Oops, it is getting late. Maybe I should further clarify that my goal is to
manipulate the torsion angles that define atom positions in Cartesian space
as in a Z-matrix. I find the (OBMol.NumAtoms() - 3) atom quadruples that I
want to use with SetTorsion, but the way SetTorsion works (as described
earlier) does not seem to be compatible with want I want to do.
On Sun, Jul 17, 2011 at 1:45 AM, Martin Kamp Jensen <
martin.kamp.jen...@gmail.com> wrote:
> 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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