def masses_per_mole(snapshot):
"""
Returns
-------
masses_per_mole : list of openmm.unit.Quantity with length n_atoms
atomic masses (with openmm.unit attached) in units of mass/mole
"""
try:
simulation = snapshot.engine.simulation
except AttributeError:
# OpenMM snapshot not from simulation engine (setup snapshot,
# probably)
ops_topology = snapshot.topology
topology = ops_topology.mdtraj.to_openmm()
masses_per_mole = [a.element.mass for a in topology.atoms()]
else:
# standard case from simulation
system = simulation.context.getSystem()
n_particles = system.getNumParticles()
masses_per_mole = [
system.getParticleMass(i) for i in range(system.getNumParticles())
]
masses_per_mole = u.Quantity(value=np.array(
[m.value_in_unit(u.dalton) for m in masses_per_mole]),
unit=u.dalton)
return masses_per_mole
def _build_current_snapshot(self):
# TODO: Add caching for this and mark if changed
tmp = self.template
coordinates = u.Quantity(
tmp.coordinates._value +
np.random.normal(0.0, 0.02, tmp.coordinates.shape),
tmp.coordinates.unit)
velocities = u.Quantity(
np.random.normal(0.0, 0.02, tmp.velocities.shape),
tmp.velocities.unit)
return peng.Snapshot.construct(coordinates=coordinates,
box_vectors=tmp.box_vectors,
velocities=velocities,
engine=self)
def empty_snapshot_from_openmm_topology(topology, simple_topology=False):
"""
Return an empty snapshot from an openmm.Topology object
Velocities will be set to zero.
Parameters
----------
topology : openmm.Topology
the topology representing the structure and number of atoms
simple_topology : bool
if `True` only a simple topology with n_atoms will be created.
This cannot be used with complex CVs but loads and stores very fast
Returns
-------
openpathsampling.engines.Snapshot
the complete snapshot with zero coordinates and velocities
"""
error_if_no_simtk_unit("empty_snapshot_from_openmm_topology")
u_nm = unit.nanometers
u_ps = unit.picoseconds
n_atoms = topology.n_atoms
if simple_topology:
topology = Topology(n_atoms, 3)
else:
error_if_no_mdtraj("empty_snaphsot_from_openmm_topology")
topology = MDTrajTopology(md.Topology.from_openmm(topology))
snapshot = Snapshot.construct(
coordinates=unit.Quantity(np.zeros((n_atoms, 3)), u_nm),
box_vectors=unit.Quantity(topology.setUnitCellDimensions(), u_nm),
velocities=unit.Quantity(np.zeros((n_atoms, 3)), u_nm / u_ps),
engine=TopologyEngine(topology)
)
return snapshot
def snapshot_from_testsystem(testsystem, simple_topology=False,
periodic=True):
"""
Construct a Snapshot from openmm topology and state objects
Parameters
----------
testsystem : openmmtools.Topology
The filename of the .pdb file to be used
simple_topology : bool
if `True` only a simple topology with n_atoms will be created.
This cannot be used with complex CVs but loads and stores very fast
periodic : bool
True (default) if system is periodic; if False, box vectors are None
Returns
-------
:class:`openpathsampling.engines.Snapshot`
the constructed Snapshot
"""
error_if_no_simtk_unit("snapshot_from_testsystem")
u_nm = unit.nanometers
u_ps = unit.picoseconds
velocities = unit.Quantity(np.zeros(testsystem.positions.shape),
u_nm / u_ps)
if simple_topology:
topology = Topology(*testsystem.positions.shape)
else:
topology = MDTrajTopology(md.Topology.from_openmm(testsystem.topology))
if periodic:
sys_box_vectors = testsystem.system.getDefaultPeriodicBoxVectors()
box_vectors = np.array([v / u_nm for v in sys_box_vectors]) * u_nm
else:
box_vectors = None
snapshot = Snapshot.construct(
coordinates=testsystem.positions,
box_vectors=box_vectors,
velocities=velocities,
engine=OpenMMToolsTestsystemEngine(topology, testsystem.name)
)
return snapshot
def _get(my_getter):
if my_getter is None:
return lambda v: u.Quantity(v, unit)
else:
return lambda v: u.Quantity(my_getter(v), unit)
def trajectory_from_mdtraj(mdtrajectory,
simple_topology=False,
velocities=None):
"""
Construct a Trajectory object from an mdtraj.Trajectory object
Parameters
----------
mdtrajectory : mdtraj.Trajectory
Input mdtraj.Trajectory
simple_topology : bool
if `True` only a simple topology with n_atoms will be created.
This cannot be used with complex CVs but loads and stores very fast
velocities : np.array
velocities in units of nm/ps
Returns
-------
openpathsampling.engines.Trajectory
the constructed Trajectory instance
"""
error_if_no_simtk_unit("trajectory_from_mdtraj")
trajectory = Trajectory()
u_nm = unit.nanometer
u_ps = unit.picosecond
vel_unit = u_nm / u_ps
if simple_topology:
topology = Topology(*mdtrajectory.xyz[0].shape)
else:
topology = MDTrajTopology(mdtrajectory.topology)
if velocities is None:
empty_vel = unit.Quantity(np.zeros(mdtrajectory.xyz[0].shape),
vel_unit)
if mdtrajectory.unitcell_vectors is not None:
box_vects = unit.Quantity(mdtrajectory.unitcell_vectors,
unit.nanometers)
else:
box_vects = [None] * len(mdtrajectory)
engine = TopologyEngine(topology)
for frame_num in range(len(mdtrajectory)):
# mdtraj trajectories only have coordinates and box_vectors
coord = unit.Quantity(mdtrajectory.xyz[frame_num], u_nm)
if velocities is not None:
vel = unit.Quantity(velocities[frame_num], vel_unit)
else:
vel = empty_vel
box_v = box_vects[frame_num]
statics = Snapshot.StaticContainer(coordinates=coord,
box_vectors=box_v,
engine=engine)
kinetics = Snapshot.KineticContainer(velocities=vel, engine=engine)
snap = Snapshot(statics=statics, kinetics=kinetics, engine=engine)
trajectory.append(snap)
return trajectory