Re: [Rdkit-discuss] How to get coordinates for each atom in molecule?

[sereina r. <ser...@gm...>]

Hi Michael,

You can get the atom positions via the conformer:

m = Chem.MolFromSmiles('c1ccccc1')
AllChem.Compute2DCoords()
pos = m.GetConformer().GetAtomPosition(0) # position of atom 0

This gives you a rdGeometry.Point3D - e.g. the x coordinates you get with:

x = pos.x

I hope this is what you were looking for.

Best,
Sereina




2014/1/24 Michał Nowotka <mm...@gm...>

> Hi,
>
> Let's say I loaded a molfile containing coordinates to RDKit mol
> object or loaded it from smiles but called
> AllChem.Compute2DCoords(mol).
> Now I would like to get coordinates for each atom. Unfortunately Atom
> class doesn't have any GetCoords method but this is understandable
> since position is optional. I tried to look into properties but it
> seems that they are stored in some stage container exported from C++:
>
> for atom in mol.GetAtoms():
>     print atom.GetPropNames()
>    ....:
> <rdkit.rdBase._vectSs object at 0xa455aec>
> <rdkit.rdBase._vectSs object at 0xa455aec>
> ...
>
>
> Some blind guesses such as: atom.GetProp('x'), atom.GetProp('X')
> failed. Mol object itself doesn't provide any method that would
> suggest that it can return coordinates....
>
> So is there any way to get this data without parsing original molfile?
>
>
> Regards,
>
> Michal Nowotka
>
>
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