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

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

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 <gre...@gm...>
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" <
> tot...@gm...> 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!
>>
>