Hi all, I have a Fe-coproporphyrin III molecule in mol format which has an iron at the center of a porphyrin ring from the ChEBI database (ChEBI ID 55376). In order for the Fe to have connectivity to the porphyrin the charge of the Fe was changed to 2- and pseudo bonds were added to surrounding Nitrogens. I would like to retain this information when I canonicalize the molecule - currently when I canonicalize the molecule the Fe is given a charge of 5 and the connectivity is lost. Is there are way to retain this information in the canonicalization step?
Many Thanks, Rudesh -- View this message in context: http://forums.openbabel.org/Canonicalize-and-retain-pseudo-charges-bonds-tp4657138.html Sent from the General discussion mailing list archive at Nabble.com. ------------------------------------------------------------------------------ CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments & Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
