Dear James,
this is a small variation on Greg's reply (he was faster than me!):
https://gist.github.com/ptosco/02af3456720d54c37ffc488056df02d4
While Greg's reply showed how to set a molecule property as a list of
per-atom partial charges, here I have set each partial charge as an atom
property. When you read in the SDF file, the partial charge for each
atom can be accessed with
partialCharge = float(atom.GetProp('molFileAlias'))
In the same way you may also associate to each a name or any other property.
Cheers,
p.
On 31/10/2016 17:11, James Johnson wrote:
Is there any supported format that outputs partial charges?
The speed of RDKit is phenomenal (0.02 seconds) vs obabel's 2 seconds,
but if I cannot output partial charges I'll be forced to use obabel.
Thank you for your time.
-James
On Mon, Oct 31, 2016 at 1:00 AM, Greg Landrum <greg.land...@gmail.com
<mailto:greg.land...@gmail.com>> wrote:
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 <mailto: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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