def load_trr(trr_file, top, velocities=True):
"""Load a TRR file, ready for use as input to an OpenMMEngine.
This is a single method to handle several peculiarities of both the TRR
format (which rounds some values) and OpenMM (which has certain
requirements of box vectors), plus the possibility that you'll want
velocities.
Parameters
----------
trr_file : string
name of TRR file to load
top : string
name of topology (e.g., ``.gro``) file to use. See MDTraj
documentation on md.load.
velocities : bool
whether to also load velocities from the TRR file; default ``True``
Return
------
:class:`.Trajectory`
the OPS trajectory, with OpenMM-reduced box vectors and velocities
(if requested)
"""
mdt = md.load(trr_file, top=top)
trr = md.formats.TRRTrajectoryFile(trr_file)
if velocities:
vel = trr._read(n_frames=len(mdt),
atom_indices=None,
get_velocities=True)[5]
else:
vel = None
traj = trajectory_from_mdtraj(mdt, velocities=vel)
return reduce_trajectory_box_vectors(traj)
def topology_from_pdb(pdb_file, simple_topology=False):
"""
Construct a Topology 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)
if simple_topology:
topology = Topology(*pdb.xyz[0].shape)
else:
topology = MDTrajTopology(pdb.topology)
return topology
def __init__(self, gro):
self.gro = gro
traj = md.load(gro)
self.topology = MDTrajTopology(traj.topology)
n_atoms = self.topology.n_atoms
n_spatial = self.topology.n_spatial
descriptor = SnapshotDescriptor.construct(
snapshot_class=self.SnapshotClass,
snapshot_dimensions={
'n_spatial': n_spatial,
'n_atoms': n_atoms
})
super(_GroFileEngine, self).__init__(options={},
descriptor=descriptor,
template=None)
def ops_load_trajectory(filename, **kwargs):
error_if_no_mdtraj("ops_load_trajectory")
return trajectory_from_mdtraj(md.load(filename, **kwargs))
def read_frame_data(self, file_name, file_position):
traj = md.load(file_name)
xyz = traj.xyz[0]
vel = np.zeros(shape=xyz.shape)
box = traj.unitcell_vectors[0]
return (xyz, vel, box)