Dear Reinis and dear all, actually the aromaticity detection problem is only raised when dealing with charged heterocyclic systems with formats which do not support explicit formal charges (e.g., MOL2), while there are no problems with SDF and MOL files. I was initially misled about this and I erroneously made changes to kekulize.cpp which broke the test suite, as Noel pointed out. This is the reason why I reverted them, while I added some code to mol2format, also following a bug report about pyridinium ions being incorrectly perceived. Since the latter is a very commonly used format, I thought it would be a pity to incorrectly perceive aromaticity on such files, even though they do not carry explicit formal charges. However, since they do carry atom/bond type information, it is possible to use it to improve the quality of aromaticity perception.
Best, Paolo There was raised an issue about aromaticity detection problems in charged heterocycles (e.g. pyridinium). There were also some commits in the summer by ptosco for oxonium ions which were later reverted and worked around in mol2format(?). It would be good to solve this issue if possible, but I haven't looked at it closely. Reinis ------------------------------------------------------------------------------ Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel -- ========================================================== Paolo Tosco, Ph.D. Department of Drug Science and Technology Via Pietro Giuria, 9 - 10125 Torino (Italy) Tel: +39 011 670 7680 | Mob: +39 348 5537206 Fax: +39 011 670 7687 | E-mail: paolo.to...@unito.it http://open3dqsar.org | http://open3dalign.org ========================================================== ------------------------------------------------------------------------------ Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
