This is an awesome piece of software! Many thanks Greg...
On 24 August 2011 03:48, Greg Landrum <[email protected]> wrote: > 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
