Re: [Rdkit-discuss] pharmacophore align

[Taka S. <ser...@gm...>]

Dear Greg and rdkit-discuss members.

Thank you for your kindness.
Your messages are very helpful for me.
Thanks.

Taka


2012/7/22 Greg Landrum <gre...@gm...>:
> Dear Taka,
>
> On Sun, Jul 22, 2012 at 12:20 AM, Taka Seri <ser...@gm...> wrote:
>>
>> And I have one question.
>> Can I get selected pharmacophore feature positions from AtomIds?
>> Or how can I get selected pharmacophore features from AtomIds?
>> From feature object, it is easy to do that by useing "feature.GetPos()" method.
>> I want to do same thing by using AtomIds.
>
> There's not really a direct way to find the features that an atom is
> involved in, but you can find the atoms that make up a feature using
> the method MolChemicalFeature.GetAtomIds(). Given that you can do the
> following:
> def GetFeatsPerAtom(feats):
>   """  Returns a dictionary keyed by atom id, with lists of features as
>    the values
>
>   """
>   res = {}
>   for feat in feats:
>     for atomId in feat.GetAtomIds():
>       if res.has_key(atomId):
>         res[atomId].append(feat)
>       else:
>         res[atomId] = [feat]
>   return res
> (this code, which could really be improved using a python defaultdict,
> is taken from: http://rdkit.svn.sourceforge.net/viewvc/rdkit/trunk/Python/qtGui/Search3D/SearchUtils.py?revision=2&view=markup&pathrev=2
> )
>
> To get the position of the Atoms themselves, you need to use the
> owning molecule's Conformer. something like this:
> In [6]: conf = atom.GetOwningMol().GetConformer()
>
> In [7]: conf.GetAtomPosition(atom.GetIdx())
> Out[7]: <rdkit.Geometry.rdGeometry.Point3D at 0x1045ebe20>
>
> I hope this helps,
> -greg
>
>
> -greg