Hi all, After further offline discussion with Paolo, it turns out that the behaviour I was seeing was due to a bug, which has now been fixed by Paolo and accepted. Thanks Paolo for sorting this out!
Regards, Mark From: Paolo Tosco <paolo.tosco.m...@gmail.com> Sent: 27 August 2020 23:08 To: Mark Mackey <m...@cresset-group.com> Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] 2D coord for hydrogens Hi Mark, further to Fio's reply, I think the confusion stems from the fact that when you call AddHs() after MolFromSmiles() no coordinates are actually generated; these are only generated on the fly for visualization, and hence are correct before and after AddHs(), as the layout is always generated on-the-fly from scratch, rather than incrementally. Instead, when you explicitly call rdCoordGen.AddCoords() (or rdDepictor.Compute2DCoords()) a conformation is actually added, thus allowing incremental addition of coordinates when you call AddHs(). I hope this gist clarifies the above: https://gist.github.com/ptosco/1c7c83017cd1a3d8aa64fe336ae3c1f8 Cheers, p. On Thu, Aug 27, 2020 at 8:25 PM Mark Mackey <m...@cresset-group.com<mailto:m...@cresset-group.com>> wrote: Hi all, I’m trying to generate a 2D layout with sensible locations for hydrogens, and am struggling a bit. If I start from SMILES: m=Chem.MolFromSmiles('Nc1nnc2n1CCS2') m2=rdmolops.AddHs(m, False, True); Then m2 has perfectly sensible 2D cords for the hydrogens. If I use addCoords=False here then the hydrogens are all at the origin, which is more-or-less expected. If, however, I generate new 2D coords for the heavy atoms with CoordGen: m=Chem.MolFromSmiles('Nc1nnc2n1CCS2') Chem.rdCoordGen.AddCoords(m) m2=rdmolops.AddHs(m, False, True); then the 2D coords for the hydrogens are poor on the 5-membered ring, and the two hydrogens on the NH2 are superimposed. (In practise I’m starting from a 3D SDF and trying to generate 2D coords for it, hence the need for CoordGen). What am I doing wrong? Regards, Mark -- Mark Mackey Chief Scientific Officer Cresset New Cambridge House, Bassingbourn Road, Litlington, Cambridgeshire, SG8 0SS, UK tel: +44 (0)1223 858890 mobile: +44 (0)7595 099165 fax: +44 (0)1223 853667 email: m...@cresset-group.com<mailto:m...@cresset-group.com> web: www.cresset-group.com<http://www.cresset-group.com/> skype: mark_cresset _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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