Hi all, for those who are using trunk/, and I am happy to hear that an increasing number of people are courageous enough to give it a go, you may find a list of all defined atom types at this URL:
http://cdk.svn.sourceforge.net/viewvc/*checkout*/cdk/trunk/cdk/src/main/org/openscience/cdk/config/data/cdk_atomtypes.xml?revision=HEAD&content-type=text%2Fxml By setting the mime type in the URL, Firefox should pick up the associated XSLT stylesheet and create nice HTML output for display. This list is work on progress, and many elements are currently not listed at all. Additionally, you may notice many charged atom types and radicals, which are important for partial charge, IP, reaction mechanism, etc calculations. Thank to Miguel for guiding me with those. Additions, bug reports etc, always most welcome. As well, as running the CDKAtomTypeMatcher from trunk/ against your favorite molecule data set... previous tests against PubChem were quite promosing... If you like to contribute atom types, please email to this list the following information: - identifier - element - formal charge - hybridization (sp2, sp3, ...) - neighbours (aka coordination number) - pi bonds (aka number of pi electrons - lone pairs And, importantly, an example of the atom type in the wild, e.g. MolBase, MaCiE, PubChem, ... please give a URL deep linking into that database or, the database identifier. Egon -- ---- http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
