CodyA
2017-07-21 19:50:27 UTC
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.
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.