On Wed, Jul 20, 2011 at 3:00 PM, Noel O'Boyle <baoille...@gmail.com> wrote:
> Works for me from Python:
>
> >>> import pybel
> >>> mol = pybel.readstring("smi", "CCCC")
> >>> mol.make3D()
> >>> mol.OBMol.GetTorsion(1,2,3,4)
> -179.9743765482302
> >>> mol.OBMol.SetTorsion(1,2,3,4, 22.5*math.pi/180.)
> >>> mol.OBMol.GetTorsion(1,2,3,4)
> 22.500000000000004
>
My issue is actually that by changing one angle, other angles (of bonded
neighbors) would be changed as well. Then there could be a situation where
you change two different angle, and then the changes neutralize each other.
I was going to show it, but the code below results in something else than
yours even though I thought it should be the same... hmm.
OBConversion c = new OBConversion();
> c.SetInFormat("smi");
> OBMol m = new OBMol();
> c.ReadString(m, "CCCC");
> System.out.println(m.GetTorsion(1, 2, 3, 4));
> m.SetTorsion(m.GetAtom(1), m.GetAtom(2), m.GetAtom(3), m.GetAtom(4),
> 22.5*Math.PI/180);
> System.out.println(m.GetTorsion(1, 2, 3, 4));
Output:
180.0
> 180.0
> where SetTorsion is defined in the Python interface as:
> void SetTorsion(int i, int j, int k, int l, double ang)
> {
> self->SetTorsion(self->GetAtom(i), self->GetAtom(j),
> self->GetAtom(k), self->GetAtom(l), ang);
> }
>
> - Noel
>
> On 15 July 2011 21:41, 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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