[OpenBabel-Devel] Refining openbabel's aromatic atom types

2014-02-02 Thread ro...@nextmovesoftware.com
Hi Noel and Geoff,I've been investigating some of the weird SMILES strings distributed by eMolecules,that can't be read into other cheminformatics packages.  A significant fraction appearto be molecules with nonsense formal charges on aromatic atoms, which then fail tobe Kekulized given the mismatc

Re: [OpenBabel-Devel] Refining openbabel's aromatic atom types

2014-02-03 Thread ro...@nextmovesoftware.com
Hi Geoff, On 3 Feb 2014, at 05:23, Geoffrey Hutchison wrote: >> to be molecules with nonsense formal charges on aromatic atoms, which then >> fail to >> be Kekulized given the mismatched valence states. > > OK, I have an interesting test case from Noel's python testkekulize.py script. > (Sadly