Hi James,
Due to problems with the general ambiguity of the format the RDKIt does not
have a mol2 writer.
-greg
On Mon, Oct 31, 2016 at 12:22 AM +0100, "James Johnson"
<totalboron...@gmail.com> wrote:
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!
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