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

[Paolo T. <pao...@un...>]

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 <gre...@gm... 
> <mailto: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... <mailto: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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