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

[Maciek W. <ma...@wo...>]

Hi,

If you really desperately need it, there is a mockup of MolToMol2Block()
and MolToMol2File() by Jan and myself [see
https://github.com/rdkit/rdkit/pull/415], but it's still rough around the
eadges at best.

----
Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
ma...@wo...

2016-10-31 18:11 GMT+01:00 James Johnson <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!
>>>
>>
>
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