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.
Indeed - this is a common task. I have such a simplified wrapper
available but haven't added it yet. Note that there are several steps
because "adding a forcefield" isn't just a case of adding a restraint,
but also requires topology, etc. to be set up properly.
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).
You can create topology for any Hierarchy - doesn't have to be the
entire PDB, but could be a single chain, for example.