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

[Michał Nowotka]

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

[sereina riniker]

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 were looking for.

Best,
Sereina




2014/1/24 Michał Nowotka mmm...@gmail.com

 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


 --
 CenturyLink Cloud: The Leader in Enterprise Cloud Services.
 Learn Why More Businesses Are Choosing CenturyLink Cloud For
 Critical Workloads, Development Environments  Everything In Between.
 Get a Quote or Start a Free Trial Today.

 http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk
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 Rdkit-discuss mailing list
 Rdkit-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

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