Dear JP, On Tue, Nov 29, 2011 at 3:36 PM, JP <[email protected]> wrote: > Sorry for the repeated posting -- I had asked a similar question for > 2D some time ago > (http://www.mail-archive.com/[email protected]/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 [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
