[MMTK] Copy/Replace Operations

Konrad Hinsen research at khinsen.fastmail.net
Mon Oct 12 09:42:18 UTC 2009

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  

> 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 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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