Thanks for both tips, Andrew! Everything works as expected now.
> -----Original Message----- > From: Andrew Dalke [mailto:da...@dalkescientific.com] > Sent: Friday, May 19, 2017 2:13 PM > To: Markus Heller <mhel...@cdrd.ca> > Cc: rdkit-discuss@lists.sourceforge.net > Subject: Re: [Rdkit-discuss] Non-standard Heavy Atoms and CHemFP > Fingerprints > > On May 19, 2017, at 21:59, Markus Heller <mhel...@cdrd.ca> wrote: > > [In chemfp] I get the following error: > > > > [11:37:55] Explicit valence for atom # 6 Te, 4, is greater than > > permitted > > ERROR: Cannot parse the SMILES > > 'CC(C)(/C(=C\\Cl)/[Te-2](c1ccc(cc1)OC)(Cl)Cl)O' at line 155850 of > > chembl_23.fixed.smi. Exiting.[11:39:23] Explicit valence for atom # 6 > > Te, 6, is greater than permitted > > > > How should atoms non-standard heavy atoms like Te be treated? > > While this doesn't answer your question, I thought you might like to know > that you can add "--errors ignore" or "--errors report" to the command-line > to have chemfp ignore any errors from the underlying toolkit. > > As to the chemistry problem, you might want to upgrade. The release notes > for Release_2016.09.3 say: > > - Support valences of 4 and 6 for Te > (github issue #1204 from hsiaoyi0504) > > That issue is at https://github.com/rdkit/rdkit/issues/1204 . > > I confirm here that the newer version will process your SMILES string: > > % python > Python 2.7.13 (default, Dec 18 2016, 07:03:39) [GCC 4.2.1 Compatible Apple > LLVM 8.0.0 (clang-800.0.42.1)] on darwin Type "help", "copyright", "credits" > or "license" for more information. > >>> import rdkit > >>> rdkit.__version__ > '2016.09.3' > >>> from rdkit import Chem > >>> Chem.MolFromSmiles('CC(C)(/C(=C\\Cl)/[Te-2](c1ccc(cc1)OC)(Cl)Cl)O') > <rdkit.Chem.rdchem.Mol object at 0x10342c130> > > > Andrew > da...@dalkescientific.com > ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
