Dear Greg, I am not sure that is what I need/I explained myself well.
My question is: If you have a 3D molecule, and you replace a part of it with a new group based on some SMARTS expression (with no 3D coorinates) - what is the best way to keep all the 3D info for the atoms in the molecule which have not changed while creating some "sensible" co-cordinates (in the current frame) for the newly appended atoms to the molecule. 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. Is this still a rumble? Many thanks - Jean-Paul Ebejer Early Stage Researcher On 29 November 2011 16:10, Greg Landrum <greg.land...@gmail.com> wrote: > Dear JP, > > On Tue, Nov 29, 2011 at 3:36 PM, JP <jeanpaul.ebe...@inhibox.com> wrote: >> Sorry for the repeated posting -- I had asked a similar question for >> 2D some time ago >> (http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01916.html), >> but now I need the 3D case and I am stuck. >> >> Using RDKit 2011_09_01. >> >> I am simply protonating a molecule via some simple SMART replacements. >> I would like the final output molecule to have the same 3D co >> ordinates as the input one. I have code which works for the 2D case, >> (basically the below but using >> GenerateDepictionMatching2DStructure(...) instead. > > I think you're overcomplicating things. Once you have the molecule > ready to be protonated, try doing: > > Chem.AddHs(mol,addCoords=True) > > That is *supposed* to do the right thing (assuming I've understood the > request correctly). If it doesn't let me know and I will propose a > more complicated solution. > > -greg ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
