Dan already mentioned this in his reply, but I will reinforce: the RDKit
stores atom positions in conformers, so if a molecule has no conformers it
also has no atom positions. Without atom positions it doesn’t make sense to
calculate angles.
What exactly are you trying to do?
-greg
On Fri, 20 Sep 2019 at 20:16, Navid Shervani-Tabar <nshe...@gmail.com>
wrote:
> Hello,
>
> Couple weeks ago, I asked if there is an RDKit based method that can give
> the distance between two atoms between the molecule. The solution that I
> got was:
>
> from rdkit.Chem import AllChem
>
> mol = Chem.MolFromSmiles('O=CC1OC12CC1OC12')
> AllChem.EmbedMolecule(mol)
> conf = mol.GetConformer()
>
> at1Coords = np.array(conf.GetAtomPosition(bond_i.GetBeginAtomIdx()))
> at2Coords = np.array(conf.GetAtomPosition(bond_i.GetEndAtomIdx()))
>
> dist = np.linalg.norm(at2Coords - at1Coords)
>
> This was good until I tried the same for molecules such as 'CC12CCC1CC2'
> where
> there are zero conformations and the method did not work. I found the
> alternative
>
> from rdkit.Chem import rdDistGeom as molDG
>
> bound_matrix = molDG.GetMoleculeBoundsMatrix(mol)
> bond_i = mol.GetBondWithIdx(idx)
> d = bound_matrix[bond_i.GetBeginAtomIdx(), bond_i.GetEndAtomIdx()]
>
> Now getting back to my current question, I am trying to find the angle
> between two atoms using the method
>
> angle = Chem.rdMolTransforms.GetAngleDeg(conf, atom[0], atom[1], atom[2])
>
> Again, this method does not work when there are zero conformations. I was
> wondering if there are any RDKit alternatives for this that do not use
> mol.GetConformer or my best bet is to use molDG.GetMoleculeBoundsMatrix
> and trigonometry to find them.
>
> Thanks,
> Navid
>
>
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