About the best I can think of is to set a property on the molecule and
generate an SDF. This contains the information, but is somewhat ugly:
In [19]: m = Chem.MolFromSmiles('c1cccnc1OC')
In [20]: AllChem.ComputeGasteigerCharges(m)
In [21]: chgs = [x.GetDoubleProp('_GasteigerCharge') for x in m.GetAtoms()]
In [22]: m.SetProp('GasteigerCharges','\n'.join(['%.3f'%x for x in chgs]))
In [23]: from io import StringIO
In [24]: sio = StringIO()
In [25]: w = Chem.SDWriter(sio)
In [26]: w.write(m)
In [27]: w.flush()
In [28]: print(sio.getvalue())
RDKit
8 8 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
6 7 1 0
7 8 1 0
6 1 1 0
M END
> <GasteigerCharges> (1)
0.000
-0.055
-0.044
0.031
-0.222
0.212
-0.481
0.079
$$$$
Maybe there's a better solution. What are you trying to do with the partial
charge data?
-greg
On Mon, Oct 31, 2016 at 6:11 PM, James Johnson <totalboron...@gmail.com>
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>
> 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> 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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