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 o
Hi Michael,
You can get the atom positions via the conformer:
m = Chem.MolFromSmiles('c1c1')
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
Yes, exactly, thank you very much!
On Fri, Jan 24, 2014 at 12:08 PM, sereina riniker
wrote:
> Hi Michael,
>
> You can get the atom positions via the conformer:
>
> m = Chem.MolFromSmiles('c1c1')
> AllChem.Compute2DCoords()
> pos = m.GetConformer().GetAtomPosition(0) # position of atom 0
>
> T
3 matches
Mail list logo