Dear JP, On Tue, Aug 23, 2011 at 8:28 PM, JP <[email protected]> wrote: > > I am basically replacing part of an existing molecule using > ReplaceSubstructs. The replaced parts do not have any coordinate > information (as these are SMILES/SMART patterns really). If I use > AllChem.Compute2DCoords(...) the new "added" atoms get 2D > co-ordinates, but the rest of the atoms in the molecule have new > co-ordinates (but I want to keep that info). I would like to generate > 2D coordinates for the newly added (replaced) atoms only, but doing so > in the already existing co-ordinate frame.
This is there out of the box. The function you want is AllChem.GenerateDepictionMatching2DStructure (http://www.rdkit.org/new_docs/api/rdkit.Chem.AllChem-module.html#GenerateDepictionMatching2DStructure); there's an example in the Getting Started in Python document. -greg ------------------------------------------------------------------------------ EMC VNX: the world's simplest storage, starting under $10K The only unified storage solution that offers unified management Up to 160% more powerful than alternatives and 25% more efficient. Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
