Sorry, I thought I was clear about this. You could, in principal change the maximum number of bonds in data/elements.txt (e.g. that you want to allow up to 3 bonds to an oxygen).
ConnectTheDots would respect this. But I don’t think it’s a good general idea, because you’d frequently get spurious bonds. It would allow *all* oxygens to have up to 3 bonds, not just H3O+. Instead, I’m suggesting you either implement an additional pass in ConnectTheDots (i.e., before a bond is removed, check if it’s an H3O+) or a separate pass entirely, like the bond analysis for OBResidue. There are a few other strategies to bond perception in the literature, but they seem like research projects. I’d be happy to point to papers if you’re interested and have a student or someone else willing to see what works. -Geoff >> 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 implemented a call to ConnectTheDots but it does not add any more > bonds. According to the documentation for this routine .. > In other words, it may add the bond and then remove it again :( ------------------------------------------------------------------------------ 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
