debian/0000755000000000000000000000000012174552450007173 5ustar debian/chemical-structures.config0000644000000000000000000000043611543323066014351 0ustar #!/bin/bash set -e PACKAGE="chemical-structures" SOURCE="chemical-structures" VERSION="2.0" . /usr/share/debconf/confmodule # Package maintainer's commands follow: db_input medium chemical-structures/reconfigure-webserver || true db_go # End of package maintainer's commands exit 0 debian/patches/0000755000000000000000000000000012145521503010613 5ustar debian/patches/xml~l10n.xml0000644000000000000000000000160412145521503013027 0ustar --- a/xml/l10n.xml +++ b/xml/l10n.xml @@ -91,6 +91,15 @@ In MOL format (MOL 化學檔案格式) + In XYZ format + In XYZ format + Im XYZ Format + En XYZ formato + Au format XYZ + In MDL-xyzfile-formaat + In XYZ format (XYZ 化學檔案格式) + + InChI InChI InChI @@ -190,6 +199,11 @@ Names 化學名 + Other formats + Other formats + Autres formats + + Previous Previous Vorgehend debian/patches/chemstruc0000644000000000000000000000106511544023517012541 0ustar Index: chemical-structures-2.2.dfsg.0/chemstruc =================================================================== --- /dev/null +++ chemical-structures-2.2.dfsg.0/chemstruc @@ -0,0 +1,26 @@ +#!/bin/sh + +case $LANG in + fr*) + index=index_fr.html + ;; + de*) + index=index_de.html + ;; + *) + index=index_en.html + ;; +esac + +if [ -x /usr/bin/firefox ]; then + BROWSER=firefox +else + if [ -x /usr/bin/mozilla ]; then + BROWSER=mozilla + else + BROWSER=sensible-browser + fi +fi + +($BROWSER http://localhost/chemical-structures/$index &) + debian/patches/convert.cgi0000644000000000000000000000531311543335757013000 0ustar Index: chemical-structures-2.2.dfsg.0/convert.cgi =================================================================== --- /dev/null +++ chemical-structures-2.2.dfsg.0/convert.cgi @@ -0,0 +1,90 @@ +#!/usr/bin/python + +import cgi, os, tempfile +import cgitb; cgitb.enable() + +form = cgi.FieldStorage() + +""" +contentTypes were made from the package chemical-mime-data with some additions +""" + +contentTypes={ + 'alc':'chemical/x-alchemy', + 'arc':'chemical/x-msi-car', + 'c3d':'chemical/x-chem3d', + 'cac':'chemical/x-cache', + 'cache':'chemical/x-cache', + 'car':'chemical/x-msi-car', + 'cdx':'chemical/x-cdx', + 'cif':'chemical/x-cif', + 'cml':'chemical/x-cml', + 'cor':'chemical/x-msi-car', + 'dat':'chemical/x-mopac-input', + 'dx':'chemical/x-jcamp-dx', + 'gal':'chemical/x-gaussian-log', + 'gam':'chemical/x-gamess-input', + 'gamin':'chemical/x-gamess-input', + 'gau':'chemical/x-gaussian-input', + 'gjc':'chemical/x-gaussian-input', + 'gjf':'chemical/x-gaussian-input', + 'gpr':'chemical/x-gpr', + 'gpt':'chemical/x-mopac-graph', + 'hessian':'chemical/x-msi-hessian', + 'hin':'chemical/x-hin', + 'inchi':'chemical/x-inchi', + 'inchix':'chemical/x-inchi-xml', + 'inp':'chemical/x-gamess-input', + 'jdx':'chemical/x-jcamp-dx', + 'mcif':'chemical/x-mmcif', + 'mdf':'chemical/x-msi-mdf', + 'mdl':'chemical/x-mdl-molfile', + 'mmd':'chemical/x-macromodel-input', + 'mmod':'chemical/x-macromodel-input', + 'mol':'chemical/x-mdl-molfile', + 'mol2':'chemical/x-mol2', + 'moo':'chemical/x-mopac-out', + 'mop':'chemical/x-mopac-input', + 'mopcrt':'chemical/x-mopac-input', + 'mpc':'chemical/x-mopac-input', + 'msi':'chemical/x-msi-msi', + 'out':'chemical/x-mopac-out', + 'outmol':'chemical/x-dmol', + 'pdb':'chemical/x-pdb', + 'rd':'chemical/x-mdl-rdfile', + 'res':'chemical/x-shelx', + 'rxn':'chemical/x-mdl-rxnfile', + 'sd':'chemical/x-mdl-sdfile', + 'sdf':'chemical/x-mdl-sdfile', + 'tgf':'chemical/x-mdl-tgf', + 'vmd':'chemical/x-vmd', + 'xyz':'chemical/x-xyz', + 'zmt':'chemical/x-mopac-input'} + + +def output(mol, ext, debug=False): + + if contentTypes.has_key(ext): + ct=contentTypes[ext] + else: + ct='chemical/unknown' + if debug: + print "Content-type: text/html\n\n" + else: + print "Content-type: %s\nContent-Disposition: inline; filename=\"%s\"\n\n" %(ct,mol+'.'+ext) + handle,outfile=tempfile.mkstemp('.'+ext) + if os.path.exists(mol+".cml.gz"): + handle1,outfile1=tempfile.mkstemp('.cml') + os.system("zcat %s.cml.gz > %s" %(mol,outfile1)) + os.system("babel -icml %s -o%s %s" %(outfile1,ext,outfile)) + os.remove(outfile1) + else: + os.system("babel -icml %s.cml -o%s %s" %(mol,ext,outfile)) + print ''.join(open(outfile).readlines()) + os.remove(outfile) + + + +if __name__ == "__main__": + output(form["mol"].value, form["ext"].value) + debian/patches/series0000644000000000000000000000015112145511151012023 0ustar convert.cgi tools~cmlwriter.py apache.conf chemstruc src~jmol~jmol.js xml~l10n.xml build-xyz-files.patch debian/patches/tools~cmlwriter.py0000644000000000000000000001671511544025236014472 0ustar Index: chemical-structures-2.2.dfsg.0/tools/cmlwriter.py =================================================================== --- chemical-structures-2.2.dfsg.0.orig/tools/cmlwriter.py +++ chemical-structures-2.2.dfsg.0/tools/cmlwriter.py @@ -17,6 +17,86 @@ class CMLWriter: self.fout = fout self.cml = cml_handler self.l10n = l10n_handler + self.scriptFormat=""" + +""" + self.selection=""" + +""" def parseFormula(self, raw_formula): """Parse formula and return the HTML formula @@ -57,8 +137,8 @@ class CMLWriter: xhtmlout.setOutput(self.fout) xhtmlout.setTitle(title) xhtmlout.addHead(' ') - xhtmlout.addHead(' ') - xhtmlout.addHead(' ') + xhtmlout.addHead(' ') + xhtmlout.addBody(self.scriptFormat) xhtmlout.addBody(' ') @@ -152,6 +232,7 @@ class CMLWriter: 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('
  • ' + self.l10n.translate('Other formats', lang) + ' '+self.selection+'
    • ') xhtmlout.addBody(' ') xhtmlout.addBody(' ') xhtmlout.addBody('
    ') debian/patches/build-xyz-files.patch0000644000000000000000000006343412145520710014674 0ustar --- a/src/alcohols/CMakeLists.txt +++ b/src/alcohols/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/water/CMakeLists.txt +++ b/src/water/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/acid_anhydrides/CMakeLists.txt +++ b/src/acid_anhydrides/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/aldehydes/CMakeLists.txt +++ b/src/aldehydes/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/alkanes/CMakeLists.txt +++ b/src/alkanes/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/alkenes/CMakeLists.txt +++ b/src/alkenes/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/alkynes/CMakeLists.txt +++ b/src/alkynes/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/amides/CMakeLists.txt +++ b/src/amides/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/amines/CMakeLists.txt +++ b/src/amines/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/amino_acids/CMakeLists.txt +++ b/src/amino_acids/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/aromatics/CMakeLists.txt +++ b/src/aromatics/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/carbamides/CMakeLists.txt +++ b/src/carbamides/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/carbohydrates/CMakeLists.txt +++ b/src/carbohydrates/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/carboxylic_acids/CMakeLists.txt +++ b/src/carboxylic_acids/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/drugs/CMakeLists.txt +++ b/src/drugs/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/esters/CMakeLists.txt +++ b/src/esters/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/ethers/CMakeLists.txt +++ b/src/ethers/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/fatty_acids/CMakeLists.txt +++ b/src/fatty_acids/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/haloalkanes/CMakeLists.txt +++ b/src/haloalkanes/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/heteroaromatics/CMakeLists.txt +++ b/src/heteroaromatics/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/ketones/CMakeLists.txt +++ b/src/ketones/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/macrocycles/CMakeLists.txt +++ b/src/macrocycles/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/natural_products/CMakeLists.txt +++ b/src/natural_products/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/nitriles/CMakeLists.txt +++ b/src/nitriles/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/nitroalkanes/CMakeLists.txt +++ b/src/nitroalkanes/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/nucleobases/CMakeLists.txt +++ b/src/nucleobases/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/peptides/CMakeLists.txt +++ b/src/peptides/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/polycyclic_alkanes/CMakeLists.txt +++ b/src/polycyclic_alkanes/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/polycyclic_aromatics/CMakeLists.txt +++ b/src/polycyclic_aromatics/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/sulfones/CMakeLists.txt +++ b/src/sulfones/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/sulfoxides/CMakeLists.txt +++ b/src/sulfoxides/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/thioethers/CMakeLists.txt +++ b/src/thioethers/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/src/thiols/CMakeLists.txt +++ b/src/thiols/CMakeLists.txt @@ -43,6 +43,13 @@ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} ) set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}") + # Generate xyz files + set(xyz_FILE "${cml_WE}.xyz") + add_custom_command(TARGET ${CHEM_GROUP} + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE} + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}") # Generate smi files set(smi_FILE "${cml_WE}.smi") add_custom_command(TARGET ${CHEM_GROUP} --- a/tools/cmlwriter.py +++ b/tools/cmlwriter.py @@ -125,6 +125,7 @@ cml_file = entry_details.path + '.cml' mol_file = entry_details.path + '.mol' + xyz_file = entry_details.path + '.xyz' smi_file = entry_details.path + '.smi' smiles = "" if os.path.isfile(smi_file): @@ -232,6 +233,8 @@ 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
    • ') + if os.path.isfile(xyz_file): + xhtmlout.addBody('
  • ' + self.l10n.translate('In XYZ format', lang) + ' Download xyz file
    • ') xhtmlout.addBody('
  • ' + self.l10n.translate('Other formats', lang) + ' '+self.selection+'
    • ') xhtmlout.addBody(' ') xhtmlout.addBody('
    ') debian/patches/apache.conf0000644000000000000000000000112011543350011012670 0ustar Index: chemical-structures-2.2.dfsg.0/apache.conf =================================================================== --- /dev/null +++ chemical-structures-2.2.dfsg.0/apache.conf @@ -0,0 +1,14 @@ +# chemical-structures setup for Apache +# with no virtual host + +Alias /chemical-structures /usr/share/chemical-structures/ + + + AllowOverride None + DirectoryIndex index.html + Options +ExecCGI + AddHandler cgi-script .cgi + AddDefaultCharset UTF-8; + Order allow,deny + Allow from all + debian/patches/src~jmol~jmol.js0000644000000000000000000000143111544020341014073 0ustar Index: chemical-structures-2.2.dfsg.0/src/jmol/Jmol.js =================================================================== --- chemical-structures-2.2.dfsg.0.orig/src/jmol/Jmol.js +++ chemical-structures-2.2.dfsg.0/src/jmol/Jmol.js @@ -158,7 +158,12 @@ function jmolSetAppletWindow(w) { function jmolApplet(size, script, nameSuffix) { _jmolInitCheck(); - return _jmolApplet(size, null, script, nameSuffix); + /// the applets have been removed from the main repository of Debian + /// they must be provided by another package + ////////////////// + /// return _jmolApplet(size, null, script, nameSuffix); + d=window.document.getElementById("structure"); + d.innerHTML="(no Jmol applet featured)"; } //////////////////////////////////////////////////////////////// debian/control0000644000000000000000000000137012164115677010604 0ustar Source: chemical-structures Section: science Priority: optional Maintainer: Georges Khaznadar Build-Depends: debhelper (>= 9), python, po-debconf, cmake, openbabel Build-Depends-Indep: xsltproc, docbook-xsl, docbook-xml Standards-Version: 3.9.4 Package: chemical-structures Architecture: all Depends: ${misc:Depends}, debconf, python, openbabel Recommends: chemical-mime-data, apache2| httpd, iceweasel|iceape Suggests: jmol, jmol-applet Description: set of molecular structures in open formats hundreds of molecular structures, in the following classes: alcohols, aldehydes, alkanes, alkenes, amides, amines, amino_acids, aromatics, carboxylic_acids, esters, ethers, fatty_acids, haloalkanes, ketones, nitriles,nucleobases, water. debian/po/0000755000000000000000000000000012174551662007615 5ustar debian/po/templates.pot0000644000000000000000000000172411543347725012345 0ustar # SOME DESCRIPTIVE TITLE. # Copyright (C) YEAR THE PACKAGE'S COPYRIGHT HOLDER # This file is distributed under the same license as the PACKAGE package. # FIRST AUTHOR , YEAR. # #, fuzzy msgid "" msgstr "" "Project-Id-Version: PACKAGE VERSION\n" "Report-Msgid-Bugs-To: chemical-structures@packages.debian.org\n" "POT-Creation-Date: 2011-03-26 12:36+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=CHARSET\n" "Content-Transfer-Encoding: 8bit\n" #. Type: boolean #. Description #: ../chemical-structures.templates:1001 msgid "Should apache2 be restarted?" msgstr "" #. Type: boolean #. Description #: ../chemical-structures.templates:1001 msgid "" "In order to activate the new configuration, apache2 has to be restarted. You " "can also restart apache2 by manually executing 'invoke-rc.d apache2 restart'." msgstr "" debian/po/sv.po0000644000000000000000000000306411572004143010574 0ustar # Translation of chemical-structures debconf template to Swedish # Copyright (C) 2011 Martin Bagge # This file is distributed under the same license as the chemical-structures package. # # Martin Bagge , 2011 msgid "" msgstr "" "Project-Id-Version: chemical-structures 2.1.dfsg.1-3\n" "Report-Msgid-Bugs-To: chemical-structures@packages.debian.org\n" "POT-Creation-Date: 2011-03-26 12:36+0100\n" "PO-Revision-Date: 2011-06-02 14:42+0100\n" "Last-Translator: Martin Bagge / brother \n" "Language-Team: Swedish \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" "X-Poedit-Language: Swedish\n" "X-Poedit-Country: Sweden\n" #. Type: boolean #. Description #: ../chemical-structures.templates:1001 #| msgid "Should ${webserver} be restarted?" msgid "Should apache2 be restarted?" msgstr "Ska apache2 startas om?" #. Type: boolean #. Description #: ../chemical-structures.templates:1001 #| msgid "" #| "In order to activate the new configuration, ${webserver} has to be " #| "restarted. You can also restart ${webserver} by manually executing " #| "'invoke-rc.d ${webserver} restart'." msgid "" "In order to activate the new configuration, apache2 has to be restarted. You " "can also restart apache2 by manually executing 'invoke-rc.d apache2 restart'." msgstr "" "För att de nya inställningarna ska börja gälla måste apache2 startas om. Du " "kan också starta om apache2 manuellt genom att exekvera \"invoke-rc.d " "apache2 restart\"." debian/po/da.po0000644000000000000000000000233411666701553010544 0ustar # Danish translation chemical-structures. # Copyright (C) 2010 chemical-structures & nedenstående oversættere. # This file is distributed under the same license as the chemical-structures package. # Joe Hansen (joedalton2@yahoo.dk), 2010, 2011. # msgid "" msgstr "" "Project-Id-Version: chemical-structures\n" "Report-Msgid-Bugs-To: chemical-structures@packages.debian.org\n" "POT-Creation-Date: 2011-03-26 12:36+0100\n" "PO-Revision-Date: 2011-12-04 12:42+0000\n" "Last-Translator: Joe Hansen \n" "Language-Team: Danish \n" "Language: da\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" #. Type: boolean #. Description #: ../chemical-structures.templates:1001 msgid "Should apache2 be restarted?" msgstr "Skal apache2 genstartes?" #. Type: boolean #. Description #: ../chemical-structures.templates:1001 msgid "" "In order to activate the new configuration, apache2 has to be restarted. You " "can also restart apache2 by manually executing 'invoke-rc.d apache2 restart'." msgstr "" "For at aktivere den nye konfiguration, skal apache2 genstartes. Du kan " "også genstarte apache2 ved manuelt at køre »invoke-rc.d apache2 restart«." debian/po/fr.po0000644000000000000000000000415311544712605010563 0ustar # # Translators, if you are not familiar with the PO format, gettext # documentation is worth reading, especially sections dedicated to # this format, e.g. by running: # info -n '(gettext)PO Files' # info -n '(gettext)Header Entry' # Some information specific to po-debconf are available at # /usr/share/doc/po-debconf/README-trans # or http://www.debian.org/intl/l10n/po-debconf/README-trans# # Developers do not need to manually edit POT or PO files. # # Christian Perrier , 2010. msgid "" msgstr "" "Project-Id-Version: chemical-structures 2.0\n" "Report-Msgid-Bugs-To: chemical-structures@packages.debian.org\n" "POT-Creation-Date: 2011-03-26 12:36+0100\n" "PO-Revision-Date: 2010-11-06 23:13+0100\n" "Last-Translator: Georges Khaznadar \n" "Language-Team: French \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Language: fr\n" "Plural-Forms: nplurals=2; plural=(n > 1);\n" "X-Generator: Lokalize 1.0\n" #. Type: boolean #. Description #: ../chemical-structures.templates:1001 msgid "Should apache2 be restarted?" msgstr "Faut-il redémarrer Apache 2 ?" #. Type: boolean #. Description #: ../chemical-structures.templates:1001 msgid "" "In order to activate the new configuration, apache2 has to be restarted. You " "can also restart apache2 by manually executing 'invoke-rc.d apache2 restart'." msgstr "" "Pour activer la nouvelle configuration, il faut redémarrer Apache 2. " "Vous pouvez aussi redémarrer Apache 2 à la main en lançant « invoke-rc.d " "apache2 restart »." #~ msgid "Web server to reconfigure automatically:" #~ msgstr "Serveur web à reconfigurer automatiquement :" #~ msgid "" #~ "Please choose the web server that should be automatically configured to " #~ "run chemical-structures." #~ msgstr "" #~ "Veuillez choisir le serveur web à reconfigurer automatiquement pour " #~ "exécuter chemical-structures." #~ msgid "Chemical-structures supports Apache and Apache2." #~ msgstr "Chemical-structures supporte Apache et Apache2." debian/po/de.po0000644000000000000000000000254711547620065010552 0ustar # German translation of debconf templates for the chemical-structures package. # Copyright (C) 2006 Georges Khaznadar # This file is distributed under the same license as the chemical-structures # package. # Martin E. Schauer , 2010, 2011. # msgid "" msgstr "" "Project-Id-Version: chemical-structures 2.2.dfsg.0-1\n" "Report-Msgid-Bugs-To: chemical-structures@packages.debian.org\n" "POT-Creation-Date: 2011-03-26 12:36+0100\n" "PO-Revision-Date: 2011-04-08 12:34+0200\n" "Last-Translator: Martin Eberhard Schauer \n" "Language-Team: German \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "X-Generator: KBabel 1.11.4\n" #. Type: boolean #. Description #: ../chemical-structures.templates:1001 msgid "Should apache2 be restarted?" msgstr "Soll apache2 jetzt neu gestartet werden?" #. Type: boolean #. Description #: ../chemical-structures.templates:1001 msgid "" "In order to activate the new configuration, apache2 has to be restarted. You " "can also restart apache2 by manually executing 'invoke-rc.d apache2 restart'." msgstr "" "Damit die neue Konfiguration aktiviert wird, muss apache2 neu gestartet " "werden. Sie k??nnen apache2 auch manuell mit dem Befehl ??/etc/init.d/" "apache2 restart?? neu starten." debian/po/vi.po0000644000000000000000000000411111543347725010572 0ustar # Vietnamese Debconf translation for Chemical Structures. # Copyright © 2010 Free Software Foundation, Inc. # This file is distributed under the same license as the chemical-structures package. # Clytie Siddall , 2010. # msgid "" msgstr "" "Project-Id-Version: chemical-structures 2.1.dfsg.1-6\n" "Report-Msgid-Bugs-To: chemical-structures@packages.debian.org\n" "POT-Creation-Date: 2011-03-26 12:36+0100\n" "PO-Revision-Date: 2010-11-07 17:07+1030\n" "Last-Translator: Clytie Siddall \n" "Language-Team: Vietnamese \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Language: vi\n" "Plural-Forms: nplurals=1; plural=0;\n" "X-Generator: LocFactoryEditor 1.8\n" #. Type: boolean #. Description #: ../chemical-structures.templates:1001 #, fuzzy #| msgid "Should ${webserver} be restarted?" msgid "Should apache2 be restarted?" msgstr "Có nên khởi chạy lại ${webserver} không?" #. Type: boolean #. Description #: ../chemical-structures.templates:1001 #, fuzzy #| msgid "" #| "In order to activate the new configuration, ${webserver} has to be " #| "restarted. You can also restart ${webserver} by manually executing " #| "'invoke-rc.d ${webserver} restart'." msgid "" "In order to activate the new configuration, apache2 has to be restarted. You " "can also restart apache2 by manually executing 'invoke-rc.d apache2 restart'." msgstr "" "Để kích hoạt cấu hình mới thì cần phải khởi chạy lại trình phục vụ Web " "${webserver}. Bạn cũng có thể khởi chạy lại ${webserver} bằng cách thực hiện " "bằng tay câu lệnh « invoke-rc.d ${webserver} restart »." #~ msgid "Web server to reconfigure automatically:" #~ msgstr "Trình phục vụ Web cần tự động cấu hình lại:" #~ msgid "" #~ "Please choose the web server that should be automatically configured to " #~ "run chemical-structures." #~ msgstr "" #~ "Hãy chọn trình phục vụ Web nên được tự động cấu hình để chạy chemical-" #~ "structures." debian/po/pt.po0000644000000000000000000000417311544457023010601 0ustar # Translation of chemical-structures debconf messages to Portuguese # Copyright (C) 2010 the chemical-structures's COPYRIGHT HOLDER # This file is distributed under the same license as the chemical-structures package. # # Américo Monteiro , 2010. # Américo Monteiro , 2011. msgid "" msgstr "" "Project-Id-Version: chemical-structures 2.2.dfsg.0-1\n" "Report-Msgid-Bugs-To: chemical-structures@packages.debian.org\n" "POT-Creation-Date: 2011-03-26 12:36+0100\n" "PO-Revision-Date: 2011-03-29 22:54+0100\n" "Last-Translator: Américo Monteiro \n" "Language-Team: Portuguese \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Language: pt\n" "X-Generator: Lokalize 1.2\n" "Plural-Forms: nplurals=2; plural=(n != 1);\n" #. Type: boolean #. Description #: ../chemical-structures.templates:1001 #| msgid "Should ${webserver} be restarted?" msgid "Should apache2 be restarted?" msgstr "Deve o apache2 ser reiniciado?" #. Type: boolean #. Description #: ../chemical-structures.templates:1001 #| msgid "" #| "In order to activate the new configuration, ${webserver} has to be " #| "restarted. You can also restart ${webserver} by manually executing " #| "'invoke-rc.d ${webserver} restart'." msgid "" "In order to activate the new configuration, apache2 has to be restarted. You " "can also restart apache2 by manually executing 'invoke-rc.d apache2 restart'." msgstr "" "De modo a activar a nova configuração, o apache2 tem que ser " "reiniciado. Você também pode reiniciar o apache2 manualmente ao " "executar 'invoke-rc.d apache2 restart'." #~ msgid "Web server to reconfigure automatically:" #~ msgstr "Servidor web para reconfigurar automaticamente:" #~ msgid "" #~ "Please choose the web server that should be automatically configured to " #~ "run chemical-structures." #~ msgstr "" #~ "Por favor escolha o servidor web que deve ser configurado automaticamente " #~ "para correr o chemical-structures." #~ msgid "Chemical-structures supports Apache and Apache2." #~ msgstr "O chemical-structures suporta Apache e Apache2." debian/po/ru.po0000644000000000000000000000423111561230464010574 0ustar # Copyright (C) YEAR THE PACKAGE'S COPYRIGHT HOLDER # This file is distributed under the same license as the chemical-structures package. # # Yuri Kozlov , 2010, 2011. msgid "" msgstr "" "Project-Id-Version: chemical-structures 2.2.dfsg.0-2\n" "Report-Msgid-Bugs-To: chemical-structures@packages.debian.org\n" "POT-Creation-Date: 2011-03-26 12:36+0100\n" "PO-Revision-Date: 2011-05-07 11:00+0400\n" "Last-Translator: Yuri Kozlov \n" "Language-Team: Russian \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Language: Russian\n" "X-Generator: Lokalize 1.0\n" "Plural-Forms: nplurals=3; plural=(n%10==1 && n%100!=11 ? 0 : n%10>=2 && " "n%10<=4 && (n%100<10 || n%100>=20) ? 1 : 2);\n" #. Type: boolean #. Description #: ../chemical-structures.templates:1001 #| msgid "Should ${webserver} be restarted?" msgid "Should apache2 be restarted?" msgstr "Перезапустить apache2?" #. Type: boolean #. Description #: ../chemical-structures.templates:1001 #| msgid "" #| "In order to activate the new configuration, ${webserver} has to be " #| "restarted. You can also restart ${webserver} by manually executing " #| "'invoke-rc.d ${webserver} restart'." msgid "" "In order to activate the new configuration, apache2 has to be restarted. You " "can also restart apache2 by manually executing 'invoke-rc.d apache2 restart'." msgstr "" "Чтобы новая конфигурация начала действовать, нужно " "перезапустить apache2. Также вы можете перезапустить apache2 " "вручную, выполнив команду «invoke-rc.d apache2 restart»." #~ msgid "Web server to reconfigure automatically:" #~ msgstr "Веб-сервер для автоматической перенастройки:" #~ msgid "" #~ "Please choose the web server that should be automatically configured to " #~ "run chemical-structures." #~ msgstr "" #~ "Выберите веб-сервер, который нужно автоматически настроить для запуска " #~ "chemical-structures." debian/po/cs.po0000644000000000000000000000241511577377661010577 0ustar # Czech PO debconf template translation of chemical-structures. # Copyright (C) 2010 Michal Simunek # This file is distributed under the same license as the chemical-structures package. # Michal Simunek , 2010 - 2011. # msgid "" msgstr "" "Project-Id-Version: chemical-structures 2.2.dfsg.0-3\n" "Report-Msgid-Bugs-To: chemical-structures@packages.debian.org\n" "POT-Creation-Date: 2011-03-26 12:36+0100\n" "PO-Revision-Date: 2011-05-28 12:09+0200\n" "Last-Translator: Michal Simunek \n" "Language-Team: Czech \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" #. Type: boolean #. Description #: ../chemical-structures.templates:1001 msgid "Should apache2 be restarted?" msgstr "Chcete nyní restartovat apache2?" #. Type: boolean #. Description #: ../chemical-structures.templates:1001 msgid "" "In order to activate the new configuration, apache2 has to be restarted. You " "can also restart apache2 by manually executing 'invoke-rc.d apache2 restart'." msgstr "" "Chcete-li nové nastavení aktivovat, je třeba restartovat apache2. Můžete jej " "také restartovat ručně příkazem 'invoke-rc.d apache2 restart'." debian/po/POTFILES.in0000644000000000000000000000007011543323066011361 0ustar [type: gettext/rfc822deb] chemical-structures.templates debian/po/es.po0000644000000000000000000000473211706544603010567 0ustar # chemical-structures po-debconf translation to Spanish # Copyright (C) 2010 Software in the Public Interest # This file is distributed under the same license as the chemical-structures package. # # Changes: # - Initial translation # Ricardo Fraile , 2010 # - Updated translation # Javier Fernández-Sanguino , 2012 # # Traductores, si no conocen el formato PO, merece la pena leer la # documentación de gettext, especialmente las secciones dedicadas a este # formato, por ejemplo ejecutando: # info -n '(gettext)PO Files' # info -n '(gettext)Header Entry' # # Equipo de traducción al español, por favor lean antes de traducir # los siguientes documentos: # # - El proyecto de traducción de Debian al español # http://www.debian.org/intl/spanish/ # especialmente las notas y normas de traducción en # http://www.debian.org/intl/spanish/notas # # - La guía de traducción de po's de debconf: # /usr/share/doc/po-debconf/README-trans # o http://www.debian.org/intl/l10n/po-debconf/README-trans # msgid "" msgstr "" "Project-Id-Version: chemical-structures 2.1\n" "Report-Msgid-Bugs-To: chemical-structures@packages.debian.org\n" "POT-Creation-Date: 2011-03-26 12:36+0100\n" "PO-Revision-Date: 2012-01-03 03:03+0100\n" "Last-Translator: Javier Fernández-Sanguino \n" "Language-Team: Debian l10n Spanish \n" "Language: es\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "X-POFile-SpellExtra: restart invoke rc\n" #. Type: boolean #. Description #: ../chemical-structures.templates:1001 msgid "Should apache2 be restarted?" msgstr "¿Debería reiniciarse apache2?" #. Type: boolean #. Description #: ../chemical-structures.templates:1001 msgid "" "In order to activate the new configuration, apache2 has to be restarted. You " "can also restart apache2 by manually executing 'invoke-rc.d apache2 restart'." msgstr "Tiene que reiniciarse apache para activar la nueva configuración.También puede reiniciar apache2 manualmente ejecutando «invoke-rc.d apache2 restart»." #~ msgid "Web server to reconfigure automatically:" #~ msgstr "Servidor web para reconfigurar automáticamente:" #~ msgid "" #~ "Please choose the web server that should be automatically configured to " #~ "run chemical-structures." #~ msgstr "Elija el servidor web que se debe configurar automáticamente para ejecutar «chemical-structures»." debian/po/ja.po0000644000000000000000000000237112174551551010547 0ustar # Copyright (C) 2010 Nobuhiro Iwamatsu # This file is distributed under the 2-clause BSD license. # Nobuhiro Iwamatsu , 2010, 2012. # msgid "" msgstr "" "Project-Id-Version: chemical-structures_2.2.dfsg.0-10\n" "Report-Msgid-Bugs-To: chemical-structures@packages.debian.org\n" "POT-Creation-Date: 2013-07-01 14:28+0000\n" "PO-Revision-Date: 2013-07-01 23:28+0900\n" "Last-Translator: Nobuhiro Iwamatsu \n" "Language-Team: Japanese \n" "Language: ja\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" #. Type: boolean #. Description #: ../chemical-structures.templates:1001 msgid "Should apache2 be restarted?" msgstr "apache2 を再起動しますか?" #. Type: boolean #. Description #: ../chemical-structures.templates:1001 msgid "" "In order to activate the new configuration, apache2 has to be restarted. You " "can also restart apache2 by manually executing 'invoke-rc.d apache2 restart'." msgstr "" "新規の設定を有効にするには、apache2 を再起動する必要があります。'invoke-rc.d " "apache2 restart' を手動で実行することで、apache2 を再起動することもできます。" debian/po/it.po0000644000000000000000000000357511543347725010605 0ustar # ITALIAN TRANSLATION OF CHEMICAL-STRUCTURES' PO-DEBCONF FILE. # COPYRIGHT (C) 2010 THE CHEMICAL-STRUCTURES' COPYRIGHT HOLDER # This file is distributed under the same license as the chemical-structures package. # # Vincenzo Campanella , 2010. # msgid "" msgstr "" "Project-Id-Version: chemical-structures 2.1.dfsg.1-6\n" "Report-Msgid-Bugs-To: chemical-structures@packages.debian.org\n" "POT-Creation-Date: 2011-03-26 12:36+0100\n" "PO-Revision-Date: 2010-11-07 11:41+0100\n" "Last-Translator: Vincenzo Campanella \n" "Language-Team: Italian \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" #. Type: boolean #. Description #: ../chemical-structures.templates:1001 #, fuzzy #| msgid "Should ${webserver} be restarted?" msgid "Should apache2 be restarted?" msgstr "Riavviare ${webserver}?" #. Type: boolean #. Description #: ../chemical-structures.templates:1001 #, fuzzy #| msgid "" #| "In order to activate the new configuration, ${webserver} has to be " #| "restarted. You can also restart ${webserver} by manually executing " #| "'invoke-rc.d ${webserver} restart'." msgid "" "In order to activate the new configuration, apache2 has to be restarted. You " "can also restart apache2 by manually executing 'invoke-rc.d apache2 restart'." msgstr "" "Affinché la nuova configurazione venga attivata è necessario riavviare " "${webserver}. È anche possibile riavviare manualmente ${webserver} eseguendo " "«invoke-rc.d ${webserver} restart»." #~ msgid "Web server to reconfigure automatically:" #~ msgstr "Server web da riconfigurare automaticamente:" #~ msgid "" #~ "Please choose the web server that should be automatically configured to " #~ "run chemical-structures." #~ msgstr "" #~ "Scegliere il server web che deve essere configurato automaticamente per " #~ "eseguire chemical-structures." debian/chemical-structures.postinst0000644000000000000000000000372012164115625014766 0ustar #! /bin/sh # postinst script for chemical-structures # # see: dh_installdeb(1) set -e # summary of how this script can be called: # * `configure' # * `abort-upgrade' # * `abort-remove' `in-favour' # # * `abort-deconfigure' `in-favour' # `removing' # # for details, see http://www.debian.org/doc/debian-policy/ or # the debian-policy package # . /usr/share/debconf/confmodule case "$1" in configure) # make a script executable chmod +x /usr/share/chemical-structures/convert.cgi # reconfigure the webserver if necessary if [ -e /usr/share/apache2/apache2-maintscript-helper ] ; then . /usr/share/apache2/apache2-maintscript-helper apache2_invoke enconf chemical-structures.conf elif dpkg-query -f '${Version}' -W 'apache2.2-common' > /dev/null 2>&1 ; then # if the configuration uses # uncomment the next line # a2enmod -q version f=/etc/apache2/conf.d/chemical-structures.conf if [ -f $f -a ! -L $f ]; then rm $f # remove plain file if it exists fi [ -d /etc/apache2/conf.d/ ] && \ ln -sf ../conf-available/chemical-structures.conf \ /etc/apache2/conf.d/chemical-structures.conf fi db_get chemical-structures/restart-webserver if [ "$RET" = "true" ]; then if [ -x /usr/sbin/invoke-rc.d ]; then invoke-rc.d apache2 reload || true else /etc/init.d/apache2 reload || true fi fi ;; abort-upgrade|abort-remove|abort-deconfigure) ;; *) echo "postinst called with unknown argument \`$1'" >&2 exit 1 ;; esac # dh_installdeb will replace this with shell code automatically # generated by other debhelper scripts. #DEBHELPER# exit 0 debian/compat0000644000000000000000000000000212145505271010366 0ustar 9 debian/chemical-structures.postrm0000644000000000000000000000222612145517047014432 0ustar #!/bin/sh # postrm script for chemical-structures # # see: dh_installdeb(1) set -e # summary of how this script can be called: # * `remove' # * `purge' # * `upgrade' # * `failed-upgrade' # * `abort-install' # * `abort-install' # * `abort-upgrade' # * `disappear' overwrit>r> # for details, see http://www.debian.org/doc/debian-policy/ or # the debian-policy package case "$1" in purge) rm -f /etc/apache2/conf-available/chemical-structures.conf rm -f /etc/apache2/conf-enabled/chemical-structures.conf [ -x /usr/sbin/invoke-rc.d ] && [ -f /etc/init.d/apache2 ] && invoke-rc.d apache2 reload ;; remove|upgrade|failed-upgrade|abort-upgrade) #nothing to do: do nothing gracefully true; ;; *) echo "postrm called with unknown argument \`$1'" >&2 exit 1 ;; esac # dh_installdeb will replace this with shell code automatically # generated by other debhelper scripts. #DEBHELPER# exit 0 debian/chemstruc.10000644000000000000000000000442111543343437011255 0ustar '\" t .\" Title: CHEMSTRUC .\" Author: Georges Khaznadar .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: juin 17, 2006 .\" Manual: [FIXME: manual] .\" Source: [FIXME: source] .\" Language: English .\" .TH "CHEMSTRUC" "1" "juin 17, 2006" "[FIXME: source]" "[FIXME: manual]" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" chemstruc \- calls a browser to view molecular structures .SH "SYNOPSIS" .HP \w'\fBchemstruc\fR\ 'u \fBchemstruc\fR .SH "DESCRIPTION" .PP \fBchemstruc\fR is a program to browse the chemical structures coming with the package chemical\-structures\&. .PP There are currently 253 molecular structures, in the following classes: alcohols, aldehydes, alkanes, alkenes, amides, amines, amino_acids, aromatics, carboxylic_acids, esters, ethers, fatty_acids, haloalkanes, ketones, nitriles, nucleobases, water\&. .SH "AUTHOR" .PP This manual page was written by Georges Khaznadar georgesk@ofset\&.org for the Debian(TM) system (but may be used by others)\&. Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by the Free Software Foundation\&. .PP On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common\-licenses/GPL\&. .SH "AUTHOR" .PP \fBGeorges Khaznadar\fR .RS 4 Author. .RE .SH "COPYRIGHT" .br Copyright \(co 2003 Georges Khaznadar .br debian/chemical-structures.manpages0000644000000000000000000000002311543343346014672 0ustar debian/chemstruc.1 debian/copyright0000644000000000000000000000354411543323066011132 0ustar This package was debianized by Georges Khaznadar on Fri, 16 Jun 2006 11:16:38 +0200. It was downloaded from http://www.pansanel.net/chemistry/resources/chemical-structures-0.8.src.tar.gz Copyright Holder: Jerome PANSANEL License: Copyright (c) 2006 Jerome Pansanel 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. 3. Neither the name of the University nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``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 REGENTS 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. ---------------- The file Jmol.js is licensed under the LGPL 2.1, see /usr/share/common-licenses/LGPL-2.1 debian/source/0000755000000000000000000000000011543324366010475 5ustar debian/source/format0000644000000000000000000000001411543324366011703 0ustar 3.0 (quilt) debian/manpage.xml0000644000000000000000000000653011543323066011327 0ustar .
    will be generated. You may view the manual page with: nroff -man .
    | less'. A typical entry in a Makefile or Makefile.am is: DB2MAN=/usr/share/sgml/docbook/stylesheet/xsl/nwalsh/\ manpages/docbook.xsl XP=xsltproc -''-nonet manpage.1: manpage.dbk $(XP) $(DB2MAN) $< The xsltproc binary is found in the xsltproc package. The XSL files are in docbook-xsl. Please remember that if you create the nroff version in one of the debian/rules file targets (such as build), you will need to include xsltproc and docbook-xsl in your Build-Depends control field. --> Georges"> Khaznadar"> juin 17, 2006"> 1"> georgesk@ofset.org"> CHEMSTRUC"> Debian"> GNU"> GPL"> ]>
    &dhemail;
    &dhfirstname; &dhsurname; 2003 &dhusername; &dhdate;     &dhucpackage; &dhsection; &dhpackage; calls a browser to view molecular structures &dhpackage; DESCRIPTION &dhpackage; is a program to browse the chemical structures coming with the package chemical-structures. There are currently 253 molecular structures, in the following classes: alcohols, aldehydes, alkanes, alkenes, amides, amines, amino_acids, aromatics, carboxylic_acids, esters, ethers, fatty_acids, haloalkanes, ketones, nitriles, nucleobases, water. AUTHOR This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the &gnu; General Public License, Version 2 any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.     debian/dirs0000644000000000000000000000010512145510013010036 0ustar usr/share/doc/chemical-structures usr/bin etc/apache2/conf-available debian/chemical-structures.templates0000644000000000000000000000042611543341343015077 0ustar Template: chemical-structures/restart-webserver Type: boolean Default: false _Description: Should apache2 be restarted? In order to activate the new configuration, apache2 has to be restarted. You can also restart apache2 by manually executing 'invoke-rc.d apache2 restart'. debian/README.source0000644000000000000000000000074211543333613011352 0ustar The source files come from http://sourceforge.net/projects/chem-file/files/Chemical%20Structures/2.2.0/chemical-structure-source-2.2.0.tgz/download The directory containing the source tree has been renamed to chemical-structures-2.2.dfsg.0 then every jar library has been removed from the subdirectory src/jmol This package should recommend the package Jmol as soon as it will be able to enter Debian. -- Georges Khaznadar , Sat, 26 Mar 2011 10:53:15 +0100 debian/docs0000644000000000000000000000000511543323066010037 0ustar TODO debian/changelog0000644000000000000000000002037112174552032011044 0ustar chemical-structures (2.2.dfsg.0-11) unstable; urgency=low * updated the file d/po/ja.po. Closes: #717706 -- Georges Khaznadar Fri, 26 Jul 2013 21:53:55 +0200 chemical-structures (2.2.dfsg.0-10) unstable; urgency=low * modified some dependencies, relaxed them down to recommendations Closes:#669749 * improved slightly the postinst script -- Georges Khaznadar Sun, 30 Jun 2013 22:37:41 +0200 chemical-structures (2.2.dfsg.0-9) unstable; urgency=low * Changed my DEBEMAIL * included Nobuhiro Iwamatsu's last version of d/po/ja.po file (Closes: #695079) * Updated compat-level and Standards-Version * Modified the management of the configuration file for Apache2 (Closes: #669749) * modified CMakeLists.txt files to build .xyz files for molecules -- Georges Khaznadar Fri, 17 May 2013 21:50:50 +0200 chemical-structures (2.2.dfsg.0-8) unstable; urgency=low * modified the postrm scripts to allow the purge even if appache2 was previously purged. Closes: #660586 -- Georges Khaznadar Wed, 22 Feb 2012 14:33:54 +0000 chemical-structures (2.2.dfsg.0-7) unstable; urgency=low * updated the Spanish po file, thanks to Javier Fernandez-Sanguino Pen~a Closes: #656401 -- Georges Khaznadar Sat, 21 Jan 2012 15:19:54 +0100 chemical-structures (2.2.dfsg.0-6) unstable; urgency=low * merged Joe's file da.po. Closes: #650949 -- Georges Khaznadar Sun, 04 Dec 2011 15:28:34 +0100 chemical-structures (2.2.dfsg.0-5) unstable; urgency=low * updated cs.po, thanks to Michal Simunek. Closes: #628212 -- Georges Khaznadar Sun, 19 Jun 2011 15:55:07 +0200 chemical-structures (2.2.dfsg.0-4) unstable; urgency=low * updated sv.po, thanks to Martin Bagge. Closes: #628930 -- Georges Khaznadar Fri, 03 Jun 2011 00:02:15 +0200 chemical-structures (2.2.dfsg.0-3) unstable; urgency=low * updated ru.po, thanks to Yuri Kozlov. Closes: #625933 * updated Standards-Version to 3.9.2 * fixed a spelling error in debian/Redme.debian and an article in description synopsis -- Georges Khaznadar Sat, 07 May 2011 13:47:34 +0200 chemical-structures (2.2.dfsg.0-2) unstable; urgency=low * updated the files pt.po, thanks to Américo Monteiro, fr.po, thanks to Christian Perrier, de.po, thanks to Martin Eberhard Schauer, Closes: #620085, #620169, #621731 -- Georges Khaznadar Fri, 08 Apr 2011 16:48:26 +0200 chemical-structures (2.2.dfsg.0-1) unstable; urgency=low * fixed the purge script. Closes: #619570 * upgraded to the newer upstream version. -- Georges Khaznadar Sat, 26 Mar 2011 09:47:25 +0100 chemical-structures (2.1.dfsg.1-10) unstable; urgency=low * integrated Ricardo Fraile's file. Closes: #603671 * integrated Nobuhiro Iwamatsu's file. Closes: #603886 -- Georges Khaznadar Thu, 18 Nov 2010 19:18:52 +0100 chemical-structures (2.1.dfsg.1-9) unstable; urgency=low * added the Itialian translation for debconf, thanks to Vincenzo Campanella * updated the Portuguese translation for debconf, thanks to Américo Monteiro Closes: #602761 * repeated Closes stances as multiple targets did not seem to work previoulsy: Closes: #601452 Closes: #601722 Closes: #602615 * integrated Martin Bagge's sv.po file. Closes: Bug#602796 * integrated Nobuhiro Iwamatsu's ja.po file. Closes: #602983 * integrated Michal Simunek cs.po file. Closes: #603040 * integrated Joe Dalton's da.po file. Closes: #603049 * integrated Martin Eberhard's de.po file. Closes: #603370 -- Georges Khaznadar Sat, 13 Nov 2010 21:13:37 +0100 chemical-structures (2.1.dfsg.1-8) unstable; urgency=low * inserted Christian Perrier's fr.po file * replaced "seveurs" by "serveur", following Stéphane Blondon's advice * added the Vietnamese translation. Closes: #602681 -- Georges Khaznadar Sun, 07 Nov 2010 16:08:59 +0100 chemical-structures (2.1.dfsg.1-7) unstable; urgency=low * added po-debconf translations by Michal Simunek, Américo Monteiro and Yuri Kozlov, respectively for Czech, Portuguese and Russian. Closes: #600197 #601452 #601722 #602615 -- Georges Khaznadar Sat, 06 Nov 2010 18:11:00 +0100 chemical-structures (2.1.dfsg.1-6) unstable; urgency=low * modified the templates file for debconf. reworked the French translation for deboconf templates. Closes: #602364 -- Georges Khaznadar Sat, 06 Nov 2010 15:03:48 +0100 chemical-structures (2.1.dfsg.1-5) unstable; urgency=low * added Martin Eberhard Schauer's de.po file, and slightly modified one template accordingly to his suggestion. Closes: #601776 -- Georges Khaznadar Mon, 01 Nov 2010 18:30:22 +0100 chemical-structures (2.1.dfsg.1-4) unstable; urgency=low * simplified the debconf dialog about apache, thanks to Christian Perrin's hint. Closes: #600500 * added debian/po.sv.po and made a tiny modification in the description's translation of the debconf dialog about apache. Closes: #600504 -- Georges Khaznadar Mon, 18 Oct 2010 10:45:26 +0200 chemical-structures (2.1.dfsg.1-3) unstable; urgency=low * upgraded the standards to 3.9.1 and compat to 7 * added a dependency on mics:Depends * changes the rules to build the package as arch-independent * added "set -e" in the config script. * changed "dh_clean -k" to "dh_prep" in debian/rules * first publication in Debian. Closes: #593126 -- Georges Khaznadar Sun, 15 Aug 2010 19:06:11 +0200 chemical-structures (2.1.dfsg.1-2) unstable; urgency=low * recompiled with newer standards -- Georges Khaznadar Mon, 21 Jun 2010 19:38:32 +0200 chemical-structures (2.1.dfsg.1-1) unstable; urgency=low * Upgraded to the new upstream version, removed the .jar files to comply with the DFSG. * remove references to binary files from src/CMakeLists.txt * removed the references to OpenBabel2Exe -- Georges Khaznadar Fri, 04 Jan 2008 14:18:48 +0100 chemical-structures (2.0.dfsg.1-2) unstable; urgency=low * new modifications, hinted by Daniel Leidert: * added a postinst script to remove the symlinks in /etc/apache*/conf.d -- Georges Khaznadar Fri, 19 Jan 2007 18:08:57 +0100 chemical-structures (2.0.dfsg.1-1) unstable; urgency=low * many modifications, hinted by Daniel Leidert * removed any binary file from the source (src/jmol/*.jar) * downgraded the recommendations of jmol, jmol-applet to suggestion * made better build-dependencies * added a recommendation on chemical-mime-data * added a dependency on python, apache* and openbabel * updated the copyright about Jmol.js * modified convert.cgi to manage gzipped source files upon conversion. -- Georges Khaznadar Wed, 17 Jan 2007 20:39:26 +0100 chemical-structures (2.0-2) unstable; urgency=low * added a chemical format converter option to the pages containing the molecules * added a CGI script to convert the molecules * added configuration scripts to configure the webserver * modified chemstruc to open an URL with a protocol http -- Georges Khaznadar Sat, 13 Jan 2007 20:05:11 +0100 chemical-structures (2.0-1) unstable; urgency=low * Upgrade to new upstream release -- Georges Khaznadar Fri, 12 Jan 2007 11:02:42 +0100 chemical-structures (1.0-2) unstable; urgency=low * modified the dependancy: added firefox -- Georges Khaznadar Sat, 11 Nov 2006 19:51:25 +0100 chemical-structures (1.0-1) unstable; urgency=low * Upgrade to new upstream release -- Georges Khaznadar Tue, 11 Jul 2006 16:32:29 +0200 chemical-structures (0.9-1) unstable; urgency=low * Upgrade to new upstream release * modified the command chemstruc to take in account $LANG -- Georges Khaznadar Wed, 21 Jun 2006 09:31:46 +0200 chemical-structures (0.8-1) unstable; urgency=low * Initial release -- Georges Khaznadar Wed, 21 Jun 2006 09:21:45 +0200 debian/rules0000755000000000000000000000243312145510022010240 0ustar #!/usr/bin/make -f # -*- makefile -*- # Sample debian/rules that uses debhelper. # This file was originally written by Joey Hess and Craig Small. # As a special exception, when this file is copied by dh-make into a # dh-make output file, you may use that output file without restriction. # This special exception was added by Craig Small in version 0.37 of dh-make. # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 DESTDIR = $(CURDIR)/debian/chemical-structures DB2MAN = /usr/share/sgml/docbook/stylesheet/xsl/nwalsh/manpages/docbook.xsl XP = xsltproc --nonet %: dh $@ override_dh_auto_clean: find . -name *.pyc | xargs rm -f rm -rf build dh_auto_clean debian/chemstruc.1: debian/manpage.xml cd debian; $(XP) $(DB2MAN) manpage.xml override_dh_auto_configure: mkdir -p build cd build; cmake -DCMAKE_INSTALL_PREFIX=$(DESTDIR)/usr .. override_dh_auto_build: debian/chemstruc.1 ## do nothing since install would run the build again. ## cd build; make override_dh_auto_install: cd build; make install install -m 755 convert.cgi $(DESTDIR)/usr/share/chemical-structures install -m 755 chemstruc $(DESTDIR)/usr/bin install -m 644 apache.conf $(DESTDIR)/etc/apache2/conf-available/chemical-structures.conf rm -f $(DESTDIR)/usr/share/chemical-structures/jmol/LICENSE.txt debian/README.Debian0000644000000000000000000000113611561234120011223 0ustar chemical-structures for Debian ------------------------------ chemical-structure recommends Jmol (jmol-applet), which has been already packaged for Debian, see http://debian.wgdd.de/repository http://debian.wgdd.de/debian/ the following line in sources.list allows one to access the package: # for Jmol deb http://debian.wgdd.de/debian unstable main contrib non-free if you install the package JMol, you should make a soft link from /usr/share/chemical-structures/jmol to the directory where the file Jmol.js is located. -- Georges Khaznadar , Sat, 7 May 2011 14:17:20 +0200