> E.g. if I want to convert 1-methyl-pyridine I get a non-aromatic ring > with a carbon radical. This would be correct if the moleculare should be > neutral. But when I could set the total charge to +1 I would expect a > aromatic, non-radical pyridinium cation.
This is largely due to the input format. I'd suggest SDF, for example, which can specify the correct formal charge on the N atom. Other formats would probably work, but this is the most obvious standardized format. > If this is not possible for a xyz-file, do I have an alternative to > create a svg-format from a format which only hold topological > informations. All hydrogens are known. Are you saying that you don't wish to determine bonding or formal charges? I'm not sure such a format exists. Hope that helps, -Geoff ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
