[MMTK] Determine atom position given restraints

Konrad Hinsen hinsen at cnrs-orleans.fr
Tue Dec 16 10:34:29 CET 2003


On Monday 15 December 2003 23:24, Antoine Logean wrote:
> Rocco Moretti wrote:
> >Hello all,
> >
> >I'm looking to build up atom positions within a molecule atomwise, given
> >the relationships between the atoms. That is, I have a growing
> >molecule/chain, and I'd like to add on another atom to it, given
> >distance, angle and dihedral from three already positioned atoms. Is
> >there a function in MMTK to do such a thing? Is there perhaps code in
> >the hydrogen addition algorithm which I could hijack for that purpose?
> >
> >Thanks,
> >-Rocco
>
> yes
> the code is in the findPositions method of the ConfigIO module.
> The cartesian coordinate of the fourth atom are given by the
> intersection of a sphere a cone and a plane.

Indeed. It is used for defining a conformation by a Z-Matrix, but it may well 
be used for other purposes.

Konrad.
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