On Apr 26, 2018, at 10:09, Marco Stenta <marco.ste...@gmail.com> wrote: > > Dear Colleagues, > I just installed on conda env the new rdkit version > and wanted to try mmpdb but upon testing I got the error below > reverting back to rdkit=2017.09.3.0 it works fine (I still get some errors > but it goes thrugh) > > It is a bug, am I doing anything obviously wrong?
You did nothing wrong. The latest version of RDKit changed the SMILES output for wildcard atoms from "*" to "[*]". I missed this change in the release notes. It's further documented at https://github.com/rdkit/rdkit/pull/1788 The mmpdb code does a lot of manipulation of the SMILES at the syntax level, and parts of the code expected that wildcard atoms would only be in the form "[*]". I've put together a first go at a fix, which should work for both older and the newest versions of RDKit. The automated mmpdb test suite isn't that good, so I still need to do some manual testing. I won't be able to get to this until (hopefully) this evening. Until then, if you could try out http://dalkescientific.com/mmpdb-2.1b1.tar.gz or my fork of the repository at https://github.com/adalke/mmpdb and let me know if there are failures, that would help me with the testing. Cheers, 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
