Re: [IMP-dev] automatic force field restraint setup

[Daniel Russel <>]

Yeah, it seems like one should be able to just add one restraint, not the current convoluted steps. Something like the ExcludedVolumeRestraint (which wraps a ClosePairContainer and a PairsRestraint). Easy enough\ for a simple case like the example (but I can't say I've looked at the code beyond the example).

For the second question, it is not obvious to me how to create a force field for something that is not a whole subtree in a hierarchy (eg, parts of several different atom.Hierarchies, or a few parts of the same hierarchy). Ben?


On Jul 12, 2010, at 3:31 PM, Dave Barkan wrote:

> Hi all,
> 
> I was wondering if there is a quick way to set up force field restraints 
> on a hierarchy of atoms generated by read_pdb()? Right now I have to 
> explicitly set up three or four types of restraints myself (following 
> the protocol in the charm_forcefield.py example in the atom module). 
> This is likely to be re-implemented often and it would be nice if IMP 
> provided an easy way to do this.
> 
> Maybe less useful to others, but potentially to me, would be if you 
> could specify a region of the protein to which to add the forcefield 
> restraints (instead of the whole PDB you just read in).
> 
> thanks,
> db
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