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
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