I am facing a problem when manipulating an aromatic molecule:
[nH]1nnc2c1c(=O)c1[nH]nnc1c2=O
Cycles are not in kekulize form.
When I create a molecule with pybel:
>>> mol = pybel.readstring("smi","O=c1c2nn[nH]c2c(=O)c2[nH]nnc12").next()pybel create a connectivity error with 2 pentavalent carbon atom (carbonyls) in the cycle: >>> mol.write().split()[0] O=C1=C2N=NNC2C(=O)=C2NN=NC12 how to get around the problem? thanks a lot David -- View this message in context: http://forums.openbabel.org/aromatic-compounds-tp4657475.html Sent from the openbabel-devel mailing list archive at Nabble.com. ------------------------------------------------------------------------------ "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free." http://p.sf.net/sfu/SauceLabs _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
