Hi Jim, The biggest challenge here is likely to be the fact that the RKDit doesn't have a Mol2 writer.
-greg On Tue, Nov 13, 2018 at 7:05 PM James T. Metz via Rdkit-discuss < rdkit-discuss@lists.sourceforge.net> wrote: > RDkit Discussion Group, > > Given a set of small molecules as a SDF file, I would like to generate > a MOL2 > file where the atomic contributions to logP (hydrophobicity) from each > atom including > hydrogens have been calculated and are now encoded in the partial atomic > charge > "slot" in a MOL2 file. Is this possible using RDkit? > > I have found code that calculates the atomic contributions for the > Crippen > logP model and then generates a colorized 2D plot: > > >>> from rdkit.Chem import rdMolDescriptors > >>> contribs = rdMolDescriptors._CalcCrippenContribs(mol) > >>> fig = SimilarityMaps.GetSimilarityMapFromWeights(mol,[x for x,y in > contribs], ˓→colorMap='jet', contourLines=10) > > However, I would like to encode the atomic contributions as partial > atomic charges so > that this information can be written out in a MOL2 file for each atom. > > Does anyone have PYTHON/RDkit code to do this? Thank you. > > Regards, > Jim Metz > > > > > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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