Clarification of my question/confusion: It seems to me that the way it works
means that, for a group of bonded neighbors, you cannot set the torsion
angle for one of them independently of the others. If you change one torsion
angle, the others will be adjusted accordingly. This basically means that
when I read in a molecule (usually a PDB file) to a OBMol, then the
difference between torsion angles for bonded neighbors are fixed going
forward because the SetTorsion method rotates bonded neighbors when used. Or
have I completely misunderstood something?
On Fri, Jul 15, 2011 at 10:41 PM, Martin Kamp Jensen <
martin.kamp.jen...@gmail.com> wrote:
> Hello,
>
> Maybe someone can explain to me how the SetTorsion method [1] of the OBMol
> class works? The documentation is "Set the torsion defined by these atoms,
> rotating bonded neighbors." It is the latter part about rotating bonded
> neighbors I am particularly interested in. My question arises because I have
> noticed that if I use the SetTorsion method to change several torsion angles
> between bonded atoms in a molecule and then check the torsion angles using
> GetTorsion [2] then they are not identical to the values I wanted to assign
> (I am aware that GetTorsion returns a value in degrees while SetTorsion
> takes a value in radians). Further, it seems to matter in what order I
> change the angles. So it seems like changing a specific torsion angle can
> lead to other torsion angles changing. Can that be avoided?
>
> [1]
> http://openbabel.org/api/2.3/classOpenBabel_1_1OBMol.shtml#a501e76993e9deb8ec8ab24c464d4ed3c
> [2]
> http://openbabel.org/api/2.3/classOpenBabel_1_1OBMol.shtml#adfd902d8de9eeb32ea476fe916a329fd
>
> Thanks,
> Martin.
>
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