Thank you everyone for all of your help.
I decided the best solution was Mr. Wójcikowsk's pull request. Thank you!
If it wasn't for this, I would have used a different program. Make that
pull request happen! :-D
Thanks once again.
-Jonathan
On Mon, Oct 31, 2016 at 11:16 AM, Paolo Tosco <paolo.to...@unito.it> wrote:
> 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>
> 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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