Hi all, I'm looking at carbon bonded to benzene. The carbon can bond at all the equivalent carbon in the benzene, as well as several other places in my simulation.
I am trying to compare structures by their RMSD, to determine the unique bonding structures. However, when I use OpenBabel the RMSD values I get are large for visually identical structures. This is because "When aligning molecules, the atoms of the two molecules must be in the same order" In my case, the carbon-carbon bond is between Carbon 1 and carbon 13, Carbon 2 and carbon 13, etc. all of which are different order but result in the same visually identical structure. Is there any way to programmatically put the atoms of the target in the same order as reference? -- View this message in context: http://forums.openbabel.org/Put-atoms-of-target-molecule-in-same-order-as-reference-tp4660120.html Sent from the General discussion mailing list archive at Nabble.com. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
