Re: [Rdkit-devel] collecting feature suggestions for the next release

[Adrian S. <ma...@ad...>]

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
>
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