Nice subject. :-)
On Tue, Mar 13, 2012 at 6:54 PM, JP <[email protected]> wrote:
> I need to get the H atom 3D positions on hydrogen bond donors in a molecule.
> Thanks to the great documentation I found out how to get the H bond donor
> atoms, so I thought I could move from there to get the H 3D co-ordinates.
>
indeed you can, but you need to be careful that your molecule actually
includes Hs.
Here's a demonstration of how you can do that that might help:
I start from SMILES, like in your example:
In [1]: from rdkit import Chem
In [2]: m = Chem.MolFromSmiles('CCCO')
In [3]: mh = Chem.AddHs(m)
In [4]: from rdkit.Chem import AllChem
In [5]: AllChem.EmbedMolecule(mh)
Out[5]: 0
In [6]: AllChem.UFFOptimizeMolecule(mh)
Out[6]: 0
In [7]: hMatcher = '[$([#1]-O)]' # <- you would replace the "O" with
your expression for a donor
In [8]: hM = Chem.MolFromSmarts(hMatcher)
In [9]: donatableHs = mh.GetSubstructMatches(hM)
In [10]: list(donatableHs)
Out[10]: [(11,)]
In [13]: hps = [mh.GetConformer().GetAtomPosition(x[0]) for x in donatableHs]
In [14]: hps
Out[14]: [<rdkit.Geometry.rdGeometry.Point3D at 0x1046a8b78>]
Here's how to do the same thing from a mol block (from a mol file is analogous):
In [15]: mb = Chem.MolToMolBlock(mh)
In [16]: newm = Chem.MolFromMolBlock(mb,removeHs=False)
In [17]: hps = [newm.GetConformer().GetAtomPosition(x[0]) for x in donatableHs]
In [18]: hps
Out[18]: [<rdkit.Geometry.rdGeometry.Point3D at 0x1046a8af0>]
Of course, instead of matching the H directly you can also do the loop
over neighbors that you originally proposed as long as the neighbors
are actually still present in the molecular graph and not just
implicit.
Does that answer the question?
-greg
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