On 06/07/12 10:27, JP wrote: > Steifl -- that is a really crafty and less painful way how to go about > it. > > The SMILES is in fact, a wget call away - since I am processing PDB > deposited structures. > http://www.rcsb.org/pdb/rest/describeHet?chemicalID=NAG
It is not clear to me how the SMILES helps you. You still have to map between rdkit atoms and PDB atom names, do you not? How about using the monomer library? http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/dictionary.html > > Of course, this approach is not generally applicable (and for this > you'd need the perception code Greg mentioned). Hmm... I am unconvinced that you want to be doing chemistry perception. > > > For the protein I can somehow "guess" the bonds. What do you mean by "guess" here? Are you worried about histidine protonation? ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
