[Rdkit-discuss] Writing a Tripos MOL2 file with charges

[James J. <tot...@gm...>]

Hello all,

I've been trying to output my 3D mol object that has Gasteiger charges to
mol2 file format. How would I go about that? I've only found it for mol and
pdb.

Here is the code I'be been using if that helps:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
from rdkit import Chem
from rdkit.Chem import AllChem

smile = 'Cc1ccccc1'

uncharged_mol_1D = Chem.MolFromSmiles(smile)

uncharged_mol_3D = Chem.AddHs(uncharged_mol_1D)
AllChem.EmbedMolecule(uncharged_mol_3D)
AllChem.UFFOptimizeMolecule(uncharged_mol_3D)

charged_mol_3D = uncharged_mol_3D
AllChem.ComputeGasteigerCharges(charged_mol_3D)

fout = Chem.SDWriter('./charged_test.mol')
fout.write(charged_mol_3D)
fout.close()
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Thank you!