[MMTK] feature

hinsen at llb.saclay.cea.fr hinsen at llb.saclay.cea.fr
Mon Oct 18 16:04:33 CEST 2004


On Oct 18, 2004, at 0:26, Eric Zollars wrote:

> Is there a built-in way to rotate a bond in a molecule using MMTK?  For
> example, if I start with a tri-peptide what's the best way to rotate 
> one
> phi angle (or chi angle in a sidechain)?

Define all atoms on one side of the bond as a group, then rotate that 
group around the bond using rotateAroundAxis(), the two atoms of the 
bond defining the rotation axis.

One could write a utility function that takes care of the hard part 
(defining the group), provided that there is a recipe for defining the 
group that is correct in most practical applications. For example, one 
could decide that the group contains those atoms of the molecule 
containing the bond that are one one side of the bond (of course that 
could fail in the presence of cyclic bond structures). But one would 
still need a convention for deciding which side of the bond is to be 
modified.

> Also, Konrad, it appears that peptide_ct in MMTK-2.5.1 is missing
> {'HA2': 'HA', '2HA': 'HA'} in pdb_alternative.
>
Indeed, thanks!

Konrad.
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