[MMTK] transformation of one molecule in an other one?

Konrad Hinsen hinsen at cnrs-orleans.fr
Thu Jan 22 15:17:30 UTC 2009


On 22.01.2009, at 15:17, Andreas Fuchs wrote:

> I have an amorphous structure containing n molecules of the same  
> geometry. All molecules are arbitrarily translated and rotated. Now  
> I'd like to know the tranformations I have to apply to transform  
> molecule i into molecule j.
> I was thinking about trying the MMTK function findTransformation().
> Unfortunately, I cannot find the correct syntax and am net even  
> sure if I am on the right way. Has anyone had a similar problem and  
> could give me some hints?

findTransformation does the job, but it is made for a slightly  
different situation: comparing the *same* molecule in different  
configurations. To use it for your problem, you'd have to create a  
new configuration object, copy the atom positions of molecule i to  
the new configuation as the positions of molecule j, and then call  
findTransformation on molecule j.

Konrad.
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen at cnrs-orleans.fr
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