On 14 February 2012 03:29, Greg Landrum <[email protected]> wrote:
> Dear Jean-Paul,
>
> On Mon, Feb 13, 2012 at 12:18 PM, JP <[email protected]> wrote:
> > I have the indices for four atoms: how do I calculate the torsion angle
> > using rdkit ?
> >
> > I can see that the method I want is
> > here: http://www.rdkit.org/C++_Docs/TorsionAngle_8h.html
> > But is this method on the Python interface?
> >
> > I would have imagined this method to exist in the python Geom package...
>
> It's an oversight really. The only code in the RDKit for calculating
> torsions is the piece you discovered in the force field
> implementation.
>
> > If it is not available, it is not a big deal as the calculation is
> > straightforward. But if it is really missing in the python interface, it
> > just looks like a waste to have the method there and not be able to use
> it.
>
> There's no real argument against adding this to the Geom interface
> that I can come up with at the moment. I'll take a look at adding it
> for the next release.
>
>
Thanks Greg.
In geom? Or
Mol.CalcTorsionAngle(atomIdx1,atomIdx2,atomIdx3,atomIdx4, confId=default) ?
(Then I wouldn't need to worry to get the atom positions from the conformer
etc.)
Meanwhile, if others need this and cannot wait for the next release,
http://www.koders.com/python/fid0CC73E2FDE574BA11102EEC9C5C68E5BFA8B30FC.aspx?s=%22rob%22
is a good place to start.
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