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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