Dear Navid,
“Zero conformations” mains that EmbedMolecule function return false. There is
no 3D. You use the default EmbedMolecule parameters.
You can try to change them to get 3D coordinates (increase maxAttempts for
example). I don’t see another way to get realistic “Angle” between atoms.
Generally when such thing happens, you must remove molecules instead of trying
to get wrong / approximate values.
Good luck.
BR,
Guillaume
De : Navid Shervani-Tabar <nshe...@gmail.com>
Date : vendredi, 20 septembre 2019 à 20:16
À : RDKit Discuss <rdkit-discuss@lists.sourceforge.net>
Objet : [Rdkit-discuss] GetAngleDeg alternative for the case of no conformation
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
***********************************************************************************
DISCLAIMER
This email and any files transmitted with it, including replies and forwarded
copies (which may contain alterations) subsequently transmitted from Firmenich,
are confidential and solely for the use of the intended recipient. The contents
do not represent the opinion of Firmenich except to the extent that it relates
to their official business.
***********************************************************************************
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
