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

[Michał N. <mm...@gm...>]

Yes, exactly, thank you very much!

On Fri, Jan 24, 2014 at 12:08 PM, sereina riniker
<ser...@gm...> wrote:
> 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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>
>