Sam, I wouldn't trust the PDB for either bond order or connectivity. In OB the order is inferred from the distances, which are dependent on the quality of the structure and the software used for the model refinement.
For example, I found that in structures generated a version of Refmac, the oxygen double bond lenght in the DMSO is wrong, so OB assigns an sp3 hybridization to it. If you have to do that in a high-throughput fashion, I would use the ligand ID to download the actual SMILES from the ligand repository at the PDB and use that for your analysis. Best, S On 08/31/2016 01:51 PM, Sam Tonddast-Navaei wrote: > I am trying to read a small molecule from PDB file and match its atom numbers > to the same > molecule in a SDF file. I have tried both matching SMART patterns and > using OBIsomorphismMapper, both work for 70% of cases. However there are > cases for which > OpenBabel can not simply get the right SMILES from just the PDB file (e.g. > adds extra > double bonds or miss ones). For example in PDB ID 1KF6 and ligand name IPE, > if you > generate SMILES from PDB you will get OCCO/C=C/OCCO/C=C/O/C=C/O while the > correct one > should be OCCOCCOCCOCCOCCO. I would appreciate if someone can give me some > advise on this. > > Thanks, > Sam > ------------------------------------------------------------------------------------------ > NOTE: This message was trained as non-spam. If this is wrong, please correct > the training > as soon as possible. > > > ------------------------------------------------------------------------------ > > > > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Stefano Forli, PhD Assistant Professor of ISCB Molecular Graphics Laboratory Dept. of Integrative Structural and Computational Biology, MB-112A The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037-1000, USA. tel: +1 (858)784-2055 fax: +1 (858)784-2860 email: fo...@scripps.edu http://www.scripps.edu/~forli/ ------------------------------------------------------------------------------ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
