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
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
