On Wed, Dec 7, 2011 at 5:06 AM, Greg Landrum <greg.land...@gmail.com> wrote: > Dear JP, > >> I do not see how AddHs will help me when replacing [OH] with [O-], but >> that might just be me being thick. >> My problem is that ps = AllChem.ReplaceSubstructs(mol, patt, repl, >> replaceAll=True) in my original attached code throws away the 3D >> coordinates (ps[0] atoms are all on 0,0,0) - and I don't know of a way >> to regain the original co-ordinates back. > > You need two things here: > 1) the coordinates of the input molecule should be copied to the result > molecule > 2) some way to generate sensible coordinates for the new atoms. > > The first is already supposed to be happening; the fact that it's not > is a bug which I will fix > (https://sourceforge.net/tracker/?func=detail&aid=3453144&group_id=160139&atid=814650).
This bug is now fixed in svn. -greg ------------------------------------------------------------------------------ Systems Optimization Self Assessment Improve efficiency and utilization of IT resources. Drive out cost and improve service delivery. Take 5 minutes to use this Systems Optimization Self Assessment. http://www.accelacomm.com/jaw/sdnl/114/51450054/ _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
