Re: [Rdkit-devel] collecting feature suggestions for the next release
Open-Source Cheminformatics and Machine Learning
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glandrum
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From: Adrian S. <ma...@ad...> - 2008-05-29 09:39:55
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Hi Greg, I think a feature to handle PDB structures would be a great addition to RDKit, but I guess this depends if its possible to have thousands of atoms in an rdmol object. Maybe I should start to explain what kind of implementation I had in mind. Since the hierarchy in PDB structures can be fragile sometimes, the most convenient way would be to use a set theory-like representation. Basically, there could a class rdResidueAtom, subclass of rdAtom, which in addition to the inherited attributes and functions also has PDB details as attributes such as rdResidueAtom.IsHetatm rdResidueAtom.SerialNumber rdResidueAtom.AtomName rdResidueAtom.AlternateLocation rdResidueAtom.ResidueName rdResidueAtom.ChainID rdResidueAtom.ResidueNumber rdResidueAtom.InsertCode rdResidueAtom.Occupancy rdResidueAtom.BFactor the sets would be structure->NMR model->chain->residue->atom then. In an ideal case, it would be possible to access individual sets through a hierarchy/index object, e.g. -> getResidue(chainID, resName, resNum, insCode) would return all atoms with ->atomIdx() that belong to that set - and accordingly for chains, atoms etc. It would tremendously useful to have cheminformatics functions available for protein-ligand complexes, particularly to determine connectivity, aromaticity, assign implicit hydrogens, geometric functions etc. This, as a result, would simplify many tasks, for instance determining hydrogen bonding, analysing the geometry of pi-pi interactions and so on. That would make my life a lot easier at least! ;) Adrian On Sun, May 25, 2008 at 7:55 AM, Greg Landrum <gre...@gm...> wrote: > Dear all, > > I'm starting to collect suggestions for feature additions for the next > RDKit release, which should happen sometime towards the end of Q3. > These are in the feature tracker: > http://sourceforge.net/tracker/?group_id=160139&atid=814653 > in the 2008_Q3 group. > > If you have things you'd like to see added, or cleanups that you > believe need to be done, please either add them to the tracker > directly, post them to the list, or email them to me. > > Thanks, > -greg > > ------------------------------------------------------------------------- > 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/ > _______________________________________________ > Rdkit-devel mailing list > Rdk...@li... > https://lists.sourceforge.net/lists/listinfo/rdkit-devel > |