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 > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev