[MMTK] help on start

Konrad Hinsen hinsen at cnrs-orleans.fr
Wed May 14 07:02:41 UTC 2008


On 08.05.2008, at 17:21, Arturas Ziemys wrote:

> I'm potentially new user of MMTK. The reason using MMTK for me is  
> to develop some humble code. But first I want to understand MMTK  
> code and I have general few questions:
> 1) I there any additional material (except the manual and the code  
> itself) to study/look-at about the general idea of the "flow" or  
> general concept/logic how things are done or expected to be done?  
> Python vs. C objects, etc....

Don't forget the examples, which are all simplified versions of real- 
life applications. There are also some published real-life  
applications that you can look at:

	http://dirac.cnrs-orleans.fr/plone/Members/hinsen/software-for- 
normal-mode-calculations-on-a-protein-crystal

	http://dirac.cnrs-orleans.fr/DomainFinder/

	http://dirac.cnrs-orleans.fr/plone/software/nmoldyn/

	http://dirac.cnrs-orleans.fr/plone/software/screwfit/screwfit/

	http://dirac.cnrs-orleans.fr/plone/software/densityfit/

> 2) Is the any clue how docking code should be started ? Any  
> examples or references ?

It all depends on the methods used. Do you want to dock rigid units,  
or flexible molecules? If flexible, what is your model for the  
internal flexibility?

> 3) Should the flow be changed in program if I decide to develop and  
> use new potentials ?

No. One of the design goals of MMTK was the possibility to add new  
potentials that work just like the built-ins. Any code that uses the  
documented APIs for energy calculations will work with potentials  
implemented later.

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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