From: gilleain t. <gil...@gm...> - 2008-08-20 22:19:22
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Hi, About the PDBReader; I also noticed a problem with it (now fixed) to do with the CONECT records, but I agree that it makes sense for a chemistry development kit to focus on chemical, not biological formats. The PDB fixed-width files (as opposed to mmCIF or the xml file formats) are notoriously difficult to handle because (I understand) some crystallographers do odd things with the files. There are cleaned versions of the data, but that can't be checked for or guaranteed. Even though macromolecules are of course chemicals, I would also vote for using the Biojava classes. This is part of a bigger issue that the Bioclipse project faces of different projects having different core models for the data. JMol uses its own classes for macromolecules, which are not CDK Molecules. In fact, an even bigger question (off topic, really) is the large amount of unused and duplicated classes from bioclipse plugins in the project. I would be interested to know what the smallest size it could be is. But that's a tale for another time, and another mailing list, I suppose :) gilleain On Wed, Aug 20, 2008 at 10:31 PM, Rajarshi Guha <rg...@in...> wrote: > Hi, the ACS is finally ended and I can get back to code! I noticed in > the commits that the QM code has its own module. What is the role of > QM code in the CDK? Do we seriously plan to implement QM/semi- > emperical algo's? > > On a related note, why does the CDK need an implementation of a PDB > reader? Why not use BioJava and provide a transformer class that > converts the BioJava object to a CDK object? I spoked with Raphael in > Philly, and he noted that round tripping does not work with the PDB > (PDBWriter makes files that PDBReader cannot read). > > I can see the CDK being used in metabolomics and hence the need for > PDB support - but given the format can be fiddly, why not just use > BioJava? > > ------------------------------------------------------------------- > Rajarshi Guha <rg...@in...> > GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 > ------------------------------------------------------------------- > So the Zen master asked the hot-dog vendor, > "Can you make me one with everything?" > - TauZero on Slashdot > > > > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > |