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
"""
n_atoms = topology.n_atoms
if simple_topology:
topology = Topology(n_atoms, 3)
else:
topology = MDTrajTopology(md.Topology.from_openmm(topology))
snapshot = Snapshot.construct(
coordinates=u.Quantity(np.zeros((n_atoms, 3)), u.nanometers),
box_vectors=u.Quantity(topology.setUnitCellDimensions(), u.nanometers),
velocities=u.Quantity(np.zeros((n_atoms, 3)),
u.nanometers / u.picoseconds),
engine=TopologyEngine(topology))
return snapshot
def snapshot_from_pdb(pdb_file, simple_topology=False):
"""
Construct a Snapshot from the first frame in a pdb file without velocities
Parameters
----------
pdb_file : str
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
Returns
-------
:class:`openpathsampling.engines.Snapshot`
the constructed Snapshot
"""
pdb = md.load(pdb_file)
velocities = np.zeros(pdb.xyz[0].shape)
if simple_topology:
topology = Topology(*pdb.xyz[0].shape)
else:
topology = MDTrajTopology(pdb.topology)
snapshot = Snapshot.construct(
coordinates=u.Quantity(pdb.xyz[0], u.nanometers),
box_vectors=u.Quantity(pdb.unitcell_vectors[0], u.nanometers),
velocities=u.Quantity(velocities, u.nanometers / u.picoseconds),
engine=FileEngine(topology, pdb_file))
return snapshot
def snapshot_from_pdb(pdb_file, simple_topology=False):
"""
Construct a Snapshot from the first frame in a pdb file without velocities
Parameters
----------
pdb_file : str
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
Returns
-------
:class:`openpathsampling.engines.Snapshot`
the constructed Snapshot
"""
pdb = md.load(pdb_file)
velocities = np.zeros(pdb.xyz[0].shape)
if simple_topology:
topology = Topology(*pdb.xyz[0].shape)
else:
topology = MDTrajTopology(pdb.topology)
snapshot = Snapshot.construct(
coordinates=u.Quantity(pdb.xyz[0], u.nanometers),
box_vectors=u.Quantity(pdb.unitcell_vectors[0], u.nanometers),
velocities=u.Quantity(velocities, u.nanometers / u.picoseconds),
engine=FileEngine(topology, pdb_file)
)
return snapshot
def _build_current_snapshot(self):
# TODO: Add caching for this and mark if changed
state = self.simulation.context.getState(getPositions=True,
getVelocities=True,
getEnergy=True)
snapshot = Snapshot.construct(
coordinates=state.getPositions(asNumpy=True),
box_vectors=state.getPeriodicBoxVectors(asNumpy=True),
velocities=state.getVelocities(asNumpy=True),
engine=self
)
return snapshot
def snapshot_from_testsystem(testsystem, simple_topology=False):
"""
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
Returns
-------
:class:`openpathsampling.engines.Snapshot`
the constructed Snapshot
"""
velocities = u.Quantity(
np.zeros(testsystem.positions.shape), u.nanometers / u.picoseconds)
if simple_topology:
topology = Topology(*testsystem.positions.shape)
else:
topology = MDTrajTopology(md.Topology.from_openmm(testsystem.topology))
box_vectors = \
np.array([
v / u.nanometers for v in
testsystem.system.getDefaultPeriodicBoxVectors()]) * u.nanometers
snapshot = Snapshot.construct(
coordinates=testsystem.positions,
box_vectors=box_vectors,
velocities=velocities,
engine=OpenMMToolsTestsystemEngine(topology, testsystem.name)
)
return snapshot
def snapshot_from_testsystem(testsystem, simple_topology=False):
"""
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
Returns
-------
:class:`openpathsampling.engines.Snapshot`
the constructed Snapshot
"""
velocities = u.Quantity(np.zeros(testsystem.positions.shape),
u.nanometers / u.picoseconds)
if simple_topology:
topology = Topology(*testsystem.positions.shape)
else:
topology = MDTrajTopology(md.Topology.from_openmm(testsystem.topology))
box_vectors = \
np.array([
v / u.nanometers for v in
testsystem.system.getDefaultPeriodicBoxVectors()]) * u.nanometers
snapshot = Snapshot.construct(coordinates=testsystem.positions,
box_vectors=box_vectors,
velocities=velocities,
engine=OpenMMToolsTestsystemEngine(
topology, testsystem.name))
return snapshot
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
"""
n_atoms = topology.n_atoms
if simple_topology:
topology = Topology(n_atoms, 3)
else:
topology = MDTrajTopology(md.Topology.from_openmm(topology))
snapshot = Snapshot.construct(
coordinates=u.Quantity(np.zeros((n_atoms, 3)), u.nanometers),
box_vectors=u.Quantity(topology.setUnitCellDimensions(), u.nanometers),
velocities=u.Quantity(
np.zeros((n_atoms, 3)), u.nanometers / u.picoseconds),
engine=TopologyEngine(topology)
)
return snapshot
