On 13/10/2016 05:04, Bin Song wrote: > Hello everyone, > > A new user of Rdkit and new subscriber of the mailing list reporting here. > > I have a question to ask, as stated in the subject. I have googled and > consulted the > documentation of rdkit, but found no answer. Basically, I want to run a > search with a smarts > string on my molecule. I am interested in the hydrogen atoms bonded to an > atom that is part > of the match, as GetSubstructMatches does not return the idx of hydrogens. > Because I am > looking at crystal structures, I want the idx of hydrogen so that I get the > 3D coordinates > of the hydrogen to perform further computations. If anyone has any tips and > good ideas, > please let me know.
Are you sure? I use HasSubstrMatch to match hydrogens. see set_atom_type() here: https://github.com/pemsley/coot/blob/master/pyrogen/atom_types.py I think that this is more or less what you want to do. (As you might be able to work out, I too have an interest in hydrogens on ligands in protein ligand crystal structures.) Paul. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
