n.m" # n = number of lines, up to 5 # m = binary mask for dottedness, up to 31 (0x1F) # 00001 first line of bond dotted # 00010 second line of bond dotted # 00011 first and second line of bond dotted, etc. # new feature: connect may use numeric bond orders, including "partial n.m" # new feature: preliminary work on functionalized state # new feature: global/local functions (to applet, for instance # in general, functions are global -- common to all applets. # first-character "_" indicates this function is a LOCAL function, private to this applet. # ----------------------------------------------------------------------------- #version=11.3.28 # critical bug fix for color command not coloring objects properly # new feature: bondOrders 2.5 and -2.5 PartialTriple and partialTriple2 # ----------------------------------------------------------------------------- #version=11.3.27 # critical bug fix for functions not returning values # bug fix for atomarray[i] not selecting properly # bug fix for write not working with VAR # bug fix for application not accepting pastes into the # console consisting of multiple lines # bug fix for bondOrder command not properly treating 4.0 or 0.5 # bug fix for decimals not represented properly in error messages # ----------------------------------------------------------------------------- #version=11.3.26 # new feature: _1 parameter for "first atom" in second expression of connect: # connect 3.0 (_H and connected(_N) (_O and not within(chain,_1)) hbond # new feature: better reporting of PMESH file format errors # code cleanup: pmesh moved to shapespecial; privatized # bug fix within(chain,xxx) not working # bug fix for() as first command in script or line # bug fix we were not exporting error free xhtml 1.1. # bug fix for WebPageMaker not writing files # bug fix for PAUSE causes app to hang -- this is a reversion of use of SwingUtilities.invokeLater(), # which actually will not work in ScriptWindow. We need the direct execution in # order to avoid the event queue from stopping itself. # ----------------------------------------------------------------------------- #version=11.3.25 # bug fix compiler not recognizing "axes =" or "measures = " # bug fix for WebPageMaker creating uncompressed PNG # bug fix for WebPageMaker not stripping \ in load file names # ----------------------------------------------------------------------------- #version=11.3.24 # critical bug fix for 11.3.23 compiler not recognizing line endings # bug fix for show state for draw in multi-model environment # bug fix? for background model not available for multiple frame range (e.g. frame 2.0) or after invalid frame number # # new feature: within(distance,isWithinAllModels,atomExpression) # # allows finding atoms within a specified distance of other atoms in OTHER models: # # select within(5.0,true,model=2.1) # TRUE indicates we should check all models # select within(5.0,false,model=2.1) # FALSE -- only model 2.1 # select within(5.0,model=2.1) # default is FALSE # ----------------------------------------------------------------------------- #version=11.3.23 # VERSION full script flow control support: # if / else if / else / end if # for / end for # while / end while # # var i = 4 # if (i = 3) # print "i=3" # else if (i = 4) # print "i=4" # else if (i = 5) # print "i=5" # end if # # var i = 5 # while ( i > 0) # print "atom " + i + " " + {atomno=i}.ident + " is at " + {atomno=i}.xyz # i = i - 1 # end while # # n = {*}.size # for (i = 1; i <= n; i = i + 1) # for (j = i + 1;j <= n; j = j + 1) # # var dist = {atomno=i}.distance({atomno=j}) # # if (dist < 1.77) # print "i-j: " + i + "," + j + " " + dist%2 # measure {atomno=i} {atomno=j} # endif # # end for # end for # # var i = 4 # while ( i > 0) # print "in while: i="+i # if (i = 2);print "i is 2";endif # i = i - 1 # end while # # # ----------------------------------------------------------------------------- #version=11.3.22 # Changes to webexport package only # New Features: textboxes for entry of author name and title for browser window # persistence across launches of authorname and applet size # automatic gzip of large structure/quantum files. # Bug? fix: update the page templates to XHTML 1.1 # Minor fixes to instruction .html files. # tweak: using "var" keyword prevents display of global variable value # ----------------------------------------------------------------------------- #version=11.3.21 # # bug fix: isosurface of MOs not properly displaying color in saved state # bug fix: state saving of @ definitions has extra = sign. # # new feature: fully functional user-defined functions: # # MACROS (no parameters) # # function mymacro # background red # color atoms blue # end function # # function mymacro2 # background black # color atoms cpk # end function # # background white # delay 2 # # mymacro # # delay 2 # # mymacro2 # # # SUBROUTINES (parameters, but no return) # # function drawline(id,a,b) # var x = script("draw line"+ id + " {atomno=" + a + "} {atomno=" + b + "}") # end function # # drawline(1,3,5) # drawline(2,10,12) # # # FUNCTIONS (parameters and returns) # # function d(a,b) # return a.distance(b) # end function # # x = d({atomno=3},{atomno=4}) # print x # # SHOW AND WRITE: # # show functions # # write functions macros.spt # # ----------------------------------------------------------------------------- #version=11.3.20 # bug fix for arrows way too fat (introduced in 11.3.19) :( # ----------------------------------------------------------------------------- #version=11.3.19 # bug fix: critical arrow fix of 11.3.17 for 2-point arrows # bug fix: write PNG default was 0 compression. -q flag was OK for setting 0-9 # bug fix: ragged arrow tip # ----------------------------------------------------------------------------- #version=11.3.18 # critical bug fix for 11.3.17 in regard to serialization of arrays # also introduces # # reset ALL # resets all user-created variables # # also "exitJmol" typed into the script window for the application does that. # # ----------------------------------------------------------------------------- #version=11.3.17 # bug fix: problem with unescaping comma-separated point strings "{1,2,3}" as a point. # bug fix: drawn arrows scale improperly when zooming; arrow heads off-kilter # new feature: set defaultDrawArrowScale # 0.5 initially # Drawn arrows now have a head size that can be set and a dimension that # scales with the model, so arrow head:atom size ratio remains constant # # new feature: setting Jmol,Rasmol,Shapely,Amino,Roygb,Rwb # color schemes makes those colors the default colors for these schemes. # rename byResidue_jmol --> byResidue_shapely # rename byResidue_rasmol --> byResidue_amino # new feature: array variables saved as arrays # prior to 11.3.17, you could not do: # # x = "this is a test".split(" ") # y = x[3] # # because x was only saved as a string, not an array # now x is saved as an array, so this is no problem. # # new feature Jmol math point(x,y,z) function # # point(a,b,c) or point("{x,y,z}") # # x = point(y[3], y[6], y[2]) # x = point("{2,3,5}") # # needed because, with simple numbers, just # # x = {3.0,4.0,5.0} # # works, but # # x = {r,g,b} # # does(did) not. # # new feature: Jmol math array element assignment: # # a = "2,3,4,5".split(",") # # a[3] = "now the 4 becomes this phrase" # a[a[2]] = "not any more; now it's this" # a[0] = "setting the final element" # a[6] = "expanding the array" # print a # # 2 # 3 # not any more; now it's this # setting the final element # # expanding the array # # works with strings as well: # # a = "this is a test" # a[8] = " not" # print a # >> a = "this is not a test" # # new feature: Jmol math x = array(a,b,,,,) # # x = array(3,4,5,6) # print x[3] # >> 5 # # new feature: Jmol math plane(x,y,z,w) function # # plane(a,b,c,d) or plane("{x,y,z,w}") # or through three points: # plane({atomExprOrPoint},{atomExprOrPoint},{atomExprOrPoint}) # or through three points with a reference point # plane({atomExprOrPoint},{atomExprOrPoint},{atomExprOrPoint},{atomExprOrPoint}) # # x = plane(y[3], y[6], y[2], 3.0) # x = plane("{2,3,5,4}") # x = plane({_H}[1],{_H}[2],{_H}[3],{_C}[1]) # new feature: print command prints a variable expression # # print x # print x * 3 # print x[4] + x[3] # print x.split(" ")[2][0] # new feature: aPlane.distance({some atoms}) # new feature: someArray.add("string") adds string to right of each item # new feature: someArray.sub("string") adds string to left of each item # colorManager clean-up # ----------------------------------------------------------------------------- #version=11.3.16 # bug fix: Eval RPN processor for list[n] addition operator not doing selection # new feature: MOPAC mgf file UHF orbital reading -- preliminary only # new feature: byElement and byResidue color schemes allow # customized element and residue coloring schemes. # built-in include: byElement_Jmol, byElement_Rasmol, # byResidue_Jmol (shapely) and byResidue_Rasmol (amino) # with abbreviations byElement == byElementJmol; byResidue == byResidue_Jmol # color atoms "byresidue_Jmol" # # Users can set up their own byElement and byResidue color schemes # simply by preficing a name with "byElement" or "byResidue": # # color "byElement_Mine=[x......] [x......] [x......] ..." # 0(unknown) 1(H) 2(He) ... # # then: # # color atoms "byElement_Mine" # # RANGE min and max are ignored for byElement and byResidue schemes, # and there is no scaling done ever, so effectively these prefixes # make the correlated value a simple index into the array. # This is what one would want for something that should be a given # for a specific element or residue # # Residue indexes in order correspond to the groupID of an atom: # # 0 noGroup, # 1 ALA, ARG, ASN, ASP, CYS, # 6 GLN, GLU, GLY, HIS, ILE, # 11 LEU, LYS, MET, PHE, PRO, # 16 SER, THR, TRP, TYR, VAL, # 21 ASX, GLX, UNK, # 24 A, +A, G, +G, I, +I, # 30 C, +C, T, +T, U, +U # # so this opens the door to user-created residue coloring schemes. # # color "byResidue_Mine=[x......] [x......]..." # nogroup ALA ... # # then # # color cartoons "byResidue_Mine" # ----------------------------------------------------------------------------- #version=11.3.15 # new feature: fully customizable popup menu -- see file jmol.mnu # # load menu jmol.mnu # # applet parameter param=menuFile value="jmol.mnu" # # application parameter -m filename # # mostly untested # # new feature: show menu # new feature: getProperty menu # # These deliver the current menu (as translated) in jmol.mnu format # ----------------------------------------------------------------------------- #version=11.3.14 # new feature: fully customizable popup menu -- see file jmol.mnu # # load menu jmol.mnu # # applet parameter param=menuFile value="jmol.mnu" # # largely untested # bug fix: HDO not recognized as "water" # bug fix: rotateSelected MOLECULAR not around {0 0 0} # bug fix: -g ignored on -n option, even if -w is present # bug fix: unknown color palette could cause error # new feature: %l atomic element number # new feature: APPLICATION -q (quality) option # new feature: lcaoCartoon, mo, isosurface, pmesh: color [translucent [n]|opaque] [colors...] # adjustment: setting JPG default quality to 75, not 100 # new feature: {r,g,b} can be used in place of [r,g,b] for indicating color, # allowing programmatic color definition: # # r = 255; g = 255; b = 0; # background {@r,@g,@b} # new feature: expanded color command for properties # # color atoms property partialcharge "rwb" range -1.0 1.0 # # and reverse with range inverted: # # color atoms property partialcharge "rwb" range 1.0 -1.0 # new feature: unlimited user-defined color schemes: # # select none; # color "myname=[xff00ff] [xffff00] [xff00ff]" # # colors must be [xRRGGBB] format for this one # new feature: fully remappable isosurface using COLOR command: # # isosurface s1 molecular map mep # color $s1 "bwr" # color $s1 "rwb" range -0.2 0.2 # APPLICATION adjustment to console window scaling/size # ----------------------------------------------------------------------------- #version=11.3.13 # this version introduces fully customizable color schemes # # new feature: .color for numbers and points delivers the # color associated with a given value in the current # coloring or propertyColorScheme. # (some number).color gives a color triple as a point {x y z} # {x y z}.color gives a hexadecimal string [xRRGGBB] # # # select atomno=3;color yellow # x = {atomno=3}.color # gives {255.0, 255.0, 0.0} # x = {atomno=3}.color.color # gives "[xFFFF00]" # # set propertyColorScheme "bwr" # x = {atomno=3}.partialcharge.color # # new feature: color ["schemeName"] RANGE [min] [max] # allows setting of color range and scheme so that color # values can be determined. This would be used for making # a color key using positionable ECHO text boxes: # # color "bwr" absolute -0.1 0.1 # x = (0.01).color # gives the point-color associated with that number # set echo myecho 100 100 # position # echo " " # just some space # color echo @x; background echo @x # color this bar the color of 0.01 # # new feature: show colorscheme "schemeName" # delivers "colorscheme = " followed by a string of color values. # without the scheme name, returns the current colorscheme listing # For example: show colorscheme "low" delivers: # # colorscheme = [xff0000] [xff2000] [xff4000] [xff6000] [xff8000] [xffa000] [xffc000] [xffe000] [xfff000] [xffff00] [xf0f000] # # setting an array variable to the color values: # # list = script("show colorscheme \"low\"")[15][0].split(" ") # # new feature: set userColorScheme [list of color names] # creates a colorscheme referred to as "user" and its reverse, "resu" # based on a list of color values: # # set userColorScheme red green [x00FFFF] blue # color atoms property partialcharge "user" range -1.0 1.0 # ----------------------------------------------------------------------------- #version=11.3.12 # bug fix: zoomTo 100% # bug fix: set language fr needs quotes but should not # bug fix: load multiple files inline causes null pointer exception # # new feature: APPLICATION: File|Export...|Export to Web Page # ----------------------------------------------------------------------------- #version=11.3.11 # bug fix: lcaoCartoon for sp center requires "sp2" not "sp" # bug fix: mo not showing titles # # new feature: lcaoCartoon rotate [x|y|z] degrees create "px" # new feature: adds Jaguar PLT plot file reader for isosurface # isosurface sign red blue "myfile.plt" # ----------------------------------------------------------------------------- #version=11.3.10 # bug fix: script window using swing thread start not from event queue # bug fix: state of multi-polymer protein cannot be restored # bug fix: dots nn% not operational # bug fix: molecular dipole and multiple frames # # new feature: molecular dipole for Gaussian files # # new feature: simple calculation of approximate dipole moment from charge distributions. # dipole molecular # from file value if provided # dipole calculate molecular # from "center of gravity" of charges calculation # # new feature: show frame # based on models in the current frame set, displays information about frames # # new feature: application option for web page export # # new feature: write JPG n "filename" # where n is the quality (<=100) # ----------------------------------------------------------------------------- #version=11.3.9 # bug fix for isosurface mapping of planes by MEP (see 11.3.2) # new feature: symmetryRange: load "someFile" {mmm nnn 1|0} range x.x where x.x is a maximum distance away from closest atom in the base cell # new feature: synchronization of applets using JavaScript # new feature: synchronization of applets using Jmol scripts: # # synchronize .|>|*|appletId[syncId] ON|OFF|SLAVE|command # # The synchronize (sync) command allows two or more applets to be synchronized in # terms of orientation. Move one with the mouse, and the other moves as well. # In addition, the sync command allows ANY command to be sent to one or more # other applets directly, without the intervention of JavaScript. # # Applets are identified by appletId (jmolApplet0, for instance) # along with an optional bracketed sync group identifier -- generally a random # number that identifies the page containing the controlling applet. If the # syncId is not given, then the ID for the page containing the controlling applet # is used. This feature is important for cross-frame synchronization only. # # # . this applet only # > all applets except this one # * all applets # appletId id of a specific applet # [syncId] (optional) a unique string of digits -- brackets included # # ON sync as driver (default) # OFF turn sync off # SLAVE turn sync on, but not as driver # command command to send # # for example: # # sync * # synchronize all applets as drivers # sync jmolApplet1 #syncs this applet with jmolApplet1 both as drivers # sync > "set echo top left;echo OK" # sends OK to top left of all OTHER applets # sync jmolApplet2[254678942] OFF # turns sync off for an applet ON A DIFFERENT PAGE # # or in a different FRAME # sync . OFF # turns sync off for this applet # # new Jmol.js feature: jmolGetSyncId(); jmolSetSyncId(id); # allows control over the sync ID via javascript. jmolSetSyncId(id) # should be called prior to jmolApplet() and should incorporate some sort of # random digits and no space characters. (A number is good.) # This should only be necessary for multi-frame pages. # ----------------------------------------------------------------------------- #version=11.3.8 # bug fix: isosurface color -- not operating for some isosurface types # bug fix: isosurface "xxxx.cube" -- not assigning proper default colors # bug fix: gamess reader MO fix # bug fix: state save of STRUCTURE misplaced # feature: adds adjustable scale for unitcell axes # ----------------------------------------------------------------------------- #version=11.3.7 # bug fix: reading of JVXL files for orbitals loses phase information # bug fix: ACD/Labs nonstandard cml "builtin" property reader # bug fix: isosurface interior cavity was not setting meshdata surfaceSet null # bug fix: select dna can select rna if chain is mixed hybrid dna+rna # ----------------------------------------------------------------------------- #version=11.3.6 # bug fix: inappropriate draw pick spinning for single point # bug fix: dots not available in multimodel mode # bug fix: multiple isosurface cavities incorrect in a multimodel environment # bug fix: isosurface cavity not filled completely # bug fix: nested ifs can cause last endif to throw error # bug fix: compiler bug working with very small real numbers # bug fix: Support for mol2 files with blank line after comments. # ----------------------------------------------------------------------------- #version=11.3.5 # bug fix: ACD/Labs nonstandard cml "builtin" property reader # note that xmlReader (SAX reader) is now set to ignore all DOCTYPE declarations # bug fix: odydata fix for files with \r\n for line ending # bug fix for PDB remediated T/DT difference of C5M/C7 # bug fix: set spin X was case-selective # bug fix: echo text not re-orienting on resize of applet or application # bug fix: multiple isosurface cavities in a multimodel environment # bug fix: missing set picking ident in popup window # bug fix: popup menu set picking label not working # ----------------------------------------------------------------------------- #version=11.3.4 # rough export of VRML using # # write VRML "myfile.wrl" # # includes colored balls and sticks; uncolored isosurfaces # ----------------------------------------------------------------------------- #version=11.3.3 # bug fix pmesh not working # bug fix for state after calculate surface, calculate hbonds, configuration, dynamic variable definition in multimodel environment (ModelSet::addStateScript) # NEW FEATURES from the 2007 Gordon Research Conference on Visualization in Science and Education: # # internal dataFrame concept # # new command: ramachandran # # new command: quaternion [w x y z] [derivative] # # TODO: frame menu # TODO: write VMRL # preliminary Maya export -- sets the stage for any number of export frameworks. # ----------------------------------------------------------------------------- #version=11.3.2 # bug fix: set picking label # bug fix: minus-sign "fix" in 11.3.1 broke all {x -y z} notation # bug fix: state for phased atomic orbitals does not preserve red/blue color # bug fix: mo opaque causing "invalid argument" when no MOs # bug fix: isosurface cavity molecular caused exception # feature: adds isosurface capability to map MO and MEP data onto planes # ----------------------------------------------------------------------------- #version=11.3.1 # bug fix: debugscript on;center 3-5; "-" missing # bug fix: zoomTo (5-7) read as "5 to -7" # bug fix: move with time < 0.03 seconds causes molecule to disappear # bug fix: hover interruption # bug fix: image offsets in creating JPG image if model has been moved by CTRL-ALT-LEFT drag # ----------------------------------------------------------------------------- #version=11.3.0 # perspectiveModel 11 default # bug fix for 3D text echo staying in window # bug fix for draw text+translucency # bug fix for draw text not hovering for points # bug fix for multiple draw objects in show state # bug fix for spin save reversed direction # bug fix for CdkAdapter not having auxiliaryInfo data # # adds the ability to find the coordinate of a specific # draw object vertex using $objName[vertexId] as in # draw p perp plane (atomno=1) (atomno=2) # x = $p[3] # draw pt1 $p[1] # ----------------------------------------------------------------------------- #version=11.1.49 # bug fix for Gaussian file reader fix for very large negative MO coefficients # bug fix for move not releasing isInMotion # bug fix for x = "testing"[0], x = "testing"[-1], "testing".split("t")[0], and "testing".split("t")[-1] # bug fix for select {*}[0], {*}[-1], etc., which now counts from the end back # adds proper indents on debugscript for if/else/endif # allows "jmolscript:" for embedded scripts and callbacks # ----------------------------------------------------------------------------- #version=11.1.48 # bug fix for gamess reader MO fix # bug fix for mopac GRAPHF file fix (resolver thought MOL) # bug fix for lcaocartoon "lp" fix for AX3E and AX2E # ----------------------------------------------------------------------------- #version=11.1.47 # bug fix for compound document reader not reading enough short segment pointers # bug fix for Spartan reader not recognizing 5D orbital problem # bug fix for animation skipping frames # ----------------------------------------------------------------------------- #version=11.1.46 # bug fix for Jvxl.jar standalone application not having complete set of class files (jvxl) # adds inline help support for Jmol application running under Java 6 (Java 1.6.xx) # bug fix for inappropriate pre-JVM12 menu items not disabled # ----------------------------------------------------------------------------- #version=11.1.45 # bug fix for animFrameCallback not indicating animation direction # bug fix for help not working and help URL not displaying (app) # bug fix for app not writing state from File...Export menu (app) # bug fix for retaining the last-saved file type selected for Image export (app) # bug fix for "wait" not recognizing if it is just a syntax check (app) # ----------------------------------------------------------------------------- #version=11.1.44 # bug fix for inability to specify fractional coordinates: adds fx, fy, fz as # select fx < 0.5 and fy < 0.5 and fz < 0.5 # aveFracX = {molecule=1}.fx # bug fix for inability to use x,y,z,fx,fy,fz with cartesian points # bug fix for select BONDS ({...}) not preserved in state # bug fix for geosurface not always restored from saved state # bug fix for strandcount saved explicitly forces bioshape load # ----------------------------------------------------------------------------- #version=11.1.43 # bug fix for labels mysteriously disappearing. Also probably taking up HUGE amounts of hashtable space. # bug fix for hydrogen bond calculation with incomplete nucleic acid definitions. # bug fix for "set picking draw" crashing Jmol # bug fix for strandCount not carrying over to meshRibbon # bug fix for geosurface/dots save/restore state exception # bug fix for save state using "measurements off" instead of "set measurements off" # ----------------------------------------------------------------------------- #version=11.1.42 # bug fix for lack of updating of certain variable predefined expressions # bug fix for smiles nonfunctional # bug fix for load append and structure commands # bug fix for load files losing structure and cartoons # bug fix for multiple frames displayed does not show Select...Elements menu # bug fix for select @x not functioning where x = {atom expression} or x = "atom expression" # bug fix for {atom expression}.ident nonfunctional # code refactoring Frame --> ModelSet and ModelLoader # code refactoring modelframe --> modelset package # code refactoring shapebio --> shapebio + molsetbio packages # code refactoring dissociates Mps.MpsShape from Mps as BioShape # code refactoring removes Mps.Mpsmodel # code refactoring Mps --> BioShapeCollection # code refactoring greatly simplifies BioShapeCollection subclasses # ----------------------------------------------------------------------------- #version=11.1.41 # bug fix for load with explicit spacegroup not respecting normalization choice # bug fix for symop=nijk selecting base atoms when not appropriate # bug fix for select specialposition non-functional # bug fix for adding atoms but mads[] going stale # slight redefinition of "special position" # bug fix for structure loss on load append. (structure is supposed to be recalculated). # adds language switching for Open / Save dialog boxes and full menuing system in Jmol application # adds "structure" command -- structure [helix|sheet|turn|none] (atom expression) # adds "save/restore structure" command # ----------------------------------------------------------------------------- #version=11.1.40 # bug fix for backgroundModel and save state # bug fix for load append with spacegroups causing atoms to be repositioned # bug fix for anim playrev in loop mode causing animation to stall # ----------------------------------------------------------------------------- #version=11.1.39 # several bug fixes: # # bug fix for mo data misreading in smol files # bug fix for lcaoCartoon "s" giving incomplete spheres # bug fix for select symop=3555 not giving proper atoms when load "" {444 666 0} # bug fix for PDB files not supplying information about residues for the popup menu. # bug fix in frame range 1.0 when file 1 has only one model. # ----------------------------------------------------------------------------- #version=11.1.38 # bug fix for opaque triangles missing one pixel on right side when translucent objects are present. # bug fix for label alignments sometimes not being saved properly in the state # bug fix for animFrameCallback giving multiple callbacks -- still there, but identified now # in terms of whether animation is on or not in the 7th parameter being 1 or 0: # # function animFrameCallback(app,frame,fileno,modelno,firstno,lastno,isRunning){...} # ----------------------------------------------------------------------------- #version=11.1.37 # fixes bugs in draw and unicode label state definitions # adds simplistic to text, including echo, label, hover, etc. # fixes popup menu to better deal with multiple file context # update of Turkish translation # ----------------------------------------------------------------------------- #version=11.1.36 # build: renames applet files JmolApplet0*.jar and JmolAppletSigned0*.jar # # bug fixes for isosurface in multi-file environment # # bug fix and additional work in relation to translations # # zoomTo (atom expression) 0 # # with options # # zoomTo (atom expression) 0+n # zoomTo (atom expression) 0-n # zoomTo (atom expression) 0*n # zoomTo (atom expression) 0/n # # also # # moveTo timeSec {x y z w} (atom expression) 0 [zoom factor] # and # moveTo timeSec {x y z w} 0 transX transY (atom expression) 0 [zoom factor] # # where [zoom factor] is x, where x > 0 # or # [0] [[+ | - | * | /] x] # # # app fix for Edit...preferences not properly refreshing for axes and boundbox # ----------------------------------------------------------------------------- #version=11.1.35 # fix for x = {...}.resno and {...}.groupID # fix for select resno=-1 # first version of pt_BR translation # ----------------------------------------------------------------------------- #version=11.1.34 # language submenu # ----------------------------------------------------------------------------- #version=11.1.33 # bug fixes -- draw state, menu not updating, language submenu # ----------------------------------------------------------------------------- #version=11.1.32 # adds capability to define a property for selected atoms: # # select xxx # property_x = n.m # ----------------------------------------------------------------------------- #version=11.1.31 # adds capability to read data from selected fields (white-space delimited columns) in a file # # propertyDataField = 0 # no fields -- just read tokens # propertyDataField = 2 # data are in field 2 (second from the left) # propertyAtomNumberField = 1 # data must match atomNo in field 1 and will be in # the field specified by propertyDataField # ----------------------------------------------------------------------------- #version=11.1.30 # full support for switching languages, including a new "language" menu item # # Jmol.js: # # jmolSetCallback("language", "de") # # Jmol scripting: # # language = "de" # # Menu: # # new language submenu with checkboxes. # # allows for efficient specific file reader options for the applet (particularly) # # adds _spinning variable # # adds LOAD xxx::myfile xxx indicating file type xyz, mol, etc. # # not important generally. # # adds PQR reader option, at least for PDB2PQR generated output # # better spin control during zoomTo and moveTo # spinning now detects that a zoomTo or moveTo operation is occurring # or the user is manipulating the model with the mouse, and pauses 1 second # for that operation to complete before resuming spinning # # hover now is turned off during spinning or user manipulation of the model # # zoomTo and moveTo the same location changed to no time delay # ----------------------------------------------------------------------------- #version=11.1.29 # code: totally reorganized isosurface code; new org/jmol/jvxl packages # # adds (1) isosurface functionxy "file:data.dat" ... # adds (2) isosurface functionxy "functionName" {x0 y0 z0} {-ni ...} ... # adds (3) isosurface functionxy "functionName" {x0 y0 z0} {-ni ...}{-nj ...} ... # # (1) "file:" allows reading of xy data from files for graphing f(x,y) # (2) ni<0 indicates JavaScript functionName will return a single string that # should be parsed for numeric data. # (3) ni<0, nj<0 indicates that JavaScript will fill the fourth parameter # of the function with an array of f[nX][nY] data values: # # Jmol: # # isosurface s1 functionXY "xyData" {-2 -2 -2} {21 0.1 0 0} {21 0 0.1 0} {21 0 0 0.1} # # JavaScript: (slow) # # function xyData(app, x, y) { # return func(x, y) # } # # Jmol: # # isosurface s2 functionXY "xyDataAsString" {-2 -2 -2} {-21 0.1 0 0} {21 0 0.1 0} {21 0 0 0.1} # # JavaScript: (much faster) # # function xyDataAsString(app, nX, nY) { # var s # for (var i = 0; i < nX; i++) # for (var j = 0; j < nY; j++) # s += "x_"+i+"\ty_"+j+"\t"+func(i,j)+"\n" # # //non-numeric formatting allowed but not necessary # # return s # } # # Jmol: # # isosurface s3 functionXY "xyDataAsArray" {-2 -2 -2} {-21 0.1 0 0} {-21 0 0.1 0} {21 0 0 0.1} # # JavaScript: (very fast) # # function xyDataAsArray(app, nX, nY, fxy) { # for (var i = 0; i < nX; i++) # for (var j = 0; j < nY; j++) # fxy[i][j] = func(i,j) # } # # (2) and (3) are very fast; (1) is the original method, but it is slow. # # MAYSCRIPT expanded # # for the Wiki or any application where absolutely no JavaScript # is to be allowed, simply remove the MAYSCRIPT parameter, which # now covers all aspects of JavaScript interaction from within Jmol # # # adds applySymmetryToBonds (default: FALSE) # # applySymmetryToBonds # # When set TRUE, this flag instructs Jmol when applying symmetry # to atoms, as in "load xxx.cif {1 1 1}", to also apply symmetry # to the bonds indicated in the file. The flag is useful when # normal Jmol autobonding would not properly connect atoms, but # the model is "molecular" -- the base atom coordinates are correct # for whole molecules. The flag should NOT be used in cases where # the application of symmetry operations creates new bonds that # were not present in the original set, as for quartz.cif, where # there is only one bond initially, and after applying symmetry # new bonds are created that are between atoms that were created # using two different symmetry operations. # # adds isosurface HOMO/LUMO [+/- n] # # better isosurface plane rendering, especially in regard to meshes # bug fix in isosurface contour -n going WAY back to before 10.9.60 # refactoring of all isosurface-related classes # support for Spartan MO HOMO # # adds isosurface POCKET [cavity] sasurface # adds isosurface INTERIOR [cavity] sasurface # # adds load TRAJECTORY -- for a single file with multiple models all with # the same number of atoms. Atom locations can also be updated on the # fly using the data statement. # # adds TRAJECTORY n command -- like FRAME or MODEL, but never more # than one model at a time displayed, because there is only one set # of atoms. # # adds script: option for callbacks set from within Jmol. That is, callbacks # can either be to host page JavaScript functions or to Jmol scripts. This # will allow interactive sessions without external JavaScript. # # set pickcallback "script: script doCallback.spt" # # adds resizeCallback because certain positioning of echos and sizing of the # structure may require method intervention after the resizing # # adds translucency for echo and hover, both text and backgrounds # # adds echo script to defined state # # adds hourglass cursor during MO/Isosurface operations # # fixes inoperative "set pickingstyle measures on" # ----------------------------------------------------------------------------- #version=11.1.28 # adds # # a = script("some script command") # a = javascript("some javascript") # # putting output into a from commands such as "show" or "getProperty", for instance. # # reinstates tempManager properly. # # adds support for CAChe CSF files with MOPAC (AM1, PM3, etc.), # Density Functional, and Extended Huckel Gaussian/Slater-based molecular orbitals. # # CHANGES DEFAULT RENDERING FOR MOLECULAR ORBITALS TO: MESH NOFILL FRONTONLY # # adds MOPAC 2007 graphf output reader (gpt2 files, MOPAC molecular orbitals) # based on the VERY latest version (not released yet), which includes # "MOPAC-Graphical data" on the first line, character index 6. # # adds # # mo HOMO [+/- n] # mo LUMO [+/- n] # # fixes bugs found by FindBugs: # # labels: default z setting for labels (set labelFront, set labelGroup, set labelAtom) # was not being recorded properly # move: with slab or zoom was doing integer math # GhemicalMMReader -- was incorrectly assigning aromatic to bond type 4 via fall-through of switch # # adds xodydata reading of "boundary" as unitcell # enhances default axis rendering for axes unitcell # # adds expanded isosurface-related commands: # # draw list # isosurface list # lcaocartoon list # (mo list) -- not particularly useful # pmesh list # # Listing gives id, number of vertices, number of polygons, visibility, # and title (usually the command that was given that created this isosurface) # # CHANGED BEHAVIOR FOR ISOSURFACE COMMAND WITHOUT ID INDICATED: # # Now if no ID is indicated, the previous ID is used for all commands # EXCEPT "isosurface delete", which deletes all isosurfaces. # # This is a change from Jmol 10.2 and 11.0, where if you leave # off the ID, a new isosurface is created. # # This was a needed change to prevent unwanted multiple isosurfaces. # # CHANGED BEHAVIOR FOR ISOSURFACE DEFAULT COLOR # # The default isosurface color no longer changes shade among 5 possible shades. # That was necessary only because it was easy to mistakenly make multiple # isosurfaces that otherwise would look the same. # ----------------------------------------------------------------------------- #version=11.1.27 # fixes two state bugs: # 1) dots/geosurface not being saved properly in state # 2) animation parameters not being saved properly in state # ----------------------------------------------------------------------------- #version=11.1.26 # fixes two nasty bugs relating to isosurfaces and JVXL files. # -- JVXL files created from molecular orbitals will show up with no color # in 11.1.0 - 11.1.25 because of a missing number in the definition line :( # -- JVXL files created from molecular orbitals will show unwanted cross-over # surfaces from + to -. # ----------------------------------------------------------------------------- #version=11.1.25 # --fully dissociates geosurface from dots; # --allows coloring and transparency of geosurface # similarly to the way stars are colored # ----------------------------------------------------------------------------- #version=11.1.24 # refactored Geodesic3D, Dots, DotsRenderer # independent dots/geosurface # # isosurface CAVITY # ----------------------------------------------------------------------------- #version=11.1.23 # fixes a number of bugs, some critical # # adds isosurface CAVITY x.xx -- a new way to depict the cavities of # a molecule in terms of color. # ----------------------------------------------------------------------------- #version=11.1.21/22 # adds # # load file "=xxxx" and set loadFormat "http://....../%FILE..... # load files ..... # just a cleaner version of loading multiple files. # load append ..... # APPENDS the file(s) or model(s) as new frames onto the current set. # data append ..... # same thing, but inline # # isosurface MODEL n # pmesh MODEL n # isosurface within x.x (what) # # Introduces "real" color translucency # # color xxxx translucent N # # where N is -1 to 9. # # OR OR # translucent -1 same as Jmol 10.2 # translucent 0.0 opaque # through # translucent 1.0 transparent (invisible) # # translucent 2 0.125 32 1/8 translucency (slightly translucent) # translucent 3 0.25 64 2/8 translucency # translucent 4 0.375 96 3/8 translucency # translucent 5 0.5 128 4/8 translucency (default) # translucent 6 0.625 160 5/8 translucency # translucent 7 0.75 192 6/8 translucency # translucent 8 0.825 224 7/8 translucency (very sheer) # translucent 9 1.00 255 8/8 transparent (invisible) # ----------------------------------------------------------------------------- #version=11.1.20 # cleans up axes/boundbox/unitcell business # # allows for individually colored axes: # # color axis1 ... # color axis2 ... # color axis3 ... # color axes ... (of course) # # and these objects are considered more like background -- # colors and sizes persist past file load # # to turn on and off without messing with size, just use # # showAxes = true # showBoundBox = true # # etc. # ----------------------------------------------------------------------------- #version=11.1.19 # allows comparison of user-defined atom properties in SELECT: # # select property_myprop < 1e-5; # # and # # x = {carbon}[5].property_test # x = {carbon}.property_test.min # x = {carbon}.property_test.max # # etc. # # This is it! :) # ----------------------------------------------------------------------------- #version=11.1.18 # introduces user-definable atom properties that can be used # to color isosurfaces: # # x = load("file.dat"); # isosurface variable x # simple 100% vdw radius mapping # # select 1.3 # data "property_myprop @x" # isosurface property_myprop # # allows isosurface mapping of general atom properties: # # isosurface sasurface colorscheme bwr map property temperature # # adds "bwr" colorscheme as opposed to "rwb", which I think is backward. # # isosurface -- now supports APBS ( ) # molecular electrostatic potential output files # # write -- modified to allow unquoted filename in # write isosurface file.name # # jvxl 1.0 -- adds ANGSTROMS flag on line with # of atoms (line 3) # ----------------------------------------------------------------------------- #version=11.1.17 # deprecation of SET # ------------------ # # The "SET" command is no longer necessary. Anything that could have # been set using "SET x .... " can now be set using # # x = .... # # This allows for a much cleaner interface because we simply make # settings in a normal sort of way: # # axes on # axes = molecular # # measures = angstroms # # It will take a bit more to make it all consistent, but the idea # is that there are then some special reserved variables that # mean something special when set, like "bondmode" # # This build allows for the applet to be "bare-bones" -- only the # essential classes included in the Jar file; others never included # or possibly in accompanying jar files, such as, perhaps, JmolPopupMenu.jar, # JmolNavigation.jar, JmolBio.jar, Jm olSurface.jar, JmolXtal.jar, etc. # # Then a developer can slim down the download. The minimum is 697K, # about 58% of the full package. All that gets you is atoms, bonds, # and measures. # ----------------------------------------------------------------------------- #version=11.1.16: # First incompatibility found: # # set echo myecho (atomno=3) or (atomno=5) # 1) adds two new modifiers: # .min # .max # # as in: # # x = {*}.bonds.length.max #the longest bond length # x = {*}.atoms.max #the last atom # # 2) extends find() to sets of lines. For example: # # longLine={*}.bonds.label("%=, %LENGTH").lines.find({*}.bonds.length.max) # message @longLine # longest = longLine%(longLine.find(",")-1) # b = {*}.bonds[longest] # select b_set;color bonds yellow # # NOTE: _set removed in 11.3.41: # select @b;color bonds yellow # # ----------------------------------------------------------------------------- #version=11.1.15: # APPLICATION: adds undo/redo to a fixed depth of 50 commands # # TYPE CONVERSION # # We have eight different variable types now: # boolean True/False # integer 0, 1, 2, .... # decimal 3.5, 3.25E-3 # string "test" "3.5" # point {2.3 3.4 5.6} {0 1/2 1} # plane {0 1 1 0} # atomset {oxygen} # bondset {oxygen}.bonds # plane and bondset are new; arithmetic operations are not fully developed. # These can be mixed and matched to good effect. Certain relatively # intuitive rules apply. Usually the operand on the left sets # the overall type, allowing for easy type conversion depending upon # operand order: # int + float: # 0 + 3.6 ==> 3 (int on left rounds float on right) # 3.6 + 0 ==> 3.6 (float on left sets result) # # int/float + string: # 0.0 + "3.5" ==> 3.5 (string converted to float) # 0 + "3.5" ==> 3 (string converted to float, then int) # "3.5" + 0 ==> "3.50" (integer converted to string) # "3.5" + 0.0 ==> "3.50.0" (float converted to string) # # 1.0 + {carbon}.xyz ==> 1 + distance from {0 0 0} to {carbon} center # {carbon}.xyz + 1 ==> {carbon} center point offset by {1 1 1} # # x = {carbon}.xyz * {1 0 0} ==> (dot product) # # Now x is the average x coordinate of carbon # # Boolean expressions are a bit different in that the operators # AND, OR, XOR, and NOT all require conversion to boolean UNLESS both # operands are atom expressions, in which case these operate directly on the # atom sets and return a new atom set, just like in SELECT. # # 3 and 0.5 ==> TRUE (both are nonzero) # false OR 2.0 ==> true (2.0 is not 0, so it is TRUE) # {oxygen} and {molecule=1} ==> all oxygen atoms in the first molecule # # x = ({oxygen} and {molecule=1}).xyz # # x is now the center point of all oxygen atoms in the first molecule # # In standard math, boolean TRUE evaluates to 1.0; FALSE evaluates to 0.0 # # true + 2.0 ==> 3.0 ("TRUE" evaluates to 1.0 in math operations) # 2 + true ==> 3 ("TRUE" evaluates to 1.0 and is then turned into an integer) # # # ATOM EXPRESSION AUTOMATIC DEFINE # # When you set a variable to a value, and that value is a point, plane, or atom expression, # then Jmol automatically registers the result as follows: # # points: # x = "{x y z}" # # planes: # x = "{x y z w}" # # atom expressions: # x = n # x_set = "({i j k ...})" # # NOTE: "set x" removed in 11.3.40: # NOTE: _set removed in 11.3.41: # # x = {oxygen}.xyz # y = {carbon}.xyz # draw @x # draw @y # draw line1 @x @y # # and # # x = {carbon}[3][5] # select @x # color green # x = {carbon}[3][5] # select @x # color green # # x = {carbon or oxygen}.bonds # select BONDS @x # color bonds green # # DATA() function and variable option for DATA command # # x = data({atomno < 10},"xyz") # x = data({atomno < 10},"mol") # x = data({atomno < 10},"pdb") # # data "model @x" # # write data t.xyz # write data t.mol # write data t.pdb # # # Better BITSET implementation # # CHANGE: default string value for a bitset is now the ({n:m}) # string format, which can be used in numerous commands. # # To get the count within a string context, just use .size: # # x = "number selected is " + {selected}.size # # or force integer math: # # x = "number selected is " + (0 + {selected}) # # merges math functions within(), connected(), substructure() into molecular math # # adds connected() both for finding atoms and for identifying bonds: # xAtoms = connected(3, {carbon}) # xBonds = connected(1.3,2.5,"single", {carbon} {oxygen}) # # adds # x.atoms # to go along with x.bonds # # adds distance({carbon},{oxygen}) # adds angle({carbon}[4],{oxygen}[3], {nitrogen}[2]) # # angle function accepts from three or four # atom expressions or XYZ coordinates and returns a decimal number for # the distance, angle, or dihedral relating these points. # When more than one atom is involved, average positions are used. # # Note that when more than one atom is involved in a set, # the following are different: # # x1 = {molecule=1}.distance{molecule=2} # x2 = {molecule=1}.xyz - {molecule=2}.xyz # # x1 is a NUMBER that is the "average distance measured # from each molecule 1 atom to the average molecule 2 position" # x2 is a point representing the VECTOR from the "average position of molecule 2" # to the "average position of molecule 1" # # The following are all equivalent: # # x3 = {molecule=1}.xyz.distance{molecule=2} # x4 = 0.0 + ({molecule=1}.xyz - {molecule=2}.xyz) # x5 = ({molecule=1}.xyz - {molecule=2}.xyz).distance{0 0 0} # x6 = distance({molecule=1} {molecule=2}) # # They are all the distance from the center of molecule 1 # to the center of molecule 2 # # # x = load("filename") # # The string data in the file are loaded into the string. # If the file does not exist, then the string contains the error message. # # # Implements ({i j:k m n}) bitset option across all commands # # RESET varName # # reset varName # clears that variable definition # # # "UNSPECIFIED" and "QUADRUPLE" BOND TYPES # # An additional bond type is now avaiable: "UNSPECIFIED". # This shows up in the MOL2 reader and may be selected for and modified using, for example: # # select connected(unspecified) # color bonds red # # or # # select connected(unspecified) # connect (selected) single modify # # In addition, we now can depict quadruple bonds. # ----------------------------------------------------------------------------- #version=11.1.14: # DYNAMIC MEASUREMENTS # # Now that we can move atoms so easily, we don't want those measurements getting stale. # # set dynamicMeasurements # # allows measurements to be recalculated on the fly. # # # MEASUREMENT FORMAT STRINGS # # Measurement format strings can be set using # # measure "format string..." # # where the format string may have the following keys: # # %= 1-based index # %VALUE the value of the measurement # %UNITS the units for the measurement # %x1 atom property "x" for atom 1 # %x2 atom property "x" for atom 2 # %x3 atom property "x" for atom 3 # %x4 atom property "x" for atom 4 # # for example: # # measure "%a1 -- %VALUE %UNITS --- %a2" # # # MATH OPERATOR PRECEDENCE AND PARENTHESES # # Jmol 11.1.14 supports full standard operator precedence and parentheses # in IF, SET, and %{} expressions # # degUnsat = ({carbon} * 2 + {nitrogen} + 2 - {hydrogen}) / 2 # # # BRACES INDICATE ATOM EXPRESSIONS # # Use {} in IF, SET and %{} for designating atom expressions. # We are still using () for "embedded expressions" in all other commands. # # nOxygen = {oxygen} # xOxygen = {oxygen}.x # ptOxygen = {oxygen.xyz} # # a = {oxygen}.temperature # message %{{carbon}.x} # if {O22}.bondCount > 2;goto ... # # but # # draw line1 (atomno=2) (atomno=3) # # # ATOM EXPRESSION ITEM SELECTOR [n] # # In SET, IF, and %{ } in MESSAGE and ECHO you can now specify a subset of the # atom expression. # # x = {carbon}[3] # the third carbon atom # x = {carbon}[3][5] # the third through fifth carbon atoms # x = {carbon}[3][0] # the third through last carbon atoms # # This also works in standard select expressions, but using () instead: # # select (carbon)[3] # the third carbon atom # # and anywhere an embedded expression might be found: # # measure ((_C)[1]) ((_C)[2]) # # # POINTS IN IF, SET, and %{} # # Points in IF, SET, and %{} can be designated using the standard {x y z} # notation WITHOUT commas. This is because we have to distinguish between # atom expressions {1,2,3} and coordinates {x y z}, and this seems to me the # simplest way to do it. (Comma means "or" in atom expressions.) In all other # instances, the commas are fine, including "SET UNITCELL" and "SET DEFAULTLATTICE". # # x = {1 1 0} + {oxygen}.xyz # # { }.distance ATOM PROPERTY FOR SET, IF, and %{} # # d = {oxygen and * /1}.distance{oxygen and * /2} # set echo top left # echo the O-O distance is %{{oxygen and * /1}.distance{oxygen and * /2}} # # message %{{atomno=3}.distance{atomno=4}} # message %{{atomno=3}.distance{1/2 1/2 1/2}} # # # { }.label "xxxx" ATOM PROPERTY FOR IF, SET, and %{} # # The .label format provides a convenient means of delivering a wide range of # atom-based data back to the user with whatever formatting is desired. # # x2 = {atomno=3).label("atom %a\t" + (atomno=3).xyz) # xyzFile = "" + {selected}.size + "\n\n" + {selected}.label("%a %x %y %z") # # # "....".lines # # The .lines operator splits a string into an array based on line termination. # # WRITE VAR "filename" (application only) # # pdbAtomData = {selected and not hetero}.label("ATOM %5i %-4a%1A%3n %1c%4R%1E %8.3x%8.3y%8.3z%6.2Q%6.2b %2e%2C") # pdbHeteroData = {selected and hetero}.label("HETATM%5i %-4a%1A%3n %1c%4R%1E %8.3x%8.3y%8.3z%6.2Q%6.2b %2e%2C") # pdbFile = pdbAtomData + pdbHeteroData # write VAR pdbFile "test.pdb" # # molFileData = "line1\nline2\nline3\n"+(""+{selected}.size)%-3+(""+{selected}.bonds.size)%-3+" 0 0 0\n"+{selected}.labels("%-10.4x%-10.4y%-10.4z %2e 0 0 0 0 0")+{selected}.bonds.labels("%3D1%3D2%3ORDER 0 0 0") # # # GETPROPERTY "evaluate" # # You can now use getProperty to get expression information directly: # # getproperty "evaluate" "{*}.xyz" # # or on a web page the following returns a valid XYZ file for molecule 1: # # var info = jmolGetPropertyAsJavaObject("evaluate", '"" + {molecule=1} + "\n\n" + {molecule=1}.label("%a %x %y %z")') # # # SELECTED ATOMS FROM ATOM EXPRESSIONS # # You can select atoms from an atom expression using [n]. # "[0]" means "and everything after". # # x = {atom expression}[3].ident # x = {atom expression}[3][0].xyz # 3 and after (average position) # x = {atom expression}[3][5].x # 3-5 (average x) # # # SELECTED BONDS FROM EXPRESSIONS # # You can select bonds from an atom expression # # x = {atom expression}.bonds.ident # x = {atom expression}.bonds[3].ident # # # BOND INFORMATION # # You can specify how to label a set of bonds using format strings. # Numbers are currently in Angstroms. Keys are # # %# sequential number # %= file 1-based index # %ORDER the bond order # %TYPE the bond type # %LENGTH the bond length # %x1 atom property "x" for atom 1 # %x2 atom property "x" for atom 2 # # The special atom properties %D1 and %D2 give sequential numbers for the # atoms FOR THIS SET OF BONDS. This is so that a proper subfile of type MOL # could be generated. # # x = {atom expression}.bonds[3].label("%# %3ORDER %TYPE %a1 %a2 %6.3LENGTH") # # # EXPANDED MODULUS % OPERATOR IN IF, SET, AND %{} # # Usually modulus is reserved for integer math, so we # extend that here to add some useful "modulus-like" capability: # # string modulus for trimming and padding # "test" %3 ==> left trim: "tes" # "test" %6 ==> right pad: "test " # "test" %-3 ==> right trim: "est" # "test" %-6 ==> left pad: " test" # # float modulus for rounding and scientific notation # 3.5456 %3 ==> "3.546" (STRING!) # 3545.6 %-3 ==> "3.55E+3" (STRING!) # # 0.0 + 3.5456 %3 ==> 3.546 (float) # 0.0 + 3545.6 %-3 ==> 3550.0 # # point modulus for getting base unit cell equivalent position # {3/2 1/2 1/1} % 0 ==> {1/2 1/2 0} # ----------------------------------------------------------------------------- #version=11.1.13: # DATA "coord set" # invertSelected POINT .... # invertSelected PLANE .... # invertSelected HKL ...... # rotateSelected .... # rotateSelected spin .... # full state support for "tainting" atom positions using translateSelected or invertSelected # # set allowRotateSelected # then use ALT-LEFT for rotating just the selected molecule # # this all definitely needs some work and discussion in terms of user interface via mouse # # # write coords xxxx.spt # load xxxx.spt # minimal -- just coord. # script xxxx.spt # this is the full state load # # x = (some atom expression).atomProperty -- takes an average if more than one atom # for example: # # x = (* /1).temperature # x = (C5).bondcount # # note that you can even say: # set echo top left # echo average position= {%{(selected).x},%{(selected).y},%{(selected).z}} # # and it will AUTOMATICALLY update with new values as you select different atoms. # ----------------------------------------------------------------------------- #version=11.1.12: # app fix for console entry messing up cursor position; # allows for scripting during pause or interrupt of running script using ! as first character of script # new: within(x.x,plane,$plane1) # fix for "draw off" not recorded in save state # fix for within(integer,...) bug using RasMol units # fix for _modelnumber showing up as 2001 # reconfigures _modelNumber as x.y for single models; x.x - y.y for range # adds _currentFileNumber # adds _currentModelNumberInFile # disallows user setting of variables with _ as first character # adds @variableName in any command # adds frame x.x - y.y # adds frame 0.0 # adds frame range x.x - y.y # adds file command # adds select file= # tunes select model= chemical-structures-2.2.dfsg.0.orig/src/jmol/LICENSE.txt0000644000175000017500000006350011225104065023133 0ustar georgeskgeorgesk GNU LESSER GENERAL PUBLIC LICENSE Version 2.1, February 1999 Copyright (C) 1991, 1999 Free Software Foundation, Inc. 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. 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To apply these terms, attach the following notices to the library. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. Copyright (C) This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA Also add information on how to contact you by electronic and paper mail. You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the library, if necessary. Here is a sample; alter the names: Yoyodyne, Inc., hereby disclaims all copyright interest in the library `Frob' (a library for tweaking knobs) written by James Random Hacker. , 1 April 1990 Ty Coon, President of Vice That's all there is to it! chemical-structures-2.2.dfsg.0.orig/src/jmol/COPYRIGHT.txt0000644000175000017500000000532011225104065023415 0ustar georgeskgeorgesk Copyright 1998-2007 The Jmol Development Team This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. Complete source code for the Jmol application, the Jmol applet, and surrounding utilities is available from http://www.jmol.org This software uses several external libraries and resources: JUnit Used for unit testing. Distributed by the IBM Public License (see doc/ibm.license.html). See http://www.junit.org/. The Chemical Development Kit Used for reading and writing CML and ShelX. Distributed by Lesser GNU Public License See http://cdk.sf.net/. AElfred Used for XML parsing. Distributed free and without warranty. Copyright (C) 1997,1998 by Microstar Software Ltd. See http://www.microstar.com/aelfred.html. SAX Used for event-based XML parsing. Distributed free and without warranty. See http://www.megginson.com/SAX/. Acme Image encoders Used for exporting images in GIF and PPM formats. Distributed free and without warranty. Copyright (C) 1996,1998 by Jef Poskanzer. See http://www.acme.com/. JPEG Encoder Used for exporting images in JPEG format. Distributed free and without warranty (see doc/jpegEncoder.license). Copyright (c) 1998 James R. Weeks and BioElectroMech. See http://www.obrador.com/essentialjpeg/. Java Analysis Studio Used for graphs. Distributed by the GNU Lesser General Public License (see doc/lgpl.license), and requires providing the source code (see http://jas.freehep.org/source.htm). See http://jas.freehep.org/. Unofficial Java3D vecmath package Used for linear algebra. Distributed free and without warranty. Copyright (C) 1997,1998,1999 by Kenji Hiranabe. See http://www.esm.co.jp/divisions/open-sys/java/vecmath/. JFA Icon collection Used for icons in menus and toolbars. Distributed free and without warranty. Copyright (C) 1998 by Dean S. Jones. See http://jfa.javalobby.org/projects/icons/ Jakarta Commons CLI Used for parsing command line optinos. Distributed with The Apache Software License, Version 1.1. Copyright (c) 1999-2001 The Apache Software Foundation. See http://jakarta.apache.org/commons/cli/. chemical-structures-2.2.dfsg.0.orig/src/jmol/CMakeLists.txt0000644000175000017500000000237211112716045024052 0ustar georgeskgeorgesk################################################################# # Local variable settings # ################################################################# set(LOCAL_TARGET jmol) message(STATUS "Generating ${LOCAL_TARGET} Makefile") file(GLOB jmol_SRCS *.jar *.js) set(jmol_SRCS ${jmol_SRCS} COPYRIGHT.txt LICENSE.txt README.txt ) set(jmol_files "") add_custom_target(${LOCAL_TARGET} ALL) ################################################################# # jmol file handle # ################################################################# foreach(jmol_SRC_FILE ${jmol_SRCS}) get_filename_component(jmol_FILE ${jmol_SRC_FILE} NAME) add_custom_command(TARGET ${LOCAL_TARGET} COMMAND cp ${jmol_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${jmol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(jmol_files ${jmol_files} ${jmol_FILE}) endforeach(jmol_SRC_FILE) ################################################################# # Install files # ################################################################# install(FILES ${jmol_files} DESTINATION ${SHARE_HOME}/jmol) chemical-structures-2.2.dfsg.0.orig/src/jmol/LEAME.txt0000644000175000017500000001544711225617132022707 0ustar georgeskgeorgesk============================================================================== === Jmol === ============================================================================== Jmol es un visor de molculas y un editor; es de cdigo abierto y est escrito en Java. Toda la informacin est disponible en http://www.jmol.org/ Las preguntas o comentarios relativos a su uso deben enviarse a jmol-users@lists.sourceforge.net (en ingls) Las preguntas, comentarios y sugerencias relativos a su desarrollo deben enviarse a jmol-developers@lists.sf.net (en ingls) Lista de archivos incluidos: -------------------- - LEAME.txt Este archivo. - README.txt La versin en ingls de este archivo. - COPYRIGHT.txt Informacin sobre los derechos de copia. - LICENSE.txt Los trminos de uso y distribucin de Jmol (licencia GNU LGPL). - Jmol.jar El archivo ejecutable de la aplicacin Jmol (un programa escrito en Java). Funciona como cualquier otro programa: se abre en su propia ventana, se puede redimensionar o minimizar, se puede arrastrar y soltar archivos sobre l, tiene una barra superior de men, puede abrir y grabar archivos, etc. Puede ejecutarse desde la lnea de comandos (particularmente, usando los archivos por lotes que se describen a continuacin) pero, si Java est correctamente configurado en tu sistema, normalmente basta con hacer doble clic en este archivo. - jmol (Un tipo de archivo por lotes para iniciar la aplicacin Jmol) - jmol.bat Archivo por lotes para iniciar la aplicacin en Windows. - jmol.mac (Un tipo de archivo por lotes para iniciar la aplicacin Jmol) - jmol.sh Un archivo de instrucciones para iniciar la aplicacin Jmol en sistemas de tipo Unix, por ejemplo Linux, BSD, Solaris o Cygwin para Windows. - JmolApplet.jar La miniaplicacin ("applet"), es decir, una versin del programa que slo funciona cuando est incrustada en una pgina web. Se trata en este caso de un archivo "todo en uno" o "monoltico" que se mantiene principalmente por compatibilidad con pginas antiguas que lo invoquen explcitamente. El mtodo recomendado actualmente es el uso de la versin subdividida (JmolApplet0.jar etc., descrita ms abajo). En particular, Jmol.js utiliza la versin subdividida. Te puede interesar utilizar este archivo si quieres mantener sencillo tu sitio web, o si slo quieres actualizar un archivo jar cuando lleguen versiones nuevas de Jmol. Sin embargo, este Jmol se cargar algo ms lentamente que las versiones subdivididas, puesto que es preciso que se descargue al equipo del usuario el programa completo, con todos sus componentes, antes de que se pueda mostrar una estructura. Para llamar a JmolApplet.jar desde Jmol.js: a) ponlo en la misma carpeta que contiene la pgina HTML que lo requiere y no uses jmolInitialize() o bien b) identifcalo explcitamente en jmolInitialize(), por ejemplo: jmolInitialize("carpeta-que-contiene-los-archivos-jar", "JmolApplet.jar") - JmolAppletSigned.jar Una versin equivalente de la miniaplicacin, pero en este caso es una miniaplicacin "firmada" o "confiable" (terminologa de seguridad en el lenguaje Java). Esto significa que para ejecutarse debe previamente ser autorizada por el usuario visitante de la pgina web y, de ser as, habr menos restricciones de seguridad para el acceso a archivos. Por ejemplo, podr acceder a archivos en cualquier parte del ordenador del usuario y en cualquier otro servidor web. Habitualmente, los usuarios recibirn un aviso prguntndoles si quieren "aceptar el certificado" o si "confan" en la miniaplicacin; sin embargo, esta prestacin de seguridad no siempre est activada. Si decides usar JmolAppletSigned.jar, debes tener esto en cuenta. Aparte de la lectura de archivos, Jmol no utiliza ninguna otra capacidad de las miniaplicaciones firmadas, como acceder al portapapeles del sistema o grabar archivos. Usa la miniaplicacin firmada slo si sabes lo que ests haciendo y has tenido en cuenta las cuestiones de seguridad. Para llamar a JmolAppletSigned.jar desde Jmol.js: jmolInitialize("carpeta-que-contiene-los-archivos-jar", "JmolAppletSigned.jar") - Jmol.js Esta es la bilioteca de funciones, escrita en el lenguaje JavaScript, que ayuda en la preparacin de pginas web que usen la miniaplicacin Jmol sin necesidad de conocer y escribir cdigo detallado especfico para la miniaplicacin. Esta biblioteca usa por defecto la versin subdividida de la miniaplicacin (firmada o no). Est documentada en detalle en http://jmol.org/jslibrary/ - JmolApplet0.jar y JmolApplet0(diversosSufijos).jar La miniaplicacin se divide en varios trozos de acuerdo con su funcionalidad, de modo que si una pgina no precisa determinado componente, ste no se descargar desde el servidor. Aun as, se recomienda que pongas todos los archivos JmolApplet0*.jar en el servidor, incluso si tus pginas no usan sus prestaciones, pues tanto el men emergente como la consola permiten a los usuarios acceder a funciones de Jmol que t no hayas previsto. El conjunto de todos estos archivos es equivalente al archivo nico JmolApplet.jar. Esta versin subdividida es la que se usa de forma predeterminada si utilizas Jmol.js. Para ello, basta usar la forma ms simple de jmolInitialize(), indicando slo la carpeta que contiene el conjunto de archivos jar: jmolInitialize("carpeta-que-contiene-los-archivos-jar") por ejemplo, jmolInitialize(".") (si los archivos jar estn en la misma carpeta que la pgina web) jmolInitialize("../jmol") (si los archivos jar estn en una carpeta paralela, llamada 'jmol') - JmolAppletSigned0.jar y JmolAppletSigned0(diversosSufijos).jar La versin firmada de la miniaplicacin subdividida. Esta versin permite que el usuario acceda a archivos en cualquier parte de su ordenador y en cualquier servidor web. Habitualmente, los usuarios recibirn un aviso pidindoles que acepten el certificado para **cada uno** de los archivos jar que se pueden cargar (actualmente, 16). Por esta razn, es probable que esta versin no sea de uso habitual. El conjunto de todos estos archivos es equivalente al archivo nico JmolAppletSigned.jar. Para llamar a esta versin desde Jmol.js: a) jmolInitialize("carpeta-que-contiene-los-archivos-jar", true) o bien b) jmolInitialize("carpeta-que-contiene-los-archivos-jar", "JmolAppletSigned0.jar") --------------------------- Teniendo en cuenta las descripciones anteriores, observars que el paquete de distribucin de Jmol contiene 4 copias completas de la miniaplicacin (firmada or no, subdividida o no). --------------------------- chemical-structures-2.2.dfsg.0.orig/src/alcohols/0000755000175000017500000000000011225622315022152 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/alcohols/heptan-1-ol.cml0000644000175000017500000001013510662517661024707 0ustar georgeskgeorgesk Heptan-1-ol 116.2013 116.1201151 -36 176 chemical-structures-2.2.dfsg.0.orig/src/alcohols/octan-1-ol.cml0000644000175000017500000001071210662517661024535 0ustar georgeskgeorgesk Octan-1-ol 130.2279 130.1357652 -15 195 chemical-structures-2.2.dfsg.0.orig/src/alcohols/4R-octan-4-ol.cml0000644000175000017500000001020210662517661025015 0ustar georgeskgeorgesk (4R)-Octan-4-ol 130.2279 130.1357652 chemical-structures-2.2.dfsg.0.orig/src/alcohols/2S-hexan-2-ol.cml0000644000175000017500000000711510662517661025022 0ustar georgeskgeorgesk (2S)-Hexan-2-ol 102.1748 102.1044651 138 chemical-structures-2.2.dfsg.0.orig/src/alcohols/butan-1-ol.cml0000644000175000017500000000577510662517661024557 0ustar georgeskgeorgesk Butan-1-ol 74.1216 74.0731649 -90 117 chemical-structures-2.2.dfsg.0.orig/src/alcohols/index.xml0000644000175000017500000003527311142231213024004 0ustar georgeskgeorgesk Alcohols Alcohols Alkohole Alcools Alcoholen Alcohols 醇類 2-Methylpropan-1-ol 2-Méthylpropan-1-ol 2-Methylpropan-1-ol 2-甲基-1-丙醇 2-methylpropan-1-ol Isobutanol Isobutanol Isobutanol 異丁醇 Jerome Pansanel 2006-05-10 2-Methylpropan-2-ol 2-Méthylpropan-2-ol 2-Methylpropan-2-ol 2-甲基-2-丙醇 2-methylpropan-2-ol tert-Butanol tert-Butanol tert-Butanol 第三丁醇 Jerome Pansanel 2006-05-10 (2R,3R,4R,5S)-Hexane-1,2,3,4,5,6-hexol (2R,3R,4R,5S)-Hexan-1,2,3,4,5,6-hexol (2R,3R,4R,5S)-Hexane-1,2,3,4,5,6-hexol (2R,3R,4R,5S)-Hexane-1,2,3,4,5,6-hexol (2R,3R,4R,5S)-己-1,2,3,4,5,6-六醇) 2R_3R_4R_5S-hexane-1_2_3_4_5_6-hexol D-Sorbitol D-Sorbitol D-Sorbitol D-山梨醇 Jerome Pansanel 2006-05-10 (2R)-Butan-2-ol (2R)-Butan-2-ol (2R)-Butan-2-ol (2R)-丁醇 2R-butan-2-ol Jerome Pansanel 2006-05-10 (2S)-Butan-2-ol (2S)-Butan-2-ol (2S)-Butan-2-ol (2S)-丁醇 2S-butan-2-ol Jerome Pansanel 2006-05-10 (2S)-Heptan-2-ol (2S)-Heptan-2-ol (2S)-Heptan-2-ol (2S)-庚-2-醇 2S-heptan-2-ol Jerome Pansanel 2006-05-10 (2S)-Hexan-2-ol (2S)-Hexan-2-ol (2S)-Hexan-2-ol (2S)-己-2-醇 2S-hexan-2-ol Jerome Pansanel 2006-05-10 (2S)-Octan-2-ol (2S)-Octan-2-ol (2S)-Octan-2-ol (2S)-辛-2-醇 2S-octan-2-ol Jerome Pansanel 2006-05-10 (2S)-Pentan-2-ol (2S)-Pentan-2-ol (2S)-Pentan-2-ol (2S)-戊-2-醇 2S-pentan-2-ol Jerome Pansanel 2006-05-10 (3S)-Heptan-3-ol (3S)-Heptan-3-ol (3S)-Heptan-3-ol (2S)-庚-3-醇 3S-heptan-3-ol Jerome Pansanel 2006-05-10 (3S)-Hexan-3-ol (3S)-Hexan-3-ol (3S)-Hexan-3-ol (3S)-己-3-醇 3S-hexan-3-ol Jerome Pansanel 2006-05-10 (3S)-Octan-3-ol (3S)-Octan-3-ol (3S)-Octan-3-ol (3S)-辛-3-醇 3S-octan-3-ol Jerome Pansanel 2006-05-10 (4R)-Octan-4-ol (4R)-Octan-4-ol (4R)-Octan-4-ol (4R)-辛-4-醇 4R-octan-4-ol Jerome Pansanel 2006-05-10 Butan-1-ol Butan-1-ol Butan-1-ol 丁-1-醇 butan-1-ol Jerome Pansanel 2006-05-10 Ethane-1,2-diol Ethane-1,2-diol Ethane-1,2-diol 乙-1,2-二醇 ethane-1_2-diol Ethylene glycol Ethylenglykol Éthylène glycol Ethylene glycol 乙二醇 Jerome Pansanel 2006-05-10 Ethanol Ethanol Ethanol 乙醇 ethanol Jerome Pansanel 2006-05-10 Heptan-1-ol Heptan-1-ol Heptan-1-ol 庚-1-醇 heptan-1-ol Jerome Pansanel 2006-05-10 Heptan-4-ol Heptan-4-ol Heptan-4-ol 庚-4-醇 heptan-4-ol Jerome Pansanel 2006-05-10 Hexan-1-ol Hexan-1-ol Hexan-1-ol 己-1-醇 hexan-1-ol Jerome Pansanel 2006-05-10 Methanol Méthanol Methanol 甲醇 methanol Jerome Pansanel 2006-05-10 Octan-1-ol Octan-1-ol Octan-1-ol 辛-1-醇 octan-1-ol Jerome Pansanel 2006-05-10 Pentan-1-ol Pentan-1-ol Pentan-1-ol 戊-1-醇 pentan-1-ol Jerome Pansanel 2006-05-10 Pentan-3-ol Pentan-3-ol Pentan-3-ol 戊-3-醇 pentan-3-ol Jerome Pansanel 2006-05-10 Propan-1-ol Propan-1-ol Propan-1-ol 丙-1-醇 propan-1-ol Jerome Pansanel 2006-05-10 Propan-2-ol Propan-2-ol Propan-2-ol 丙-2-醇 propan-2-ol Isopropanol Isopropanol Isopropanol 異丙醇 Jerome Pansanel 2006-05-10 Propane-1,2,3-triol Propane-1,2,3-triol Propane-1,2,3-triol 丙-1,2,3-三醇 propane-1_2_3-triol Glycerol Glycerin Glycérine Glycérol Glycerol 甘油 Jerome Pansanel 2006-05-10 2-Methylbutan-2-ol 2-Méthylbutan-2-ol 2-Methylbutan-2-ol 2-甲基-2-丁醇 2-methylbutan-2-ol tert-Amyl alcohol tert-Amylalkohol Alcool tert-amylique tert-Amyl alcohol 三級戊醇 Jerome Pansanel 2006-07-13 Decan-1-ol Décan-1-ol Decan-1-ol 1-癸醇 decan-1-ol Decyl alcohol Decylalkohol Alcool décylique Decyl alcohol 癸醇 Jerome Pansanel 2006-07-13 Nonan-1-ol Nonan-1-ol Nonan-1-ol 1-壬醇 nonan-1-ol Nonyl alcohol Nonylalkohol Alcohol nonylique Nonyl alcohol 壬醇 Jerome Pansanel 2006-07-13 2-Aminoethanol 2-Aminoéthanol 2-Aminoethanol 乙醇胺 2-aminoethanol Jerome Pansanel 2006-07-31 But-2-yne-1,4-diol But-2-yne-1,4-diol But-2-yne-1,4-diol 丁-2-炔-1,4-二醇 but-2-yne-1_4-diol Jerome Pansanel 2006-11-09 Cyclohexanol Cyclohexanol Cyclohexanol 環已醇 cyclohexanol Jerome Pansanel 2006-11-09 Cyclopentanol Cyclopentanol Cyclopentanol 環戊醇 cyclopentanol Jerome Pansanel 2006-11-09 1,1,1,3,3,3-Hexafluoropropan-2-ol 1,1,1,3,3,3-Hexafluoropropan-2-ol 1,1,1,3,3,3-Hexafluoropropan-2-ol 1,1,1,3,3,3-六氟丙-2-醇 1_1_1_3_3_3-hexafluoropropan-2-ol Jerome Pansanel 2006-11-21 2,2,2-Trifluoroethanol 2,2,2-Trifluoroéthanol 2,2,2-Trifluoroethanol 2,2,2-三氟乙醇 2_2_2-trifluoroethanol Jerome Pansanel 2006-11-21 2-Thioethanol 2-Thioéthanol 2-Thioethanol 2-硫代乙醇 2-thioethanol 2-Mercaptoethanol 2-Mercaptoéthanol 2-Mercaptoethanol 巰基乙醇 Thioglycol Thioglycol Thioglycol 硫乙二醇 Monothio ethylene glycol Monothio éthylène glycol Monothio ethylene glycol 單硫乙二醇 Jerome Pansanel 2006-11-21 (Z)-Hex-3-en-1-ol (Z)-Hex-3-en-1-ol (Z)-Hex-3-en-1-ol (Z)-己-3-烯-1-醇 Z-hex-3-en-1-ol Jerome Pansanel 2006-11-21 (2S,3R)-Butane-1,2,3,4-tetrol (2S,3R)-Butan-1,2,3,4-tetrol (2S,3R)-Butane-1,2,3,4-tétrol (2S,3R)-Butane-1,2,3,4-tetrol (2R,3R)-1,2,3,4-丁炔 2S_3R-butane-1_2_3_4-tetrol meso-Erythritol méso-Erythritol meso-Erythritol 內消旋-丁四醇 (2S,3R)-1,2,3,4-Tetrahydroxybutane (2S,3R)-1,2,3,4-Tétrahydroxybutane (2S,3R)-1,2,3,4-Tetrahydroxybutan (2S,3R)-1,2,3,4-Tetrahydroxybutane (2S,3R)-1,2,3,4-四羥丁烷 Jerome Pansanel 2006-07-13 chemical-structures-2.2.dfsg.0.orig/src/alcohols/2-methylpropan-1-ol.cml0000644000175000017500000000602710662517661026316 0ustar georgeskgeorgesk 2-Methylpropan-1-ol 74.1216 74.0731649 -108 108 chemical-structures-2.2.dfsg.0.orig/src/alcohols/2S-pentan-2-ol.cml0000644000175000017500000000633310662517661025205 0ustar georgeskgeorgesk (2S)-Pentan-2-ol 88.1482 88.0888150 118 chemical-structures-2.2.dfsg.0.orig/src/alcohols/2-methylbutan-2-ol.cml0000644000175000017500000000657710662517661026143 0ustar georgeskgeorgesk 2-Methylbutan-2-ol 88.1482 88.0888150 -10 102 chemical-structures-2.2.dfsg.0.orig/src/alcohols/2R_3R_4R_5S-hexane-1_2_3_4_5_6-hexol.cml0000644000175000017500000001035110662517661030505 0ustar georgeskgeorgesk (2R,3R,4R,5S)-Hexane-1,2,3,4,5,6-hexol 182.1718 182.0790382 99 chemical-structures-2.2.dfsg.0.orig/src/alcohols/2-methylpropan-2-ol.cml0000644000175000017500000000601710662517661026316 0ustar georgeskgeorgesk 2-Methylpropan-2-ol 74.1216 74.0731649 24 82 chemical-structures-2.2.dfsg.0.orig/src/alcohols/propane-1_2_3-triol.cml0000644000175000017500000000535710662517661026270 0ustar georgeskgeorgesk Propane-1,2,3-triol 92.0938 92.0473441 19 chemical-structures-2.2.dfsg.0.orig/src/alcohols/decan-1-ol.cml0000644000175000017500000001224010662517661024501 0ustar georgeskgeorgesk Decan-1-ol 158.2811 158.1670653 6 230 chemical-structures-2.2.dfsg.0.orig/src/alcohols/ethane-1_2-diol.cml0000644000175000017500000000464610662517661025444 0ustar georgeskgeorgesk Ethane-1,2-diol 62.0678 62.0367794 -13 197 chemical-structures-2.2.dfsg.0.orig/src/alcohols/2-thioethanol.cml0000644000175000017500000000464610662517661025351 0ustar georgeskgeorgesk 2-Thioethanol 78.1334 78.0139358 -100 157 chemical-structures-2.2.dfsg.0.orig/src/alcohols/2S-butan-2-ol.cml0000644000175000017500000000554210662517661025032 0ustar georgeskgeorgesk (2S)-Butan-2-ol 74.1216 74.0731649 99 chemical-structures-2.2.dfsg.0.orig/src/alcohols/2S-octan-2-ol.cml0000644000175000017500000001045510662517661025024 0ustar georgeskgeorgesk (2S)-Octan-2-ol 130.2279 130.1357652 175 chemical-structures-2.2.dfsg.0.orig/src/alcohols/3S-octan-3-ol.cml0000644000175000017500000001046110662517661025023 0ustar georgeskgeorgesk (3S)-Octan-3-ol 130.2279 130.1357652 175 chemical-structures-2.2.dfsg.0.orig/src/alcohols/2R-butan-2-ol.cml0000644000175000017500000000554210662517661025031 0ustar georgeskgeorgesk (2R)-Butan-2-ol 74.1216 74.0731649 99 chemical-structures-2.2.dfsg.0.orig/src/alcohols/but-2-yne-1_4-diol.cml0000644000175000017500000000523710662517661025721 0ustar georgeskgeorgesk But-2-yne-1,4-diol 86.0892 86.0367794 56 238 chemical-structures-2.2.dfsg.0.orig/src/alcohols/nonan-1-ol.cml0000644000175000017500000001145210662517661024544 0ustar georgeskgeorgesk Nonan-1-ol 144.2545 144.1514153 -6 214 chemical-structures-2.2.dfsg.0.orig/src/alcohols/3S-hexan-3-ol.cml0000644000175000017500000000712010662517661025020 0ustar georgeskgeorgesk (3S)-Hexan-3-ol 102.1748 102.1044651 134 chemical-structures-2.2.dfsg.0.orig/src/alcohols/hexan-1-ol.cml0000644000175000017500000000734710662517661024546 0ustar georgeskgeorgesk Hexan-1-ol 102.1748 102.1044651 -52 156 chemical-structures-2.2.dfsg.0.orig/src/alcohols/Z-hex-3-en-1-ol.cml0000644000175000017500000000652010662517661025166 0ustar georgeskgeorgesk (Z)-Hex-3-en-1-ol 100.1589 100.0888150 156 chemical-structures-2.2.dfsg.0.orig/src/alcohols/CMakeLists.txt0000644000175000017500000000712411112716045024715 0ustar georgeskgeorgesk################################################################# # Local variables settings # ################################################################# set(CHEM_GROUP "alcohols") message(STATUS "Generating ${CHEM_GROUP} Makefile") set(level "1") set(index_files "") set(chemical_structure_files "") set(chemical_data_files "") add_custom_target(${CHEM_GROUP} ALL) ################################################################# # Index file handle # ################################################################# foreach(lang ${AVAILABLE_LANG}) set(index_files ${index_files} "${CMAKE_CURRENT_BINARY_DIR}/index_${lang}.html") endforeach(lang) ################################################################# # Structure file handle # ################################################################# file(GLOB cml_SRCS *.cml) set(chemical_structure_files "") foreach(cml_SRC_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_SRC_FILE} NAME_WE) set(cml_FILE "${cml_WE}.cml") # add custom command to build mol files add_custom_command(TARGET ${CHEM_GROUP} COMMAND cp ${cml_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_FILE}") if(OPENBABEL2_EXECUTABLE_FOUND) # Generate mol files set(mol_FILE "${cml_WE}.mol") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -omol ${mol_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -osmi ${smi_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${smi_FILE}") endif(OPENBABEL2_EXECUTABLE_FOUND) endforeach(cml_SRC_FILE) ################################################################# # Chemical datafile handle # ################################################################# foreach(cml_FILE ${cml_SRCS}) get_filename_component(cml_WE ${cml_FILE} NAME_WE) foreach(lang ${AVAILABLE_LANG}) set(chemical_data_files ${chemical_data_files} "${CMAKE_CURRENT_BINARY_DIR}/${cml_WE}_${lang}.html") endforeach(lang) endforeach(cml_FILE) ################################################################# # Build XHTML files # ################################################################# add_custom_command(TARGET ${CHEM_GROUP} COMMAND ${PYTHON_EXECUTABLE} ${MAKEXHTMLFILES} ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/index.xml ${level} ${AVAILABLE_LANG} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) ################################################################# # Install files # ################################################################# install(FILES ${index_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_structure_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) install(FILES ${chemical_data_files} DESTINATION ${SHARE_HOME}/${CHEM_GROUP}) chemical-structures-2.2.dfsg.0.orig/src/alcohols/2_2_2-trifluoroethanol.cml0000644000175000017500000000447610662517661027076 0ustar georgeskgeorgesk 2,2,2-Trifluoroethanol 100.0398 100.0135994 -45 76 chemical-structures-2.2.dfsg.0.orig/src/alcohols/ethanol.cml0000644000175000017500000000443010662517661024315 0ustar georgeskgeorgesk Ethanol 46.0684 46.0418648 -114 78 chemical-structures-2.2.dfsg.0.orig/src/alcohols/pentan-1-ol.cml0000644000175000017500000000656510662517661024731 0ustar georgeskgeorgesk Pentan-1-ol 88.1482 88.0888150 -78 137 chemical-structures-2.2.dfsg.0.orig/src/alcohols/cyclohexanol.cml0000644000175000017500000000703210662517661025354 0ustar georgeskgeorgesk Cyclohexanol 100.1589 100.0888150 23 160 chemical-structures-2.2.dfsg.0.orig/src/alcohols/pentan-3-ol.cml0000644000175000017500000000631010662517661024717 0ustar georgeskgeorgesk Pentan-3-ol 88.1482 88.0888150 115 chemical-structures-2.2.dfsg.0.orig/src/alcohols/1_1_1_3_3_3-hexafluoropropan-2-ol.cml0000644000175000017500000000531310662517661030513 0ustar georgeskgeorgesk 1,1,1,3,3,3-Hexafluoropropan-2-ol 168.0378 168.0009840 -4 59 chemical-structures-2.2.dfsg.0.orig/src/alcohols/2-aminoethanol.cml0000644000175000017500000000455610662517661025511 0ustar georgeskgeorgesk 2-Aminoethanol 61.0831 61.0527638 10 chemical-structures-2.2.dfsg.0.orig/src/alcohols/propan-2-ol.cml0000644000175000017500000000522110662517661024730 0ustar georgeskgeorgesk Propan-2-ol 60.0950 60.0575149 -89 82 chemical-structures-2.2.dfsg.0.orig/src/alcohols/heptan-4-ol.cml0000644000175000017500000001014110662517661024707 0ustar georgeskgeorgesk Heptan-4-ol 116.2013 116.1201151 -42 155 chemical-structures-2.2.dfsg.0.orig/src/alcohols/2S_3R-butane-1_2_3_4-tetrol.cml0000644000175000017500000000663610700413346027320 0ustar georgeskgeorgesk (2S,3R)-Butane-1,2,3,4-tetrol 122.1198 122.0579088 121 330 chemical-structures-2.2.dfsg.0.orig/src/alcohols/2S-heptan-2-ol.cml0000644000175000017500000000770610662517661025204 0ustar georgeskgeorgesk (2S)-Heptan-2-ol 116.2013 116.1201151 161 chemical-structures-2.2.dfsg.0.orig/src/alcohols/3S-heptan-3-ol.cml0000644000175000017500000000770210662517661025202 0ustar georgeskgeorgesk (3S)-Heptan-3-ol 116.2013 116.1201151 156 chemical-structures-2.2.dfsg.0.orig/src/alcohols/propan-1-ol.cml0000644000175000017500000000522310662517661024731 0ustar georgeskgeorgesk Propan-1-ol 60.0950 60.0575149 -131 97 chemical-structures-2.2.dfsg.0.orig/src/alcohols/methanol.cml0000644000175000017500000000365210662517661024477 0ustar georgeskgeorgesk Methanol 32.0419 32.0262147 -98 64 chemical-structures-2.2.dfsg.0.orig/src/alcohols/cyclopentanol.cml0000644000175000017500000000624510662517661025543 0ustar georgeskgeorgesk Cyclopentanol 86.1323 86.0731649 -19 140 chemical-structures-2.2.dfsg.0.orig/src/htdocs/0000755000175000017500000000000011225622315021632 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/src/htdocs/notices.html0000644000175000017500000000647611225117604024201 0ustar georgeskgeorgesk The Chemical Structures Project -- Notices

License

Copyright 2006-2009 The Chemical Structures Project. All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
are met:
1. Redistributions of source code must retain the above copyright
   notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright
   notice, this list of conditions and the following disclaimer in the
   documentation and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE CHEMICAL STRUCTURES PROJECT ``AS IS'' AND ANY
EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE CHEMICAL STRUCTURES PROJECT OR CONTRIBUTORS
BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Contributions

The Chemical Structures project could not succeed without the involvement of the following contributors:

  • Jean Bréfort
  • I-Yuan Chiang
  • Georges Khaznadar
  • Jérôme Kieffer
  • Patrick Lax
  • Carsten Niehaus
  • Noel O'Boyle
  • Egon Willighagen

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chemical-structures-2.2.dfsg.0.orig/src/htdocs/CMakeLists.txt0000644000175000017500000000230411225131563024371 0ustar georgeskgeorgesk################################################################# # Local variable settings # ################################################################# set(LOCAL_TARGET htdocs) message(STATUS "Generating ${LOCAL_TARGET} Makefile") file(GLOB htdocs_SRCS *.html) set(htdocs_files "") add_custom_target(${LOCAL_TARGET} ALL) ################################################################# # htdocs file handle # ################################################################# foreach(htdocs_SRC_FILE ${htdocs_SRCS}) get_filename_component(htdocs_FILE ${htdocs_SRC_FILE} NAME) add_custom_command(TARGET ${LOCAL_TARGET} COMMAND cp ${htdocs_SRC_FILE} ${CMAKE_CURRENT_BINARY_DIR}/${htdocs_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) set(htdocs_files ${htdocs_files} ${htdocs_FILE}) endforeach(htdocs_SRC_FILE) ################################################################# # Install files # ################################################################# install(FILES ${htdocs_files} DESTINATION ${SHARE_HOME}/htdocs) chemical-structures-2.2.dfsg.0.orig/VERSION0000644000175000017500000000000411225116471020622 0ustar georgeskgeorgesk2.2 chemical-structures-2.2.dfsg.0.orig/tools/0000755000175000017500000000000011225622315020717 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/tools/l10nhandler.py0000644000175000017500000000537610725742137023425 0ustar georgeskgeorgesk"""L10N file handler for Python. Exported classes: L10NHandler - L10N file handler. """ import xml.sax.handler class L10NHandler(xml.sax.handler.ContentHandler): """Class for receiving logical L10N content events. It supports L10N entities as defined in the following file: xml/l10n.dtd The order of event in this class mirrors the order of the information in the document. """ def __init__(self): """Creates an instance of the L10NHandler class. The function set the object attributes with default values. """ self.msgDict = {} self.msgid = "" self.inMsgid = False self.msg = "" self.msgLang ="" self.inMsg = False def startElement(self, name, attributes): """Signals the start of an element. The function set a variable depending on the element and the attribut. Parameters: name - contains the raw CML name of the element type as a string. attributes - contains an instance of the Attributes class. """ if name == "msgid": self.inMsgid = True if name == "msg": if attributes.has_key('xml:lang'): self.msgLang = unicode.encode(attributes["xml:lang"]) else: self.msgLang = "en" self.inMsg = True def characters(self, data): """Receives notification of character data. The parser will call this method to report each chunk of character data. Parameters: data - contains the chunk of character data. """ if self.inMsgid: self.msgid += data if self.inMsg: self.msg += data def endElement(self,name): """Signals the end of an element in non-namespace mode. Parameters: name - contains the name of the element type. """ if name == "msgid": self.inMsgid = False self.msgDict[self.msgid] = {} if name == "msg": self.inMsg = False self.msgDict[self.msgid][self.msgLang] = self.msg self.msgLang = "" self.msg = "" if name == "msgset": self.msgid = "" def translate(self, msgid, lang): """Translates a string Parameters: msgid - contains the msgid to translate. lang - contains the destination language. Returns: a string - either the translated string if the translation is available or the msgid in other cases. """ if self.msgDict.has_key(msgid) and self.msgDict[msgid].has_key(lang): return self.msgDict[msgid][lang] else: return msgid chemical-structures-2.2.dfsg.0.orig/tools/cmlwriter.py0000644000175000017500000002314411225116347023310 0ustar georgeskgeorgesk"""CML2XHTML converter for Python This module provides a convenient way to transform CML to XHTML. Exported classes: CMLWriter - Write a XHTML file with the content of a CML file """ import xhtmlwriter import os class CMLWriter: """ """ def __init__(self, fout, cml_handler, l10n_handler): """Creates an instance of the CMLWriter class. """ self.fout = fout self.cml = cml_handler self.l10n = l10n_handler def parseFormula(self, raw_formula): """Parse formula and return the HTML formula """ formula = raw_formula.strip() formula_ar = formula.split(" ") formula = "" idx = 0 subBool = False for i in formula_ar: if i == "1": idx += 1 elif idx % 2: # we are in the multiple section" formula += "" + i + "" idx += 1 else: # we are in the element section formula += i idx += 1 return formula def WriteXHTML(self, entry_details, lang, level): if entry_details.name.has_key(lang): title = entry_details.name[lang] else: title = entry_details.name['en'] cml_file = entry_details.path + '.cml' mol_file = entry_details.path + '.mol' smi_file = entry_details.path + '.smi' smiles = "" if os.path.isfile(smi_file): smiles_fin = open(smi_file,'r') smiles = smiles_fin.readline() idx = smiles.find("\t") smiles = smiles[:idx] smiles_fin.close() xhtmlout = xhtmlwriter.XHTMLWriter() xhtmlout.setOutput(self.fout) xhtmlout.setTitle(title) xhtmlout.addHead(' ') xhtmlout.addHead(' ') xhtmlout.addHead(' ') xhtmlout.addBody(' ') xhtmlout.addBody(' ') xhtmlout.addBody('
') xhtmlout.addBody('
') xhtmlout.addBody('
') xhtmlout.addBody('

' + self.l10n.translate('Properties', lang) + '

') xhtmlout.addBody('
    ') xhtmlout.addBody('
  • ' + self.l10n.translate('Name: ', lang) + title + '
    • ') xhtmlout.addBody('
  • ' + self.l10n.translate('IUPAC name: ', lang) + self.cml.name + '
    • ') xhtmlout.addBody('
  • ' + self.l10n.translate('Formula: ', lang) + self.parseFormula(self.cml.formula) + '
    • ') xhtmlout.addBody('
  • ' + self.l10n.translate('Molecular weight: ', lang) + self.cml.weight + ' g/mol
    • ') xhtmlout.addBody('
  • ' + self.l10n.translate('Monoisotopic weight: ', lang) + self.cml.monoisotopic_weight + ' g/mol
    • ') if self.cml.mpSet: if self.cml.mp.count(">"): mp = self.cml.mp.replace(">","").strip() mpK = str(int(mp) + 273) else: mpK = str(int(self.cml.mp) + 273) xhtmlout.addBody('
  • ' + self.l10n.translate('Melting point: ', lang) + self.cml.mp + ' °C ('+ mpK + ' K)
    • ') if self.cml.bpSet: if self.cml.bp.count(">"): bp = self.cml.bp.replace(">","").strip() bpK = str(int(bp) + 273) else: bpK = str(int(self.cml.bp) + 273) xhtmlout.addBody('
  • ' + self.l10n.translate('Boiling point: ', lang) + self.cml.bp + ' °C (' + bpK + ' K)
    • ') ######################################################### # Writing synonyms # # Write only if synonyms (localized or english) are # available ######################################################### if entry_details.synDict.has_key(lang): if len(entry_details.synDict[lang]) == 1: xhtmlout.addBody('
  • ' + self.l10n.translate('Synonym:', lang) ) else: xhtmlout.addBody('
  • ' + self.l10n.translate('Synonyms:', lang) ) xhtmlout.addBody('
      ') for synonym in entry_details.synDict[lang]: xhtmlout.addBody('
    • ' + synonym + '
      • ') xhtmlout.addBody('
    ') xhtmlout.addBody('
    • ') elif entry_details.synDict.has_key('en'): if len(entry_details.synDict['en']) == 1: xhtmlout.addBody('
  • ' + self.l10n.translate('Synonym:', lang) ) else: xhtmlout.addBody('
  • ' + self.l10n.translate('Synonyms:', lang) ) xhtmlout.addBody('
      ') for synonym in entry_details.synDict['en']: xhtmlout.addBody('
    • ' + synonym + ' (en)
      • ') xhtmlout.addBody('
    ') xhtmlout.addBody('
    • ') ######################################################### # Writing abbreviations # # Write only if abbreviations are available ######################################################### if len(entry_details.abbreviation): if len(entry_details.abbreviation) == 1: xhtmlout.addBody('
  • ' + self.l10n.translate('Abbreviation:', lang) ) else: xhtmlout.addBody('
  • ' + self.l10n.translate('Abbreviations:', lang) ) xhtmlout.addBody('
      ') for abbreviation in entry_details.abbreviation: xhtmlout.addBody('
    • ' + abbreviation + '
      • ') xhtmlout.addBody('
    ') xhtmlout.addBody('
    • ') xhtmlout.addBody('
') xhtmlout.addBody('
') xhtmlout.addBody('
') xhtmlout.addBody('

' + self.l10n.translate('Structure', lang) + '

') xhtmlout.addBody(' ') xhtmlout.addBody('
') xhtmlout.addBody('
') xhtmlout.addBody('

' + self.l10n.translate('Structure Download', lang) + '

') xhtmlout.addBody('
    ') xhtmlout.addBody('
  • ' + self.l10n.translate('In CML format', lang) + ' Download cml file
    • ') if os.path.isfile(mol_file): xhtmlout.addBody('
  • ' + self.l10n.translate('In MOL format', lang) + ' Download mol file
    • ') xhtmlout.addBody('
') xhtmlout.addBody('
') xhtmlout.addBody('
') xhtmlout.addBody('

' + self.l10n.translate('InChI', lang) + '

') if len(self.cml.inchi) > 80: htmlinchi = "" size = int(len(self.cml.inchi)/80) for i in range(0,size): htmlinchi += self.cml.inchi[i*80:(i+1)*80] + "
\n" htmlinchi += self.cml.inchi[size*80:len(self.cml.inchi)] else: htmlinchi = self.cml.inchi xhtmlout.addBody(' ' + htmlinchi + '') xhtmlout.addBody('
') if smiles: xhtmlout.addBody('
') xhtmlout.addBody('

' + self.l10n.translate('SMILES', lang) + '

') if len(smiles) > 80: htmlsmiles = "" size = int(len(smiles)/80) for i in range(0,size): htmlsmiles += smiles[i*80:(i+1)*80] + "
\n" htmlsmiles += smiles[size*80:len(smiles)] else: htmlsmiles = smiles xhtmlout.addBody(' ' + htmlsmiles + '') xhtmlout.addBody('
') xhtmlout.addBody('
') xhtmlout.addBody('
') xhtmlout.addFooter('

Legal Notices

') xhtmlout.write() chemical-structures-2.2.dfsg.0.orig/tools/cmlhandler.py0000644000175000017500000000676111225106270023411 0ustar georgeskgeorgesk"""CML file handler for Python. This module provides an xml handler for CML file. Exported classes: CMLHandler - CML file handler. """ import sys import xml.sax.handler class CMLHandler(xml.sax.handler.ContentHandler): """Class for receiving logical CML content events. It supports CML entities as defined by the 2.0 version. For more details, see http://www.xml-cml.org/ The order of event in this class mirrors the order of the information in the document. """ def __init__(self): """Creates an instance of the CMLHandler class. Set the object attributes with default values. """ self.id = "" self.formula = "" self.inchi = "InChI=" self.smiles = "" self.name = "" self.inName = False self.weight = "" self.inWeight = False self.monoisotopic_weight = "" self.inMonoisotopicWeight = False self.mp = "" self.mpSet = False self.inMp = False self.bp = "" self.inBp = False self.bpSet = False def startElement(self, name, attributes): """Signals the start of an element. The function set a variable depending on the element and the attributes. Parameters: name - contains the raw CML name of the element type as a string. attributes - contains an instance of the Attributes class. """ if name == "molecule": self.id = attributes["id"] if name == "formula": self.formula = attributes["concise"] if name == "identifier": self.inIdentifier = True if attributes["convention"] == "iupac:inchi": self.inchi += attributes["value"] if name == "name": self.inName = True if name == "scalar": if attributes["dictRef"] == "cml:molwt": self.inWeight = True elif attributes["dictRef"] == "cml:monoisotopicwt": self.inMonoisotopicWeight = True elif attributes["dictRef"] == "cml:mp": self.inMp = True elif attributes["dictRef"] == "cml:bp": self.inBp = True def characters(self, data): """Receives notification of character data. The parser will call this method to report each chunk of character data. Parameters: data - contains the chunk of character data. """ if self.inName: self.name += data if self.inWeight: self.weight += data if self.inMonoisotopicWeight: self.monoisotopic_weight += data if self.inMp: self.mp += data if self.inBp: self.bp += data def endElement(self,name): """Signals the end of an element. Parameters: name - contains the name of the element type. """ if name == "name": self.inName = False if name == "scalar": if self.inWeight: self.inWeight = False elif self.inMonoisotopicWeight: self.inMonoisotopicWeight = False elif self.inMp: self.inMp = False self.mp = self.mp.strip() if self.mp: self.mpSet = True elif self.inBp: self.inBp = False self.bp = self.bp.strip() if self.bp: self.bpSet = True chemical-structures-2.2.dfsg.0.orig/tools/indexwriter.py0000644000175000017500000001072211225116347023642 0ustar georgeskgeorgeskimport xhtmlwriter class IndexWriter: """Class for creating an index file """ def __init__(self, fout, index_handler, l10n_handler): """Creates an instance of the class. """ self.fout = fout self.index = index_handler self.l10n = l10n_handler def WriteXHTML(self, index_title, lang, level): """ """ xhtmlout = xhtmlwriter.XHTMLWriter() xhtmlout.setOutput(self.fout) if index_title.has_key(lang): xhtmlout.setTitle(index_title[lang]) else: xhtmlout.setTitle(index_title['en']) xhtmlout.addHead(' ') xhtmlout.addHead(' ') xhtmlout.addBody(' ') xhtmlout.addBody(' ') xhtmlout.addBody('
') """ Create a list of directories """ if len(self.index.entryList["dir"]) > 0: # Order the entry list by alphabetic order entryDict = {} for entry in self.index.entryList["dir"]: if entry.name.has_key(lang): entryDict[entry.name[lang]] = entry else: entryDict[entry.name['en']] = entry keys = entryDict.keys() keys.sort() xhtmlout.addBody('
') xhtmlout.addBody('

'+ self.l10n.translate("Directories", lang) +'

') xhtmlout.addBody(' ') xhtmlout.addBody('
') """ Create list of files """ if len(self.index.entryList["file"]) > 0: # Order the entry list by alphabetic order entryDict = {} for entry in self.index.entryList["file"]: if entry.name.has_key(lang): entryDict[entry.name[lang]] = entry else: entryDict[entry.name['en']] = entry keys = entryDict.keys() keys.sort() xhtmlout.addBody('
') xhtmlout.addBody('

' + self.l10n.translate("Names", lang) + '

') xhtmlout.addBody(' ') xhtmlout.addBody('
') xhtmlout.addBody('
') xhtmlout.addFooter('

Legal Notices

') xhtmlout.write() chemical-structures-2.2.dfsg.0.orig/tools/nameindexwriter.py0000644000175000017500000000367511112525053024505 0ustar georgeskgeorgeskimport xhtmlwriter class DataIndexWriter: def __init__(self, fout, data_list, l10n_handler): self.fout = fout self.data_list = data_list self.l10n = l10n_handler def WriteXHTML(self, title, lang): size = len(self.data_list) xhtmlout = xhtmlwriter.XHTMLWriter() xhtmlout.setOutput(self.fout + "_" + lang + ".html") xhtmlout.setTitle(title) xhtmlout.addHead(' ') xhtmlout.addHead(' ') xhtmlout.addBody(' ') xhtmlout.addBody(' ') xhtmlout.addBody('
') xhtmlout.addBody('
') xhtmlout.addBody(' ') for i in range(0, size): xhtmlout.addBody(' ') xhtmlout.addBody(' ') xhtmlout.addBody(' ') xhtmlout.addBody('
' + self.data_list[i][0] + '
') xhtmlout.addBody('
') xhtmlout.addBody('
') xhtmlout.write() chemical-structures-2.2.dfsg.0.orig/tools/make_index_files.py0000644000175000017500000000641711145307406024571 0ustar georgeskgeorgesk#!/usr/bin/python """This file generates the index filesi in the top directory: - src/name_index_lang.html - src/raw_formula_lang.html - src/index_lang.html """ import sys import os import xml.sax import l10nhandler import indexhandler import indexwriter import nameindexwriter import formulaindexwriter def get_formula_ar(file): fin = open(unicode.encode(file) + ".cml", 'r') for line in fin: if line.count("formula concise"): idx = line.find('=') + 2 line = line[idx:] idx = line.find('"') formula = line[:idx].strip() formula_ar = formula.split(" ") return formula_ar return [] def formulaCmp(tuple1, tuple2): formula1 = tuple1[0][0] formula2 = tuple2[0][0] if formula1 == formula2: return 0 count = min( len(formula1), len(formula2) ) for i in range(0, count): if i%2: if cmp( int(formula1[i]), int(formula2[i]) ) != 0: return cmp( int(formula1[i]), int(formula2[i]) ) else: if cmp( formula1[i],formula2[i]) != 0: return cmp( formula1[i], formula2[i] ) return cmp( len(formula1), len(formula2) ) sourceDir = sys.argv[1] if not os.path.isdir(sourceDir): print "Error: "+ sourceDir + ": no such directory" sys.exit(1) indexFile = sys.argv[2] level = int(sys.argv[3]) langList = sys.argv[4:] skip_dir = ['jmol','images','styles'] current_binary_dir = os.path.abspath(os.curdir) os.chdir(sourceDir + os.path.sep + "src") src_list = os.listdir(os.curdir) name_list = [] formula_list = [] # Parse l10n.xml for l10n support l10n_parser = xml.sax.make_parser() l10n_handler = l10nhandler.L10NHandler() l10n_parser.setContentHandler(l10n_handler) l10n_file = sourceDir + os.path.sep + "xml" + os.path.sep + "l10n.xml" l10n_parser.parse(l10n_file) # find the index.xml files in the subdirectories and index the data for dir in src_list: if os.path.isdir(dir) and dir not in skip_dir: os.chdir(dir) if os.path.isfile("index.xml"): index_parser = xml.sax.make_parser() index_parser.setFeature(xml.sax.handler.feature_external_ges, 0) index_handler = indexhandler.IndexHandler() index_parser.setContentHandler(index_handler) print os.path.realpath(os.path.curdir) index_parser.parse("index.xml") for entry in index_handler.entryList["file"]: name_list.append( (entry.name["en"], "./" + dir +"/" + entry.path) ) formula_list.append( [(get_formula_ar(entry.path), "./" + dir +"/" + entry.path), entry.name["en"] ]) os.chdir(os.pardir) os.chdir(current_binary_dir) name_list.sort() formula_list.sort(formulaCmp) data_index = nameindexwriter.DataIndexWriter("name_index",name_list,l10n_handler) formula_index = formulaindexwriter.DataIndexWriter("formula_index",formula_list,l10n_handler) # parse the top index file index_parser = xml.sax.make_parser() index_parser.setFeature(xml.sax.handler.feature_external_ges, 0) index_handler = indexhandler.IndexHandler() index_parser.setContentHandler(index_handler) index_parser.parse(indexFile) index = indexwriter.IndexWriter(indexFile,index_handler,l10n_handler) for lang in langList: data_index.WriteXHTML("Name index", lang) formula_index.WriteXHTML("Formula index", lang) index = indexwriter.IndexWriter("index_" + lang + ".html",index_handler,l10n_handler) index.WriteXHTML(index_handler.title,lang,level) chemical-structures-2.2.dfsg.0.orig/tools/xhtmlwriter.py0000644000175000017500000000254411225106270023664 0ustar georgeskgeorgeskimport codecs class XHTMLWriter: def __init__(self): self.fout = "" self.title = "" self.stylesheet = "" self.head = "" self.body = "" self.footer = "" def setOutput(self, fout): self.fout = fout def setTitle(self, title): self.title = title def addHead(self, line): self.head = self.head + line + "\n" def addBody(self, line): self.body = self.body + line + "\n" def addFooter(self, line): self.footer = self.footer + line + "\n" def write(self): out = codecs.open(self.fout, encoding='utf-8', mode='w') out.write('' + "\n") out.write('' + "\n") out.write('' + "\n") out.write(' ' + "\n") out.write(' ' + "\n") out.write(' '+self.title+'' + "\n") out.write(self.head) out.write(' ' + "\n") out.write(' ' + "\n") out.write(self.body) out.write(' ' + "\n") out.write(' ' + "\n") out.write(' ' + "\n") out.write('') out.close() chemical-structures-2.2.dfsg.0.orig/tools/indexhandler.py0000644000175000017500000001317211225106270023737 0ustar georgeskgeorgesk"""Index file handler for Python. Exported classes: Entry - a entry class. IndexHandler - Index file handler. """ import xml.sax.handler class Entry: """Class for common index entry. It contains each feature of an entry element. """ def __init__(self): """Creates an instance of the Entry class. Set the object attributes with default values. """ self.id = "" self.name = {} self.path = "" self.synDict = {} self.abbreviation = [] self.authors = "" self.date = "" class IndexHandler(xml.sax.handler.ContentHandler): """Class for receiving logical Index content events. It supports Index entities as defined in the project's DTD. For more details, see xml/index.dtd """ def __init__(self): """Creates an instance of the IndexHandler class. Set the object attributes with default values. """ self.title = {} self.titleLang = "" self.inTitle = False self.entry = None self.entryList = {'dir': [], 'file': []} self.inEntry = False self.nameLang = "" self.inName = False self.inDirname = False self.inFilename = False self.type = None self.synonym = "" self.synLang = "" self.inSynonym = False self.abbreviation = "" self.inAbbreviation = False self.inAuthors = False self.inDate = False def startElement(self, name, attributes): """Signals the start of an element. The function set a variable depending on the element and the attribut. Parameters: name - contains the element name as a string. attributes - contains an instance of the Attributes class. """ if name == "title": self.inTitle = True if attributes.has_key("xml:lang"): self.titleLang = unicode.encode(attributes["xml:lang"]) if self.titleLang == "": self.titleLang = "en" else: self.titleLang = "en" self.title[self.titleLang] = "" if name == "entry": self.inEntry = True self.entry = Entry() if name == "name": self.inName = True if attributes.has_key("xml:lang"): self.nameLang = unicode.encode(attributes["xml:lang"]) if self.nameLang == "": self.nameLang = "en" else: self.nameLang = "en" self.entry.name[self.nameLang] = "" if name == "dirname": self.inDirname = True self.type = "dir" if name == "filename": self.inFilename = True self.type = "file" if name == "synonym": self.inSynonym = True if attributes.has_key("xml:lang"): self.synLang = unicode.encode(attributes["xml:lang"]) if self.synLang == "": self.synLang = "en" else: self.synLang ="en" if not self.entry.synDict.has_key(self.synLang): self.entry.synDict[self.synLang] = [] if name == "abbrev": self.inAbbreviation = True if name == "authors": self.inAuthors = True if name == "date": self.inDate = True def characters(self, data): """Receives notification of character data. The parser will call this method to report each chunk of character data. Parameters: data - contains the chunk of character data. """ if self.inTitle: self.title[self.titleLang] += data elif self.inName: self.entry.name[self.nameLang] += data elif self.inDirname: self.entry.path += data elif self.inFilename: self.entry.path += data elif self.inSynonym: self.synonym += data elif self.inAbbreviation: self.abbreviation += data elif self.inAuthors: self.entry.authors += data elif self.inDate: self.entry.date += data def endElement(self,name): """Signals the end of an element. Parameters: name - contains the name of the element type. """ if name == "title": self.inTitle = False self.titleLang = "" elif name == "entry": if self.type == "file": self.entryList["file"].append(self.entry) else: self.entryList["dir"].append(self.entry) self.entry = None self.inEntry = False elif name == "name": self.inName = False self.nameLang = "" elif name == "dirname": self.inDirname = False elif name == "filename": self.inFilename = False elif name == "synonym": try: self.entry.synDict[self.synLang].append(self.synonym) except: sys.stderr.write("[ERROR] Could not append the " \ + "synonym to " % (self.synonym) \ + "the %s dictionary.\n" % (self.synLang)) self.synonym = "" self.inSynonym = False self.synLang = "" elif name == "abbrev": self.inAbbreviation = False self.entry.abbreviation.append(self.abbreviation) self.abbreviation = "" elif name == "authors": self.inAuthors = False elif name == "date": self.inDate = False chemical-structures-2.2.dfsg.0.orig/tools/make_xhtml_files.py0000644000175000017500000000354611225106270024611 0ustar georgeskgeorgesk#!/usr/bin/python """This module can transform index file into xhtml file No class or function are defined """ import sys import os import xml.sax import l10nhandler import indexhandler import indexwriter import cmlhandler import cmlwriter source_dir = sys.argv[1] if not os.path.isdir(source_dir): sys.stderror.write("[ERROR] %s: no such directory.\n" % (source_dir)) sys.exit(1) indexFile = sys.argv[2] level = int(sys.argv[3]) langList = sys.argv[4:] # Get the level into CMake ? root = os.path.realpath(os.curdir) if os.path.isfile(indexFile): # Parse l10n.xml for l10n support l10n_parser = xml.sax.make_parser() l10n_handler = l10nhandler.L10NHandler() l10n_parser.setContentHandler(l10n_handler) l10n_parser.parse(source_dir + "/xml/l10n.xml") # Parse index file index_parser = xml.sax.make_parser() index_parser.setFeature(xml.sax.handler.feature_external_ges, 0) index_handler = indexhandler.IndexHandler() index_parser.setContentHandler(index_handler) index_parser.parse(indexFile) index = indexwriter.IndexWriter(indexFile,index_handler,l10n_handler) for lang in langList: index = indexwriter.IndexWriter("index_" + lang \ + ".html",index_handler,l10n_handler) index.WriteXHTML(index_handler.title,lang,level) # Add dir entry to the index file for index_entry in index_handler.entryList["file"]: if index_entry.path != "" and os.path.isfile(index_entry.path + ".cml"): cml_parser = xml.sax.make_parser() cml_handler = cmlhandler.CMLHandler() cml_parser.setContentHandler(cml_handler) cml_parser.parse(index_entry.path + ".cml") for lang in langList: cml = cmlwriter.CMLWriter(index_entry.path + "_" + lang \ + ".html", cml_handler,l10n_handler) cml.WriteXHTML(index_entry,lang,level) chemical-structures-2.2.dfsg.0.orig/tools/formulaindexwriter.py0000644000175000017500000000615011112525053025221 0ustar georgeskgeorgeskimport xhtmlwriter class DataIndexWriter: def __init__(self, fout, data_list, l10n_handler): self.fout = fout self.data_list = data_list self.l10n = l10n_handler def get_formula(self, formula_ar): formula = "" idx = 0 subBool = False for i in formula_ar: if i == "1": idx += 1 continue if idx % 2: formula += "" + i subBool = True idx += 1 else: if subBool: formula += "" subBool = False formula += i idx += 1 if subBool: formula += "" return formula def WriteXHTML(self, title, lang): size = len(self.data_list)/3 if len(self.data_list) % 3: size += 1 xhtmlout = xhtmlwriter.XHTMLWriter() xhtmlout.setOutput(self.fout + "_" + lang + ".html") xhtmlout.setTitle(title) xhtmlout.addHead(' ') xhtmlout.addHead(' ') xhtmlout.addBody(' ') xhtmlout.addBody(' ') xhtmlout.addBody('
') xhtmlout.addBody('
') xhtmlout.addBody(' ') for i in range(0, size): xhtmlout.addBody(' ') xhtmlout.addBody(' ') if (size + i) < len(self.data_list): xhtmlout.addBody(' ') else: xhtmlout.addBody(' ') if (2*size + i) < len(self.data_list): xhtmlout.addBody(' ') else: xhtmlout.addBody(' ') xhtmlout.addBody(' ') xhtmlout.addBody('
' + self.get_formula(self.data_list[i][0][0]) + '' + self.get_formula(self.data_list[size+i][0][0]) + '' + self.get_formula(self.data_list[2*size+i][0][0]) + '
') xhtmlout.addBody('
') xhtmlout.addBody('
') xhtmlout.write() chemical-structures-2.2.dfsg.0.orig/cmake/0000755000175000017500000000000011225622315020637 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/cmake/modules/0000755000175000017500000000000011225622315022307 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/cmake/modules/FindOpenBabel2Exe.cmake0000644000175000017500000000226410627064724026502 0ustar georgeskgeorgesk# - Find OpenBabel2 executable # This module find if OpenBabel2 executable is installed and determines where # the executable is. It sets the following variables: # # OPENBABEL2_EXECUTABLE_FOUND - set to true if the OpenBabel2 executable is # found # OPENBABEL2_EXECUTABLE - path to OpenBabel2 executable # Copyright (c) 2007 Jerome Pansanel # # Redistribution and use is allowed according to the terms of the BSD license. # For details see the accompanying COPYING file. IF( OPENBABEL2_EXECUTABLE ) # in cache already SET( OPENBABEL2_EXECUTABLE_FOUND TRUE ) ELSE( OPENBABEL2_EXECUTABLE ) FIND_PROGRAM(OPENBABEL2_EXECUTABLE NAMES babel PATHS [HKEY_LOCAL_MACHINE\\SOFTWARE\\OpenBabel\\Current;BinPath] ) SET(OPENBABEL2_EXECUTABLE_FOUND) IF(OPENBABEL2_EXECUTABLE) SET(OPENBABEL2_EXECUTABLE_FOUND ON) ENDIF(OPENBABEL2_EXECUTABLE) ENDIF( OPENBABEL2_EXECUTABLE ) IF( NOT ${OPENBABEL2_EXECUTABLE_FOUND} ) IF( ${OPENBABEL2EXE_FIND_REQUIRED} ) MESSAGE( FATAL_ERROR "OpenBabel2 executable was not found on the system." ) ENDIF( ${OPENBABEL2EXE_FIND_REQUIRED} ) ENDIF( NOT ${OPENBABEL2_EXECUTABLE_FOUND} ) chemical-structures-2.2.dfsg.0.orig/TODO0000644000175000017500000000216511225131563020253 0ustar georgeskgeorgesk################################################################# # New molecule requests # ################################################################# Apiol Statine Serotonin AMP, ADP, ATP GMP, GDP, GTP Aminochlorothenoxazin dipanone prolidine hexalgon cyclic carbohydrates ################################################################# # Optimization # ################################################################# Get a better minimization of linolein ################################################################# # Misc # ################################################################# Add a custom clean target to the build system Add javascript that display a small help Melting point: The melting point of a crystalline solid is the temperature range at which it changes state from solid to liquid (?) write a cml parser to verify the integrity of each file: 1. parse against cml dtd 1. check the content of each field and value Add the version on the html pages chemical-structures-2.2.dfsg.0.orig/CMakeLists.txt0000644000175000017500000000300311120277442022314 0ustar georgeskgeorgeskproject(chemical-structures) set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake/modules) cmake_minimum_required(VERSION 2.4.0) ################################################################# # Define global variables # ################################################################# set(VERSION 2.2) set(AVAILABLE_LANG "en" "es" "de" "fr" "nl" "tw") set(SHARE_HOME ${CMAKE_INSTALL_PREFIX}/share/chemical-structures) ################################################################# # Python Settings # ################################################################# find_package(PythonInterp REQUIRED) set(MAKEINDEXFILES ${CMAKE_SOURCE_DIR}/tools/make_index_files.py) set(MAKEXHTMLFILES ${CMAKE_SOURCE_DIR}/tools/make_xhtml_files.py) ################################################################# # Open Babel Settings # ################################################################# find_package(OpenBabel2Exe) ################################################################# # Define global target # ################################################################# add_custom_target(clean_xhtml) add_custom_target(clean_structure) ################################################################# # Add subdirectories # ################################################################# add_subdirectory(src) chemical-structures-2.2.dfsg.0.orig/ChangeLog0000644000175000017500000004660611225131563021345 0ustar georgeskgeorgesk2009-07-08 17:00:43 Jerome Pansanel * Release 2.2 * Many fixes in tools * New htdocs/notices.html file * Compounds and directory are now sorted by alphabetic order * New version of Jmol included 2009-07-07 17:44:36 Jerome Pansanel * New categories added: Natural products Peptides * New structures added: carboxylic_acids/4-aminobutanoic_acid.cml ethers/tetrahydropyran.cml ketones/pyrrol-2-one.cml ketones/1_5-dihydro-2H-pyrrol-2-one.cml natural_products/norepinephrine.cml natural_products/coelenterazine.cml natural_products/D-luciferin.cml natural_products/R-adrenaline.cml peptides/aspartame.cml 2008-02-23 Jerome Pansanel * Traditionnal Chinese translation added 2009-02-04 Jerome Pansanel * The build system has been updated. The out-of-source build is now supported. 2008-01-03 15:05:40 Jerome Pansanel * Release 2.1 2008-01-01 13:45:18 Jerome Pansanel * Fix some html lines for xhtml1.0-strict compliancy * Many table element are replaced by div element * style.css is updated to fit new html 2007-12-10 12:54:05 Jerome Pansanel * Spanish translation available * Minor bug fixes 2007-12-06 14:34:22 Jerome Pansanel * Switch from RDFa to MicroFormat 2007-12-03 11:38:40 Jerome Pansanel * New structures: polycyclic_alkanes/norbornane.cml drugs/diazepam.cml aromatics/5-phenyl-1_3-dihydro-2H-1_4-benzodiazepin-2-one.cml aromatics/1H-1_4-benzodiazepine.cml aromatics/1H-1_2-benzodiazepine.cml amino_acids/L-4-nitrophenylalanine.cml 2007-11-30 13:52:33 Jerome Pansanel * RDFa support is added * Some bug fixes * Some german translation issues have been fixed * Improved formula index * French translations are available for each compound 2007-11-30 12:05:28 Jerome Pansanel * Renamed structures: water/water.cml thiols/R_butane-2-thiol.cml polycyclic_aromatics/caffeine.cml polycyclic_aromatics/acenaphthenequinone.cml polycyclic_aromatics/uric_acid.cml polycyclic_aromatics/D-warfarin.cml polycyclic_aromatics/2-Benzofuranyl_methyl_ketone.cml polycyclic_aromatics/phthalimide.cml polycyclic_aromatics/coumarin.cml polycyclic_aromatics/chromone.cml polycyclic_aromatics/N-2-hydroxyethylphthalimide.cml 2007-11-28 12:01:44 Jerome Pansanel * Renamed structures: sulfones/p-toluenesulfonic_acid.cml sulfoxides/dimethyl_sulfoxide.cml 2007-11-27 17:45:46 Jerome Pansanel * Renamed structures polycyclic_alkanes/1R-camphor.cml polycyclic_alkanes/1R-camphene.cml nitriles/isobutyronitrile.cml nitriles/butyronitrile.cml nitriles/propionitrile.cml macrocycles/porphin.cml ketones/acetone.cml ketones/p-benzoquinone.cml ketones/o-benzoquinone.cml ketones/hexafluoroacetone.cml ketones/methyl_vinyl_ketone.cml heteroaromatics/nicotinamide.cml heteroaromatics/picolinic_acid.cml heteroaromatics/picolinamide.cml heteroaromatics/nicotinic_acid.cml heteroaromatics/isonicotinamide.cml heteroaromatics/isonicotinic_acid.cml 2007-11-26 20:45:34 Jerome Pansanel * Renamed structures: haloalkanes/2-chloro-2-methylpropane.cml nucleobases/*.cml 2007-11-25 16:35:33 Jerome Pansanel * Renamed structures: fatty_acids/cervonic_acid.cml fatty_acids/arachidonic_acid.cml fatty_acids/linolenic_acid.cml fatty_acids/stearic_acid.cml fatty_acids/oleic_acid.cml fatty_acids/lauric_acid.cml fatty_acids/myristic_acid.cml fatty_acids/palmitic_acid.cml fatty_acids/linoleic_acid.cml 2007-11-24 11:30:56 Jerome Pansanel * Renamed structures: drugs/D-amphetamine.cml carboxylic_acids/D-lactic_acid.cml carboxylic_acids/D-malic_acid.cml carboxylic_acids/L-ascorbic_acid.cml carboxylic_acids/L-lactic_acid.cml carboxylic_acids/L-malic_acid.cml ethers/dipropylether.cml ethers/di-tert-butylether.cml ethers/dibutylether.cml ethers/diisopropylether.cml ethers/diethylether.cml ethers/dimethylether.cml ethers/tetrahydrofuran.cml 2007-11-23 23:10:13 Jerome Pansanel * Renamed structures: carboxylic_acids/L-tartaric_acid.cml carboxylic_acids/D-tartaric_acid.cml carboxylic_acids/citric_acid.cml amino_acids/*.cml amines/{many}.cml 2007-10-03 13:39:45 Jerome Pansanel * Many carbohydrate structures have been added: carbohydrates/d-allose.cml carbohydrates/d-altrose.cml carbohydrates/d-arabinose.cml carbohydrates/d-erythrose.cml carbohydrates/d-erythrulose.cml carbohydrates/d-fructose.cml carbohydrates/d-galactose.cml carbohydrates/d-glucose.cml carbohydrates/d-glyceraldehyde.cml carbohydrates/d-gulose.cml carbohydrates/d-idose.cml carbohydrates/d-lyxose.cml carbohydrates/d-mannose.cml carbohydrates/d-psicose.cml carbohydrates/d-ribose.cml carbohydrates/d-ribulose.cml carbohydrates/d-sorbose.cml carbohydrates/d-tagatose.cml carbohydrates/d-talose.cml carbohydrates/d-threose.cml carbohydrates/d-xylose.cml carbohydrates/d-xylulose.cml carbohydrates/dihydroxyacetone.cml 2007-08-08 10:58:37 Jerome Pansanel * Update each file to UTF-8 ( and recode ISO-8859-1..UTF-8) 2007-08-06 14:20:21 Jerome Pansanel * Update all files with new name for exact mass (monoisotopic mass) * Chage bpt and mpt to bp and mp * Uppercase for the first letter of the first word in each property title * Update indentation * Change xsd:decimal to xsd:double * Fix InChi identifiers 2007-07-18 18:30:15 Jerome Pansanel * Fix cml namespace for the 524 structures 2007-02-28 19:40:11 Jerome Pansanel * Add dutch translation * Fix InChI code * Fix width * Release 2.0.1 2007-02-27 09:47:24 Jerome Pansanel * Create formulaindexwriter and nameindexwriter from dataindexwriter * Add a sort function for chemical formula to make_index.py * Add Kelvin units * Fix src/CMakeLists.txt * Release 2.0.0 2007-02-26 15:59:25 Jerome Pansanel * Fix some translations in xml/l10n.xsl * Change many entries in src/styles/style.css * Move to cmake build system * Add a cmake module: FindOpenBabel2Exe.cmake * Add several python scripts for building and checking the webpages * Move some files to other directories: - pyridine derivatives to heteraromatics - bromosuccinimide to amides * Fix some IUPAC names 2006-11-24 13:58:25 Jerome Pansanel * Update xml/l10n.xsl * Add new structure directories: macrocycles, nitroalkanes, sulfones, sulfoxides and thiols * alcohols/Z-hex-3-en-1-ol.cml * alcohols/2_2_2-trifluoroethanol.cml * alcohols/2-thioethanol.cml * alcohols/1_1_1_3_3_3-hexafluoropropan-2-ol.cml * aldehydes/prop-2-enal.cml * alkenes/cycloocta-1_3-diene.cml * alkenes/cyclopenta-1_3-diene.cml * alkenes/cycloocta-1_3_5_7-tetraene.cml * alkenes/cycloocta-1_3_5-triene.cml * alkenes/cyclohexa-1_4-diene.cml * alkenes/cyclohexa-1_3-diene.cml * alkenes/cyclohepta-1_4-diene.cml * alkenes/cyclohepta-1_3_5-triene.cml * alkenes/cyclohepta-1_3-diene.cml * amides/N_N-dimethylacetamide.cml * amides/ethyl_carbamate.cml * amines/1R_2S-cyclohexane-1_2-diamine.cml * amines/1S_2S-cyclohexane-1_2-diamine.cml * amines/1_4-diazabicyclo_2_2_2_octane.cml * amines/2-methylpropan-2-amine.cml * amines/2S-butan-2-amine.cml * amines/N-ethylethanamine.cml * amines/N-methylmethanamine.cml * amines/N_N_N2_N2-tetramethylethane-1_2-diamine.cml * amines/cyclohexanamine.cml * amines/cyclopentamine.cml * amines/pentane-1_5-diamine.cml * aromatics/1-chloro-2-ethenylbenzene.cml * aromatics/1-chloro-2-methoxybenzene.cml * aromatics/1-chloro-3-methoxybenzene.cml * aromatics/1-chloro-4-methoxybenzene.cml * aromatics/1-phenylbutan-1-one.cml * aromatics/1_3_5-trichloro-2-methoxybenzene.cml * aromatics/2-chloro-4-nitroaniline.cml * aromatics/2-chloro-5-methylphenol.cml * aromatics/2_2-dimethyl-3H-benzofuran-7-yl_N-methylcarbamate.cml * aromatics/2_3_4_5_6-pentachlorophenol.cml * aromatics/2_4_6-trichlorophenol.cml * aromatics/4-bromo-5-methyl-2-propan-2-yl-phenol.cml * aromatics/4-chloro-2-methylphenol.cml * aromatics/4-chloro-3-methylphenol.cml * aromatics/4-chloroaniline.cml * aromatics/4-methoxybenzaldehyde.cml * aromatics/4-methylbenzoic_acid.cml * aromatics/4-octylphenol.cml * aromatics/5-chloro-2-2_4-dichlorophenoxy_phenol.cml * aromatics/E-2-chloroethenyl_benzene.cml * aromatics/E-2-phenylethenyl_benzene.cml * aromatics/benzhydrylbenzene.cml * aromatics/benzonitrile.cml * aromatics/nitrobenzene.cml * carboxylic_acids/2_2-dichloroacetic_acid.cml * carboxylic_acids/2_2_2-trichloroacetic_acid.cml * drugs/2S-1-phenylpropan-2-amine.cml * ethers/1_4_7_10_13_16-hexaoxacyclooctadecane.cml * ethers/2-2-hydroxyethoxy_ethanol.cml * haloalkanes/1-chloro-1_1_2_2_2-pentafluoroethane.cml * haloalkanes/1_1_1-trichloroethane.cml * haloalkanes/1_1_1_2_2-pentafluoroethane.cml * haloalkanes/1_1_1_2_2_2-hexafluoroethane.cml * haloalkanes/2-bromo-2-methylpropane.cml * haloalkanes/2S-2-bromobutane.cml * haloalkanes/2S-2-chlorobutane.cml * haloalkanes/difluoromethane.cml * heteroaromatics/1H-pyridine-2-thione.cml * heteroaromatics/pyridine-2-thiol.cml * ketones/1_1_1_3_3_3-hexafluoropropanone.cml * ketones/Z-4-hydroxypent-3-en-2-one.cml * ketones/but-3-en-2-one.cml * ketones/cyclohex-2-en-1-one.cml * ketones/cyclohexanone.cml * ketones/cyclopent-2-en-1-one.cml * macrocycles/molecules.xml * macrocycles/porphyrin.cml * nitriles/1_1_1-trichloroacetonitrile.cml * nitriles/2-methylpropanenitrile.cml * nitriles/butanenitrile.cml * nitriles/propanenitrile.cml * nitroalkanes/molecules.xml * nitroalkanes/nitroethane.cml * nitroalkanes/nitromethane.cml * polycyclic_alkanes/1R_4S-1_7_7-trimethylnorbornan-2-one.cml * polycyclic_alkanes/1R_4S-2_2-dimethyl-3-methylidenenorbornane.cml * polycyclic_alkanes/cubane.cml * polycyclic_aromatics/1_3_7-trimethylpurine-2_6-dione.cml * polycyclic_aromatics/2-hydroxy-3-1R-3-oxo-1-phenylbutyl_chromen-4-one.cml * polycyclic_aromatics/7_9-dihydro-3H-purine-2_6_8-trione.cml * sulfones/4-methylbenzenesulfonic_acid.cml * sulfones/benzenesulfonic_acid.cml * sulfones/methanesulfonic_acid.cml * sulfones/molecules.xml * sulfoxides/methylsulfinylmethane.cml * sulfoxides/molecules.xml * thiols/2-methylproprane-2-thiol.cml * thiols/butane-1-thiol.cml * thiols/butane-2-thiol.cml * thiols/ethane-1_2-dithiol.cml * thiols/ethanethiol.cml * thiols/heptane-1-thiol.cml * thiols/hexane-1-thiol.cml * thiols/methanethiol.cml * thiols/molecules.xml * thiols/octane-1-thiol.cml * thiols/pentane-1-thiol.cml * thiols/proprane-1-thiol.cml * thiols/proprane-2-thiol.cml 2006-11-13 14:34:03 Jerome Pansanel * Modify xml/molecule_data.xsl : using Jmol.js script * Move src/bin to src/jmol * Add complete jmol binary distribution (v10.2) to /src/jmol 2006-11-09 12:06:23 Jerome Pansanel * Add new structure directories: alkynes, drugs * Update directories.xml * Add alcohols/cyclohexanol.cml * Add alcohols/cyclopentanol.cml * Add alcohols/but-2-yne-1_4-diol.cml * Update alcohols/molecules.xml * Add alkynes/acetylene.cml * Add alkynes/but-1-yne.cml * Add alkynes/but-2-yne.cml * Add alkynes/propyne.cml * Add alkynes/molecules.xml * Add amides/acetamide.cml * Update amides/molecules.xml * Add aromatics/2-bromophenol.cml * Add aromatics/2-chlorophenol.cml * Add aromatics/2-phenylacetic_acid.cml * Add aromatics/2-pyridin-2-ylpyridine.cml * Add aromatics/3-bromophenol.cml * Add aromatics/3-chlorophenol.cml * Add aromatics/3-pyridin-3-ylpyridine.cml * Add aromatics/4-bromophenol.cml * Add aromatics/4-chlorophenol.cml * Add aromatics/4-pyridin-4-ylpyridine.cml * Add aromatics/N_N-dimethylaniline.cml * Add aromatics/anisol.cml * Add aromatics/benzoyl_chloride.cml * Add aromatis/benzamide.cml * Add aromatics/bromobenzene.cml * Add aromatics/chlorobenzene.cml * Add aromatics/pyridine-2-carboxamide.cml * Add aromatics/pyridine-2-carboxylic_acid.cml * Add aromatics/pyridine-3-carboxamide.cml * Add aromatics/pyridine-3-carboxylic_acid.cml * Add aromatics/pyridine-4-carboxamide.cml * Add aromatics/pyridine-4-carboxylic_acid.cml * Update aromatics/molecules.xml * Add drugs/4-acetamidophenyl_2-hydroxybenzoate.cml * Add drugs/N-4-hydroxyphenyl_acetamide.cml * Add drugs/acepromazine.cml * Add drugs/molecules.xml * Add ethers/R-2-ethoxybutane.cml * Update ethers/molecules.xml * Add haloalkanes/1-bromopropane.cml * Add haloalkanes/1_4-dichlorobut-2-yne.cml * Add haloalkanes/2-bromopropane.cml * Add haloalkanes/2-chloropropane.cml * Add haloalkanes/bromocyclohexane.cml * Add haloalkanes/bromoethane.cml * Add haloalkanes/bromomethane.cml * Add haloalkanes/bromotrifluoromethane.cml * Add haloalkanes/chloro-chloromethoxy_methane.cml * Add haloalkanes/chlorocyclohexane.cml * Update haloalkanes/molecules.xml * Add polycyclic_aromatics/acenaphthene-1_2-dione.cml * Add polycyclic_aromatics/acenaphthene.cml * Add polycyclic_aromatics/acenaphthylene.cml * Update polycyclic_aromatics/molecules.xml * Add polycyclic_alkanes/abietic_acid.cml * Update polycyclic_alkanes/molecules.xml 2006-10-17 10:43:45 Jerome Pansanel * Update german translations in alcohols/molecules.xml * Update german translations in aldehydes/molecules.xml * Update german translations in alkanes/molecules.xml * Update german translations in alkenes/molecules.xml * Update german translations in amides/molecules.xml * Update german translations in amines/molecules.xml * Update german translations in amino_acids/molecules.xml * Update german translations in aromatics/molecules.xml * Update german translations in carbamides/molecules.xml * Update german translations in carbohydrates/molecules.xml * Update german translations in carboxylic_acids/molecules.xml 2006-10-16 13:44:03 Jerome Pansanel * Add alkanes/1S_2S-1-ethyl-2-methylcyclopentane.cml * Update alkanes/molecules.xml * Add alkenes/3Z_3-ethylhepta-1_3-diene.cml * Update alkenes/molecules.xml * Add aromatics/tris_4-dimethylaminophenyl_methanol.cml * Add aromatics/tris_4-aminophenyl_methanol.cml * Add aromatics/triphenylmethanol.cml * Add aromatics/4_bis_4-dimethylaminophenyl_methylene-2_5-\ cyclohexadien-1-iminium.cml * Update aromatics/molecules.xml * Add polycyclic_aromatics/1_1-benzofuran-2-yl_ethanone.cml * Update polycyclic_aromatics/molecules.xml 2006-10-11 16:45:11 Jerome Pansanel * Release 1.05 * Remove 8Z_12Z_16Z_19Z-docosa-8_12_16_19-tetraenoic_acid.cml (Structure was false and non-relevant) * Update fatty_acids with MOPAC/PM3 optimized structures 2006-10-03 08:43:10 Jerome Pansanel * Update alcohols with MOPAC/PM3 optimized structures * Update aldehydes with MOPAC/PM3 optimized structures * Update alkanes with MOPAC/PM3 optimized structures * Update alkenes with MOPAC/PM3 optimized structures * Update amides with MOPAC/PM3 optimized structures * Update amines with MOPAC/PM3 optimized structures * Update amino_acids with MOPAC/PM3 optimized structures * Update aromatics with MOPAC/PM3 optimized structures * Update carbamides with MOPAC/PM3 optimized structures * Update carbohydrates with MOPAC/PM3 optimized structures * Update carboxylic_acid with MOPAC/PM3 optimized structures * Update esters with MOPAC/PM3 optimized structures * Update ethers with MOPAC/PM3 optimized structures * Update haloalkanes with MOPAC/PM3 optimized structures * Update heteroaromatics with MOPAC/PM3 optimized structures * Update ketones with MOPAC/PM3 optimized structures * Update nitriles with MOPAC/PM3 optimized structures * Update nucleobases with MOPAC/PM3 optimized structures * Update polycyclic_alkanes with MOPAC/PM3 optimized structures * Update polycyclic_aromatics with MOPAC/PM3 optimized structures * Update thioethers with MOPAC/PM3 optimized structures * Update water with MOPAC/PM3 optimized structures 2006-06-29 08:43:10 Jerome Pansanel * Add cyclohexa-2,5-diene-1,4-dione * Add cyclohexa-2,4-diene-1,6-dione * Add benzene-1,2-diol * Add benzene-1,3-diol * Add benzene-1,4-diol * Add 2,4,6-trimethylaniline * Change make.sh to Makefile * Add chemwt.xml to xml directory 2006-06-28 08:02:52 Jerome Pansanel * Update README 2006-06-27 08:51:28 Jerome Pansanel * Release 1.0 * Add (2R,3R)-2-Amino-3-hydroxy-butanoic acid (D-allo-Threonine) * Add (2S,3R)-2-Amino-3-methyl-pentanoic acid (L-allo-Leucine) * Add Linolein 2006-06-26 08:51:28 Jerome Pansanel * Add Pyrrolidine * Add missing mpt values * Add missing bpt values 2006-06-23 21:26:45 Jerome Pansanel * Add Butoxybutane * Add missing mpt values * Add missing bpt values 2006-06-22 08:34:56 Jerome Pansanel * Add formula to each cml file * Add InChI (version 1) to each cml file * Add property:molwt to each cml file * Add property:exact_molwt to each cml file * Add property:mpt tag to each cml file * Add property:bpt tag to each cml file * Add some bpt and mpt values * Update l10n.xml * Update molecule_data.xsl 2006-06-20 08:01:04 Jerome Pansanel * Release 0.9 * Fixes some issues in amino_acids directory * Remove "(),[]" from molecule filenames 2006-06-19 19:12:26 Jerome Pansanel * Add l10n.xml (Localization) * Add l10n.xsl (Internationalization) * update make.sh (add support for fr and de languages) 2006-06-16 08:47:39 Jerome Pansanel * change applet to object in molecule_data.xsl * add README 2006-06-15 08:39:11 Jerome Pansanel * release version 0.8 * add src/images/cml.png * add src/images/mol.png * add xsl style sheet for cml files * add Jmol applet * update directory_index.xsl * update molecule_index.xsl * use xsltproc by default (was sabcmd) 2006-06-14 18:12:50 Jerome Pansanel * add xsl stylesheet for directories and molecules * update make.sh * add some translation (german and french) 2006-06-13 18:48:19 Jerome Pansanel * change structure mol file to cml file type (was mol file type) * add filename tag to index.xml * change description tag to comments * update the index files * fix make.sh 2006-05-09 09:23:14 Jerome Pansanel * add new molecule types: - fatty acids - nucleobases 2006-05-08 14:12:23 Jerome Pansanel * add new molecule types: - amides - amines - amino acids - aromatics - esters - ethers - nitriles * remove molecule types: - others * create build script make.sh * add licensing informations (COPYING file) 2006-05-05 10:33:52 Jerome Pansanel * add new molecule types: - alcohols - aldehydes - alkanes - alkenes - carboxylics_acid - others - haloalkanes - ketones - other - water chemical-structures-2.2.dfsg.0.orig/xml/0000755000175000017500000000000011225622315020357 5ustar georgeskgeorgeskchemical-structures-2.2.dfsg.0.orig/xml/index.dtd0000644000175000017500000000257010732745725022204 0ustar georgeskgeorgesk chemical-structures-2.2.dfsg.0.orig/xml/l10n.xml0000644000175000017500000002123011225116445021653 0ustar georgeskgeorgesk Abbreviation: Abbreviation: Abkürzung: Abreviatura : Abréviation : Afkorting: Abbreviation 縮寫: Abbreviations: Abbreviations: Abkürzungen: Abreviaturas : Abréviations : Afkortingen: Abbreviations 縮寫: Back to index Back to index Zurück zum Index Regresar al índice Retour à l'index Terug naar de index Back to index 回到目錄 Boiling point: Boiling point: Siedepunkt: Punto de ebullición : Point d'ébullition : Kookpunt: Boiling point 沸點: Comments Comments Kommentar Comentarios Commentaires Commentaar Comments 備註 Directories Directories Verzeichnisse Directorios Répertoires Mappen Directories 目錄 Formula: Formula: Formel: Fórmula : Formule brute : Molecuulformule: Formula 化學式: Formula index Formula index Formelindex Índice de fórmulas Index des formules Index met molecuulformules Formula index 依化學式排列 In CML format In CML format Im CML Format En CML formato Au format CML In CML-formaat In CML format (CML 化學檔案格式) In MOL format In MOL format Im MOL Format En MOL formato Au format MOL In MDL-molfile-formaat In MOL format (MOL 化學檔案格式) InChI InChI InChI InChI InChI InChI InChI (InChI 文字化學式) SMILES SMILES SMILES SMILES SMILES SMILES SMILES (SMILES 文字化學式) InChI: InChI: InChI: InChI : InChI : InChI: InChI (InChI 文字化學式): IUPAC name: IUPAC name: IUPAC Name: Nombre IUPAC : Nom IUPAC : IUPAC-naam: IUPAC name (IUPAC 化學名): Melting point: Melting point: Schmelzpunkt: Punto de fusión : Point de fusion : Smeltpunt: Melting point 熔點: Molecular weight: Molecular weight: Molekülmasse: Masa molecular : Masse moléculaire : Moleculair gewicht: Molecular weight 分子量: Monoisotopic weight: Monoisotopic weight: Monoisotopisches Gewicht: Masa monoisótopica : Masse monoisotopique : Exacte massa: Monoisotopic weight 單同位素分子量: Name Name Name Nombre Nom Naam Name 化學名稱 Name: Name: Name: Nombre : Nom : Naam: Name 化學名稱: Name index Name index Namensindex Índice del nombre Index des noms Index met namen Name index 依化學名稱排列 Names Names Namen Nombres Noms Namen Names 化學名 Previous Previous Vorgehend Anterior Précédent Vorige Previous 前一頁 Properties Properties Eigenschaften Propiedades Propriétés Eigenschappen Properties 性質 Structure Structure Struktur Estructura Structure Structuur Structure 立體結構 Synonym: Synonym: Synonym: Sinónimo : Synonyme : Synoniem: Synonym 俗名/別名: Synonyms Synonyms Synonyme Sinónimos Synonymes Synoniemen Synonyms 俗名/別名 Synonyms: Synonyms: Synonyme: Sinónimos : Synonymes : Synoniemen: Synonyms 俗名/別名: Structure Download Structure Download Struktur laden Descargar la estructura Téléchargement de la structure De structuur downloaden Structure Download 下載分子結構檔案