def __init__(self, ff_type=None, system_file=None, **kwargs):
"""Two pathways can be used starting from FF-specific files
or OpenMM XML system. Additional kwargs are variously used
depending on the forcefield / pathway that was chosen.
supported ff_type
-----------------
amber :: give a prmtop and an inpcrd
openmm :: give an XML file for the system
supported kwargs
----------------
topology :: system-specific or not depending on FF
coordinates :: source of coordinates for initial state
"""
assert (ff_type is None) or (system_file is None)
# This dict will store the API calls
# along with atom groups and force
# parameters needed to generate all
# the given restraints
self._restraints = dict()
self._topology = None
topofile = kwargs.get("topology", None)
coordfile = kwargs.get("coordinates", None)
if ff_type is not None:
if ff_type.lower() == "amber":
prmtop = AmberPrmtopFile(topofile)
inpcrd = AmberInpcrdFile(coordfile)
self.system = prmtop.createSystem(
nonbondedMethod=NoCutoff
) #CutoffNonPeriodic - according to Ada, this would be good bc its what amber does - preliminary tests show that this hurts small/medium proteins
self._topology = Topology.from_openmm(prmtop.topology)
self._positions = inpcrd
elif system_file is not None:
self.load_xml(system_file)
if topofile:
if topofile.endswith(".pdb"):
# this line is a bit silly but Topology class
# doesn't seem to directly load PDB so keeps
# the imports clean
self._topology = Topology.from_openmm(
PDBFile(topofile).topology)
else:
# Inspect and set ff_type
# TODO ff_type as instance attribute
pass
def show_conformations(self,centers_indices=None, rotations_indices=None, nodes_labels=None,
least_rmsd_fit='receptor', center_rmsd_fit='receptor'):
tmp_molcomplex = self.get_conformations(centers_indices, rotations_indices, nodes_labels)
tmp_mdtraj_topol = _mdtraj_topology.from_openmm(tmp_molcomplex.topology)
tmp_mdtraj_traj = _mdtraj_trajectory(tmp_molcomplex.positions/unit.nanometer,tmp_mdtraj_topol)
tmp_view = _nv_show_mdtraj(tmp_mdtraj_traj)
del(tmp_molcomplex, tmp_mdtraj_topol, tmp_mdtraj_traj)
return tmp_view
def subset(self, selector):
"""
Returns a list of atom indices corresponding to a MDTraj DSL
query. Also will accept list of numbers, which will be coerced
to int and returned.
"""
if isinstance(selector, (list, tuple)):
return map(int, selector)
selector = SELECTORS.get(selector, selector)
mdtop = MDTrajTopology.from_openmm(self.handler.topology)
return mdtop.select(selector)
def render_traj(topology, positions):
traj = Trajectory(positions / unit.nanometers,
Topology.from_openmm(topology))
return (show_mdtraj(traj).add_ball_and_stick('all').center_view(zoom=True))