Conceptually, what SetTorsion does is to take a single bond and rotate
it (not just move the one atom you specify in the command). As you've
found, this is not quite what you were looking for. Open Babel can
read and write z-matrices so there must be some code in there for
doing what you suggest - you should probably look at some of those
z-matrix formats. Alternatively, you could edit SetTorsion to avoid
considering the other parts of the molecule that are attached to the
end of the bond) and send in the patch.
- Noel
On 21 July 2011 18:23, Martin Kamp Jensen <martin.kamp.jen...@gmail.com> wrote:
> 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.
>> >> >
>> >> >
>> >> > ------------------------------------------------------------------------------
>> >> > AppSumo Presents a FREE Video for the SourceForge Community by Eric
>> >> > Ries, the creator of the Lean Startup Methodology on "Lean Startup
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>> >> > optimize your ideas and identify your business strategy.
>> >> > http://p.sf.net/sfu/appsumosfdev2dev
>> >> > _______________________________________________
>> >> > OpenBabel-discuss mailing list
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>> >> >
>> >> >
>> >
>> >
>
>
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