Re: [Rdkit-discuss] pharmacophore align

[Greg L. <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