[MMTK] Copy/Replace Operations

[Konrad Hinsen]

On 08.10.2009, at 22:36, tezcan at ecs.umass.edu wrote:

> I am trying to modify/transform a sidechain of a residue, save it  
> and replace sidechains with modified versions as necessary.
> Following might give you a better idea of what I am trying to do: 
> (suppose I have a function called modify()):

In your example, modify() is not a function but a method on residue  
objects. There is no such method in MMTK, so I wonder where it comes  
from.

> What is the proper way of doing this type of copy/replace operations  
> in MMTK?

The proper way is the use of indexed assignment:

	universe.protein[0][1] = new_second_residue

Some caveats:
1) The new residue should be newly created, not taken from an existing  
peptide chain.
2) Residues, like all groups and molecules in MMTK, cannot be  
modified. They are created from a database description or from a  
molecule factory and are immutable after creation. This is done to  
permit reasonably efficient operations on them. Only chain molecules  
can be modified, by substituting residues as shown above.

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: research at khinsen dot fastmail dot net
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