On Thu, May 7, 2009 at 9:07 PM, Loren Lenzen <[email protected]> wrote: > 3) It appears that the SMILES parser doesn't recognize the heavier metals > (e.g. Eu). How much of the periodic table is left out? Is there a way to > capture these atoms without them returning a CDKexception.
SMILES requires atom type perception, and the current algorithm does indeed not do the full periodic table yet. The full list of recognized atom types for the cdk-1.2.x branch is available at: http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk;a=blob;f=src/main/org/openscience/cdk/dict/data/cdk-atom-types.owl;h=2069fd449679a2ed5dbb1d80f1aeae322a681438;hb=refs/heads/cdk-1.2.x > 5) What method is used for the IteratingMDLReader to detect ID tags. I > tried using the IMolecule.getproperties() method, but it returned null > strings. I am currently using a v2000 MDL database for this experiment. IDs get typically stored as IAtom.getID() and IBond.getID(). But I don't remember MDL molfiles to have IDs... the have atom numbers... Can you give an example MDL molfile with atom IDs? > 6) I would prefer that the IteratingMDLReader return IAtomContainer objects > instead of IMolecule objects, because some mol files contain multiple > molecules. Is this a simple hack of the readers or is there more to it than > that? IMolecule extends IAtomContainer, but an MDL molfile indeed does not restrict the content to be a single molecule, so it should strictly speaking not return an IMolecule but an IAtomContainer... I filed: http://sourceforge.net/tracker/?func=detail&aid=2788763&group_id=20024&atid=120024 > P.S. Thanks for all your help so far. I work with very large and very > diverse databases. If there is a bug in any of these classes (at least > under real-world conditions) I am sure to find it. Where do I go to submit > bug reports? Bugs can be filed in CDK's SourceForge bug track system at: http://sourceforge.net/tracker/?func=browse&group_id=20024&atid=120024 Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------------ The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
