Dear Michal, Chem.AddHs() has the option “addCoords” which is normally set to False. So, using
mol = Chem.AddHs(mol, addCoords=True) should solve your problem. Best, Sereina On 20 Aug 2014, at 19:07, Michał Nowotka <[email protected]> wrote: > Hello, > > Imagine I have a compound with some 2D coordinates I really like: > > mol > > Now I would like to add hydrogens to it: > > mol = Chem.AddHs(mol) > > The problem is, all new hydrogen atoms will have (0,0,0) coordinates, > which doesn't look to good... > > I could force recomputing 2D coords for the whole compound: > > AllChem.Compute2dCoords(mol) > > But this will ruin my beautiful layout of the original, non-hydrogen part... > > Is it possible to layout hydrogens around my compound after I add them? > > Regards, > Michał Nowotka > > ------------------------------------------------------------------------------ > Slashdot TV. > Video for Nerds. Stuff that matters. > http://tv.slashdot.org/ > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ------------------------------------------------------------------------------ Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
