In this example, a PDB file is read in and scored using the CHARMM forcefield. It is similar to the 'charmm_forcefield.py' example, but fully works through each step of the procedure using lower-level IMP classes. This is useful if you want to customize the way in which the forcefield is applied.
18 topology = ff.create_topology(prot)
23 topology.apply_default_patches()
28 topology.add_atom_types(prot)
33 topology.add_missing_atoms(prot)
36 topology.add_coordinates(prot)
45 bonds = topology.add_bonds(prot)
46 angles = ff.create_angles(bonds)
47 dihedrals = ff.create_dihedrals(bonds)
48 impropers = topology.add_impropers(prot)
90 ff.add_well_depths(prot)
106 pair_filter.set_bonds(bonds)
107 pair_filter.set_angles(angles)
108 pair_filter.set_dihedrals(dihedrals)
109 nbl.add_pair_filter(pair_filter)
119 print m.evaluate(
False)