def apply_forcefield(structure, forcefield, debug=False):
"""Apply a forcefield to a Topology. """
if not structure.bonds:
warn("Structure contains no bonds: \n{}\n".format(structure))
if isinstance(forcefield, string_types):
if forcefield.lower() in ["opls-aa", "oplsaa", "opls"]:
if os.path.isdir("oplsaa.ff"):
ff_path = "oplsaa.ff/forcefield.itp"
else:
ff_path = os.path.join(gmx.GROMACS_TOPDIR, "oplsaa.ff/forcefield.itp")
elif forcefield.lower() in ["trappeua"]:
ff_path = os.path.join(gmx.GROMACS_TOPDIR, "trappeua.ff/forcefield.itp")
else:
ff_path = forcefield
# TODO: this is a patchwork fix until rules and FF files become one
forcefield = forcefield.lower()
for alias in OPLS_ALIASES:
if alias in forcefield:
forcefield = "oplsaa"
ff = GromacsTopologyFile(ff_path, parametrize=False)
find_atomtypes(structure.atoms, forcefield, debug=debug)
if hasattr(structure, "box"):
ff.box = structure.box
ff.atoms = structure.atoms
ff.bonds = structure.bonds
ff.residues = structure.residues
create_bonded_forces(ff)
ff.parametrize()
return ff
