Thanks for the quick reply. This feature would be extremely useful. I think it is a graph isomorphism problem.
I’m not following the first method that you proposed. But the second method you mentioned definitely works. In my case, I need to shuffle the atoms of the benzene such that they rotate 60 degrees (360/6) around the ring. Perhaps, I’ll try all 5 permutations and take the lowest RMSD as the correct RMSD . Sent from Mail for Windows 10 From: Noel O'Boyle [via Open Babel] Sent: Saturday, July 22, 2017 11:57 AM To: CodyA Subject: Re: Put atoms of target molecule in same order as reference I should probably add this feature. In the meanwhile, one way would be to generate canonical labels and then shuffle the atoms of both into that order. Alternatively, if there's a way to get the mapping between two molecules, you would just need to shuffle the atoms of one of them. (on my phone so hard to provide details) - Noel On 22 Jul 2017 3:48 p.m., "CodyA" <[hidden email]> wrote: 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 [hidden email] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ 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 [hidden email] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss If you reply to this email, your message will be added to the discussion below: http://forums.openbabel.org/Put-atoms-of-target-molecule-in-same-order-as-reference-tp4660120p4660123.html To unsubscribe from Put atoms of target molecule in same order as reference, click here. NAML 54636F7ED890412FBF93D9793BBF54F8.png (206 bytes) <http://forums.openbabel.org/attachment/4660124/0/54636F7ED890412FBF93D9793BBF54F8.png> -- View this message in context: http://forums.openbabel.org/Put-atoms-of-target-molecule-in-same-order-as-reference-tp4660120p4660124.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
