On 11/01/16 16:56, Geoffrey Hutchison wrote: >> 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. Indeed. > > 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 > I implemented a call to ConnectTheDots but it does not add any more bonds. According to the documentation for this routine "This method adds single bonds between all atoms closer than their combined atomic covalent radii, then "cleans up" making sure bonded atoms are not closer than 0.4A and the atom does not exceed its valence. It implements blue-obelisk:rebondFrom3DCoordinates. "
In other words, it may add the bond and then remove it again :( -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se ------------------------------------------------------------------------------ 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
