bodr-10/0000755000175000017500000000000012205735330007223 500000000000000bodr-10/install-sh0000755000175000017500000003325512201027520011146 00000000000000#!/bin/sh # install - install a program, script, or datafile scriptversion=2011-11-20.07; # UTC # This originates from X11R5 (mit/util/scripts/install.sh), which was # later released in X11R6 (xc/config/util/install.sh) with the # following copyright and license. # # Copyright (C) 1994 X Consortium # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to # deal in the Software without restriction, including without limitation the # rights to use, copy, modify, merge, publish, distribute, sublicense, and/or # sell copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 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Fixed all atomic masses accordingly to the latest publication of the IUPAC. * elements/mass.bibxml: Added latest atomic table publication. * tests/AtWt.xsl: Fixed handling of non-breaking spaces and the latest IUPAC website. * isotopes/isotopes.*: Added the half-lives of 209Th and 238Th (fixes #9) * elements/elements.xml: Fixed the groups of Ds and Mt * elements/elements.xml|symbols.bibxml: Lv and Fl got official names * README, COPYING: in agreement with the following email, changed the license to CCZero * elements/elements.xml: Fixed description for Copernicium. * crystal/space-groups.xml: fixed Hall name for group 205. * elements/elements.xml: Fixed atomic weight for Rutherfordium accordingly to IUPAC AtWt table. Release version 9 2010-04-25 * Atomic weights have been updated to correspond with the IUPAC table (KDE#192551). * Minor bug-fixes in the elements database (KDE#192616). * Fix in the space group table. * Added name for element 112: copernicum (KDE#235313). * Updated mass of H2 to current value from webelements.com (closes #2989934 on sf.net) Release version 8 2008-03-02 * Uses CML 2.5, with two tweaks: missing Rg and Ds; allow inside * Fixes the distcheck errors: correct dictionary schematron (closes #1905375 on sf.net) Release version 7 2008-03-01 * Adds spacegroup information * Removed unnecessary paths (closes #1713504 sf.net) * Make system fixes * Output PUBLIC and SYSTEM IDs for XHTML * Adding documentation for discoveryDate * Added information about elements 112-118 Release version 6 2007-03-10 * The .txt source files now mention the license too, instead of '??' * updated elemental masses according to a 2006 IUPAC publication (closes SF bug #1660527) Release version 5 2006-12-27 * The actinoids are now listed as 'other metal' (closes SF bug #1603063) * The acidity information was removed (closes SF bug #1603066) Release Version 4 2006-10-16 * Isotope and element data now conforms a Schematron convention. * XML files are now valid CML 2.3 files * Fixed name of C.W.Scheele * Added element crystal structure data * Added country where elements were discovered Release Version 3 2006-06-07 * Fixed a stupid mistake in the newly shipped pkgconfig file. See Version 2 for other changes. Release Version 2 2006-06-07 * Fixed missing root node in isotopes.xml. * Fixed build issues. * Added isotope info: decay and spin. * Added HTML bibliography for elements.xml Release Version 1 2006-02-08 * first tar.gz release bodr-10/missing0000755000175000017500000001533112201027520010534 00000000000000#! /bin/sh # Common wrapper for a few potentially missing GNU programs. scriptversion=2012-06-26.16; # UTC # Copyright (C) 1996-2013 Free Software Foundation, Inc. # Originally written by Fran,cois Pinard , 1996. # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2, or (at your option) # any later version. # This program 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. 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bodr-10/bibtexml-xslt/COPYING0000644000175000017500000004311012176645770013012 00000000000000 GNU GENERAL PUBLIC LICENSE Version 2, June 1991 Copyright (C) 1989, 1991 Free Software Foundation, Inc. 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Library General Public License instead.) You can apply it to your programs, too. 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If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. 9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation. 10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. NO WARRANTY 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. 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 program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program 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 General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Also add information on how to contact you by electronic and paper mail. If the program is interactive, make it output a short notice like this when it starts in an interactive mode: Gnomovision version 69, Copyright (C) year name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program. You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the program, if necessary. Here is a sample; alter the names: Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (which makes passes at compilers) written by James Hacker. , 1 April 1989 Ty Coon, President of Vice This General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Library General Public License instead of this License. bodr-10/bibtexml-xslt/harvard-helper.xsl0000644000175000017500000000742712176645770015426 00000000000000 , ` : ' in , , pp. , p. , vol. , no. , . . & , (eds) (ed.) , : bodr-10/bibtexml-xslt/html-harvard.xsl0000644000175000017500000001324612176645770015107 00000000000000

.

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Pauling The Nature of the Chemical Bond 1960 3rd Cornell Univ. USA J.E. Huheey, E.A. Keiter, and R.L. Keiter Inorganic Chemistry: Principles of Structure and Reactivity 1993 4th HarperCollins New York, USA A.L. Allred J. Inorg. Nucl. Chem. 1961 17 215 http://www.webelements.com/ bodr-10/elements/ionization.bibxml0000644000175000017500000000116112176645770014357 00000000000000 W.C. Martin, A. Musgrove, S. Kotochigova, and J.E. Sansonetti Ground Levels and Ionization Energies for the Neutral Atoms (version 1.3) 2003 http://physics.nist.gov/IonEnergy 2005 http://physics.nist.gov/IonEnergy National Institute of Standards and Technology Gaithersburg, MD. bodr-10/elements/symbols.bibxml0000644000175000017500000000242412176646565013672 00000000000000 Pure Appl. Chem. 1997 69 12 2471-2473 Pure Appl. Chem. 2003 75 10 1613-1615 Pure Appl. Chem. 2004 76 12 2101-2103 Tatsumi, K. and Corish, J. Pure Appl. Chem. 2010 82 3 753-755 10.1351/PAC-REC-09-08-20 Loss, R.D. and Corish, J. Pure Appl. Chem. 2012 84 7 1669-1672 10.1351/PAC-REC-11-12-03 bodr-10/elements/crystalstructures.xml0000644000175000017500000016661512176645770015364 00000000000000 470.0 470.0 340.0 90.0 90.0 120.0 424.2 424.2 424.2 90.0 90.0 90.0 351.0 351.0 351.0 90.0 90.0 90.0 228.58 228.58 358.43 90.0 90.0 90.0 506.0 506.0 506.0 58.06 58.06 58.06 246.4 246.4 671.1 90.0 90.0 120.0 386.1 386.1 626.5 90.0 90.0 120.0 540.3 342.9 508.6 90.0 132.53 90.0 550.0 328.0 728.0 90.0 90.0 90.0 442.9 442.9 442.9 90.0 90.0 90.0 429.06 429.06 429.06 90.0 90.0 90.0 320.94 320.94 524.08 90.0 90.0 120.0 404.95 404.95 404.95 90.0 90.0 90.0 543.09 543.09 543.09 90.0 90.0 90.0 1145.0 505.3 1126.1 71.84 90.37 71.56 1043.7 1284.5 2436.9 90.0 90.0 90.0 622.35 445.61 817.85 90.0 90.0 90.0 525.6 525.6 525.6 90.0 90.0 90.0 532.8 532.8 532.8 90.0 90.0 90.0 558.84 558.84 558.84 90.0 90.0 90.0 330.9 330.9 527.33 90.0 90.0 120.0 295.8 295.8 468.55 90.0 90.0 120.0 303.0 303.0 303.0 90.0 90.0 90.0 291.0 291.0 291.0 90.0 90.0 90.0 891.25 891.25 891.25 90.0 90.0 90.0 286.65 286.65 286.65 90.0 90.0 90.0 250.71 250.71 406.95 90.0 90.0 120.0 352.4 352.4 352.4 90.0 90.0 90.0 361.49 361.49 361.49 90.0 90.0 90.0 266.49 266.49 494.68 90.0 90.0 120.0 451.97 766.33 452.6 90.0 90.0 90.0 565.75 565.75 565.75 90.0 90.0 90.0 375.98 375.98 1054.75 90.0 90.0 120.0 905.4 908.3 1160.1 90.0 90.81 90.0 672.65 464.51 870.23 90.0 90.0 90.0 570.6 570.6 570.6 90.0 90.0 90.0 558.5 558.5 558.5 90.0 90.0 90.0 608.49 608.49 608.49 90.0 90.0 90.0 364.74 364.74 573.06 90.0 90.0 120.0 323.2 323.2 514.7 90.0 90.0 120.0 330.04 330.04 330.04 90.0 90.0 90.0 314.7 314.7 314.7 90.0 90.0 90.0 273.5 273.5 438.8 90.0 90.0 120.0 270.59 270.59 428.15 90.0 90.0 120.0 380.34 380.34 380.34 90.0 90.0 90.0 389.07 389.07 389.07 90.0 90.0 90.0 408.53 408.53 408.53 90.0 90.0 90.0 297.94 297.94 561.86 90.0 90.0 120.0 325.23 325.23 494.61 90.0 90.0 90.0 583.18 583.18 318.19 90.0 90.0 90.0 430.7 430.7 1127.3 90.0 90.0 120.0 445.72 445.72 592.9 90.0 90.0 120.0 718.02 471.02 981.03 90.0 90.0 90.0 620.23 620.23 620.23 90.0 90.0 90.0 614.1 614.1 614.1 90.0 90.0 90.0 502.8 502.8 502.8 90.0 90.0 90.0 377.2 377.2 1214.4 90.0 90.0 120.0 362.0 362.0 599.0 90.0 90.0 120.0 367.25 367.25 1183.54 90.0 90.0 120.0 365.8 365.8 1179.9 90.0 90.0 120.0 362.1 362.1 2625.0 90.0 90.0 120.0 458.1 458.1 458.1 90.0 90.0 90.0 363.6 363.6 578.26 90.0 90.0 120.0 360.1 360.1 569.36 90.0 90.0 120.0 359.3 359.3 565.37 90.0 90.0 120.0 357.73 357.73 561.58 90.0 90.0 120.0 355.88 355.88 558.74 90.0 90.0 120.0 353.75 353.75 555.46 90.0 90.0 120.0 548.47 548.47 548.47 90.0 90.0 90.0 350.31 350.31 555.09 90.0 90.0 120.0 319.64 319.64 505.11 90.0 90.0 120.0 330.13 330.13 330.13 90.0 90.0 90.0 316.52 316.52 316.52 90.0 90.0 90.0 276.1 276.1 445.6 90.0 90.0 120.0 273.44 273.44 431.73 90.0 90.0 120.0 383.9 383.9 383.9 90.0 90.0 90.0 392.42 392.42 392.42 90.0 90.0 90.0 407.82 407.82 407.82 90.0 90.0 90.0 300.5 300.5 300.5 70.52 70.52 70.52 345.66 345.66 552.48 90.0 90.0 120.0 495.08 495.08 495.08 90.0 90.0 90.0 667.4 611.7 330.4 90.0 110.33 90.0 335.9 335.9 335.9 90.0 90.0 90.0 514.8 514.8 514.8 90.0 90.0 90.0 567.0 567.0 567.0 90.0 90.0 90.0 508.42 508.42 508.42 90.0 90.0 90.0 392.5 392.5 323.8 90.0 90.0 90.0 285.37 586.95 495.48 90.0 90.0 90.0 666.3 472.3 488.7 90.0 90.0 90.0 618.3 482.2 1096.3 90.0 101.79 90.0 346.81 346.81 1124.1 90.0 90.0 120.0 349.6 349.6 1133.1 90.0 90.0 120.0 341.6 341.6 1106.9 90.0 90.0 120.0 338.0 338.0 1102.5 90.0 90.0 120.0 bodr-10/TODO0000644000175000017500000000166512176645770007662 00000000000000BODR 9 ----------------------------------------------------------------------- - create test-sheet to check our bo:mass values (including the error-values) against the one in http://www.chem.qmul.ac.uk/iupac/AtWt/ - implement spell check of our database (aspell, ispell? - aspell can handle XML) http://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl?ele=&all=all&ascii=html&isotype=some http://www.nndc.bnl.gov/masses/ http://nucleardata.nuclear.lu.se/nucleardata/toi/listnuc.asp?sql=&HlifeMin=1e30&tMinStr=1e30+s&HlifeMax=1e40&tMaxStr=1e+40+s BODR 8 ----------------------------------------------------------------------- - integrate typing, residues, etc - add a XSLT to create HTML for the element and isotope lists - add help on how XSLT can be used to create TXT - have the Schematron check for undefined dictionary references (Schematron/xmllint does not seem to like the document() function :( ) - check bug reports on SF bodr-10/schemas/0000755000175000017500000000000012205735327010654 500000000000000bodr-10/schemas/Makefile.am0000644000175000017500000000023212176645770012636 00000000000000 EXTRA_DIST = \ bibtexml.xsd \ cml25.xsd \ elements.schematron \ isotopes.schematron \ dictionary.schematron MAINTAINERCLEANFILES = \ Makefile.in bodr-10/schemas/elements.schematron0000644000175000017500000000366512176645770014520 00000000000000 Convention for CML format for the BODR element data file. The root element must specify @convention="bodr". The root must be <list>. The document must contain a <metadataList>. The <atom> element must have an @id attribute. The <metadataList> element must the title of the document. The <metadataList> element must specify the license of the document. The <metadataList> element must at least specify one contributor. The atomic number must be given for each entry. The element symbol must be given for each entry. bodr-10/schemas/isotopes.schematron0000644000175000017500000000466312176645770014550 00000000000000 Convention for CML format for the BODR element data file. The root element must specify @convention="bodr:isotopes". The root must be <list>. The document must contain a <metadataList>. Each element must specify at least one <isotope>. The <isotopeList> element must have an @id attribute. The <isotope> element must have an @id attribute. The <isotope> element must have an @number attribute. The <isotope> element must have an @elementType attribute. The <metadataList> element must the title of the document. The <metadataList> element must specify the license of the document. The <metadataList> element must at least specify one contributor. The atomic number must be given for each entry. The exact mass must be given for each entry. bodr-10/schemas/bibtexml.xsd0000644000175000017500000011120412176645770013132 00000000000000 BibteXML bibliography schema Author: Z.W. Hendrikse Version: Adapted from $Revision: 1.1.1.1 $ Copyright: GPL An abstract of the work. The authors affiliation. A Table of Contents. Copyright information. Digital Object Identifier number. Key words used for searching or possibly for annotation. The language the document is in. The Library of Congress Call Number, also seen as lib-congress. A location associated with the entry, such as the city in which a conference took place. The Mathematical Reviews number. The price of the document. The physical dimensions of a work. The WWW Universal Resource Locator that points to the item being referenced. This often is used for technical reports to point to the ftp site where the postscript source of the report is located. Category of this bibitem, added by Zeger W. Hendrikse. The bibteXML equivalent of the @article tag. An article from a journal or magazine. Required fields: author, title, journal, year. Optional fields: volume, number, pages, month, note. The bibteXML equivalent of the @book tag. A book with an explicit publisher. Required fields: author or editor, title, publisher, year. Optional fields: volume or number, series, address, edition, month, note. The bibteXML equivalent of the @booklet tag. A work that is printed and bound, but without a named publisher or sponsoring institution. Required fields: title. Optional fields: author, howpublished, address, month, year, note. The bibteXML equivalent of the @conference tag. The same as INPROCEEDINGS, included for Scribe compatibility. The bibteXML equivalent of the @inbook tag. A part of a book, which may be a chapter (or section or publisher or sponsoring institution. Required fields: author or editor, title, chapter and/or pages, publisher, year. Optional fields: fields: volume or number, series, type, address, edition, month, note. The bibteXML equivalent of the @incollection tag. A part of a book having its own title. Required fields: author, title, booktitle, publisher, year. Optional fields: editor, volume or number, series, type, chapter, pages, address, edition, month, note. The bibteXML equivalent of the @inproceedings tag. An article in a conference proceedings. Required fields: author, title, booktitle, year. Optional fields: editor, volume or number, series, pages, address, month, organization, publisher, note. The bibteXML equivalent of the @manual tag. Technical documentation. Required field: title. Optional fields: author, organization, address, edition, month, year, note. The bibteXML equivalent of the @mastersthesis tag. A Master's thesis. Required fields: author, title, school, year. Optional fields: type, address, month, note. The bibteXML equivalent of the @misc tag. Use this type when nothing else fits. Required fields: none. Optional fields: author, title, howpublished, month, year, note. The bibteXML equivalent of the @phdthesis tag. A PhD thesis. Required fields: author, title, school, year. Optional fields: type, address, month, note. The bibteXML equivalent of the @proceedings tag. The proceedings of a conference. Required fields: title, year. Optional fields: editor, volume or number, series, address, month, organization, publisher, note. The bibteXML equivalent of the @techreport tag. A report published by a school or other institution, usually numbered within a series. Required fields: author, title, institution, year. Optional fields: type, number, address, month, note. The bibteXML equivalent of the @unpublished tag. A document having an author and title, but not formally published. Required fields: author, title, note. Optional fields: month, year. Usually the address of the publisher or other type of institution. For major publishing houses, van Leunen recommends omitting the information entirely. For small publishers, on the other hand, you can help the reader by giving the complete address. An annotation. It is not used by the standard bibliography styles, but may be used by others that produce an annotated bibliography. The name(s) of the author(s), in the format described in the LaTeX book. Title of a book, part of which is being cited. See the LaTeX book for how to type titles. For book entries, use the title field instead. A chapter (or section or whatever) number. The database key of the entry being cross referenced. The edition of a book-for example, ``Second''. This should be an ordinal, and should have the first letter capitalized, as shown here; the standard styles convert to lower case when necessary. Name(s) of editor(s), typed as indicated in the LaTeX book. If there is also an author field, then the editor field gives the editor of the book or collection in which the reference appears. How something strange has been published. The first word should be capitalized. The sponsoring institution of a technical report. A journal name. Abbreviations are provided for many journals; see the Local Guide. Used for alphabetizing, cross referencing, and creating a label when the ``author'' information (described in Section [ref: ] is missing. This field should not be confused with the key that appears in the \cite command and at the beginning of the database entry. The month in which the work was published or, for an unpublished work, in which it was written You should use the standard three-letter abbreviation, as described in Appendix B.1.3 of the LaTeX book. As XML Schema supports a special month format, it is decided to allow e.g. 05 (for May) too. Any additional information that can help the reader. The first word should be capitalized. The number of a journal, magazine, technical report, or of a work in a series. An issue of a journal or magazine is usually identified by its volume and number; the organization that issues a technical report usually gives it a number; and sometimes books are given numbers in a named series. The organization that sponsors a conference or that publishes a manual. One or more page numbers or range of numbers, such as 42-111 or 7,41,73-97 or 43+ (the `+" in this last example indicates pages following that don"t form a simple range). To make it easier to maintain Scribe-compatible databases, the standard styles convert a single dash (as in 7-33) to the double dash used in TeX to denote number ranges (as in 7-33). The publisher's name. The name of the school where a thesis was written. The name of a series or set of books. When citing an entire book, the the title field gives its title and an optional series field gives the name of a series or multi-volume set in which the book is published. The work's title, typed as explained in the LaTeX book. The work's title, typed as explained in the LaTeX book. The volume of a journal or multivolume book. The year of publication or, for an unpublished work, the year it was written. Generally it should consist of four numerals, such as 1984. Although the standard styles can handle any year whose last four nonpunctuation characters are numerals, such as `(about 1984)", it is decided here to keep the year limited to four numerals, as such a type is pre-defined in XML Schema. bodr-10/schemas/cml25.xsd0000644000175000017500000210556512176645770012265 00000000000000 Describes whether child elements are sequential or parallel. There is no default. The type of an alternative. This adds semantics to an _alternative_ and might be used by an RDF or related engine. An enumeration of allowed angle units. May be obsolete. An identifier for an atom. Of the form prefix:suffix where prefix and suffix are purely alphanumeric (with _ and -) and prefix is optional. This is similar to XML IDs (and we promote this as good practice for atomIDs. Other punctuation and whitespace is forbidden, so IDs from (say) PDB files are not satisfactory. The prefix is intended to form a pseudo-namespace so that atom IDs in different molecules may have identical suffixes. It is also useful if the prefix is the ID for the molecule (though this clearly has its limitation). Atom IDs should not be typed as XML IDs since they may not validate. An array of atomRefs. The atomRefs cannot be schema- or schematron-validated. Instances of this type will be used in array-style representation of bonds and atomParitys. It can also be used for arrays of atomIDTypes such as in complex stereochemistry, geometrical definitions, atom groupings, etc. A reference to two distinct existing atoms in order. A reference to three distinct existing atoms in order. A reference to four distinct existing atoms in order. A reference to an existing atom. An array of references to bonds. The references cannot (yet) cannot be schema- or schematron-validated. Instances of this type will be used in array-style representation of electron counts, etc. It can also be used for arrays of bondIDTypes such as in complex stereochemistry, geometrical definitions, bond groupings, etc. A reference to an existing bond. A reference to a bond may be made by atoms (e.g. for multicentre or pi-bonds), electrons (for annotating reactions or describing electronic properties) or possibly other bonds (no examples yet). The semantics are relatively flexible. A box in 3-space. Defined by 6 real numbers (x1 y1 z1 x2 y2 z2). By default these are Cartesian coordinates (with units specified elsewhere - responsibility of schema creator.) If there is a means of specifying oblique axes (e.g. crystallographic cell) the box may be a parallelipiped. The components are grouped in threes ans separated by a semicolon to avoid problems of guessing the convention. enumerated type of cellParameter The chirality of a system or molecule. This is being actively investigated by a IUPAC committee (2002) so the convention is likely to change. No formal default. A pair of floats representing a complex number. This example is schema-invalid as it has three floats An x/y coordinate pair. An x/y coordinate pair consisting of two real numbers, separated by whitespace or a comma. In arrays and matrices, it may be useful to set a separate delimiter An x/y/z coordinate triple. An x/y/z coordinate triple consisting of three real numbers, separated by whitespace or commas. In arrays and matrices, it may be useful to set a separate delimiter. An array of coordinateComponents for a single coordinate. An array of coordinateComponents for a single coordinate where these all refer to an X-coordinate (NOT x,y,z).Instances of this type will be used in array-style representation of 2-D or 3-D coordinates. Currently no machine validation. Currently not used in STMML, but re-used by CML (see example). Array of counts. Normally, but not always, integers. can be used with a number of elements 2005-11-01: PMR the combination of dataType and list does not work with JUMBO5.0 - so for the meantime we have removed the restriction A count multiplier for an object. Many elements represent objects which can occur an arbitrary number of times in a scientific context. Examples are action, object or molecules. 2005-10-16. Changed to positiveNumerType. an enumerated type for all dataTypes in STM. dataTypeType represents an enumeration of allowed dataTypes (at present identical with those in XML-Schemas (Part2- datatypes). This means that implementers should be able to use standard XMLSchema-based tools for validation without major implementation problems. It will often be used an an attribute on scalar, array or matrix elements. Note: the attribute xsi:type might be used to enforce the type-checking but I haven't worked this through yet. A single non-whitespace character to separate components in arrays. Some STMML elements (such as array) have content representing concatenated values. The default separator is whitespace (which can be normalised) and this should be used whenever possible. However in some cases the values are empty, or contain whitespace or other problematic punctuation, and a delimiter is required. Note that the content string MUST start and end with the delimiter so there is no ambiguity as to what the components are. Only printable characters from the ASCII character set should be used, and character entities should be avoided. When delimiters are used to separate precise whitespace this should always consist of spaces and not the other allowed whitespace characters (newline, tabs, etc.). If the latter are important it is probably best to redesign the application. At present there is a controlled pattern of characters selected so as not to collide with common usage in XML document The values in the array are "A", "B12", "" (empty string) and "D and E" note the spaces A dictionaryPrefix used to identify a dictionary, units, convention or other metadata. 2005-12-12: PMR. Added for use with dictionary The dictionary prefix must conform to XSD. Allowed values for dimension Types in quantities. These are the 7 types prescribed by the SI system, together with the "dimensionless" type. We intend to be somewhat uncoventional and explore enhanced values of "dimensionless", such as "angle". This may be heretical, but we find the present system impossible to implement in many cases. Used for constructing entries in a dictionary of units An angl. (formally dimensionless, but useful to have units). Orientation of the eigenvector matrix. Specifies whether the rows or columns of the (square) matrix correspond to the eigenvectors. For example, in molecular orbitals the vectors are normally represented as columns, and each column would correspond to a different eigenvalue 2006-01-13: PMR. Created. The columns are the eigenvectors. The columns are the eigenvectors. An array of elementTypes. Instances of this type will be used in array-style representation of atoms. Allowed elementType values. The periodic table (up to element number 118. In addition the following strings are allowed: Du. ("dummy") This does not correspond to a "real" atom and can support a point in space or within a chemical graph. R. ("R-group") This indicates that an atom or group of atoms could be attached at this point. Any isotope of hydrogen. There are no special element symbols for D and T which should use the isotope attribute. A point or object with no chemical semantics. Examples can be centroids, bond-midpoints, orienting "atoms" in small z-matrices. Note "Dummy" has the same semantics but is now deprecated. A point at which an atom or group might be attached. Examples are abbreviated organic functional groups, Markush representations, polymers, unknown atoms, etc. Semantics may be determined by the role attribute on the atom. The basis of an error value. Errors in values can be of several types and this simpleType provides a small controlled vocabulary. Array of error estimate values. An observed or calculated estimate of the error in the value of a numeric quantity. It should be ignored for dataTypes such as URL, date or string. The statistical basis of the errorValueType is not defined - it could be a range, an estimated standard deviation, an observed standard error, etc. This information can be added through _errorBasisType_. An estimate of the error in the value of a quantity. An observed or calculated estimate of the error in the value of a numeric quantity. It should be ignored for dataTypes such as URL, date or string. The statistical basis of the errorValueType is not defined - it could be a range, an estimated standard deviation, an observed standard error, etc. This information can be added through _errorBasisType_. OBSOLETE An array of floats. An array of floats or other real numbers. Not used in STM Schema, but re-used by CML and other languages. Array of formalCharges. Used for electron-bookeeping. This has no relation to its calculated (fractional) charge or oxidation state. The formal charge on an object. Used for electron-bookeeping. This has no relation to its calculated (fractional) charge or oxidation state. Format of a spectrum. The data structure of the spectrum. (Not the format of the data). This describes how the data structure is to be interpreted. one dimensional spectru. Data are represented by two _array_s, one representing the independent variable (e.g. wavelength, mass number) and the other the measured dependent variable (absorption, intensity, etc.). This can normally be plotted directly with the independent variable as the x-axis. The order of the points is not necessarily significant and may be increasing or decreasing. Two dimensional spectru. Data are represented by a single symmetric _matrix_ with both axes identical (i.e. the same independent variable). A typical example is a "2D 1HNMR spectrum". The dependent variable is represented by the matrix elements. This can normally be plotted as a square symmentric about a diagonal. Two dimensional spectrum with different axe. Data are represented by non-square _matrix_ with independent axes. A typical example is a "2D 1H 13C NMR spectrum". The dependent variable is represented by the matrix elements. . A concise representation for a molecular formula. This MUST adhere to a whitespaced syntax so that it is trivially machine-parsable. Each element is followed by its count (which may be decimal), and the string is optionally ended by a formal charge (of form d or -d, i.e. no '+') NO brackets or other nesting is allowed. 2005-08-30: allowed decimal points Domain of an FT spectrum. Indicates whether a spectrum is raw FID or has been transforme. Data are raw, so will normally require transforming. Data have been transformed. This value indicates that an FT experiment and transformation have been performe. This was not known to be an FT experiment. (It may have been, but the author or abstracter omitted to mention it). The head linker in a polymeric repeat unit A polymeric chain may be described by liniing the head of one repeat unit to the tail or head of another. The head attribute indicates the atom id (normally on an atom of elementType="R") which acts as the head 2006-05-20: PMR added Array of hydrogenCounts. The total number of hydrogen atoms bonded to an atom or contained in a molecule, whether explicitly included as atoms or not. It is an error to have hydrogen count less than the explicit hydrogen count. There is no default value and no assumptions about hydrogen Count can be made if it is not given. If hydrogenCount is given on every atom, then the values can be summed to give the total hydrogenCount for the (sub)molecule. Because of this hydrogenCount should not be used where hydrogen atoms bridge 2 or more atoms. The total number of hydrogen atoms bonded to an object. The total number of hydrogen atoms bonded to an atom or contained in a molecule, whether explicitly included as atoms or not. It is an error to have hydrogen count less than the explicit hydrogen count. There is no default value and no assumptions about hydrogen Count can be made if it is not given. If hydrogenCount is given on every atom, then the values can be summed to give the total hydrogenCount for the (sub)molecule. Because of this hydrogenCount should not be used where hydrogen atoms bridge 2 or more atoms. An array of ids or idRefs. See idType. A unique ID for an element. This is not formally of type ID (an XML NAME which must start with a letter and contain only letters, digits and .-_:). It is recommended that IDs start with a letter, and contain no punctuation or whitespace. The function in XSLT will generate semantically void unique IDs. It is difficult to ensure uniqueness when documents are merged. We suggest namespacing IDs, perhaps using the containing elements as the base. Thus mol3:a1 could be a useful unique ID. However this is still experimental. Inheritance mechanism. A reference to an existing element can be used to supplement values such as coordinates. The inheritance attribute determines whether the values are supplemented, overwritten or deleted. In the example: <molecule id="m1" view="initial"> <atomArray> <atom id="a1" x3="0.1"/> </atomArray> </molecule> <!-- this adds more information --> <molecule ref="m1" view="initial" inherit="supplement"> <atomArray> <atom id="a1" hydrogenCount="1"/> </atomArray> </molecule> <!-- this will overwrite the previous values --> <molecule ref="m1" inherit="overwrite" view="final" id="m2"> <atomArray> <atom id="a1" x3="0.1"/> </atomArray> </molecule> <!-- this will delete the previous values --> <molecule ref="m1" inherit="delete" view="restart"> <atomArray> <atom id="a1" hydrogenCount=""/> </atomArray> </molecule> The first molecule/@ref adds complementary information, the second changes the values. Software is allowed to generate two independent copies of the molecule and reference them by different IDs (m1 and m2). This mechanism is necessary to manage the implied inheritance of partial information during minimisations and dynamics. It requires careful software implementation. Values from this element will be merged. The merging is element-specific with the intention that information from the current element will not conflict with the existing information. It is an error if there is a conflict. Values from this element will replace existing information. The merging is element-specific with the intention that information from the current element will replace the existing information. Components of this element will de deleted if they exist. An array of integers. An array of integers; for re-use by other schemas. Not machine-validatable. The numeric representation of an isotope. In core CML this represents a single number; either the combined proton/neutron count or a more accurate estimate of the nuclear mass. This is admittedly fuzzy, and requires a more complex object (which can manage conventions, lists of isotopic masses, etc.) See isotope. The default is "natural abundance" - whatever that can be interpreted as. Delta values (i.e. deviations from the most abundant istopic mass) are never allowed. A fractional representation of the spin of the nucleus. Allowed lattice types. lattice with A centering. A lattice which uses the translation operator {0, 0.5, 0.5}. User-defined lattice-type. This definition must be by reference to a namespaced dictionary entry. An unbounded line in 3-space. Defined by 6 real numbers, conventionally an arbitrary point on the line and a vector3. There is no significance to the point (i.e. it is not the "end of the line") and there are an infinite number of ways of representing the line. DANGER. Line3 now uses the point3 and vector3 attributes and the line3Type may be OBSOLETED. The type of the link. A container for locators. A link to an element. A labelled link. symbolic represention of l amd m. takes avlues of s, p, px, dxy, dx2y2, f, etc. A 4x4 transformation matrix This is the base for extending the transform3 element. Allowed matrix types. Many are square matrices. By default all elements must be included. For symmetric, antisymmetric and diagonal matrices some compression is possible by not reporting the identical or forced zero elements. These have their own subtypes, usually with UT or LT appended. Use these with caution as there is chance of confusion and you cannot rely on standard software to read these. The matrix type fixes the order and semantics of the elements in the XML element but does not mandate any local syntax. Thus an application may insert newline characters after each row or use a <row> element. Rectangular with no semantic constraints and ordered rowwise (i.e. the column index runs fastest). 1 2 3 4 0 3 5 6 Square with no semantic constraints. 1 2 78 3 4 -1 -34 2 7 Square symmetric with all elements explicit. 1 2 3 2 7 1 3 1 9 Square symmetric with the diagonal and lower triangle explicit and the upper triangle omitted. Rows are of length 1, 2, 3... 1 2 7 3 1 9 is equivalent to 1 2 3 2 7 1 3 1 9 Square symmetric with the diagonal and upper triangle explicit. Rows are of length n, n-1, ... 2, 1 1 7 9 2 -1 34 is equivalent to 1 7 9 7 2 -1 9 -1 34 Square antisymmetric with all elements explicit. The diagonal is necessarily zero. 0 -2 3 2 0 1 -3 -1 0 Square symmetric with the lower triangle explicit and diagonal and upper triangle omitted. Rows are of length 1, 2,... n-1. -7 -9 1 is equivalent to 0 7 9 -7 0 -1 -9 1 0 Square symmetric with the upper triangle explicit and diagonal and lower triangle omitted. Rows are of length n-1, n-2,... 2,1. 7 9 -1 is equivalent to 0 7 9 -7 0 -1 -9 1 0 Symmetric. Elements are zero except on the diagonal. No compressed representation available (use array element). 1 0 0 0 3 0 0 0 4 Square. Elements are zero below the diagonal 1 2 3 4 0 3 5 6 0 0 4 8 0 0 0 2 Square. Elements below the diagonal are zero and omitted, and rows are of length n, n-1, ... , 2, 1. 1 2 3 4 3 5 6 4 8 2 is equivalent to 1 2 3 4 0 3 5 6 0 0 4 8 0 0 0 2 Square. Elements are zero above the diagonal 1 0 0 7 3 0 9 2 4 Square. Elements above the diagonal are zero and omitted, and rows are of length 1, 2, ...n. 1 3 7 9 2 3 is equivalent to 1 0 0 3 7 0 9 2 3 Square. Diagonal elements are 1 and off-diagonal are zero. 1 0 0 0 1 0 0 0 1 Square. When multiplied by its transpose gives the unit matrix. 0 -1 0 1 0 0 0 0 1 Square. Each row corresponds to an eigenvector of a square matrix. Elements are real. The length of the eigenvectors is undefined, i.e. they are not required to be normalised to 1. 0 -1 0 1 0 0 0 0 1 The rotation is defined by the matrix premultiplyin a column vector (x, y) . 0 -1 1 0 produces (-y, x), i.e. a rotation of -90 degrees. A third column defining the translation is added to a rotation22. 0 -1 22 1 0 33 produces (-y + 22, x + 33), i.e. a rotation of -90 degrees followed by a translation of (22, 33). User-defined matrix-type. This definition must be by reference to a namespaced dictionary entry. The maximum INCLUSIVE value of a quantity. The maximum INCLUSIVE value of a sortable quantity such as numeric, date or string. It should be ignored for dataTypes such as URL. The use of min and max attributes can be used to give a range for the quantity. The statistical basis of this range is not defined. The value of max is usually an observed quantity (or calculated from observations). To restrict a value, the maxExclusive type in a dictionary should be used. The type of the maximum is the same as the quantity to which it refers - numeric, date and string are currently allowed Type of spectral measurement. The nature of the measured data. This is not an exhaustive list and should only be used if it affects the storage or immediate processing. Data are transmittance, so "peaks" are usually troughs. Data are absorbanc. so "peaks" are normally peaks. The name of the metadata. Metadata consists of name-value pairs (value is in the "content" attribute). The names are from a semi-restricted vocabulary, mainly Dublin Core. The content is unrestricted. The order of metadata has no implied semantics at present. Users can create their own metadata names using the namespaced prefix syntax (e.g. foo:institution). Ideally these names should be defined in an STMML dictionary. 2003-03-05: Added UNION to manage non-controlled name. The extent or scope of the content of the resource. Coverage will typically include spatial location (a place name or geographic coordinates), temporal period (a period label, date, or date range) or jurisdiction (such as a named administrative entity). Recommended best practice is to select a value from a controlled vocabulary (for example, the Thesaurus of Geographic Names [TGN]) and that, where appropriate, named places or time periods be used in preference to numeric identifiers such as sets of coordinates or date ranges. An account of the content of the resource. Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. An unambiguous reference to the resource within a given context. Recommended best practice is to identify the resource by means of a string or number conforming to a formal identification system. Example formal identification systems include the Uniform Resource Identifier (URI) (including the Uniform Resource Locator (URL)), the Digital Object Identifier (DOI) and the International Standard Book Number (ISBN). The physical or digital manifestation of the resource. Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats). A reference to a related resource. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. Information about rights held in and over the resource. Typically, a Rights element will contain a rights management statement for the resource, or reference a service providing such information. Rights information often encompasses Intellectual Property Rights (IPR), Copyright, and various Property Rights. If the Rights element is absent, no assumptions can be made about the status of these and other rights with respect to the resource. The topic of the content of the resource. Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme. A name given to the resource. Typically, a Title will be a name by which the resource is formally known. The nature or genre of the content of the resource. Type includes terms describing general categories, functions, genres, or aggregation levels for content. Recommended best practice is to select a value from a controlled vocabulary (for example, the working draft list of Dublin Core Types [DCT1]). To describe the physical or digital manifestation of the resource, use the FORMAT element. An entity responsible for making contributions to the content of the resource. Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity. An entity primarily responsible for making the content of the resource. Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity. An entity responsible for making the resource available. Examples of a Publisher include a person, an organisation, or a service. Typically, the name of a Publisher should be used to indicate the entity. A Reference to a resource from which the present resource is derived. The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A language of the intellectual content of the resource. Recommended best practice for the values of the Language element is defined by RFC 1766 [RFC1766] which includes a two-letter Language Code (taken from the ISO 639 standard [ISO639]), followed optionally, by a two-letter Country Code (taken from the ISO 3166 standard [ISO3166]). For example, 'en' for English, 'fr' for French, or 'en-uk' for English used in the United Kingdom. A date associated with an event in the life cycle of the resource. Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format. Entry contains information relating to chemical safety. Typically the content will be a reference to a handbook, MSDS, threshhold or other human-readable strin. Part or whole of the information was computer-generated. Typically the content will be the name of a method or a progra. 3D structure included. details include. The minimum INCLUSIVE value of a quantity. The minimum INCLUSIVE value of a sortable quantity such as numeric, date or string. It should be ignored for dataTypes such as URL. The use of min and min attributes can be used to give a range for the quantity. The statistical basis of this range is not defined. The value of min is usually an observed quantity (or calculated from observations). To restrict a value, the minExclusive type in a dictionary should be used. The type of the minimum is the same as the quantity to which it refers - numeric, date and string are currently allowed An identifier for an molecule. Of the form prefix:suffix where prefix and suffix are purely alphanumeric (with _ and -) and prefix is optional. This is similar to XML IDs (and we promote this as good practice for moleculeIDs. Other punctuation and whitespace is forbidden, so IDs from (say) PDB files are not satisfactory. The prefix is intended to form a pseudo-namespace so that molecule IDs in different molecules may have identical suffixes. It is also useful if the prefix is the ID for the molecule (though this clearly has its limitation). molecule IDs should not be typed as XML IDs since they may not validate. 2006-11-24: PMR created. An array of moleculeRefs. Typical applications are the annotation of peaks in chromatograms and mapping reactions. The context of the id resolution is the childOrSibling concept. A reference to two distinct existing molecules in order. At present used for joining molecules or fragments(with join). 2006-11-24: PMR created A reference to an existing molecule. An array of namespaceURIs with required protocol. used to identify dictionaries, units, conventions or other metadata. 2005-12-17: PMR. Added for use with unitList An XML QName with required prefix. A string referencing a dictionary, units, convention or other metadata. The purpose is to allow authors to extend the vocabulary through their own namespaces without altering the schema. The prefix is mandatory. This convention is only used within CML and related languages; it is NOT a generic URI. The namespace prefix must start with an alpha character and can only contain alphanumeric and '_'. The suffix can have characters from the XML ID specification (alphanumeric, '_', '.' and '-' A namespaceURI with required protocol. used to identify a dictionary, units, convention or other metadata. Not yet confirmant with XSD 2005-12-10: PMR. Added for use with dictionary The namespace prefix must start with a protocol. The number of non-hydrogen atoms attached to an atom. Obsolete in core CML. Only useful in CML queries. A non-signed angle. Re-used by _angle_. Note that we also provide positiveAngleType (e.g. for cell angles) and torsionAngleType for _torsion_. A nonNegative number. Note that we also provide positiveNumber to avoid inclusive zero. The maximum number is 1.0E+999 since 'unbounded' is more difficult to implement. This is greater than Eddington's estimate of the number of particles in the universe so it should work for most people. Array of atomic occupancies. Primarily for crystallography. Values outside 0-1 are not allowed. A floating point number between 0 and 1 inclusive Originally for crystallographic occupancy but re-usable for fractional yield, etc. An array of bond orders. See order. Bond order. This is purely conventional and used for bond/electron counting. There is no default value. The emptyString attribute can be used to indicate a bond of unknown or unspecified type. The interpretation of this is outside the scope of CML-based algorithms. It may be accompanied by a convention attribute on the bond which links to a dictionary. Example: <bond convention="ccdc:9" atomRefs2="a1 a2"/> could represent a delocalised bond in the CCDC convention. Hydrogen bond. Carries no semantics but will normally be between a hydrogen atom and an element with lone pairs. Partial bond. Can be used for a partial bond in a transition state, intermolecular interaction, etc. There is no numeric value associated and the bond order could be anywhere between 0 and single. Single bond. synonymous with "1. Single bond. Intermediate between 1 and . Could be used for a transition state or a delocalised system. Double bond. Double bond. Intermediate between 2 and . Could be used for a transition state or a delocalised system. Triple bond. Triple bond. Aromatic bond. Multiplicity of a peak. Uses a semi-controlled vocabulary. A single maximum within the peak rang. Two maxima (not necessarily equal) within the peak rang. Three maxima (not necessarily equal) within the peak rang. Four maxima (not necessarily equal) within the peak rang. Five maxima (not necessarily equal) within the peak rang. Six maxima (not necessarily equal) within the peak rang. Several maxima (not necessarily equal) within the peak rang. User contributed vocabulary of type foo:ba. Shape of a peak. Semi-controlled vocabulary such as broad or sharp. A sharp peak. A broad peak. A brodening of a peak suggesting the presence of a smaller incompletely resolved component. User contributed vocabulary of type foo:bar. type of a peakStructure. Semi-controlled vocabulary such as coupling or splitting. A coupling such as in NMR. A splitting such as in NMR. User contributed vocabulary. The width of a peak. At present we allow a peakWidth to be positive or exactly zero (to signal that the peak should not be integrated). An unbounded plane in 3-space. Defined by 4 real numbers, conventionally a vector3 normal to the plane and a signed scalar representing the distance to the origin. The vector must not be of zero length (and need not be normalized. The first three numbers are the vector, followed by the distance A point in 3-space. The 3 components can have any signed value. A non-signed angle such as a cell angle. Re-used by _crystal_. Note that we also provide nonNegativeAngleType (e.g. for bond angles). A positive number. Note that we also provide nonNegativeNumber with inclusive zero. The maximum number is (quite large) since 'unbounded' is more difficult to implement. The format of the reaction. This is provided for machine-understanding of the format of the reaction steps and components. Semantics are semi-controlled. The commonest representation with reactantList and productList. A list of molecules representing snap shots on a reaction pathway. The role of the reaction within a reactionList. Semantics are semi-controlled. On reactionList signifies that the children are the complete description of the reaction. The overall reaction in a multi-step reaction. Normally this would be the first reaction in a reactionList and the individual steps are held in a following sibling reactionList. The rate-determining step in a multi-step reaction. This implies also that the reaction has a role of step. A step in a multi-step reaction. This reaction will normally be a child of reactionList. a reactionList containing steps Examples could be "myDict:step1", "foo:chainPropagation", etc. The sequence of steps in a reactionStepList. By default the reactions in a reactionStepList are assumed to take place in sequence (e.g. one or more products of reaction n are used in reaction n+1 or later. However there are cases where it is known that reactions take place in parallel (e.g. if there is no overlap of molecular identities). Alternatively there are points at which there are two or more competing reactions which may depend on conditions or concentrations. A small semi-controlled vocabulary is suggested. The semantic of these are not fully explored, but we suggest that consecutive and simultaneous should be the first to be supported The order of the steps is unknown. The reaction proceeds through the steps in the order given. The reaction may proceed through either (or possibly both) of the contained reactions or reactionScheme, but it may not be known which. The two or more independent reaction/List children proceed independently. The semantic type of the reaction. This is provided for machine-understanding of the topology or logic of the reaction steps and components (i.e. not for a general classification for which label is more appropriate.) Semantics are semi-controlled. Some terms are appropriate to multistep reactions, and can be used with or without explicit steps. A reaction in which one or more reactive reaction intermediates (frequently radicals) are continuously regenerated, usually through a repetitive cycle of elementary steps (the 'propagation step') (IUPAC GoldBook). A reaction or process generating free radicals (or some other reactive reaction intermediates) which then induce a chain reaction. For example, in the chlorination of alkanes by a radical mechanism the initiation step is the dissociation of molecular chlorine. IUPAC Compendium of Chemical Terminology 2nd Edition (1997). The steps in a chain reaction in which reactive intermediates are destroyed or rendered inactive, thus ending the chain. IUPAC Compendium of Chemical Terminology 2nd Edition (1997) . A reaction which can proceed in the forward direction as readily as in the reverse direction (IUPAC GoldBook). A reference to an existing object. A reference to an existing element in the document. The target of the ref attribute must exist. The test for validity will normally occur in the element's _appinfo_. Any DOM Node created from this element will normally be a reference to another Node, so that if the target node is modified a the dereferenced content is modified. At present there are no deep copy semantics hardcoded into the schema. The semantic of reference are normally identical to an idType (e.g. "a123b"). Howevere there are some cases where compound references are required, such as "a123b:pq456". It is likely that this will be superseded at by RDF or Xpointer, but as long as we have non-uniqueIds this is a problem Type of relatedEntry. Type represents a the type of relationship in a relatedEntry element. instruction to create repeat of the object. The attribute contains an index, its start value (normally 1) and its end value as in "i 3 10" which would make 8 repeat of the object. In selected attribute values the string _i_ acts as a macro and would be replaced by the value of i. EXPERIMENTAL. It can also have variables as the values. 2006-05-20: PMR added. The sequence of steps in a reactionList. By default the reactions in a reactionStepList are assumed to take place in sequence (e.g. one or more products of reaction n are used in reaction n+1 or later. However there are cases where it is known that reactions take place in parallel (e.g. if there is no overlap of molecular identities). Alternatively there are points at which there are two or more competing reactions which may depend on conditions or concentrations. A small semi-controlled vocabulary is suggested. The order of the steps is unknow. The reaction proceeds through the steps in the order give. The reaction may proceed through either of the contained reactions or reactionScheme. The two or more independent reaction/List children proceed independently. This can be extended to synthetic chemistry where two parts of the synthesis are conducted in parallel. Allowed shapes of arrayList. Rectangular, triangular or irregular. Rectangular. Triangular decreasing in size from ncols to 1. Triangular increasing in size from 1 to ncols. Irregular shape. User-defined arrayList-type. This definition must be by reference to a namespaced dictionary entry. The size of an array. The size of an array. Redundant, but serves as a check for processing software (useful if delimiters are used). Signifies real or reciprocal space. Likely to be used on types such as lattice, plane, point. A synonym for reciprocal. A synonym for reciprocal. User-defined space-type. No obvious possibilities, but who know. The type of the spectrum. An infrared spectrum. The measurement should denote transmittance or absorbanc. A "simple" mass spectrum. This excludes experiments such as GC/MS, MS/MS, etc. though these could be constructed out of individual spectra with some care. The spectrum may be continuous ( data or a peakList). An NMR spectrum. This can include any experiment which creates a "1D" or "2D" data array. The symmetry of the spectrum can be specified but the details of the NMR experiment (COSY, NOESY, etc.) are not part of CMLSpect. They can be described though the normal dictRef mechanism. A spectrum somewhere in the UV VIS region of the spectrum. The measurement should denote transmittance or absorbance. A sphere in 3-space. Defined by 4 real numbers, conventionally a point3 at the centre of the sphere and a nonNegative scalar for the radius. State of a substance or property. The state(s) of matter appropriate to a substance or property. It follows a partially controlled vocabulary. It can be extended through namespace codes to dictionaries. An aqueous solutio. Gas or vapor. The default state for computation on isolated molecule. A glassy stat. Normally pure liquid (use solution where appropriate. The nematic phas. The smectic phas. A soli. A solid solutio. A (liquid) solutio. Bond stereochemistry as a string. This is purely conventional. There is no default value. The emptyString attribute can be used to indicate a bond of unknown or unspecified type. The interpretation of this is outside the scope of CML-based algorithms. It may be accompanied by a convention attribute which links to a dictionary. A cis bond. A trans bond. A wedge bond. A hatch bond. empty or missing. An array of strings, separated by whitespace. An array of strings, separated by whitespace. If the strings have embedded whitespace or may be empty (zero-length), a non-whitespace single-character delimiter must be used. At present no machine validation Type of the substanceList. Extension is allowed through the "other" value. Allowed types of table. rowBased, arrayBased, contentBased. 2006-11-03: formlized 3 table types rowBased. Based on child arrayList containing arrays or lists child tableContent User-defined table-type. This definition must be by reference to a namespaced dictionary entry. The tail linker in a polymeric repeat unit A polymeric chain may be described by liniing the tail of one repeat unit to the head or tail of another. The tail attribute indicates the atom id (normally on an atom of elementType="R") which acts as the tail 2006-05-20: PMR added The type of a torsion angle. Type of unitList. Required to differentiate between the two types of unitList (units and unitTypes) child elements are unit child elements are unitType Scientific units. These will be linked to dictionaries of units with conversion information, using namespaced references (e.g. si:m). Distinguish carefully from _unitType_ which is an element describing a type of a unit in a _unitList_. A vector in 3-space. No constraints on magnitude (i.e. could be zero. Version of a document or code. Forms include 1, 0.9, 1.1.3, 1.2alpha, etc. The name of an XMLElement. (Distinguish from a chemical element as in elementTypeType). Currently used for assigning XMLElement types to references (e.g. to='a1' toType='atom'). Semantics are not controlled and in principle elements outside the CML tagSet could be used. Implementers cannot assume that namespace prefixes can be resolved and default usage is probably the local name. Abbreviation. Abbreviation for units, terms, etc. Describes whether child elements are sequential or parallel. There is no default. The type of an alternative. This adds semantics to an _alternative_ and might be used by an RDF or related engine. Restricts units to radians or degrees. An array of atom IDs. Normally an attribute of an array-based element. A reference to a map providing mappings between atoms The map will normally be contained within the same document and referenced by its ID. It will contain a list of links with from and to attributes linking atoms. The topology of the linking is defined by the application - it could be overlay of molecular fragments, reactant/product mapping, etc. The reserved phrase "USE_IDS" assume that the sets of atoms are of equal size and have 1:1 mapping between each id. This is another way of saying that the atoms mapped by a given ID are "the same atom". A reference to an atom. Used by bond, electron, etc. The first atoms in each bond. Currently only used in bondArray in CML2 array mode. The second atoms in each bond. Only used in bondArray in CML2 array mode. An array of references to atoms. Typical use would be to atoms defining a plane. A reference to a list of atoms. Used by bonds, electrons, atomSets, etc. References to two different atoms. Available for any reference to atoms but normally will be the normal reference attribute on the bond element. The order of atoms is preserved and may matter for some conventions (e.g. wedge/hatch or donor bonds. A list of three references to atoms. Typically used for defining angles, but could also be used to define a three-centre bond. A list of 4 references to atoms. Typically used for defining torsions and atomParities, but could also be used to define a four-centre bond. An atomSet describing the region. Any point falling within atomOffset of any atom in the set lies within the region. This means the region could consist of disjoint fragments. The IDs for an array of bond. Required in CML2 array mode. A reference to a map providing mappings between bonds The map will normally be contained within the same document and referenced by its ID. It will contain a list of links with from and to attributes linking bonds. The topology of the linking is defined by the application - it could be overlay of molecular fragments, reactant/product mapping, etc. The reserved phrase "USE_IDS" assume that the sets of bonds are of equal size and have 1:1 mapping between each id. This is another way of saying that the bonds mapped by a given ID are "the same bond". A reference to a bond. used by electron, etc. A reference to a list of bonds. Used by electrons, bondSets, etc. A parallelipiped box. By default the box uses isometric Cartesians axes but can also be linked to lattice Vector. Any point falling within the box or on a boundary is within the regio. builtin children. CML1-only - now deprecated. Error array for cellParameter 3 numbers giving error limits on paremters. The type of a cellParameter. length or angle The chirality of a system or molecule. This is being actively investigated by a IUPAC committee (2002) so the convention is likely to change. No formal default. Number of columns. A concise formula. The string represents an (unstructured) formula i.e. no submolecules. Recommended to use the format "H 2 O 1", etc. The constant to add to the raw data. add *after* applying any multiplier. Additive constant to generate SI equivalent. The amount to add to a quantity in non-SI units to convert its representation to SI Units. This is applied *after* multiplierToSI. It is necessarily zero for SI units. Constraint on a parameter. Semantics not yet finalised. We anticipate "fixed", "none" and symbolic relationships to other parameters. content of metadata. A reference to a convention. There is no controlled vocabulary for conventions, but the author must ensure that the semantics are openly available and that there are mechanisms for implementation. The convention is inherited by all the subelements, so that a convention for molecule would by default extend to its bond and atom children. This can be overwritten if necessary by an explicit convention. It may be useful to create conventions with namespaces (e.g. iupac:name). Use of convention will normally require non-STMML semantics, and should be used with caution. We would expect that conventions prefixed with "ISO" would be useful, such as ISO8601 for dateTimes. There is no default, but the conventions of STMML or the related language (e.g. CML) will be assumed. The value of an element with a _convention_. When convention is used this attribute must be present and element content must be empty. The count of the object. No fixed semantics or default, normally integers. It is presumed that the element can be multiplied by the count value. Array of object counts. No fixed semantics or default, normally integral. It is presumed that the element can be multiplied by the count value. General formula for the repeat count of the element. Experimental. No fixed semantics or default. The data type of the object. Normally applied to scalar/array objects but may extend to more complex one. default value in an enumeration. A non-whitespace string (value is irrelevant) indicates that the content of this enumeration is the default value (usually of a scalar). It is an error to have more than one default. If the scalar in an instance document has no value (i.e. is empty or contains only whitespace) its value is given by the default. If the scalar in the instance is empty and no enumerations have a default attribute, an application may throw an error. A flag indicated that the element can detach/delete itself. An element containg this attribute may only have a transient existence (e.g. a template to create other elements) and this attribute shows that the element can be deleted at the appropriate stage. The time at which this is called is application dependent. At present the presence of the attribute is sufficient to trigger this; later a controlled vocabulary will be developed. 2006-05-21: PMR added attribute. A delimiter character for arrays and matrices. By default array components ('elements' in the non-XML sense) are whitespace-separated. This fails for components with embedded whitespace or missing completely: Example: In the protein database ' CA' and 'CA' are different atom types, and and array could be: <array delimiter="/" dictRef="pdb:atomTypes">/ N/ CA/CA/ N/</array> Note that the array starts and ends with the delimiter, which must be chosen to avoid accidental use. There is currently no syntax for escaping delimiters. The namespacePrefix for a data item. The dictionaryPrefix is associated with elements such as dictionaries and units and allows them to be referenced namespaces. The dictionaryPrefix is normally unbound but it may be necessary to hardcode them occasionally. Thus if a value is fixed (e.g. "xsd:double") the prefix must be identified and fixed. A reference to a dictionary entry. Elements in data instances such as _scalar_ may have a dictRef attribute to point to an entry in a dictionary. To avoid excessive use of (mutable) filenames and URIs we recommend a namespace prefix, mapped to a namespace URI in the normal manner. In this case, of course, the namespace URI must point to a real XML document containing _entry_ elements and validated against STMML Schema. Where there is concern about the dictionary becoming separated from the document the dictionary entries can be physically included as part of the data instance and the normal XPointer addressing mechanism can be used. This attribute can also be used on _dictionary_ elements to define the namespace prefix Dimensionality of a coordinate system. Note that this means that coordinates of higher dimensionality are ignored or an error is flagged. Thus z3 and dimensionality='2' are incompatible. At present higher dimensionalities than 3 (cf. Wondratschek) are not supported. The labelling of the axes id not controlled. ?? should we have an explicit attribute for labelling convention?. The basis of the dimension. Normally taken from the seven SI types but possibly expandable. The duration of the action. Semantics undefined. The orientation of the eigenvector matrix. Describes whether the vectors are columns or rows. No default, so effectively mandatory unless you want to make implementers guess and break applications. A reference to a map providing mappings between electrons The map will normally be contained within the same document and referenced by its ID. It will contain a list of links with from and to attributes linking electrons. The topology of the linking is defined by the application - it could be reactant/product mapping, etc. The reserved phrase "USE_IDS" assume that the sets of electrons are of equal size and have 1:1 mapping between each id. This is another way of saying that the electrons mapped by a given ID are "the same electron". The identity of a chemical element. Normally mandatory on _atom_, _isotope_, etc. The identity of a chemical element. Normally mandatory on _atom_, _isotope_, etc. The end value. The end value in any allowable XSD representation of data. The end condition. At present a human-readable string describing some condition when the ac tion should end. As XML develops it may be possible to add machine-processable semantics in this field. Basis of the error estimate. Value of the error. Reports the author's estimate of the error in a scalar value. Only meaningful for dataTypes mapping to real number. Array of error values. Reports the author's estimate of the error in an array of values. Only meaningful for dataTypes mapping to real number. A flag on 'arg' to indicate that the value can be calculated. This is still experimental. if eval="_ijk_+3" and the value of the ijk was 2, this would change the value of the arg to 5. Only + and - are currently allowed 2006-05-21: PMR added attribute. Information identifying the name of a file or other resource. This allows an element (such as cml) to carry limited information about provenance such as the name of the document used to provide the content. It is not a complete solution but can help to protect a document becoming separated from its external metadata. It is restricted to the basic XML character set (printable ANSI) and whitespace (which should anyway be discouraged) is normalized to single space (attribute values cannot carry newlines). Quotation marks and other horrors (as used in some OS) should be avoided. A reference to a functional form. Currently used for potential. The formalCharge on the object. NOT the calculated charge or oxidation state. No formal default, but assumed to be zero if omitted. It may become good practice to include it. An array of formalCharges. Used in CML2 Array mode. NOT the calculated charge or oxidation state. No formal defaults, but assumed to be zero if omitted. It may become good practice to include it. Format of a spectrum. The data structure of the spectrum. (Not the format of the data). This describes how the data structure is to be interpreted. Simple chemical formula. This attribute should only be used for simple formulae (i.e. without brackets or other nesting for which a _formula_ child element should be used. The attribute might be used as a check on the child elements or for ease of representation. Essentially the same as _concise_ attribute on _formula. Number of digits after the point. This is used in dictionaries to define precision. However it might be replaced by xsd:facet. The base of one or more links. On link elements the value is the single id of an element within the document or context specified in map@fromRef attributes. It must identify the element uniquely. The reserved value 'null' implies that no mapping has been provided for the object(s) in the 'to' attribute. This implies no semantics but may be used by software to keep count of which elements have been mapped. For multiple targets use 'fromSet'. 2005-06-18: updated docs The context for the 'from' links in a map. A reference to the unique 'id' attribute of an element defining the context for links in a map. This may be required when id attributes may not be unique within a document. The id should either reference an element uniquely or should be taken as the first ancestor (of the map) with such an id. This is fairly horrid but may be required when documents are assembled without establishing unique ids (e.g. concatenation of files). As an example a map referencing linked atoms in two molecules might use the containing 'reaction' element as its uniquifying context. 2005-06-18: created A set of ids representing the base of a link. For a partial mapping where a number of 'from' elements are known to link to a number of 'to' elements it can be useful to aggregate these into a single attribute value. The primary use is to assert that n links exist between a set of n 'from' elements and n 'to' elements but that the precise links are unknown. The semantics of the reference are the same as for 'from' and all the elements must be of the same type (which can be specified with 'fromType' either on the link or the containing map). No order information is implied. In general there will be the same number of idRefs in the 'toSet' and all implicit links will share the same attributes (e.g. 'role'). In many cases the sets will be later split into discrete links thorugh further calculation or experiment (e.g. peak assignment). Sets should never be used as a lazy or concise alternative where the all the links are explicitly known. 2005-06-18: created The type of the base of a link. The local tagname of the referenced element (e.g. 'molecule' or 'peakGroup'). This acts as a partial check on the integrity of the link. Software can assume that the referenced element is of a given tytpe and can create an object supporting that type. This attribute can be attached to the 'map' attribute and requires all contained links to be of this type. This can be overridden by a 'toType' attribute on indivdual links, but it may also be useful to split the map into maps od different link types. 2005-06-18: created Domain of an FT spectrum. Indicates whether a spectrum is raw FID or has been transforme. address of a resource. Links to another element in the same or other file. For dictionary/@dictRef requires the prefix and the physical URI address to be contained within the same file. We can anticipate that better mechanisms will arise - perhaps through XMLCatalogs. At least it works at present. Number of hydrogens. The total number of hydrogens bonded to the atom or molecule. It is preferable to include hydrogens explicitly, and where this is done their count represents the minimum (and may thus override this attribute). It is dangerous to use this attribute for electron-deficient molecules (e.g. diborane) or hydrogen bonds. There is NO DEFAULT and the absence of this attribute must not be given any meaning. Array of hydrogenCounts. Normally used in CML2 array mode. The total number of hydrogens bonded to the atom or molecule. It is preferable to include hydrogens explicitly, and where this is done their count represents the minimum (and may thus override this attribute). It is dangerous to use this attribute for electron-deficient molecules (e.g. diborane) or hydrogen bonds. There is NO DEFAULT and the absence of this attribute must not be given any meaning. A unique ID for an element. Id is used for machine identification of elements and in general should not have application semantics. It is similar to the XML ID type as containing only alphanumerics, '_', ',' and '-' and and must start with an alphabetic character. Ids are case sensitive. Ids should be unique within local scope, thus all atoms within a molecule should have unique ids, but separated molecules within a document (such as a published article) might have identical ids. Software should be able to search local scope (e.g. all atoms within a molecule). However this is under constant review. Allows a referring element to generate a unique id. idgen can hold a unique identifier which is copied into the id attribute of the referenced element. This avoids multiple copies of the referenced object with duplicate ids. EXPERIMENTAL 2006-05-22: PMR added. Inheritance mechanism. A reference to an existing element can be used to supplement values such as coordinates. The inheritance attribute determines whether the values are supplemented, overwritten or deleted. In the example: <molecule id="m1" view="initial"> <atomArray> <atom id="a1" x3="0.1"/> </atomArray> </molecule> <!-- this adds more information --> <molecule ref="m1" view="initial" inherit="supplement"> <atomArray> <atom id="a1" hydrogenCount="1"/> </atomArray> </molecule> <!-- this will overwrite the previous values --> <molecule ref="m1" inherit="overwrite" view="final" id="m2"> <atomArray> <atom id="a1" x3="0.1"/> </atomArray> </molecule> <!-- this will delete the previous values --> <molecule ref="m1" inherit="delete" view="restart"> <atomArray> <atom id="a1" hydrogenCount=""/> </atomArray> </molecule> The first molecule/@ref adds complementary information, the second changes the values. Software is allowed to generate two independent copies of the molecule and reference them by different IDs (m1 and m2). This mechanism is necessary to manage the implied inheritance of partial information during minimisations and dynamics. It requires careful software implementation. An inline representation of the object. This can represent a wide range of information from formal serialization as ASCII through to domain-specific textual representations. It will often be used in conjunction with the "convention" attribute. For example it could be used to represent IUPAC formula, SMILES strings, TeX equations, etc. Characters should conforma to the XML character set, and XML markup (lt and amp) should be escaped. IT SHOULD NEVER BE USED FOR INLINE XML Area under a peak. Unfortunately units are usually arbitrary and not related to the x- and y- axis units, and in this case _peakUnits_ should be use. A symmetry species. No fixed semantics, though we may provide a controlled-extensible list in the future. The isotope for an element. A real number describing the isotope. Probably obsolet. Reference to a description of the isotopic composition of an atom. Used when more than one atom shares the same isotopic composition (e.g. when H/D have been scrambled over some or all of the atoms in a molecule.. The integer number for an isotope. The number representing the isotope. By default it does not point to a fuller description of the isotope (use isotopeRef). Reference to a fuller description of the isotope. The description may be found in an external collection (e.g. IUPAC) or within the current document. indicates whether a unit is an SI or derived SI unit. required on SI unit elements with value 'true'. Optional on other units with attribute 'false'. A unitList should contain either SI units or non-SI units but not both. The k vector. The k-vector with 3 components. A reference to a kpoint. Used by band, etc. 2006-01-21: PMR. Created The secondary quantum number. takes values 0, 1, etc. A label. The semantics of label are not defined in the schema but are normally commonly used standard or semi-standard text strings. This attribute has the the same semantics as the more common _label_ element. The primitivity of a lattice. No default. The semantics of this are software-dependent (i.e. this Schema does not check for consistency between spacegroups, symmetry operators, etc. Length of a scalar. Probably will be replaced with xsd:schema tool. The type of the link. A list of values. Normally for iterations. 2006-06-09: PMR Created.. symbolic represention of l amd m. takes avlues of s, p, px, dxy, dx2y2, f, etc. The azimuthal quantum number. takes values -1, 0, 1, etc. An attribute providing a mandatory unique ID for an element. This is a horrible hack. It should be possible to add 'required' to the attributeGroup where used... (Maybe it is and I am still fighting Schema Wars. Type of matrix. Mainly square, but extensible through the _xsd:union_ mechanis. Maximum value allowed for an element or attribute. maximum exclusive value. by analogy with xsd:schema. minimum inclusive value. by analogy with xsd:schem. maximum length of a scalar. by analogy with xsd:schem. Maximum values for numeric _matrix_ or _array. A whitespace-separated list of the same length as the array in the parent element. Type of spectral measurement. The nature of the measured data. This is not an exhaustive list and should only be used if it affects the storage or immediate processing. The metadata type. This is likely to be the Dublin Core name or something similar. The use of "type" is an infelicitous misnomer and we shall try to remove it. The minimum value allowed for an element or attribute. minimum exclusive value. by analogy with xsd:schema. minimum inclusive value. by analogy with xsd:schema. minimum length of a scalar. by analogy with xsd:schema. Minimum values for numeric _matrix_ or _array. A whitespace-separated lists of the same length as the array in the parent element. A reference to a molecule. Used by spectrum, etc. A reference to one or more molecules. Uses the id attribute as the target identification. The order of molecules is preserved. It is not necessarily an error to have repeated references to the same molecule 2005-11-22: PMR. added this attribute. References to two different molecules. Available for any reference to molecules but normally will be the normal reference attribute on the join element. The order of molecules is preserved and may matter. 2006-11-24: PMR created The scale by which to multiply raw data or a unit. The scale is applied *before* adding any constant. The attribute may be found on a data item (scalar, array, matrix, etc.) or a user-defined unit. Multiplier to generate SI equivalent. The factor by which the non-SI unit should be multiplied to convert a quantity to its representation in SI Units. This is applied *before* _constantToSI_. Necessarily unity for SI unit. The principal quantum number. Takes values 1, 2, 3, etc. Name of the object. A string by which the object is known. Often a required attribute. The may or may not be a semi-controlled vocabulary. The namespace for a data item. The namespace is associated with elements such as dictionaries and units and allows them to be referenced through free namespace prefixes. A number determined by context Used for isotope number in isotope, and rotational symmetry number in symmetry for calculation of entropy, etc. 2003-03-30: added number attribut. The class of an object. The type of this information. This is not controlled, but examples might include: label summary note usage qualifier It might be used to control display or XSL filtering. The attribute is named 'objectClass' to avoid clashes with other class attributes and inappropriate conversion to foo.getClass(). Occupancy for an atom. Normally only found in crystallography. Defaults to 1.0. The occupancy is required to calculate the molecular formaula from the atoms. Array of occupancies. Normally only found in crystallography. Defaults to 1.0. The occupancy is required to calculate the molecular formula from the atoms. The order of the bond. There is NO default. This order is for bookkeeping only and is not related to length, QM calculations or other experimental or theoretical calculations. The order of the bond. There is NO default. This order is for bookkeeping only and is not related to length, QM calculations or other experimental or theoretical calculations. parameter name passed to an element This is still experimental. 2006-06-09: PMR added attribute. raplaces attribute on parent This is still experimental. Creates, overwriting if necessary, an attribute on parent. Example: <foo> <arg parentAttribute="bar">zubbo</arg> will create an attribute bar="zubbo" on <foo> 2006-06-09: PMR added attribute. A dictRef-like reference to the id of the parent SI unit. This parent should occur in this or another dictionary and be accessible through the dictRef mechanism. This attribute is forbidden for SI Units themselves. The mechanism holds for base SI units (7) and all compound (derived) units made by combinations of base Units. Pattern constraint. Based on xsd:schema. Height of a peak. For 1-dimensional data (e.g. y vs x) hould use the same units as the appropriate axis (e.g. y). Multiplicity of a peak. Uses a semi-controlled vocabulary. Shape of a peak. Semi-controlled vocabulary such as broad or sharp. Type of this structure. Semi-controlled vocabulary such as coupling or splitting. Units for a peak or peak integral. For 2-dimensional spectra the units represent the observation. For an integral they are usually arbitrary and not related to the x- and y- axis units. Thus NMR spectra may use hydrogen count as the units for the peak area. Is the axis periodic. Any or all of the axes may be periodic or aperiodic. An example could be a surface where 2 periodic axes (not necessarily orthogonal) are used to describe the coordinates in the surface, perhaps representing lattice vectors of a 3D crystal or 2D layer. The third vector is orthogonal and represents coordinates normal to the surface. In this case only the direction, not the magnitude of the vector is important. Periodicity of the system. This represents the number of dimensions (or coordinate axes) along periodic behaviour occurs and can be supported by symmetry operators or other transformations. Periodicity must never exceed dimensionality. A point in 3 dimensions. can be used for any complex geometrical object, such as line. A point group. No fixed semantics, though Schoenflies is recommended over Hermann-Mauguin. We may provide a controlled-extensible list in the future. SpaceGroup multiplicity. Normally for an atom. This attribute gives the pointGroup multiplicity of the molecule and is independent of any atomic information. No default, and it may take any positive integer value (though values are normally between 1 and 60 (for icosahedral). It represents the number of symmetry operations (without any translations) that transform the atom into itself. Thus an atom on a centre of symmetry can have a pointGroupMultiplicity of 2. The pointGroupMultiplicity can be deduced from a knowledge of the coordinates and the pointGroup operators and so is formally redundant but this is a useful convenience operator. Distinguish carefully from occupancy which represents incomplete occupation of a site. The power to which a dimension should be raised. Normally an integer. Must be included, even if unity. The power to which a dimension should be raised. Normally an integer. Must be included, even if unity. Is the dimension preserved during algebra. Experimental. The idea is to support concepts like volume/volume where algebraically these cancel out. preserve="yes" is intending to support preservation during derivation of new unitTypes. Keyword signifying how object is to be processed. Semantics depend on the parent element 2006-05-20: PMR added A ratio in the range 0 to 1. Currently used for ratios between brached reactions but re-usable for other concepts. Format of the reaction component. Indicates how the components of reactionScheme, reactionStepList, etc. should be processed. No controlled vocabulary. One example is format="cmlSnap" asserts that the processor can assume that the reactants and products can be rendered using the CMLSnap design. Note that the reaction can be interpreted without reference to the format, which is primarily a processing instruction. Role of the reaction. The sequence of steps in a reactionStepList. By default the reactions in a reactionStepList are assumed to take place in sequence (e.g. one or more products of reaction n are used in reaction n+1 or later. However there are cases where it is known that reactions take place in parallel (e.g. if there is no overlap of molecular identities). Alternatively there are points at which there are two or more competing reactions which may depend on conditions or concentrations. A small semi-controlled vocabulary is suggested. The semantic of these are not fully explored, but we suggest that consecutive and simultaneous should be the first to be supported Type of the reaction. Recommended unit. a facet on a numeric dictionary entry. A reference to an element of given type. ref modifies an element into a reference to an existing element of that type within the document. This is similar to a pointer and it can be thought of a strongly typed hyperlink. It may also be used for "subclassing" or "overriding" elements.
When referring to an element most of the "data" such as attribute values and element content will be on the full instantiated element. Therefore ref (and possibly id) will normally be the only attributes on the pointing element. However there may be some attributes (title, count, etc.) which have useful semantics, but these are element-specific A list of regions creating a union. The union of a series of regions produces a larger region (possibly disjoint). Any point belonging to any of the referenced regions is a member of this region. Type of relatedEntry. Type represents a the type of relationship in a relatedEntry element. Role of the object. How the object functions or its position in the architecture. No controlled vocabulary. Number of rows. The sequence of steps in a reactionList. By default the reactions in a reactionStepList are assumed to take place in sequence (e.g. one or more products of reaction n are used in reaction n+1 or later. However there are cases where it is known that reactions take place in parallel (e.g. if there is no overlap of molecular identities). Alternatively there are points at which there are two or more competing reactions which may depend on conditions or concentrations. A small semi-controlled vocabulary is suggested. Serial number or other id. Currently only on module. Modules with the same _role_ attribute can be distinguished by _serial_. This is often an integer but other schemes may be used. shape of object. Mainly square, but extensible through the _xsd:union_ mechanism. The namespace for SI Units dictionary. Main use is on unitList to identify the dictionary holding the SI Units. Array of namespaces locating SI Units dictionaries. Main use is on unitList to identify the dictionaries holding the SI Units. The size of an array or matrix. A space group. No fixed semantics, though Hermann-Mauguin or Hall is recommended over Schoenflies. We may provide a controlled-extensible list in the future. SpaceGroup multiplicity. Normally for an atom. This attribute gives the spaceGroup multiplicity of the molecule and is independent of any atomic information. No default, and it may take any positive integer value (though values are normally between 1 and 192. It represents the number of symmetry operations (without cell translations) that transform the atom into itself. Thus an atom on a centre of symmetry can have a spaceGroupMultiplicity of 2. The spaceGroupMultiplicity can be deduced from a knowledge of the coordinates and the spaceGroup operators and so is formally redundant but this is a useful convenience operator. Some crystallographic experiments report this attribute as, for example, the IUCr CIF item 'atom_site_symmetry_multiplicity'. Distinguish carefully from occupancy which represents incomplete occupation of a site. The spaceType of the lattice. Usually real or reciprocal. No default. The semantics of this are software-dependent (i.e. this Schema does not check for consistency for unitTypes, etc. The type of the spectrum. A sphere. Currently describes a region. Any point falling within the sphere or on its surface is within the region. The spin of a system. Supports fractional values. Currently the spin of a nucleus. The normal fraction representing the spin of the isotope. Spin multiplicity. Normally for a molecule. This attribute gives the spin multiplicity of the molecule and is independent of any atomic information. No default, and it may take any positive integer value (though values are normally between 1 and 5. The start value. The start value in any allowable XSD representation The start condition. This can describe the condition(s) that has to be met before an action can begin, such as in a recipe. Semantics are unexplored but could be used to control robotic operations. The physical state of the substance. No fixed semantics or default. The step value. The step value in any allowable XSD representation Type of the substanceList. Extension is allowed through the "other" value. A flag on 'arg' to indicate that the value can be substituted. This is still experimental. The value may be an XPath expression, at present all attributes (".//@*") are processed. If an attribute contains _ijk_ where the name of the arg is 'ijk' this string is replaced by the value of ijk, e.g. if arg with name ijk has a value of 2 then 'm_ijk__z3' becomes 'm2_z3'. substitute="." replaces this element by its value 2006-05-21: PMR added attribute. A symbol. No semantics. However it should contain only ASCII characters and we may have to develop an escaping mechanism. Used on _atomicBasisFunction_, _unit_, etc. Is the molecule oriented to the symmetry No formal default, but a molecule is assumed to be oriented according to any _symmetry_ children. This is required for crystallographic data, but some systems for isolated molecules allow specification of arbitrary Cartesian or internal coordinates, which must be fitted or refined to a prescribed symmetry. In this case the attribute value is false. type of table. controls content Indicates whether the structure is a tautomer. Currently used with IChI _identifier_ element. Semantics, vocabulary and usage are application-dependent. A term in a dictionary. The term should be a noun or nounal phrase, with a separate definition and further description. The test condition on an if element. No controlled format yet. 2006-06-09: PMR Created.. A title on an element. No controlled value. The target of one or more links. On link elements the value is the single id of an element within the document or context specified in map@toContext attributes. It must identify the element uniquely. The reserved value 'null' implies that no mapping has been provided for the object(s) in the 'from' attribute. This implies no semantics but may be used by software to keep count of which elements have been mapped. For multiple targets use 'toSet'. 2005-06-18: updated docs The context for the 'from' links in a map. A reference to the unique 'id' attribute of an element defining the context for links in a map. This may be required when id attributes may not be unique within a document. The id should either reference an element uniquely or should be taken as the first ancestor (of the map) with such an id. This is fairly horrid but may be required when documents are assembled without establishing unique ids (e.g. concatenation of files). As an example a map referencing linked atoms in two molecules might use the containing 'reaction' element as its uniquifying context. 2005-06-18: created A set of ids representing the base of a link. For a partial mapping where a number of 'to' elements are known to link to a number of 'from' elements it can be useful to aggregate these into a single attribute value. The primary use is to assert that n links exist between a set of n 'to' elements and n 'from' elements but that the precise links are unknown. The semantics of the reference are the same as for 'to' and all the elements must be of the same type (which can be specified with 'toType' either on the link or the containing map). No order information is implied. In general there will be the same number of idRefs in the 'fromSet' and all implicit links will share the same attributes (e.g. 'role'). In many cases the sets will be later split into discrete links thorugh further calculation or experiment (e.g. peak assignment). Sets should never be used as a lazy or concise alternative where the all the links are explicitly known. 2005-06-18: created total digits in a scalar. based on xsd:schema. The type of the base of a link. The local tagname of the referenced element (e.g. 'molecule' or 'peakGroup'). This acts as a partial check on the integrity of the link. Software can assume that the referenced element is of a given tytpe and can create an object supporting that type. This attribute can be attached to the 'map' attribute and requires all contained links to be of this type. This can be overridden by a 'toType' attribute on indivdual links, but it may also be useful to split the map into maps od different link types. 2005-06-18: created Type of the object. A qualifier which may affect the semantics of the object. A reference to the type of a unit. Needed to differentiate the rather unhappy polymorphism of unitList/unit and unitList/unitType. 2005-12-17 PMR: Added Scientific units on an element. These must be taken from a dictionary of units. There should be some mechanism for validating the type of the units against the possible values of the element. unitsRef attribute on CML1 elements. CML1-only - now deprecated. A reference to the type of a unit. Used in defining the unit and doing symbolic algebra on the dimensionality. Value of a scalar object. The value must be consistent with the dataType of the object. A vector in 3 dimensions. can be used for any complex geometrical object, such as line. The version of the element cml or identifier elements can currently have versions. They may be dependent on the date of release and this attribute is highly recommended. There is no controlled syntax. Weight of the element. Currently the weight of the kPoint, derived from the symmetry such as the inverse of the multiplicity in real space. Thus a point at 0,0,0 in monoclinic space might be 0.25. The lowest value possible is probably 1/48.0 (in m3m). 2003-09-15 (added at suggestion of Jon Wakelin). Whitespace. Attached to entry. This may be obsolete. x2 coordinate for an object. Used for displaying the object in 2 dimensions. Unrelated to the 3-D coordinates for the object. The orientation of the axes matters as it can affect the chirality of object. array of x2 coordinate. Normally used in CML2 array mode. Used for displaying the object in 2 dimensions. Unrelated to the 3-D coordinates for the object. The orientation of the axes matters as it can affect the chirality of object. The x coordinate of a 3 dimensional object. The default units are Angstrom. (The provision for other units is weak at present.) Objects are always described with a right-handed coordinate system. An array of x3 coordinate. Normally used in CML2 array mode. Fractional x coordinate. normally xFract, yFract and zFract should all be present or absent. If present a _crystal_ element should also occur. Array of fractional x coordinate. normally xFract, yFract and zFract should all be present or absent. If present a _crystal_ element should also occur. Maximum xValue. Annotates x-axis data with a maximum value. This need not be algorithmically deducible from the data and is typically used for the extent of a _peak_ or _peakGroup_. It uses xUnits or the same units as the data. There may or may not be a _xMin_ attribute but if so xMax should be greater than or equals to it. Minimum xValue. Annotates x-axis data with a minimum value. This need not be algorithmically deducible from the data and is typically used for the extent of a _peak_ or _peakGroup_. It uses xUnits or the same units as the data. There may or may not be a _xMax_ attribute but if so xMin should be less than or equals to it. Units for x axis. All x-axis data must have unambiguous units. Ideally the data and _xMin_ or _xValue_ should share the same units but different xUnits can be used as long as it is clear.. Value along an x axis. Annotates x-axis data with a value. It is typically used for the location of a _peak_ or _peakGroup_. It uses xUnits or the same units as the data. An unsigned interval along an x axis. It is typically used for the width of a _peak_ or _peakGroup_ but could be used for any range. It uses xUnits or the same units as the data. y2 coordinate for an object. Used for displaying the object in 2 dimensions. Unrelated to the 3-D coordinates for the object. The orientation of the axes matters as it can affect the chirality of object. array of y2 coordinate. Normally used in CML2 array mode. Used for displaying the object in 2 dimensions. Unrelated to the 3-D coordinates for the object. The orientation of the axes matters as it can affect the chirality of object. The y coordinate of a 3 dimensional object. The default units are Angstrom. (The provision for other units is weak at present.) Objects are always described with a right-handed coordinate system. An array of y3 coordinate. Normally used in CML2 array mode. Fractional y coordinate. normally xFract, yFract and zFract should all be present or absent. If present a _crystal_ element should also occur. Array of fractional y coordinate. normally xFract, yFract and zFract should all be present or absent. If present a _crystal_ element should also occur. Yield of a reaction or reactionStep. Yields can be given on either element. They should lie in the range 0 to 1 inclusive (i.e. percentages will need to be converted). Software may use yield to calculate amounts of substances created during a reaction or series of reactions. Maximum yValue. Annotates y-axis data with a maximum value. This need not be algorithmically deducible from the data and is typically used for the extent of a _peak_ or _peakGroup_. It uses yUnits or the same units as the data. There may or may not be a _yMin_ attribute but if so yMax should be greater than or equals to it. Minimum yValue. Annotates y-axis data with a minimum value. This need not be algorithmically deducible from the data and is typically used for the extent of a _peak_ or _peakGroup_. It uses yUnits or the same units as the data. There may or may not be a _yMax_ attribute but if so yMin should be less than or equal to it. Units for y axis. All y-axis data must have unambiguous units. Ideally the data and _yMin_ or _yValue_ should share the same units but different yUnits can be used as long as it is clear. Value along a y axis. Annotates y-axis data with a value. It is typically used for the location of a _peak_ or _peakGroup_. It uses yUnits or the same units as the data. An unsigned interval along a y axis. It is typically used for the width of a _peak_ or _peakGroup_ but could be used for any range. It uses yUnits or the same units as the data. The number of molecules per cell. Molecules are defined as the _molecule_ which directly contains the _crystal_ element. The z coordinate of a 3 dimensional object. The default units are Angstrom. (The provision for other units is weak at present.) Objects are always described with a right-handed coordinate system. An array of z3 coordinate. Normally used in CML2 array mode. Fractional y coordinate. normally xFract, yFract and zFract should all be present or absent. If present a _crystal_ element should also occur. Array of fractional z coordinate. normally xFract, yFract and zFract should all be present or absent. If present a _crystal_ element should also occur. The abundance of an isotope. The abundance of an isotope in an isotopeList. Values are expressed in percentages. An action which might occur in scientific data or narrative. An action which might occur in scientific data or narrative. The definition is deliberately vague, intending to collect examples of possible usage. Thus an action could be addition of materials, measurement, application of heat or radiation. The content model is unrestricted. _action_ iself is normally a child of _actionList_. The start, end and duration attributes should be interpreted as XSD dateTimes and XSD durations. This allows precise recording of time of day, etc, or duration after start of actionList. A convention="xsd" attribute should be used to enforce XSD. a numerical value, with a units attribute linked to a dictionary. a human-readable string (unlikely to be machine processable) startCondition and endCondition values are not constrained, which allows XSL-like test attribute values. The semantics of the conditions are yet to be defined and at present are simply human readable. The order of the action elements in the document may, but will not always, define the order that they actually occur in. A delay can be shown by an action with no content. Repeated actions or actionLists are indicated through the count attribute. Number of times the action should be repeated. A container for a group of actions. ActionList contains a series ofactions or nestedactionLists. An alternative name for an entry. At present a child of _entry_ which represents an alternative string that refers to the concept. There is a partial controlled vocabulary in _alternativeType_ with values such as : synonym acronym abbreviation The amount of a substance. The units attribute is mandatory and can be customised to support mass, volumes, moles, percentages, or ratios (e.g. ppm). An angle between three atoms. It can be used for: Recording experimentally determined bond angles (e.g. in a crystallographic paper). Providing the angle component for internal coordinates (e.g. z-matrix). A documentation container similar to annotation in XML Schema. A documentation container similar to annotation in XML Schema. At present this is experimental and designed to be used for dictionaries, units, etc. One approach is to convert these into XML Schemas when the documentation and appinfo children will emerge in their correct position in the derived schema. It is possible that this may develop as a useful tool for annotating components of complex objects such as molecules. A container similar to appinfo in XML Schema. A container for machine processable documentation for an entry. This is likely to be platform and/or language specific. It is possible that XSLT, RDF or XBL will emerge as generic languages. See _annotation_ and _documentation_ for further information. An example in XSLT where an element _foo_ calls a bespoke template. Allows a processor to inspect the role of the appinfo and process accordingly. An argument for a function. Arguments can be typed and have explicit or free values. They can also carry out substitutions in the parent element and its children (substitute, still experiemental) and delete itself after this. 2006-02-14: PMR. Added atomType as child 2006-05-21: PMR. Added substitute and delete attributes A homogenous 1 dimensional array of similar object. These can be encoded as strings (i.e. XSD-like datatypes) and are concatenated as string content. The size of the array should always be >= 1. The default delimiter is whitespace. The _normalize-space()_ function of XSLT could be used to normalize all whitespace to single spaces and this should not affect the value of the array elements. To extract the elements __java.lang.StringTokenizer__ could be used. If the elements themselves contain whitespace then a different delimiter must be used and is identified through the delimiter attribute. This method is mandatory if it is required to represent empty strings. If a delimiter is used it MUST start and end the array - leading and trailing whitespace is ignored. Thus size+1 occurrences of the delimiter character are required. If non-normalized whitespace is to be encoded (e.g. newlines, tabs, etc) you are recommended to translate it character-wise to XML character entities. Note that normal Schema validation tools cannot validate the elements of array (they are defined as string) However if the string is split, a temporary schema can be constructed from the type and used for validation. Also the type can be contained in a dictionary and software could decide to retrieve this and use it for validation. When the elements of the array are not simple scalars (e.g. scalars with a value and an error, the scalars should be used as the elements. Although this is verbose, it is simple to understand. If there is a demand for more compact representations, it will be possible to define the syntax in a later version. the size attribute is not mandatory but provides a useful validity check): Alternative to units Must be used in conjunction with unitType 2005-10-26: added Alternative to units Must be used in conjunction with unitType 2005-10-26: added Alternative to units Must be used in conjunction with multiplierToSI and/or constantToSI 2005-10-26: added A list of arrays or lists. A major use of arrayList is to contain data within rectangular tables. However there is no absolute requirement and the table can have any shape. The shape attribute hould be used to assert rectangularity. 2006-11-03: created An atom. Atoms can only be chosen from the periodic table and superatoms such as "Phe" or "Tyr" are not allowed. The elementType of an atom is identified by that attribute. There are two additional elementTypes, "Du" (for an object which does not have an identifiable nucleus but is useful in calculations and definitions (such as a centroid); and "R" which describes a generic fragment. Although atoms have an elementType, they do not, by default, support arbitrary atomTypes for which the <atomType> element should be used. 2006-01-12: PMR. Added vector3 child to support accelerations, velocities, dipole, etc. 2006-06-01: PMR. Added documentation. The main content model of the atom. name can be used for atom labels, etc. More than one name can be used if required. scalar contains any scalar properties of the atom (examples are chemical shift, B-value, etc.) linked through dictRef (CmlDictRefType). array contains any properties of the atom describable by a homogeneous array linked through dictRef (CmlDictRefType). matrix contains any properties of the atom describable by a homogeneous matrix linked through dictRef (CmlDictRefType). An example is the polarizability tensor atomParity (CmlAtomParityElement) the required way of defining atom-based chirality electron a away of associating electron(s) with the atom Most useful in _formula_ but possibly useful in _atomArray_ where coordinates and connectivity is not defined. No formal default, but assumed to be 1. This can be used to describe the purpose of atoms whose _elementType_s are __dummy__ or __locant__. Vocabulary not controlled. 2005-11-27: Added PMR 2005-11-27: Added PMR A container for a list of atoms. A child of _molecule_ and contains _atom_ information. There are two strategies: Create individual _atom_ elements under _atomArray_ (in any order). This gives the greatest flexibility but is the most verbose. Create *Array attributes (e.g. of _elementTypeArrayType_ under _atomArray_. This requires all arrays to be of identical lengths with explicit values for all atoms in every array. This is NOT suitable for complexType atom children such as _atomParity_. It also cannot be checked as easily by schema- and schematron validation. The _atomIDArray_ attribute is mandatory. It is allowed (though not yet recommended) to add _*Array_ children such as _floatArray_ The attributes are directly related to the scalar attributes under _atom_ which should be consulted for more info. Example - these are exactly equivalent representations An atomicBasisFunction. An atomic atomicBasisFunction which can be linked to atoms, eigenvalues/vectors etc. Normally contained within _basisSet_ Normally these are atom-centered functions, but they can also serve as "ghost" functions which are centered on points. These can be dummy atoms so that the atomRef mechanism can still be used. This information is required to interpret the eignevector components and map them onto the atom list. However this mapping is normally implicit in the program and so it may be necessary to generate basisSet information for some programs before XML technology can be automatically used to link the components of the CCML document. The atom owning this atomicBasisFunction. This reference is required to tie the reported eigenvector components to the list of atoms. This is provided for completeness but we do not see it being widely used and the symbolic representation (lm) is more valuable. This is a local annotation of the ABF and unlikely to be enumeratable. Thus a split s-orbital could have 3 ABFs with "s", "s'", "s''" but they would all have lm="s". This is a "standard" representation of the ABF, but not enumerated until we decide whether it can be formalised. Examples are "px", "dxy", etc. Note that d-orbitals and higher may be represented with redundant ABFs, e.g. 6 d-orbitals. The more standard the representation, the more useful this will be for searching. The stereochemistry round an atom centre. It follows the convention of the MIF format, and uses 4 distinct atoms to define the chirality. These can be any atoms (though they are normally bonded to the current atom). There is no default order and the order is defined by the atoms in the atomRefs4 attribute. If there are only 3 ligands, the current atom should be included in the 4 atomRefs. The value of the parity is a signed number. (It can only be zero if two or more atoms are coincident or the configuration is planar). The sign is the sign of the chiral volume created by the four atoms (a1, a2, a3, a4): | 1 1 1 1 | | x1 x2 x3 x4 | | y1 y2 y3 y4 | | z1 z2 z3 z4 | Note that atomParity cannot be used with the *Array syntax for atoms. A set of references to atoms. An atomSet consists of a number of unique references to atoms throught their ids. atomSets need not be related to molecules (which are generally created by aggregation of explicit atoms). Two or more atomSets may reference the same atom, and atomSets may be empty. atomSets have many potential uses such as: identifying functional groups results of substructure matching identifying atoms with particular roles in a calculation The atomSet may be referenced from elsewhere in the document and you are encouraged to use locally unique id attributes on atomSets. An atomType. atomTypes are used in a wide variety of ways in computational chemistry. They are normally labels added to existing atoms (or dummy atoms) in the molecule and have a number of defined properties. These properties are usually in addition to those deducible from the elementType of the atom. AtomTypes usually depend on the chemical or geometrical environment of the atom and are frequently assigned by algorithms with chemical perception. However they are often frequently set or "tweaked" by humans initiating a program run. AtomTypes on an atom have no formal relation to its elementType, which only describe the number of protons in the nucleus. It is not unknown (though potentially misleading) to use an "incompatible" atomType to alter the computational properties of an atom (e.g. pretend this K+ is a Ca++ to increase its effective charge). atomTypes will also be required to describe pseudoAtoms such as "halogen" (generic) or "methyl group" (unified atom). Atoms in computations can therefore have an atomType child with a "ref" attribute. An atomType contains numeric or other quantities associated with it (charges, masses, use in force-fields, etc.) and also description of any perception algorithms (chemical and/or geometrical) which could be used to compute or constrain it. This is still experimental. atomTypes are referred to by their mandatory name attribute. An atom refers to one or more atomTypes through atomType/@ref children examples not yet teste. The name will usually be namespaced as 'gulp:si', 'tripos:c.3', etc. It must occur except for atomType/@re. A container for one or more atomTypes. It can contain several atomTypes. A band or Brillouin zone. Not yet finalised. 2006-01-21: PMR. added kpointRef and deprecated kpointList. Band energies associated with this kpoint. The energy units must be given. kpoints should be described in kpointList and referenced. A container for bands. Experimental. A container for one or more atomicBasisFunctions. This can contain several orbitals. A bond between atoms, or between atoms and bonds. _bond_ is a child of _bondArray_ and contains bond information. Bond must refer to at least two atoms (normally using _atomRefs2_) but may also refer to more for multicentre bonds. Bond is often EMPTY but may contain _electron_, _length_ or _bondStereo_ elements. Validate Bonds One or more electrons associated with the bond. The _bondRef_ on the _electron_ should point to the id on the bond. We may relax this later and allow reference by context. The stereo convention for the bond. only one convention allowed. This is designed for multicentre bonds (as in delocalised systems or electron-deficient centres. The semantics are experimental at this stage. As an example, a B-H-B bond might be described as <bond atomRefs="b1 h2 b2"/. This is designed for pi-bonds and other systems where formal valence bonds are not drawn to atoms. The semantics are experimental at this stage. As an example, a Pt-|| bond (as the Pt-ethene bond in Zeise's salt) might be described as <bond atomRefs="pt1" bondRefs="b32"/. A container for a number of bonds. _bondArray_ is a child of _molecule_ and contains _bond_ information. There are two strategies: Create individual bond elements under bondArray (in any order). This gives the greatest flexibility but is the most verbose. Create *Array attributes (e.g. of orderArrayType under bondArray. This requires all arrays to be of identical lengths with explicit values for all bonds in every array. This is NOT suitable for complexType bond children such as _bondStereo_ nor can IDs be added to bonds.. It also cannot be checked as easily by schema- and schematron validation. The _atomRef1Array_ and _atomRef2Array_ attributes are then mandatory. It is allowed (though not yet recommended) to add _*Array_ children such as _floatArray_ The attributes are directly related to the scalar attributes under _atom_ which should be consulted for more info. Example - these are exactly equivalent representations A set of references to bonds. An bondSet consists of a number of unique references to bonds throught their ids. bondSets need not be related to molecules (which are generally created by aggregation of explicit bonds). Two or more bondSets may reference the same bond, and bondSets may be empty. bondSets have many potential uses such as: identifying functional groups results of substructure matching identifying bonds with particular roles in a calculation The bondSet may be referenced from elsewhere in the document and you are encouraged to use locally unique id attributes on bondSets. A container supporting cis trans wedge hatch and other stereochemistry. An explict list of atomRefs must be given, or it must be a child of bond. There are no implicit conventions such as E/Z. This will be extended to other types of stereochemistry. At present the following are supported: No atomRefs attribute. Deprecated, but probably unavoidable. This must be a child of bond where it picks up the two atomRefs in the atomRefs2 attribute. Possible values are C/T (which only makes sense if there is exactly one ligand at each end of the bond) and W/H. The latter should be raplaced by atomParity wherever possible. Note that W/H makes no sense without 2D atom coordinates. atomRefs4 attribute. The 4 atoms represent a cis or trans configuration. This may or may not be a child of bond; if so the second and third atomRefs should be identical with the two atomRefs in the bond. This structure can be used to guide processors in processing stereochemistry and is recommended, since there is general agreement on the semantics. The semantics of bondStereo not related to bonds is less clear (e.g. cumulenes, substituted ring nuclei) etc.It is currently an error to have more than one bondStereo referring to the same ordered 4-atom list atomRefs attribute. There are other stereochemical conventions such as cis/trans for metal complexes which require a variable number of reference atoms. This allows users to create their own - at present we do not see CML creating exhaustive tables. For example cis/trans square-planar complexes might require 4 (or 5) atoms for their definition, octahedral 6 or 7, etc. In principle this is very powerful and could supplement or replace the use of cis-, mer-, etc. the atomRefs and atomRefs4 attributes cannot be used simultaneously. The type of a bond. Bond types are used to describe the behaviour of bonds in forcefields, functional groups, reactions and many other domains. They are not as well formalised as atomTypes and we provide less semantic support. BondTypes are referred to by their mandatory _name_ attribute. The bondType name. The name will usually be namespaced as 'gulp:si', 'tripos:c.3', etc. It must occur except when the ref attribute is given. A container for one or more bondTypes. _bondTypeList_ can contain several bondTypes. A set of 3 cell parameters. Either 3 lengths or 3 angles. A general container for CML elements. Often the root of the CML (sub)document. Has no explicit function but can serve to hold the dictionary and namespace and version information, and is a useful tag to alert CML processors and search/XMLQuery tools that there is chemistry in the document. Can contain any content, but usually a list of molecules and other CML components. The fileId attribute can be used to preserve the origin of the information, though metadat should also be used. Can be nested. No specific restrictions.. An element to hold any combination of heterogeneous element children complexObject can be used as it stands but will often be extended by schema definitions in dictionary entries. A container for one or more experimental conditions. This can contain several conditions. These include (but are not limited to) intensive physical properties (temperature, pressure, etc.), apparatus (test-tube, rotary evaporator, etc.). Actions can be represented elsewhere by actionList and solvents or other substances by substanceList. Copies an element Experimental. copies contained element 2006-06-09: PMR. Created A crystallographic cell. Required if fractional coordinates are provided for a molecule. Originally there were precisely SIX child scalars to represent the cell lengths and angles in that order. There are no default values; the spacegroup is also included. This is now deprecated and replaced by cellParameter 2006-03-06 PMR: added cellParameter child OLD STYLE: All 6 cell parameters must be given, even where angles are fixed by symmetry. The order is fixed as a,b,c,alpha,beta,gamma and software can neglect any title or dictRef attributes. Error estimates can be given if required. Any units can be used, but the defaults are Angstrom (10^-10 m) and degrees. NEW STYLE: Two cellParameter children are given The definition for an entry. The definition should be a short nounal phrase defining the subject of the entry. Definitions should not include commentary, implementations, equations or formulae (unless the subject is one of these) or examples. The definition can be in any markup language, but normally XHTML will be used, perhaps with links to other XML namespaces such as CML for chemistry. From the IUPAC Dictionary of Medicinal Chemistry Descriptive information. This can occur in objects which require textual comment such as entry. Entries should have at least one separate definitions. description is then used for most of the other information, including examples. The class attribute has an uncontrolled vocabulary and can be used to clarify the purposes of the description elements. A dictionary. A dictionary is a container for _entry_ elements. Dictionaries can also contain unit-related information. The dictRef attribute on a dictionary element sets a namespace-like prefix allowing the dictionary to be referenced from within the document. In general dictionaries are referenced from an element using the __dictRef__ attribute. 2005-12-15. PMR. added namespace and dictionaryPrefix. A dimension supporting scientific unit. This will be primarily used within the definition of units. Two dimensions are of the same type if their 'name' attributes are (case-sensitive) identical. Dimensions of the same typecan be algebraically combined using the 'power' attributes. Normally dimensions will be aggregated and cancelled algebraically, but the 'preserve' attribute can be used to prevent this. Thus a velocity gradient over length can be defined as: whereas cancelling the dimensions would give: Documentation in the annotation of an entry. A container similar to documentation in XML Schema. This is NOT part of the textual content of an entry but is designed to support the transformation of dictionary entrys into schemas for validation. This is experimental and should only be used for dictionaries, units, etc. One approach is to convert these into XML Schemas when the documentation and appinfo children will emerge in their correct position in the derived schema. Do NOT confuse documentation with the description or the definition which are part of the content of the dictionary If will probably only be used when there is significant appinfo in the entry or where the entry defines an XSD-like datatype of an element in the document. An element to hold eigenstuff. Holds an array of eigenvalues and a matrix of eigenvectors. No current semantics. Suggest it is developed for the chemical/physical role, e.g. "molecular obitals", "inertial matrix", "vibrational modes", "phonons", etc. An electron. Since there is very little use of electrons in current chemical information this is a fluid concept. I expect it to be used for electron counting, input and output of theochem operations, descriptions of orbitals, spin states, oxidation states, etc. Electrons can be associated with atoms, bonds and combinations of these. At present there is no hardcoded semantics. However, _atomRef_ and similar attributes can be used to associate electrons with atoms or bond. A dictionary entry. The original design for validation with attribute-based constraints is ponderous and fragile. In future constraints will be added through appinfo in annotation. We shall develop this further in the near future. 2003-03-30: added metadataList to content mode. An enumeration of value. An enumeration of string values. Used where a dictionary entry constrains the possible values in a document instance. The dataTypes (if any) must all be identical and are defined by the dataType of the containing element. An expression that can be evaluated. Experimental. This is essentially a mathematical function, expressed currently in reverse Polish notation but we expect to move to MathML. CML-1 dataType DEPRECATED. CML-1 dataType DEPRECATED. Iterates through a list or list of values Experimental. 2006-06-09: PMR. Created A molecular formula. It is defined by atomArrays each with a list of elementTypes and their counts (or default=1). All other information in the atomArray is ignored. formula are nestable so that aggregates (e.g. hydrates, salts, etc.) can be described. CML does not require that formula information is consistent with (say) crystallographic information; this allows for experimental variance. An alternative briefer representation is also available through the concise. This must include whitespace round all elements and their counts, which must be explicit. 2005-10-16. The semantics are now the following. A formula must have one or both: A concise attribute A single atomArray child, using array format. it must also have a formalCharge attribute if atomArray is used and the charge is non-zero. The concise, formalCharge and atomArrary information must always be consistent and software should throw an error if not. Until now there was no way of holding inline formula other than concise (although JUMBO5.0 is capable of reading them). We now extend formula.xsd to incorporate this through the attribute "inline" which requires the use of the "convention" attribute. The contents of inline are purely textual. It can be used with or without atomArray or concise but there is no guarantee that it can be interpreted as a meaningful chemical formula or that there is consistency. In some cases a document supplies several formula representations (e.g. the IUCr's CIF). In this case a molecule (or crystal) element might contain several formula children. The semantics of which to use are application dependent. Allows for fractional components. The charge on the formula. Mandatory if non-zero (i.e. cannot rely on concise) An inline representation of the formula. There are no controlled semantics and it need not be compatible with concise or atomArray. A container for a fragment fragment is a container for a molecule, potentially to be joined to other fragments. In addition there may be fragmentLists which represent branches from the molecule. There may also be a join child which is normally only found if there is a @countExpression. 2006-11-23: created fragment normally contains molecules branches from the moelcule. the inter-fragment join. Normally it only makes sense with @countExpression. No formal semantics (yet). A container for one or more fragments and joins. fragmentList can contain several fragments and joins. The normal content model is join fragment join fragment... 2006-07-20: PMR Added A gradient. A container for a quantity or quantities representing the gradient of other quantities. At present just takes a scalar child. A structured identifier. Supports compund identifiers such as IChI. At present uses the V0.9 IChI XML representation verbatim but will almost certainly change with future IChIs. The inclusion of elements from other namespaces causes problems with validation. The content model is deliberately LAX but the actual elements in IChI will fail the validation as they are not declared in CML. For simple scalar values the value attribute can be used with empty content. Where an identifier has several components a series of label elements can be used. 2003-07-10: Fixed count on identifier children.. 2003-03-12: Added isotopic and atoms.. CML-1 dataType DEPRECATED. CML-1 dataType DEPRECATED. A specific isotope. Defines an isotope in terms of exact mass and spin. Differentiate from isotopeList which defines a mixture of isotope. A container for one or more isotopes. Can contain several isotopes. These may be related in several ways. This allows the definition of natural abundance and averged enrichment. Command to join two groups. EXPERIMENTAL. join will normally use atomRefs2 to identify 2 R atoms (i.e. elementType="R" that should be joined. The atoms to which the R atoms are attached are then joined by a new bond and the R groups are then deleted. It is currently an error if these atoms already have a connecting bond. 2006-05-20: PMR added. 2006-11-24: PMR deleted @left, @linkOnParent, @right, @repeat. 2006-11-24: PMR modified content model 2006-11-24: PMR added @moleculeRefs2 A kpoint. Not yet finalised. 2006-01-21: PMR. Created A container for kpoints. Experimental. A text string qualifying an object. A label can be used to identify or distinguish elements, add keywords or classifications and similar processes. It is usually interpretable by domain-aware humans (e.g. C3'-endo, but not a34561). It is usually either built in a semantically rich fashion (e.g. C2'-alpha-H) or belongs to a controlled vocabulary. It is possibly accessed by software in a domain-specific manner. It differs from description which is free text. The distinction between titles, names and labels is fuzzy, but we think this is worth making. Labels may be necesssary to identify objects within programs, while names are more likely to be reserved for database searches. Titles are likely to be freer text and not recommended for precise object retrieval. Labels should not contain whitespace. Punctuation marks are often necessary, but should not be gratuitously used. Punctuation clashing with XML character entities should be avoided; if this is not possible it should be escaped. From IUPAC Dictionary of Medicinal Chemistry A lattice of dimension 3 or less. Lattice is a general approach to describing periodic systems. It can have variable dimensionality or periodicity, and could be finite. _lattice_ is more general than _crystal_ in cmlCore which is used primarily for reporting crystallographic experiments.`A lattice can be described by latticeVectors, cell axes and angles, or metric tensors, etc. (only axes/angles are allowed under crystal). The dimensionality is enforced through a _system_ parent element. All appropriate cell parameters must be given, even where angles are fixed by symmetry. The order is fixed as a,b,c,alpha,beta,gamma and software can neglect any title or dictRef attributes. Error estimates can be given if required. Any units can be used, but the defaults are Angstrom (10^-10 m) and degrees. To be developed for lower dimensionality. A vector3 representing a lattice axis. a lattice can be represented by 1-3 non-linearly dependent latticeVectors. If the dimensionality is less than 3 latticeVectors are the preferred method. Similarly, if the axes show a mixture of periodicity and non-periodicity latticeVectors can support this. The number of periodic vectors must correspond with the periodicity attribute on a system element. The vector must not be zero and units must be given. (Zero vectors must not be used to reduce dimensionality). A lattice vector defaults to periodic.. Any or all of the axes may be periodic or aperiodic. An example could be a surface where 2 periodic axes (not necessarily orthogonal) are used to describe the coordinates in the surface, perhaps representing lattice vectors of a 3D crystal or 2D layer. The third vector is orthogonal and represents coordinates normal to the surface. In this case only the direction, not the magnitude of the vector is important. A length between two atoms. This is either an experimental measurement or used to build up internal coordinates (as in a z-matrix) (only one allowed). We expect to move length as a child of _molecule_ and remove it from here. A line in 3-space. A line characterised by one or two endpoints. 2006-01-02: the 6-number content has caused much confusion and will be obsoleted in favour of the point3 and vector3 attributes An internal or external link to other objects. Semantics are similar to XLink, but simpler and only a subset is implemented. This is intended to make the instances easy to create and read, and software relatively easy to implement. The architecture is: A single element (link) used for all linking purposes. The link types are determined by the type attribute and can be:. locator. This points to a single target and must carry either a ref or href attribute. locator links are usually children of an extended link. arc. This is a 1:1 link with both ends (from and to) defined. extended. This is usually a parent of several locator links and serves to create a grouping of link ends (i.e. a list of references in documents). Many-many links can be built up from arcs linking extended elements All links can have optional role attributes. The semantics of this are not defined; you are encouraged to use a URI as described in the XLink specification. There are two address spaces: The href attribute on locators behaves in the same way as href in HTML and is of type xsd:anyURI. Its primary use is to use XPointer to reference elements outside the document. The ref attribute on locators and the from and to attributes on arcs refer to IDs (without the '#' syntax). Note: several other specific linking mechanisms are defined elsewhere in STM. relatedEntry should be used in dictionaries, and dictRef should be used to link to dictionaries. There are no required uses of link in STMML but we have used it to map atoms, electrons and bonds in reactions in CML Relation to XLink. At present (2002) we are not aware of generic XLink processors from which we would benefit, so the complete implementation brings little extra value. Among the simplifications from Xlink are: type supports only extended, locator and arc label is not supported and ids are used as targets of links. show and actuate are not supported. xlink:title is not supported (all STM elements can have a title attribute). xlink:role supports any string (i.e. does not have to be a namespaced resource). This mechanism can, of course, still be used and we shall promote it where STM benefits from it The to and from attributes point to IDs rather than labels The xlink namespace is not used It is not intended to create independent linkbases, although some collections of links may have this property and stand outside the documents they link to The type of the object/element in the 'from' attributes. Requires the objects referenced by the 'from' attributes to have a given elementType. Can be overridden by 'from' attributes in individual links. 2005-06-18: created The type of the object/element in the 'to' attributes. Requires the objects referenced by the 'to' attributes to have a given elementType. Can be overridden by 'to' attributes in individual links. 2005-06-18: created The set of ids in the base of the link. 2005-06-18: created The set of ids in the target of the link. 2005-06-18: created The id of the ancestral element of objects referenced by 'from' attributes. Provides a context for uniquifying the references in the 'from' attributes. Thus atoms referenced by ids should be unique within a given molecule and the id of this could be the 'fromContext'. 2005-06-18: created The id of the ancestral element of objects referenced by 'to' attributes. Provides a context for uniquifying the references in the 'to' attributes. Thus atoms referenced by ids should be unique within a given molecule and the id of this could be the 'toContext'. 2005-06-18: created The role of the link. Xlink adds semantics through a URI; we shall not be this strict. We shall not normally use this mechanism and use dictionaries instead. The target of the (locator) link, outside the document. A generic container with no implied semantics. A generic container with no implied semantics. It just contains things and can have attributes which bind conventions to it. It could often act as the root element in an STM document. A container for links Usage is now standardized with map as the container and link as the individual links. The links are often effectively typed pointers to other parts of the document. The type can be set for all links by the 'fromType' and 'toType' attributes, either in the map, which then applied to all links by default, or in individual links, when it overrides the map setting. Since ids may not be unique within a document the refs can be given context with the 'fromRef' and 'toRef' attributes in the map element. If more than one context is used it may be better to use multiple maps. The role of map, and its relationship to RDF is still being developed. Currently (2005) map has primarily been used to map atoms between reactants and products, but we also expect shortly to extend it to peak assignments and several otherr areas. A map consists of a number of links, which can be directional, relating two elements through their ids. Reference is through the mandatory 'to' and 'from' attributes which must point to existing id attributes on elements. The type of the dereferenced element can be specified in 'toType' and 'fromType' which, while redundant, is an aid to software and acts as a check on referential type integrity. In principle any element can be linked to any other, with 1:1, 1:n, and n:m topology. We expect maps to be used for precise chemical concepts such as reactions, peak assignments, electron management, molecular superpositions, etc. and that these are supported by bespoke code. For other links, especially with complex topology, users should consider whether RDF may be more appropriate. In some cases partial mapping is known (e.g. one set of atoms maps to another set), but the precise links are unknown. (This is not the same as n:m mapping where n*m precise links would be expected). In some cases there may be objects such as atomSets or peakGroups which could be linked to support this. Alternatively the 'fromSet' and 'toSet' attributes can be used to hold a list of ids. Thus from='a1 a2' to='b3 b4' might imply that there were two precise links (either {a1=>b3, a2=>b4} or {a1=>b4, a2=>b3}). This is most likely to be used in intermediate documents where more precise semantics can be added later. The ids must all refer to elements of the same type. Note that a 'to' link referencing a single atomSet (toType='atomSet') is not the same as a 'toSet' of toType='atom' with multiple atomIds. The first would require an 'atomSet' element in the document; the second would not. The precise semantics such as the order of ids are application-dependent. If the order is known in both the toSet and fromSet then individual links should be used rather than adding the burden of deconstruction on the implementer. 2005-06-18: added typing and role and updated docs. 2006-08-05: added ref attribute. The type of the object/element in the 'from' attributes. Requires the objects referenced by the 'from' attributes to have a given elementType. Can be overridden by 'from' attributes in individual links. 2005-06-18: created The type of the object/element in the 'to' attributes. Requires the objects referenced by the 'to' attributes to have a given elementType. Can be overridden by 'to' attributes in individual links. 2005-06-18: created The id of the ancestral element of objects referenced by 'from' attributes. Provides a context for uniquifying the references in the 'from' attributes. Thus atoms referenced by ids should be unique within a given molecule and the id of this could be the 'fromContext'. 2005-06-18: created The id of the ancestral element of objects referenced by 'to' attributes. Provides a context for uniquifying the references in the 'to' attributes. Thus atoms referenced by ids should be unique within a given molecule and the id of this could be the 'toContext'. 2005-06-18: created The role of the map. Semantics are undefined, and can be used to provide a small semi-controlled vocabulary for identifying maps of different types. 2005-06-18: created A rectangular matrix of any quantities. By default matrix represents a rectangular matrix of any quantities representable as XSD or STMML dataTypes. It consists of rows*columns elements, where columns is the fasting moving index. Assuming the elements are counted from 1 they are ordered V[1,1],V[1,2],...V[1,columns],V[2,1],V[2,2],...V[2,columns], ...V[rows,1],V[rows,2],...V[rows,columns] By default whitespace is used to separate matrix elements; see array for details. There are NO characters or markup delimiting the end of rows; authors must be careful!. The columns and rows attributes have no default values; a row vector requires a rows attribute of 1. matrix also supports many types of square matrix, but at present we require all elements to be given, even if the matrix is symmetric, antisymmetric or banded diagonal. The matrixType attribute allows software to validate and process the type of matrix. The mechanism of a reaction. In some cases this may be a simple textual description or reference within a controlled vocabulary. In others it may describe the complete progress of the reaction, including topological or cartesian movement of atoms, bonds and electrons and annotation with varying quantities (e.g. energies). For named reaction mechanisms ("Diels-Alder", "ping-pong", "Claisen rearrangement", etc.) the name element should be used. For classification (e.g. "hydrolysis"), the label may be more appropriate. In more detailed cases the mechanism refers to components of the reaction element. Thus bond23 might be cleaved while bond19 is transformed (mapped) to bond99. The mechanismComponent can be used to refer to components and add annotation. This is still experimental. IUPAC Compendium of Chemical Terminology 2nd Edition (1997) describes a mechanism as: A detailed description of the process leading from the reactants to the products of a reaction, including a characterization as complete as possible of the composition, structure, energy and other properties of reaction intermediates, products and transition states. An acceptable mechanism of a specified reaction (and there may be a number of such alternative mechanisms not excluded by the evidence) must be consistent with the reaction stoichiometry, the rate law and with all other available experimental data, such as the stereochemical course of the reaction. Inferences concerning the electronic motions which dynamically interconvert successive species along the reaction path (as represented by curved arrows, for example) are often included in the description of a mechanism. It should be noted that for many reactions all this information is not available and the suggested mechanism is based on incomplete experimental data. It is not appropriate to use the term mechanism to describe a statement of the probable sequence in a set of stepwise reactions. That should be referred to as a reaction sequence, and not a mechanism. CMLReact provides reactionScheme and annotions to describe the reaction sequence and both it and mechanism could co-occur within a reactionScheme container. 2006-02-28 PMR: changed content model to choice. An information component within a reaction mechanism. Information components can represent both physical constituents of the reaction or abstract concepts (types of bond cleavage, thermodynamics, etc.). There are several ways that components of the reaction can be annotated and/or quantified. One approach will be to refer to specific bonds and atoms through their ids and use mechanismComponent to describe their role, properties, etc. Another is to use mechanismComponent to identify types of bond formed/broken without reference to actual atoms and bonds (initially through the name element). Yet another will be to include information on the reaction profile. This is still experimental. A general container for metadata. A general container for metadata, including at least Dublin Core (DC) and CML-specific metadata In its simple form each element provides a name and content in a similar fashion to the meta element in HTML. metadata may have simpleContent (i.e. a string for adding further information - this is not controlled). A general container for metadata elements. MetadataLists can have local roles (e.g. a bibliographic reference could be a single meteadatList with, say, 3-6 components). The role attribute is used in an uncontrolled manner for this. MetadataLists can also be nested, but metadata and metadataList children should not occur on the same level of the hierarchy. A module in a calculation. Many programs are based on discrete modules which produce chunks of output. There are also conceptual chunks such as initialisation, calculation and summary/final which often have finer submodules such as cycle, iteration, snapshot, etc. There is no controlled vocabulary but a typical structure is shown in the example. One of the challenges of CCML is to find communality between different programs and to use agreed abstractions for the modules. The module can have a program-specific name through its title or dictRef (e.g. "MINIM", "l201") and a generic role ("dynamicsCalculation", "equilibration", etc.). In general role will be controlled by CCML. A container for atoms, bonds and submolecules. molecule is a container for atoms, bonds and submolecules along with properties such as crystal and non-builtin properties. It should either contain molecule or *Array for atoms and bonds. A molecule can be empty (e.g. we just know its name, id, etc.) "Molecule" need not represent a chemically meaningful molecule. It can contain atoms with bonds (as in the solid-sate) and it could simply carry a name (e.g. "taxol") without formal representation of the structure. It can contain "sub molecules", which are often discrete subcomponents (e.g. guest-host). Molecule can contain a <list> element to contain data related to the molecule. Within this can be string/float/integer and other nested lists Normally molecule will not contain fragment or fragmentList Revised content model to allow any order of lengths, angles, torsions 2003-01-01.. Added role attribute 2003-03-19.. 2006-05-21. PMR changed content model to (A|B|C...)* 2006-11-24. PMR removed @tail, @head, @countExpression, @repeat The float|integer|string children are for compatibility with CML-1 and are deprecated. scalar|array|matrix should be used instead. No formal semantics (yet). The role describes the purpose of the molecule element at this stage in the information. Examples can be "conformation", "dynamicsStep", "vibration", "valenceBondIsomer", etc. This attribute may be used by applications to determine how to present a set of molecule elements. A container for one or more molecules. moleculeList can contain several molecules. These may be related in many ways and there is are controlled semantics. However it should not be used for a molecule consisting of descendant molecules for which molecule should be used. A moleculeList can contain nested moleculeLists. 2006-07-20: PMR Added metadataList contains metadata. list is for experimental and other data. moleculeList normally contains molecules but we make provision for nested moleculeLists if required. The molecules can be a set of reference molecules which occur in the molecules and can be referenced. This makes the molecules more readable and normalizes data when molecules are used more than once. A string identifying a object. name is used for chemical names (formal and trivial) for molecules and also for identifiers such as CAS registry and RTECS. It can also be used for labelling atoms. It should be used in preference to the title attribute because it is repeatable and can be linked to a dictionary. Constraining patterns can be described in the dictionary and used to validate names. An object which might occur in scientific data or narrative. Deliberately vague. Thus an instrument might be built from sub component objects, or a program could be composed of smaller modules (objects). object could be used to encapsulate graphical primitives (e.g. in reaction schemes, drawings of apparatus, etc.). Unrestricted content model. An observation or occurrence. A container for any events that need to be recorded, whether planned or not. They can include notes, measurements, conditions that may be referenced elsewhere, etc. There are no controlled semantics. An operator within an expression. Experimental. An operator acts on one or more arguments (at present the number is fixed by the type). The formulation is reverse Polish so the result (with its dataType) is put on a stack for further use. A parameter describing the computation. A parameter is a broad concept and can describe numeric quantities, objects, keywords, etc. The distinction between keywords and parameters is often fuzzy. ("MINIM" might mean "minimize", while "MINIM=3" might require three iterations to be run. It may help to think of control keywords as boolean parameters. Numeric parameters can describe values in molecules, forcefields or other objects. Often the parameters will be refined or otherwise varied during the calculation. Some parameters may be fixed at particular values or relaxed at different stages in the calculation. Parameters can have errors, gradients and other indications of uncertainty. String/character parameters are often abbreviated in program input, and this is supported through the regex and ignoreCase attributes. ????? Parameters will usually be defined separately from the objects and use the ref attribute to reference them. Parameters can be used to describe additional constraints. This will probably require the development of a microlanguage and until then may use program-specific mechanisms. A common approach will be to use an array of values (or objects) to represent different input values for (parts of) the calculation. Thus a conformational change could be specified by an array of several torsion angles. A parameter will frequently have a dictRef pointing to a dictionary which may have more information about how the parameter is to be used or the values it can take. The allowable content of parameters may be shown by a "template" in the appinfo; this is stil experimental. This is a shorthand for a single scalar value of the parameter. It should only be used with the ref attribute as it inherits all the dataTyping of the referenced element. It must not be used for defining new parameters as it has no mechanism for units and dataTyping. [This may change?]. Used to define concepts such as independent and dependent variables A container for one or more parameters. parameterList can contain several parameters. 2006-02-16:PMR. Added parameterList as child An object in space carrying a set of properties. particles have many of the characteristics of atoms but without an atomic nucleus. It does not have an elementType and cannot be involved in bonding, etc. It has coordinates, may carry charge and might have a mass. It represents some aspect of a computational model and should not be used for purely geometrical concepts such as centroid. Examples of particles are "shells" (e.g. in GULP) which are linked to atoms for modelling polarizability or lonepairs and approximations to multipoles. Properties such as charge, mass should be scalar/array/matrix children. Used in a similar manner to atomType. Examples might be "lonePair", "polarizable Oxygen", etc. A peak; annotated by human or machine. A peak can describe: A single point in a spectrum. Usually a maximum but could be a shoulder, inflexion or indeed any point of interest. A continuous range of values within a spectrum, defined by maximum and minimum values on either/both axes The finer structure of the peak can be given with one or more peakStructure children The units should always be given. (The raw spectral data may unfortunately use different units and no assumptions should be made). The content model includes atom, bond, molecule, but these are deprecated and should be replaced by atomRefs, etc. 2005-11-22: PMR. Added moleculeRefs Allows inter alia the provenance of the peak assignment to be recorde. 2005-11-9. DEPRECATED; use atomRefs 2005-11-9. DEPRECATED; use bondRefs 2005-11-9. DEPRECATED; use moleculeRefs when developed 2005-11-9. PMR, added Atoms contributing to this peak The primary set of atoms responsible for the peak such as an NMR peak. Coupling constants and similar splitting should not use this but peakStructure. At present there is no substructure to this attribute or concept and only one attribute is allowed. It may be combined with bondRefs. Even single atoms should use atomRefs, not atomRef. Bonds contributing to this peak The primary set of bonds responsible for the peak such as an IR frequency. At present there is no substructure to this attribute or concept and only one attribute is allowed. It may be combined with atomRefs. Molecule(s) contributing to this peak The molecule or molecule responsible for the peak. At present there is no substructure to this attribute or concept and only one attribute is allowed. This might, for example, be used to manage a mass spectrum or chromatogram A list of closely related peaks or peakGroups. Distinguish between peakList (primarily a navigational container) and peakGroup where the peaks (or groups) have some close relation not shared by all peaks. All descendants must use consistent units. 2005-11-22. added atomRefs, bondRefs and moleculeRefs and deprecated atom, bond, molecule children Allows inter alia the provenance of the peak assignment to be recorde. 2005-11-22. DEPRECATED; use atomRefs 2005-11-22. DEPRECATED; use bondRefs 2005-11-22. DEPRECATED; use moleculeRefs Atoms contributing to this peak The primary set of atoms responsible for the peak such as an NMR peak. Coupling constants and similar splitting should not use this but peakStructure. At present there is no substructure to this attribute or concept and only one attribute is allowed. It may be combined with bondRefs. Even single atoms should use atomRefs, not atomRef. Bonds contributing to this peak The primary set of bonds responsible for the peak such as an IR frequency. At present there is no substructure to this attribute or concept and only one attribute is allowed. It may be combined with atomRefs. Molecule(s) contributing to this peak The molecule or molecule responsible for the peak. At present there is no substructure to this attribute or concept and only one attribute is allowed. This might, for example, be used to manage a mass spectrum or chromatogram A list of peaks or peakGroups. Distinguish between peakList (primarily a navigational container) and peakGroup where the peaks (or groups) have some close relation not shared by all peaks. All peaks and peakGroups should use the same units. Allows inter alia the provenance of the peak assignment to be recorde. The structure of a peak. Primarily to record couplings and other fine structure. At present we have tested this on HNMR spectra, C13 NMR and simple IR. We believe that other types of spectroscopy (ESR, NQR, etc) can be represented to some extent, but there may be systems beyond the current expressive power. For molecules without symmetry we believe that most of the important types of NMR coupling can be represented. Thus an atom which gives rise to two couplings can have two child PeakStructures, and this is shown in example1. <cml xmlns="http://www.xml-cml.org/schema"> <!-- Ha ... Hb ... Hc1, Hc2 --> <molecule id="m1"> <atomArray> <atom id="a1" elementType="H"> <label value="Ha"/> </atom> <atom id="a2" elementType="H"> <label value="Hb"/> </atom> <atom id="a3" elementType="H"> <label value="Hc1"/> </atom> <atom id="a4" elementType="H"> <label value="Hc2"/> </atom> </atomArray> </molecule> <spectrum id="spectrum2" title="test peaks"> <peakList> <peak id="p1" title="Ha" atomRefs="a1" peakShape="sharp" xUnits="unit:ppm" xValue="6.0"> <peakStructure type="coupling" peakMultiplicity="doublet11" value="12" units="unit:hertz" atomRefs="a2"/> </peak> <peak id="p2" title="Hb" atomRefs="a2" peakShape="sharp" xUnits="unit:ppm" xValue="7.0"> <peakStructure type="coupling" peakMultiplicity="doublet11" value="12" units="unit:hertz" atomRefs="a1"/> <peakStructure type="coupling" peakMultiplicity="triplet121" value="15" units="unit:hertz" atomRefs="a3 a4"/> </peak> <peak id="p3" title="Hc" atomRefs="a3 a4" peakShape="sharp" xUnits="unit:ppm" xValue="8.0"> <peakStructure type="coupling" peakMultiplicity="doublet11" value="15" units="unit:hertz" atomRefs="a2"/> </peak> </peakList> </spectrum> </cml> Where a peak is due to symmetry-related atoms there are different couplings to symmetrical atoms. Thus in an AA'BB' system there can be two couplings to the A atoms and we need nested peakStructures to represent these. In this case the order of the atoms in the peak@atomRefs maps to the order of the grandchildren. See example2. <!-- AA'BB' where there are 2 Ha and 2 Hb with two couplings J1 Ha ... Hb and Ha' ... Hb' J2 Ha ... Hb' and Ha' ... Hb --> <molecule id="m1"> <atomArray> <atom id="a1" elementType="H"> <label value="Ha"/> </atom> <atom id="a2" elementType="H"> <label value="Ha'"/> </atom> <atom id="a3" elementType="H"> <label value="Hb"/> </atom> <atom id="a4" elementType="H"> <label value="Hb'"/> </atom> </atomArray> </molecule> <spectrum id="spectrum2" title="test peaks"> <peakList> <!-- the ORDER of a1 and a2 is linked to the ORDER of the grandchildren elements, i.e. a1 couples to atoms in ps11 and ps21 while a2 relates to atoms is ps21 and ps22 --> <peak id="p1" title="Ha" atomRefs="a1, a2" peakShape="sharp" xUnits="unit:ppm" xValue="6.0"> <peakStructure id="ps1" type="coupling" peakMultiplicity="doublet" value="10" units="unit:hertz"> <peakStructure id="ps11" atomRefs="a3"/> <peakStructure id="ps12" atomRefs="a4"/> </peakStructure> <peakStructure id="ps2" type="coupling" peakMultiplicity="doublet" value="2" units="unit:hertz"> <peakStructure id="ps21" atomRefs="a4"/> <peakStructure id="ps22" atomRefs="a3"/> </peakStructure> </peak> </peakList> </spectrum> </cml> Allows inter alia the provenance of the peakStructure assignment to be recorded. Allows identification of couplings in symmetric systems. May also be usable for other complicated systems. The atoms to which the peakStructure refers. Allows identification of the atoms to which the peak is coupled (not the atoms contributing to the primnary reference for which peak should be used). It may be combined with bondRefs. Even single atoms should use atomRefs, not atomRef. Bonds contributing to this peakStructure Even a single bond should use bondRefs, not bondRef A plane in 3-space. An oriented plane of indefinite extent. A point in 3-space. An explicit potential. This represents the actual function for the potential (i.e. with explicit values) rather than the functional form, which will normally be referenced from this. The functional form of a potential. This has generic arguments and parameters rather than explicit ones. It is essentially a mathematical function, expressed currently in reverse Polish notation. A container for explicit potentials. Experimental. A product within a productList. product describes a product species which is produced in a reaction. See reactant for discussion of catalysis and solvents. A product will normally be identified by name(s), formula, or molecule and at least one of these should normally be given. Amount(s) of product can be given after this identification and can describe mass, volume, percent yield, etc. but not stoichiometry A container for one or more products. productList can contain several products. These may be related in several ways, including single list of products grouping of products of parallel reactions . A productList can contain nested productLists. The semantics of this are currently undefined. The number of copies of the productList involved in the stoichiometric reaction. Probably not useful for simple reactions but could be used for parallel reactions. A container for a property. property can contain one or more children, usually scalar, array or matrix. The dictRef attribute is required, even if there is a single scalar child with the same dictRef. The property may have a different dictRef from the child, thus providing an extension mechanism. Properties may have a state attribute to distinguish the state of matter Semantics are not yet controlled but could include thermochemistry, kinetics or other common properties. A container for one or more properties. propertyList can contain several properties. These include (but are not limited to) observations, or numeric quantities. A reactant within a reactantList. reactant describes a reactant species which takes part in a reaction. Catalysts and supports are not normally classified as reactants, but this is subjective. Enzymes (or parts of enzymes) may well be reactants, as could be substances which underwent chemical change but were restored to their original state. reactant is a powerful concept as it can support stoichiometry (atom and molecule counting), mapping (for mechanisms), etc. Solvents are best contained within substanceList. A reactant will normally be identified by name(s), formula, or molecule and at least one of these should normally be given. Amount(s) of reactant can be given after this identification and can describe mass, volume, etc. but not stoichiometr. The role of the reactant within a reactantList. Semantics are not yet controlled but could be limiting, oxidant, etc. TODO: a reactant might have multiple roles so this may have to become an element. The number of copies of the reactant involved in the stoichiometric reaction. Could be non-integer but should not be used for actual ratios of materials added (for which amount should be used). A container for one or more reactants. reactantList can contain several reactants. These may be related in several ways, including lists of related reactants reactant schemes multi-step reactants parallel and/or coupled reactants . A reactantList can contain nested reactantLists. The semantics of this are currently undefined. A chemical reaction or reaction step. reaction is a container for reactants, products, conditions, properties and possibly other information relating to the reaction, often within a reactionList. Partial semantics exist: name the name(s) of the reaction reactantList (normally only one) the grouped reactants spectatorList substances with well-defined chemistry which are involved in the reaction but do not change. Examples are side groups in proteins, cofactors, etc. The division between specattor and substance is subjective. substance or substanceList substances present in the reaction but not classified as reactants. Examples might be enzymes, catalysts, solvents, supports, workup, etc. condition conditions of the reaction. These may be text strings, but ideally will have clearer semantics such as scalars for temperature, etc. productList the grouped products. This allows for parallel reactions or other semantics. property properties (often physical) associated with the reaction. Examples might be heat of formation, kinetics or equilibrium constant. Reaction normally refers to an overall reaction or a step within a reactionList. For a complex "reaction", such as in enzymes or chain reactions, it may be best to use reactionScheme to hold the overall reaction and a reactionList of the individual reaction steps. The semantics of the content model are metadataList for general metadata label for classifying or describing the reaction (e.g. "hydrolysis") identifier for unique identification. This could be a classification such as EC (enzyme commission) or an IChI-like string generated from the components. these are followed by the possible components of the reaction and/or a reactionList of further details. . This allows any objects to be attached to the reaction, but particularly graphical primitives such as lines, arrows, etc. These should be provided as elements where possible (e.g. SVG) and should have references to the chemical objects they interact with (i.e. not simply relying on geometry). Markers with IDs can be included as part of the graphics object and their ids linked to the chemical elements using link. The yield of the reaction. Note that this lies in the range 0-1. A container for one or more reactions or reactionSchemes with no interrelations. A reactionList aggregates reactions and reactionSchemes but implies no semantics. The most common uses are to create small collections of reactions (e.g. databases or publications). A container for two or more related reactions and their relationships. Where reactions are closely related (and often formally dependent on each other) they should be contained within the reactionStepList of a reactionScheme. The semantics which have informed this design include: Steps within an organic synthesis. Two or more individual (primitive) steps provding the detailed mechanism for an overall reaction. Coupled or sequential reactions within biochemical pathways. This design is general because "reaction" is used in several ways. A biochemical pathway (e.g. oxidation of glucose to CO2 and water) involves many coupled enzyme reactions proceeding both in parallel and in sequence. Each of these steps ("reactions" in their own right) is itself complex and can include several mechanistics steps which are themselves reactions with products, reactants, etc. reactionScheme can therefore include reactionStepLists (with more reactionScheme children) which provide a more detailed view of the individual components. Where a set of reactions are primitives... The semantics of the content model are metadataList for general metadata label for classifying or describing the reaction (e.g. "hydrolysis") identifier for unique identification. This could be a classification such as EC (enzyme commission) or an IChI-like string generated from the components. these are followed by the possible components of the reaction and/or a reactionList of further details. A child of reactionStepList and a container for reaction or reactionScheme. reactionStep is always contained within reactionStepList and is designed to manage "sub-reactions" which have close relationships. These will often involve reactions which, taken together, describe a higher level reaction or reaction type. Examples are: biochemical pathways synthetic reaction schemes multi-step reactions parallel and/or coupled reactions . A reactionStep normally contains a single reaction or reactionScheme. It can have attributes such as yield and ratio which can be used by the parent reactionStepList. The name applies to the overall schema of reactions. label is for additional textual information and classification. reactionStepList normally contains reactions but we make provision for nested reactionSchemes if required. The yield of the reactionStep. Note that this lies in the range 0-1. The ratio of this step to one or more sibling steps. Note that this lies in the range 0-1. It is meaningless to use this unless there are siblings, in which case it refers to the relative molar fluxes through each. The "percentage yields" will need to be transformed to this range. There is no requirement that the sum of fluxes through a group of siblings sum to 1.0, though they should not sum to more. A container for one or more related reactionSteps. reactionStepList is always contained within reactionScheme and is designed to manage "sub-reactions" which have close relationships. These will often involve reactions which, taken together, describe a higher level reaction or reaction type. Examples are: biochemical pathways synthetic reaction schemes multi-step reactions parallel and/or coupled reactions . A reactionStepList contains reactionSteps (each of which contains reactions and/or reactionSchemes (e.g. where part of the process is known in greater detail)). It may not directly contain child reactionStepLists. The child reactionSteps can have attributes such as yield and ratio which describe the relationship of the component steps. Guidance on use: reactionScheme describes a complex of reactions with metadata, one (or more) overall reactions and a reactionStepList with the overall component reactions. reactionStepList aggregates and structures the individual subreactions. reactionList is a container for reactions and reactionSchemes with no semantics (e.g. a book or database of selected reactions). The name applies to the overall schema of reactions. label is for additional textual information and classification. reactionStepList normally contains reactionSteps. The reactiveCentre in a reaction. This describes the set(s) of bonds and atoms involved in the reaction. The semantics are flexible, but a common usage would be to create atomSet(s) and bondSet(s) mapping to groups which undergo changes. A region of the system. Under development. A subdivision of the system to which special protocols or properties may be attached. Typical regions could be defined by the presence of atoms belonging to an atomSet or geometrical boundaries. A region element will not always contain other elements, but may have references from other elements. It may create a protocol, e.g. atoms within a region might be replaced by a continuum model or be subject to a field. Semantics yet to be determined. Regions can be created by the unions of two or more regions. This allows a region to be built from a series of (say) spheres or boxes filling space. An entry related in some way to a dictionary entry. The range of relationships is not restricted but should include parents, aggregation, seeAlso and so on. DataCategories from ISO12620 can be referenced through the namespaced mechanism. The related entry. An analytical or spectral sample. The sample should contain information on what things were in the sample and their roles. It can include molecule, substance and substanceList. Typical rolos include solvent, mulling agents, salt disks, molecular supports, etc. but should not cover apparatus or conditions. A molecular description. A substance in the sample. A list of substances in the sample. An element to hold scalar data. scalar holds scalar data under a single generic container. The semantics are usually resolved by linking to a dictionary. scalar defaults to a scalar string but has attributes which affect the type. scalar does not necessarily reflect a physical object (for which object should be used). It may reflect a property of an object such as temperature, size, etc. Note that normal Schema validation tools cannot validate the data type of scalar (it is defined as string), but that a temporary schema can be constructed from the type and used for validation. Also the type can be contained in a dictionary and software could decide to retrieve this and use it for validation. Alternative to units Must be used in conjunction with unitType 2005-10-26: added Alternative to units Must be used in conjunction with unitType 2005-10-26: added Alternative to units Must be used in conjunction with multiplierToSI and/or constantToSI 2005-10-26: added A spectator object in a reaction. Objects are often present during a reaction which are not formally involved in bond breaking/formation and which are not modified during the reaction. They may be catalysts, but may also be objects which in some way constrain or help the reaction to take place (surfaces, micelles, groups in enzyme active sites, etc.). In some cases molecules present in a reaction mixture may act as spectators in steps in which they are not transformed. No controlled vocabulary. Examples could be 'host', 'hydrophobic ligand', 'charge-stabilizer', etc.. A container for spectators in a reaction. A spectrum and relevant data or metadata. The spectrum construct can hold metadataList, sample (which can contain molecule), conditionList (mainly for physical/chemical conditions, not instrumental), spectrumData for the actual data and instrumental settings/procedure and peakList for the assigned peaks. This approach puts the spectrum as the primary object of interest. It could also be possible to make spectrum a child of molecule (although a reference using ref might be preferable). A (complete) description of the thing to which the spectrum relates. May contain molecule or substanceList. Solvents, mulls, etc should be described here. The conditions relating to the spectrum (complementary to substanceList. A list of peaks. This may occur independently of the xaxis/yaxis data. The molecule to which the spectrum refers. Although this may also be contained in the sample element it is useful to state it here. No default. Data for the spectrum. This is primarily to record the data in interchangeable format and machine and manufacturers settings and can include other MLs in this area (AniML, SpectroML, etc.). We recommend ASCII representations of data and this is the only format that CMLSpect implementers have to support, but we also allow for the carriage of JCAMP and other data (in ML wrappers such as AniML). All numeric data should carry units and dictionary references if possible to allow for semantic interoperability. The x-axis/es, usually including the list of points at which data are recorded. Mandatory if y-axis data are given. Multiple x-axes are initially reserved for multiple scales rather than different measurements (for which an additional spectrum should be used). The y-axis/es, usually including the list of points at which data are recorded. Mandatory if x-axis data are given. Multiple y-axes are initially reserved for multiple scales rather than different measurements (for which an additional spectrum should be used). A container for one or more spectra. spectrumList can contain several spectra. These may be related in several ways, including lists of related spectra bundle of common analytical spectra (NMR, IR, UV...) repeat measurements . A spectrumList can contain nested spectrumLists. metadataList contains metadata. list is for experimental and other data. spectrumList normally contains spectrums but we make provision for nested spectrumLists if required. The molecules can be a set of reference molecules which occur in the spectrums and can be referenced. This makes the spectrums more readable and normalizes data when molecules are used more than once. A sphere in 3-space. An element to hold stmml data. stmml holds stmml data under a single generic container. Other namespaces may be present as children. No semantics implied. CML-1 dataType (DEPRECATED). CML-1 dataType DEPRECATED. A chemical substance. substance represents a chemical substance which is deliberately very general. It can represent things that may or may not be molecules, can and cannot be stored in bottles and may or may not be microscopic. Solutions and mixtures can be described by _substanceList_s of substances. The type attribute can be used to give qualitative information characterising the substance ("granular", "90%", etc.) and _role_ to describe the role in process ("desiccant", "support", etc.). There is currently no controlled vocabulary. Note that reaction is likely to have more precise semantics. The amount of a substance is controlled by the optional _amount_ child. Added property as a child 2002-12-29 role depends on context, and indicates some purpose associated with the substance. It might indicate 'catalyst', 'solvent', 'antoxidant', etc. but is not limited to any vocabulary. A list of chemical substances. Deliberately very general - see substance. substanceList is designed to manage solutions, mixtures, etc. and there is a small enumerated controlled vocabulary, but this can be extended through dictionaries. substanceList can have an amount child. This can indicate the amount of a solution or mixture; this example describes 100 ml of 0.1M NaOH(aq). Although apparently longwinded it is precise and fully machine-interpretable Added role attribute, 2003-03-12. Molecular, crystallographic or other symmetry. symmetry provides a label and/or symmetry operations for molecules or crystals. Point and spacegroups can be specified by strings, though these are not enumerated, because of variability in syntax (spaces, case-sensitivity, etc.), potential high symmetries (e.g. TMV disk is D17) and non-standard spacegroup settings. Provision is made for explicit symmetry operations through <matrix> child elements. By default the axes of symmetry are defined by the symbol - thus C2v requires z to be the unique axis, while P21/c requires b/y. Spacegroups imply the semantics defined in International Tables for Crystallography, (Int Union for Cryst., Munksgaard). Point groups are also defined therein. The element may also be used to give a label for the symmetry species (irreducible representation) such as "A1u" for a vibration or orbital. The matrices should be 3x3 for point group operators and 3x4 for spacegroup operators. The use of crystallographic notation ("x,1/2+y,-z") is not supported - this would be <matrix>1 0 0 0.0 0 1 0 0.5 0 0 1 0.0<matrix>. The default convention for point group symmetry is Schoenflies and for spacegroups is "H-M". Other conventions (e.g. "Hall") must be specfied through the convention attribute. This element implies that the Cartesians or fractional coordinates in a molecule are oriented appropriately. In some cases it may be useful to specify the symmetry of an arbitarily oriented molecule and the <molecule> element has the attribute symmetryOriented for this purpose. It may be better to use transform3 to hold the symmetry as they have fixed shape and have better defined mathematical operators. 2005-11-03 PMR. Added transform3 as children. The rotational symmetry number. Used for calculation of entropy, etc. The complete system of components in a calculation. There is no controlled vocabulary. A rectangular table of any quantities. By default table represents a rectangular table of any simple quantities representable as XSD or CML dataTypes. There are three layouts, columnwise, rowwise and without markup. In all cases it is essential that the columns, whether explicit or otherwise, are homogeneous within the column. Also the metadata for each column must be given explicitly.
  • columns: There is a single arrayList child containing (homogeneous) child elements (array or listof size rows data. This is the "normal" orientation of data tables but the table display could be transposed by XSLT transformation if required. Access is to columns, and thence to the data within them. DataTyping, delimiters, etc are delegated to the arrays or lists, which must all be of the same size.
  • rows: with explicit trows. The metadata is carried in a theader element of size cols. Within each trow the data are contained in tcells
  • content: The metadata is carried in a theader element of size cols. data are contained in a single tableContent with columns moving fastest. Within the content the data are whitespace (or delimiter) separated.
For verification it is recommended that tables carry rows and columns attributes. The type of the tables should also be carried in a tableTypeattribute> Validity contraints (XPath expression in table context) type @tableType @rows actual rowCount @columns actual columnCount tableHeader arrayList tableRowList tableContent column based columnBased recommended ./arrayList/@size or arrayList/*[self::array or self::list]/@size optional ./arrayList/@size or count(arrayList/*[self::array or self::list]) forbidden required forbidden forbidden row based rowBased recommended ./tableRowList/@size or count(tableRowList/tableRow) recommended count(tableHeader/tableHeaderCell) or count(tableRowList/tableRow/tableCell) required forbidden required forbidden content based contentBased required only by analysing tde table recommended count(tableHeader/tableHeaderCell) required forbidden forbidden required A cell in a row of a table. tableCell is a data container of the table and only occurs as a child of tableRow. Normally it contains simpleContent, but may also contain a single child element (which could itself have complex or mixed content). However tableCell should NOT directly contain multiple children of any sort or mixed content. (It is declared as mixed content here to allow either text or element content, but not both.). The metadata for tableCells must be declared in a tableHeader/tableHeaderCell system Unmarked content of a table. This only occurs as simpleContent or a tableContent elements. It contains table/@rows * table/@columns items arranged rowwise (i.e. columns is fastest moving). Metadata for columns must be defined in tableHeader. The items of the table are ASCII strings. They can be separated by whitespace or by a defined single character delimiter as in array. The data must be rectangular and each implicit column must have consistent semantics. It can be used to hold CSV-like data (indeed CSV data can be directly entered as long as there are no quoted commas in which cas a different delimiter (or the safer tableRowList) should be used. Unlike tableRowList or arrayList (both of which can hold ASCII strings or XML elements, tableContent can only hold strings. Header for a table. Used for rowBased or contentBased tables when it is mandatory. Contains the metadata as tableHeaderCells which should match the (implicit) columns in number and semantic type. It is forbidden for arrayList tables as each array/list contains the metadata. Metadata for a column of a table. Only used when in rowBased or contentBased tables, and then as a direct child of tableHeader. There must be as many tableHeaderCells as there are implicit columns in tableRowList or tableContent. These cells carry the metadata and/or semantics for each column. These are similar to the attributes in array but without the lsist of minValue, errors etc. However they can (and should) carry all the units metadata. Alternative to units Must be used in conjunction with unitType 2005-10-26: added Alternative to units Must be used in conjunction with unitType 2005-10-26: added Alternative to units Must be used in conjunction with multiplierToSI and/or constantToSI 2005-10-26: added A row in a rowBased table. A direct child of tableRowList containing tableCells. At present all tableRows in a tableRowList must have the same count of tableCells and their semantics must correspond to the tableHeader in the table. No cells can be omitted and there is no spanning of cells. There is no need for a size attribute as the count is simply count(tableCell). List of rows in rowBased table. Metadata for rows must be defined in tableHeader. A torsion angle ("dihedral") between 4 distinct atoms. The atoms need not be formally bonded. It can be used for: Recording experimentally determined torsion angles (e.g. in a crystallographic paper). Providing the torsion component for internal coordinates (e.g. z-matrix). Note that the order of atoms is important. 2006-02-07: PMR. Fixed torsionAngleUnits A transform in 3-space. A 3-D transform. Conventionally a 4x4 matrix. The transition state in a reaction. This will normally contain a molecule which in its 2D representation will have partial bonds. These are yet to be formalized for the molecule element. Although spectators may stabilise or otherwise interact with the transitionState they are not contained within it. A propertyList is provided to capture transitionState properties. Still experimental. A scientific unit. A scientific unit. Units are of the following types: SI Units. These may be one of the seven fundamental types (e.g. meter) or may be derived (e.g. joule). An SI unit is identifiable because it has no parentSI attribute and will have a unitType attribute. 2005-122-17 - this may be obsolete; PMR nonSI Units. These will normally have a parent SI unit (e.g. calorie has joule as an SI parent). Constructed units. These use a syntax of the form: <unit id="g.s-1" name="gram per second" unitType="myUnitType:massPerTime"> <unit units="units:g" power="1"/> <unit units="siUnits:s" power="-1"/> </unit> This defines a new unit (g.s-1) which is composed from two existing units (units:g and siUnits:s) to create a new unit. The conversion to SI is computed from the two child units and may be added as a 'multiplierToSI' attribute. Only siUnits or units with 'multiplierToSI' can be used as child units; 'constantToSI cannot be used yet. If the new unit points to a unitType then the dimension can be checked. Thus if the published dimension of massPerTime does not agree with mass.length-1 an error is throwable. Alternatively a new unitType can be added as a child. The relationship of a unit to its SI parent is potentially complex and inconsistencies may arise. The following are available: parentSI. This points to the ID of a parent SI unit. If this ID is the same as the current unit the implication is that this is an SI unit. isSI. a boolean indicating whether the current unit is SI. multiplierToSI and constantToSI. If these are 1.0 and 0.0 (or missing) the implication is that this unit is SI. However this is fragile as units can be defined without these attributes and a unit could coincidentally have no numeric differences but not be an SI unit. 2003:04-09 Description or parentSI attribute enhanced. 2006:03-21 Added metadata and metadataList to content. Child unit used to build new unit. These children must have 'units' and 'power' attributes. Child unitType describing type of new unit. This can be added by the author (in which case they are responsible for checking consistency) or calculated by the software from the child units. Reference to a unit. This is used for the identification of child units when new units are composed from existing ones. Athough the syntax looks unusual it takes advantage of the tools for resolving units. See above for syntax. Abbreviation for the unit. This may be obsolete and symbol should be preferred. Symbol for the unit. This may be used for typographical display but NOT for identification as there is considerable variation in use. 2006-01-29: PMR. Added attribute. Power of unit used to create new one. Only allowed on child units A container for several unit entries. Usually forms the complete units dictionary (along with metadata). Note: this used to hold both units and unitTypes (though in separate files). This was unwieldy and unitTypeList has been created to hold unitTypes. Implementers are recommended to change any unitList/unitType to unitTypeList/unitType 2005-12-15. PMR. added namespace and dictionaryPrefix. 2005-12-17. PMR. added siNamespace . 2006-01-28. PMR. deprecated use for holding unitType. 2006-01-28: PMR. use unitTypeList. 2006-01-28: PMR. use unitTypeList. Maps dictRef prefix to the location of a dictionary. This requires the prefix and the physical URI address to be contained within the same file. We can anticipate that better mechanisms will arise - perhaps through XMLCatalogs. At least it works at present. The type of a scientific unit. Mandatory for SI Units, optional for nonSI units since they should be able to obtain this from their parent. For complex derived units without parents it may be useful. Used within a unitList Distinguish carefully from unitsType which is primarily used for attributes describing the units that elements carry 2006-02-06: PMR. Added preserve and symbol attributes. A container for several unitType entries. Usually forms the complete unitTypes dictionary (along with metadata). Note: unitTypes used to be held under unitList, but this was complicated to implement and unitTypeList makes a clean separation. 2006-01-28. PMR. created. Maps dictRef prefix to the location of a dictionary. This requires the prefix and the physical URI address to be contained within the same file. We can anticipate that better mechanisms will arise - perhaps through XMLCatalogs. At least it works at present. A vector in 3-space. The vector may have magnitude but is not rooted on any points (use line3). The x-axis. A container for all information relating to the x-axis (including scales, offsets, etc.) and the data themselves (in an array). Note: AniML uses "xValues" so avoid confusion with this. The x-data. These must match the y-data in number and order. There are tools to allow scaling and transformation (though unscaled data must be very carefully defined). The y-axis. A container for all information relating to the y-axis (including scales, offsets, etc.) and the data themselves (in an array). The y-data. These must match the x-data in number and order. There are tools to allow scaling and transformation (though unscaled data must be very carefully defined). A zMatrix. A container for length, angle and torsion, which must be arranged in the conventional zMatrix format. bodr-10/schemas/dictionary.schematron0000644000175000017500000000435612176645770015047 00000000000000 Convention for CML format for the BODR element data file. The root element must specify @convention="bodr:dictionary". The root must be <dictionary>. The document must contain a <annotation>. The document <annotation> must contain a <documentation>. The document <appinfo> must contain at least one <contributor>. The document must contain a <entry>. The <metadataList> element must the date of the document. The <metadataList> element must specify the license of the document. 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The number of the element. This is the number of protons of an atom. The symbol of an element. Every chemical element has a IUPAC-approved symbol which consists of one, two or three letters. Every chemical element has an IUPAC-approved name. IUPAC Official Masses exact masses of the most common isotopes for each element Ionization potential Electron affinity of an element Electronegativity after Pauli. On this scale, the most electronegative chemical element (fluorine) is given an electronegativity value of 3.98; the least electronegative element (francium) has a value of 0.7, and the remaining elements have values in between. For example: Xe 4f14 5d10 6s2 6p2. In this example, Xe stands for the electronic configuration of Xenon. Acidic behaviour of the elements. 0 means acidic, 1 means basic, 2 means neutral and 3 means amphoteric For example, an '1' means the element is in the first group. Together with the block you can find out if that means 1a or 1b. # hcp: hexagonal close packed # fcc: face centered cubic # bcc body centered cubic # hdp: hexagonal close packed # ccp: cubic close packed # d : diamond # sc : simple cubic # tet: tetragonal # rh : rhombohedral # or : orthorhombic # mono: monoclinic # Alkali_Earth # Alkaline_Earth # Non-Metal # Metalloids # Transition # Other_Metal # Halogene (group 7) # Noblegas (group 8) # Rare_Earth (the so called f-Block) Each element has a location in the periodic table. The reason lays in the the orbital structure of the element. This creates four block in the table: s,p,d and f, named after the orbit in which the last electron is located. The boilingpoint of an element is the temperatur at 101.3hPa at which the element is becomming vaporous. The meltingpoint of an element is the temperatur at 101.3hPa at which the element is becomming liquid. The name of an element has a origin. Often the name comes from old legends (see Cobalt) but sometime it is named after somebody (Einsteinium). The covalent radius for the element A is half the distance of the compound A-A. The van-der-Waals-radius is Conventional color for structure visualization In the given year the date has been described first. A "0" means that the element has always been known to mankind (for example Carbon). bodr-10/ChangeLog0000644000175000017500000003627012200163127010717 000000000000002013-08-06 Daniel Leidert * elements/elements.xml: Changed atom IDs of Lv and Fl and their name histories. Fixed all atomic masses accordingly to the latest publication of the IUPAC. * elements/mass.bibxml: Added latest atomic table publication. * tests/AtWt.xsl: Fixed handling of non-breaking spaces and the latest IUPAC website. 2013-08-02 Egon Willighagen * isotopes/isotopes.*: Added the half-lives of 209Th and 238Th (fixes #9) * INSTALL: typo fix 'applcations' * elements/elements.xml: Fixed the groups of Ds and Mt * elements/elements.xml|symbols.bibxml: Lv and Fl got official names * README, COPYING: in agreement with the following email, changed the license to CCZero: Date: Thu, 26 Jan 2012 21:21:28 +0100 Delivered-To: egon.willighagen@gmail.com Message-ID: Subject: BODR relicensing to CCZero From: Egon Willighagen To: BlueObelisk-Discuss Content-Type: text/plain; charset=ISO-8859-1 2012-05-02 Daniel Leidert * elements/elements.xml: Fixed description for Copernicium. 2010-05-04 Jean Brefort * crystal/space-groups.xml: fixed Hall name for group 205. 2010-04-27 Daniel Leidert * elements/elements.xml: Fixed atomic weight for Rutherfordium accordingly to IUPAC AtWt table. * AUTHORS: Added myself. 2010-04-25 Egon Willighagen * elements/elements.xml: Added IUPAC accept name for element 112. (KDE #235313) * elements/elements.xml: Updates mass of H2 to current value from webelements.com 2009-08-02 Jean Brefort * crystal/space-groups.xml: fixed group 229. 2009-05-16 Carsten Niehaus * elements/elements.xml: Synced elements.xml with the copy in Kalziums code repository. There it was spellchecked and several language issues have been found 2009-05-16 Daniel Leidert * elements/elements.xml (Uuo): Removed boiling point (unknown; just a predicted at 320-380K). Fixed discovery date - discovered in 2002 and 2005 but published 2006 (KDE #192478). 2009-05-15 Daniel Leidert * elements/elements.xml (Cm): Fixed electronic configuration (KDE #192616). (Bh,Db,Hs,Lu,Mo,Mt,Ni,Rf,Rg,Sg,UUh,Yb,Zn): Fix atom weights accordingly to the 2007 Atomic Masses table by the IUPAC (KDE #192551). (F, Cl, Br, I, At, Uus): Typo fix: s/Halogene/Halogen. Thanks to Jean Bréfort for catching this. * tests/AtWt.xsl, tests/Makefile.am: Added a stylesheet to check the atomic weights in our database against the IUPAC table. The check target will do the test. * configure.ac (AC_CONFIG_FILES), Makefile.am (SUBDIRS): Added tests. 2008-03-29 Carsten Niehaus * elements/elements.xml: Remove patch from 2008-03-17 for legal reasons. For details, ask me or Egon. 2008-03-17 Egon Willighagen * elements/*.txt: removed in favor of the .xml source * isotopes/*.txt: ditto * scripts/elements.pl: obsolete, because .xml is the source now * scripts/isotopes.pl: ditto * scripts/crystalstructure.rb: ditto 2008-03-17 Carsten Niehaus * isotopes/isotopes.xml: Remove halflifes with a value of -1 * elements/elements.xml: Rework the name origin. * elements/nameorigin.bibxml: Adding the file 2008-03-10 Daniel Leidert * COPYING: Updated copyright. Reformatting to textwidth of 80 characters. 2008-03-10 Carsten Niehaus * elements/elements.xml: Element 118 had a wrong nameOrigin * elements/nameorigin.txt: Element 118 had a wrong nameOrigin 2008-03-01 Egon Willighagen * schemas/cml25.xsd: added Rg and Ds as element symbols * schemas/cml25.xsd: allow inside * schemas/dictionary.convention: extra validation for the dictionary 2008-03-01 Egon Willighagen * NEWS: BODR 7 released, made place for BODR 8 changes * schemas/cml23.xsd, cml25.xsd: Replaced CML 2.3 with CML 2.5 (closes SF bug #1905374) 2008-03-01 Egon Willighagen * ChangeLog: Fixed Carsten's name 2008-03-01 Egon Willighagen * NEWS: Making a release * TODO: Updated 2008-02-18 Daniel Leidert * scripts/elements.pl: Make sure that values exist for mass and exactMass (workaround for non-existent element 117). * elements/colors.txt: Added colors for elements 117, 118. Adjusted values for 109-116 (please fix yourself if necessary). * elements/elements.xml: Regenerated from source. 2008-02-18 Daniel Leidert * elements/blocks.txt: Added elements 117, 118. * elements/boilingpoint.txt: Added elements 96-98, 118. * elements/dates.txt: Added for elements 112-116, 118. * elements/dates.bibxml: Added related biblographic information. * elements/density.txt: Added for elements 99, 103-116. * elements/discovery_countries.txt: Added for elements 116, 118. * elements/family.txt: Added for elements 112-118. * elements/mass.txt: Added for element 118. * elements/names.txt: Added for elements 117, 118. Fixed formatting issue for element 116. * elements/nameorigin.txt: Added for elements 112-118. * elements/periods.txt: Added element 112-118. * elements/symbols.txt: Added for elements 117, 118. * THANKS: Patches provided by Ryan Kavanagh . 2008-01-30 Carsten Niehaus * elements.pl: Improving the elements.pl script. It is now using a regular expressing instead of a strange check of the invalid atomic number * elements.pl: Fing the bug that discoverydates are not used when no person (discoverer) is known for that element. * elements.xml: Regenerated * blueobelisk-dictionary.xml: Adding documentation for discoveryDate 2007-12-18 Daniel Leidert * Makefile.am (docsdir): Use the docdir variable. 2007-10-19 Daniel Leidert * bodr.pc.in: Re-added pkgdatadir (closes #1713504 sf.net). 2007-08-13 Daniel Leidert * bodr.pc.in: Removed unnecessary paths (closes #1713504 sf.net). * configure.ac: Added backwards-compatible snippet to determine the docdir variable/option value, that is available in newer autoconf versions, to ste the installation path of biblio HTML output. * bibtexml-xslt/html-harvard.xsl: Output PUBLIC and SYSTEM IDs for XHTML. Further fixed indentation. * crystal/Makefile.am: Added creation of biblio-html output and its installation. * crystal/space-groups.bibxml: Fixed invalid XML. * isotopes/Makefile.am: Replaced GNU make specific pattern. * dicts/Makefile.am: Ditto. * elements/Makefile.am: Ditto. Also set the installation path for biblio HTML to docdir. 2007-08-12 Jean Brefort * Makefile.am: add sace groups descriptions. * configure.ac: ditto. * crystal/Makefile.am: ditto. * crystal/space-groups.bibxml: ditto. * crystal/space-groups.xml: ditto. 2007-02-27 Egon Willighagen * THANKS, AUTHORS: added a few email addresses * elements/masses.txt: update elemental masses according to a new IUPAC publication (closes #1660527) * THANKS: added Kevin Daughtridge for masses.txt patch 2007-02-26 Egon Willighagen * elements/*.txt: now list the MIT license instead of '??' 2007-01-24 Carsten Niehaus * elements/nameorigin.txt: Fix a typo for element 16 2007-01-17 Daniel Leidert * configure.ac (AC_INIT): Post release version bump to version 6. (AM_INIT_AUTOMAKE): Fixed obsolete usage. Output all warnings to inform about possible problems. 2007-01-17 Daniel Leidert * autogen.sh: Improved in many ways. Debug output option added. * schemas/Makefile.am: Added. * configure.ac (AC_CONFIG_FILES): Added schemas/Makefile. * Makefile.am (SUBDIRS): Added schemas directory. * scripts/crystalstructure.rb: Added executable bit to fix build error. * dicts/Makefile.am (XMLLINT_FLAGS_*, check-local): * isotopes/Makefile.am (XMLLINT_FLAGS_*, check-local): * elements/Makefile.am (XMLLINT_FLAGS_*, check-local, crystal_DATA) (element_DATA, EXTRA_DIST): Fixed xmllint usage and build issues (`make distcheck' errors). 2006-12-29 Egon Willighagen * scripts/elements.pl: Do not output acidity information, as source cannot be validated (closes SourceForge bug #1603066) * elements/family.txt: The actinoids are no longer listed as rare earths but as 'other metal' (closes SourceForge bug #1603063) 2006-10-16 Egon Willighagen * configure.ac, Makefile.am: added dicts subdir * dicts/Makefile.am: install the BO dictionary 2006-10-15 Jean Brefort * configure.ac: enable xmllint test. * bodr.pc.in: add datarootdir. * elements/Makefile.am: make check-local works. * isotopes/Makefile.am: make check-local works. 2006-10-15 Egon Willighagen * scripts/elements.pl: Tidied up Perl code * scripts/elements.pl: Disabled density which is not an element property * schema/elements.schematron, elements/Makefile.am: Extra validation * schema/isotopes.schematron, isotopes/Makefile.am: Extra validation * scripts/isotopes.pl: Do not create an entry for Xx 2006-09-02 Carsten Niehaus * elements/elements.xml: Refreshed * scripts/elements.pl: Activated the code which generates the XML for the Density * isotopes/isotopes.xml: Refreshed * isotopes/halflife.txt: More data * isotopes/decay.txt: More data 2006-09-02 Carsten Niehaus * elements/elements.xml: Refreshed * scripts/elements.pl: Activated the code which generates the XML for the country where an element has been discovered 2006-09-01 Carsten Niehaus * elements/elements.xml: Changes xsd:String to xsd:string as it is defined in the standard 2006-09-01 Carsten Niehaus * elements/dates.txt: Correct the name of K. W. Scheele to C. W. Scheele for Carl W. Scheele. We looked it up, both spellings are accepted but his birthname is Carl, not Karl. 2006-08-31 Carsten Niehaus * elements/dates.txt: Correct the name of K. W. Scheele. Tungsten named him "Scheel" * elements/dates.txt: Add the second name of K. W. Scheele to Chlorine 2006-08-15 Carsten Niehaus * elements/crystalstrutures.txt: Make Si ccp as that is the same as fcc * elements/crystalstrutures.txt: Make Mn sc (simple cubic) * scripts/crystalstrutures.rb: Remove the check for fcc as it is no longer needed * scripts/crystalstrutures.rb: Add check for simple cubic * scripts/crystalstrutures.rb: Fix title=""-generation (we had "b" twice) 2006-08-15 Carsten Niehaus * elements/crystalstrutures.xml: Improve the id to be SymbolNumber 2006-06-07 Daniel Leidert * configure.ac: Increased version number. Added xmllint macro (for validation purposes, but did not activate it yet). * scripts/Makefile.am (EXTRA_DIST): Added crystalstructure.rb. * isotopes/Makefile.am: Cleaned the file a bit. (check-local, XMLLINT_FLAGS): Added target, that should check the resulting XML files (not activated yet). * elements/Makefile.am: Ditto. (check-local, XMLLINT_FLAGS): Ditto. (EXTRA_DIST, CLEANFILES, crystalstructures_SRCS, xml_DATA, docs_DATA) (crystalstructures_BIBXML): Added crystalstructures* stuff. * acinclude.m4 (MP_PROG_XSLTPROC): Polished. (MP_PROG_XMLLINT): Added (for XML checking). 2006-08-15 Carsten Niehaus * elements/crystalstrutures.xml: Improve the id to be SymbolNumber * elements/boilingpoint.bibxml: Fix broken link to www.webelements.com. * elements/radii-covalent.bibxml: Ditto. * elements/meltingpoint.bibxml: Ditto. * elements/electroneg-pauling.bibxml: Ditto. * elements/crystalstructures.bibxml: Ditto. 2006-08-13 Egon Willighagen * scripts/elements.pl: now creates valid CML 2.3. * scripts/isotopes.pl: Ditto. * scripts/crystalstructures.rb: Ditto. 2006-08-11 Carsten Niehaus * created crystalstrutures.xml. The file contains information about the crystals the pure elements form * removed crystallographic information from elements.xml. The information moved (extended) to crystalstrutures.xml * added crystalstrutures.rb, a script which generates crystalstrutures.xml 2006-06-07 Daniel Leidert * configure.ac (PACKAGE_VERSION): Post release version bump to 3. * NEWS: Added information for release version 3. 2006-06-07 Daniel Leidert * bodr.pc.in: Fixed the directory-settings (sorry for that stupid mistake and thanks to Jean Bréfort). 2006-06-07 Daniel Leidert * INSTALL: Fixed/Removed some old/outdated instructions. 2006-06-07 Egon Willighagen * scripts/elements.pl: added Dublic Core license note * scripts/isotopes.pl: likewise 2006-06-07 Egon Willighagen * Makefile.am: added THANKS 2006-06-07 Egon Willighagen * THANKS: added Daniel Leidert 2006-06-07 Egon Willighagen * INSTALL: fixed program title 2006-06-07 Daniel Leidert * bibtexml-xslt/Makefile.am: Added MAINTAINERCLEANFILES. (EXTRA_DIST): Fixed the files which must be shipped (all imported XML files must be shipped). * configure.ac (AC_CONFIG_FILES): Added the Makefile in bibtexml-xslt. Added the MP_PROG_XSLTPROC macro to determine the xsltproc application location. * elements/Makefile.am (EXTRA_DIST, CLEANFILES, MAINTAINERCLEANFILES) (ELEMENTS_BIBXML, docs_DATA, elements_biblio.html) elements_biblio.bxml): Several fixes and improvements. 2006-06-07 Egon Willighagen * bibtexml-xslt/: added XSLT sheets to convert BibTeXML to HTML * elements/Makefile.am: convert *.bibxml to HTML 2006-06-07 Daniel Leidert * bodr.pc.in: datadir should be pkgdatadir and the value should be determined. 2006-06-07 Daniel Leidert * bodr.pc.in: Added datadir variable. * acinclude.m4: Added. Contains xsltproc macro. 2006-05-19 Daniel Leidert * autogen.sh: Removed autoheader run. Added possibility to link or copy auto* files, including a fix for a possible failure situation. * LICENSE: Moved to COPYING. * bodr.pc.in: Added a pkgconfig file. * configure.ac: Ditto. Removed config.h(.in) relevant stuff (not necessary for us). Added test for Perl modules. (PACKAGE_VERSION): Version bump to 2 as 1 is already released. * Makefile.am: Cleaning. Adding stuff to support the maintainer-clean target. * Makefile.am: Ditto. Introducing an implicit rule to build the XML file to install. Added installation target for the pkgconfig file. * elements/Makefile.am: Ditto. * scripts/Makefile.am: Ditto (necessary to support the implicit rules). * NEWS: Updated. 2006-05-19 Daniel Leidert * COPYING: Removed. 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-x,-y,1/2+z x,-y,1/2-z -x,y,-z -x,-y,-z x,y,1/2-z -x,y,1/2+z x,-y,z# x,1/2+y,1/2+z -x,1/2-y,z x,1/2-y,-z -x,1/2+y,1/2-z -x,1/2-y,1/2-z x,1/2+y,-z -x,1/2+y,z x,1/2-y,1/2+z x,y,z -x,-y,z x,-y,1/2-z -x,y,1/2-z -x,-y,-z x,y,-z -x,y,1/2+z x,-y,1/2+z x,1/2+y,1/2+z -x,1/2-y,1/2+z x,1/2-y,-z -x,1/2+y,-z -x,1/2-y,1/2-z x,1/2+y,1/2-z -x,1/2+y,z x,1/2-y,z x,y,z -x,-y,z x,-y,1/2-z -x,y,1/2-z -x,-y,-z x,y,-z -x,y,1/2+z x,-y,1/2+z 1/2+x,y,1/2+z 1/2-x,-y,1/2+z 1/2+x,-y,-z 1/2-x,y,-z# 1/2-x,-y,1/2-z 1/2+x,y,1/2-z 1/2-x,y,z 1/2+x,-y,z x,y,z -x,-y,1/2+z x,-y,-z -x,y,1/2-z -x,-y,-z x,y,1/2-z -x,y,z x,-y,1/2+z 1/2+x,y,1/2+z 1/2-x,-y,z 1/2+x,-y,1/2-z 1/2-x,y,-z 1/2-x,-y,1/2-z 1/2+x,y,-z 1/2-x,y,1/2+z 1/2+x,-y,z x,y,z 1/2-x,1/2-y,z -x,y,-z 1/2+x,1/2-y,-z -x,1/2-y,1/2-z 1/2+x,y,1/2-z x,1/2-y,1/2+z 1/2-x,y,1/2+z 1/2+x,1/2+y,z -x,-y,z 1/2-x,1/2+y,-z x,-y,-z 1/2-x,-y,1/2-z x,1/2+y,1/2-z 1/2+x,-y,1/2+z -x,1/2+y,1/2+z x,y,z 1/2-x,-y,z -x,y,1/2-z 1/2+x,-y,1/2-z -x,-y,-z 1/2+x,y,-z x,-y,1/2+z 1/2-x,y,1/2+z 1/2+x,1/2+y,z -x,1/2-y,z 1/2-x,1/2+y,1/2-z x,1/2-y,1/2-z 1/2-x,1/2-y,-z x,1/2+y,-z 1/2+x,1/2-y,1/2+z -x,1/2+y,1/2+z x,y,z -x,1/2-y,1/2-z -x,-y,z x,-y,-z -x,y,-z x,1/2+y,1/2-z -x,1/2+y,1/2+z x,1/2-y,1/2+z 1/2+x,1/2+y,z 1/2-x,-y,1/2-z 1/2-x,1/2-y,z 1/2+x,1/2-y,-z 1/2-x,1/2+y,-z 1/2+x,y,1/2-z 1/2-x,y,1/2+z 1/2+x,-y,1/2+z x,y,z -x,1/2-y,z x,-y,1/2-z -x,1/2+y,1/2-z -x,-y,-z x,1/2+y,-z -x,y,1/2+z x,1/2-y,1/2+z 1/2+x,1/2+y,z 1/2-x,-y,z 1/2+x,1/2-y,1/2-z 1/2-x,y,1/2-z 1/2-x,1/2-y,-z 1/2+x,y,-z 1/2-x,1/2+y,1/2+z 1/2+x,-y,1/2+z x,y,z -x,-y,z x,-y,-z -x,y,-z 1/2-x,-y,1/2-z 1/2+x,y,1/2-z 1/2-x,y,1/2+z 1/2+x,-y,1/2+z x,1/2+y,1/2+z -x,1/2-y,1/2+z x,1/2-y,1/2-z -x,1/2+y,1/2-z 1/2-x,1/2-y,-z 1/2+x,1/2+y,-z 1/2-x,1/2+y,z 1/2+x,1/2-y,z x,y,z 1/2-x,-y,z x,-y,1/2-z 1/2-x,y,1/2-z -x,-y,-z 1/2+x,y,-z -x,y,1/2+z 1/2+x,-y,1/2+z x,1/2+y,1/2+z 1/2-x,1/2-y,1/2+z x,1/2-y,-z 1/2-x,1/2+y,-z -x,1/2-y,1/2-z 1/2+x,1/2+y,1/2-z -x,1/2+y,z 1/2+x,1/2-y,z x,y,z -x,-y,z x,-y,-z -x,y,-z 1/2-x,-y,1/2-z 1/2+x,y,1/2-z 1/2-x,y,1/2+z 1/2+x,-y,1/2+z x,1/2+y,1/2+z -x,1/2-y,1/2+z x,1/2-y,1/2-z -x,1/2+y,1/2-z 1/2-x,1/2-y,-z 1/2+x,1/2+y,-z 1/2-x,1/2+y,z 1/2+x,1/2-y,z x,y,z 1/2-x,-y,1/2+z x,-y,1/2-z 1/2-x,y,-z -x,-y,-z 1/2+x,y,1/2-z -x,y,1/2+z 1/2+x,-y,z x,1/2+y,1/2+z 1/2-x,1/2-y,z x,1/2-y,-z 1/2-x,1/2+y,1/2-z -x,1/2-y,1/2-z 1/2+x,1/2+y,-z -x,1/2+y,z 1/2+x,1/2-y,1/2+z x,y,z -x,-y,z x,-y,-z -x,y,-z -x,1/2-y,1/2-z x,1/2+y,1/2-z -x,1/2+y,1/2+z x,1/2-y,1/2+z 1/2+x,y,1/2+z 1/2-x,-y,1/2+z 1/2+x,-y,1/2-z 1/2-x,y,1/2-z 1/2-x,1/2-y,-z 1/2+x,1/2+y,-z 1/2-x,1/2+y,z 1/2+x,1/2-y,z x,y,z -x,1/2-y,1/2+z x,1/2-y,-z -x,y,1/2-z -x,-y,-z x,1/2+y,1/2-z -x,1/2+y,z x,-y,1/2+z 1/2+x,y,1/2+z 1/2-x,1/2-y,z+ 1/2+x,1/2-y,1/2-z 1/2-x,y,-z 1/2-x,-y,1/2-z 1/2+x,1/2+y,-z 1/2-x,1/2+y,1/2+z 1/2+x,-y,z x,y,z -x,-y,z x,-y,-z -x,y,-z -x,1/2-y,1/2-z x,1/2+y,1/2-z -x,1/2+y,1/2+z x,1/2-y,1/2+z 1/2+x,y,1/2+z 1/2-x,-y,1/2+z 1/2+x,-y,1/2-z 1/2-x,y,1/2-z 1/2-x,1/2-y,-z 1/2+x,1/2+y,-z 1/2-x,1/2+y,z 1/2+x,1/2-y,z x,y,z -x,1/2-y,z x,1/2-y,1/2-z -x,y,1/2-z -x,-y,-z x,1/2+y,-z -x,1/2+y,1/2+z x,-y,1/2+z 1/2+x,y,1/2+z 1/2-x,1/2-y,1/2+z 1/2+x,1/2-y,-z 1/2-x,y,-z 1/2-x,-y,1/2-z 1/2+x,1/2+y,1/2-z 1/2-x,1/2+y,z 1/2+x,-y,z x,y,z -x,-y,z -x,y,-z x,-y,-z -x,-y,-z x,y,-z x,-y,z -x,y,z x,1/2+y,1/2+z -x,1/2-y,1/2+z -x,1/2+y,1/2-z x,1/2-y,1/2-z -x,1/2-y,1/2-z x,1/2+y,1/2-z x,1/2-y,1/2+z -x,1/2+y,1/2+z 1/2+x,y,1/2+z 1/2-x,-y,1/2+z 1/2-x,y,1/2-z 1/2+x,-y,1/2-z 1/2-x,-y,1/2-z 1/2+x,y,1/2-z 1/2+x,-y,1/2+z 1/2-x,y,1/2+z 1/2+x,1/2+y,z 1/2-x,1/2-y,z 1/2-x,1/2+y,-z 1/2+x,1/2-y,-z 1/2-x,1/2-y,-z 1/2+x,1/2+y,-z 1/2+x,1/2-y,z 1/2-x,1/2+y,z x,y,z -x,y,-z 1/4-x,1/4-y,1/4-z 1/4+x,1/4-y,1/4+z x,-y,-z -x,-y,z 1/4-x,1/4+y,1/4+z 1/4+x,1/4+y,1/4-z x,1/2+y,1/2+z 1/2+x,y,1/2+z 1/2+x,1/2+y,z -x,1/2+y,1/2-z 1/2-x,y,1/2-z 1/2-x,1/2+y,-z 1/4-x,3/4-y,3/4-z 3/4-x,1/4-y,3/4-z 3/4-x,3/4-y,1/4-z 1/4+x,3/4-y,3/4+z 3/4+x,1/4-y,3/4+z 3/4+x,3/4-y,1/4+z x,1/2-y,1/2-z 1/2+x,-y,1/2-z 1/2+x,1/2-y,-z -x,1/2-y,1/2+z 1/2-x,-y,1/2+z 1/2-x,1/2-y,z 1/4-x,3/4+y,3/4+z 3/4-x,1/4+y,3/4+z 3/4-x,3/4+y,1/4+z 1/4+x,3/4+y,3/4-z 3/4+x,1/4+y,3/4-z 3/4+x,3/4+y,1/4-z x,y,z 1/4-x,1/4-y,z x,1/4-y,1/4-z 1/4-x,y,1/4-z -x,-y,-z 3/4+x,3/4+y,-z -x,3/4+y,3/4+z 3/4+x,-y,3/4+z x,1/2+y,1/2+z 1/4-x,3/4-y,1/2+z x,3/4-y,3/4-z 1/4-x,1/2+y,3/4-z -x,1/2-y,1/2-z 3/4+x,1/4+y,1/2-z -x,1/4+y,1/4+z 3/4+x,1/2-y,1/4+z 1/2+x,y,1/2+z 3/4-x,1/4-y,1/2+z 1/2+x,1/4-y,3/4-z 3/4-x,y,3/4-z 1/2-x,-y,1/2-z 1/4+x,3/4+y,1/2-z 1/2-x,3/4+y,1/4+z 1/4+x,-y,1/4+z 1/2+x,1/2+y,z 3/4-x,3/4-y,z 1/2+x,3/4-y,1/4-z 3/4-x,1/2+y,1/4-z 1/2-x,1/2-y,-z 1/4+x,1/4+y,-z 1/2-x,1/4+y,3/4+z 1/4+x,1/2-y,3/4+z x,y,z -x,-y,z -x,y,-z x,-y,-z -x,-y,-z x,y,-z x,-y,z -x,y,z 1/2+x,1/2+y,1/2+z 1/2-x,1/2-y,1/2+z 1/2-x,1/2+y,1/2-z 1/2+x,1/2-y,1/2-z 1/2-x,1/2-y,1/2-z 1/2+x,1/2+y,1/2-z 1/2+x,1/2-y,1/2+z 1/2-x,1/2+y,1/2+z x,y,z -x,-y,z x,-y,1/2-z -x,y,1/2-z -x,-y,-z x,y,-z -x,y,1/2+z x,-y,1/2+z 1/2+x,1/2+y,1/2+z 1/2-x,1/2-y,1/2+z 1/2+x,1/2-y,-z 1/2-x,1/2+y,-z 1/2-x,1/2-y,1/2-z 1/2+x,1/2+y,1/2-z 1/2-x,1/2+y,z 1/2+x,1/2-y,z x,y,z 1/2-x,-y,z x,-y,-z 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Hall Ralf W. Grosse-Kunstleve 2007 August http://www.mkmc.dk/crystal/group.html 2007 August http://cci.lbl.gov/cctbx/explore_symmetry.html cctbx - Explore symmetry Per Stoltze 2007 August