Can you be a bit more specific with your question? After reading your email twice I can't figure out exactly what the problem is.
(I note in passing that PDB files are the worst possible way of storing chemical data as they typically do not contain bond orders.) - Noel On 15 November 2013 22:47, Dimitri Maziuk <dmaz...@bmrb.wisc.edu> wrote: > Hi everyone, > > I took a random molecule from PDB ligand library: > http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=sb3&operation=ccid > and > - read it in several different input formats, > - printed it out, > - compared the outputs and the original mmcif -- visually, no detailed diff. > > The inputs are PDB ideal & experimental coordinates (available from the > download tab of the above URL) files, and the strings copy-pasted from > mmCIF: > SMILES ACDLabs 10.04 > SMILES_CANONICAL CACTVS 3.341 > SMILES CACTVS 3.341 > SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 > SMILES "OpenEye OEToolkits" 1.5.0 > InChI 1.03 > > The outputs are different and don't match PDB's mmcif. > > First discrepancy: mmcif original lists an 'R' carbon and an 'S' carbon. > OpenBabel outputs two 'R' carbons in 7 out of 8 cases. In the 8th case: > inchi input, there's no chirality. > > Second discrepancy: input inchi string ends with "/t23-,24+/m0/s1". > Inchi generated by OpenBabel (2.3.2, inchi-1.04) from that is identical, > so at least it's self-consistent. For other inputs: > > - both pdb files, acdlabs smiles: ".../t23-,24-/m0/s1/i29+1" > - cactus canonical: ".../t23-,24+/m0/s1/i29+1" > - cactus and openeye: ".../t23-,24+/m1/s1" > - openeye canonical: ".../t23-,24-/m0/s1" > > Knowing RCSB I wouldn't be too surprised if their ligand file is put > together from several processing streams and their atom list doesn't > exactly match their inchi. But getting 4 different inchi strings for > allegedly the same molecule doesn't sound right to me. > > Am I missing something? > > TIA > -- > Dimitri Maziuk > Programmer/sysadmin > BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu > > > ------------------------------------------------------------------------------ > DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps > OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access > Free app hosting. Or install the open source package on any LAMP server. > Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! > http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
