On Thu, Jul 21, 2011 at 6:26 PM, Noel O'Boyle <baoille...@gmail.com> wrote:
> Your molecule does not have 3D coordinates, so torsions are all messed up.
>
Ah, I did that now and now and can show you what my original question/issue
is all about:
OBConversion c = new OBConversion();
c.SetInFormat("smi");
OBMol m = new OBMol();
c.ReadString(m, "CCCC");
m.AddHydrogens();
OBBuilder b = new OBBuilder();
b.Build(m);
System.out.println(m.GetTorsion(1, 2, 3, 10)); // C-C-C-H
System.out.println(m.GetTorsion(1, 2, 3, 11)); // C-C-C-H
System.out.println("---");
m.SetTorsion(m.GetAtom(1), m.GetAtom(2), m.GetAtom(3), m.GetAtom(10),
Math.toRadians(50));
System.out.println(m.GetTorsion(1, 2, 3, 10));
System.out.println(m.GetTorsion(1, 2, 3, 11));
System.out.println("---");
m.SetTorsion(m.GetAtom(1), m.GetAtom(2), m.GetAtom(3), m.GetAtom(11),
Math.toRadians(100));
System.out.println(m.GetTorsion(1, 2, 3, 10));
System.out.println(m.GetTorsion(1, 2, 3, 11));
Output (my comments after //):
-179.9743765482302 // Original 1, 2, 3, 10
-59.999943704013745 // Original 1, 2, 3, 11
---
49.919061598456146 // 1, 2, 3, 10 as requested
169.91902782077864 // 1, 2, 3, 11 was changed automatically to maintain 120
degree difference or something like that
---
-19.999966222322385 // 1, 2, 3, 10 was changed automatically to maintain 120
degree difference or something like that
99.99999999999997 // 1, 2, 3, 11 as requested
So it seems to be impossible to change the torsion angles (1, 2, 3, 10), and
(1, 2, 3, 11) independently of each other?
My current "way out there hack" is to have my own list of the torsion angles
and manipulate them, then calculate the Cartesian coordinates of all atoms
based on my stored values, and then finally assigning those coordinates to
all the OBAtoms of the OBMol. That's just... puh :)
> On 21 July 2011 17:21, Martin Kamp Jensen <martin.kamp.jen...@gmail.com>
> wrote:
> > 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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> >
> >
>
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