> for a number of ions, like hydronium (H3O+) and perchlorate (ClO4-) OB > does detect all bonds.
I would assume you mean “does not” detect all bonds. The maximum number of bonds for a particular element is defined in data/elements.txt (i.e. OBElement::MaxBonds() http://openbabel.org/dev-api/classOpenBabel_1_1OBElement.shtml) I’m not sure I’d “fix it” on a general basis, since OBMol::ConnectTheDots() is likely to recognize many spurious bonds. Instead, I’d probably set up some level of separate perception routine. For example, in PDB files, these are often residues and they have their own bond detection code. -Geoff ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
