Perfect, thank you! On Wed, Aug 20, 2014 at 6:13 PM, Sereina <[email protected]> wrote: > 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 >
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