def from_dict(cls, dct):
error_if_no_mdtraj("MDTrajTopology")
top_dict = dct['mdtraj']
atoms = pd.DataFrame(
top_dict['atoms'], columns=top_dict['atom_columns'])
bonds = np.array(top_dict['bonds'])
try:
md_topology = md.Topology.from_dataframe(atoms, bonds)
return cls(md_topology)
except Exception:
# we try a fix and add multiples of 10000 to the resSeq
logger.info('Normal reconstruction of topology failed. '
'Trying a fix to the 10k residue ID problem.')
for ci in np.unique(atoms['chainID']):
chain_atoms = atoms[atoms['chainID'] == ci]
indices = chain_atoms.index.tolist()
old_residue_id = 0
multiplier = 0
places = []
for row, res_id in zip(indices, list(chain_atoms['resSeq'])):
if res_id < old_residue_id:
if multiplier > 0:
atoms.loc[places, 'resSeq'] += 10000 * multiplier
places = []
multiplier += 1
if multiplier > 0:
places.append(row)
old_residue_id = res_id
if multiplier > 0:
atoms.loc[places, 'resSeq'] += 10000 * multiplier
# this function is really slow! Reads ~ 1000 atoms per second
md_topology = md.Topology.from_dataframe(atoms, bonds)
# that we have successfully created the topology using from_df
# we remove the wrong multipliers
# this is weird, but reproduces the current behaviour
for atom in md_topology.atoms:
atom.residue.resSeq %= 10000
return cls(md_topology)
def to_mdtraj(self, topology=None):
"""
Construct a mdtraj.Trajectory object from the Trajectory itself
Parameters
----------
topology : :class:`mdtraj.Topology`
If not None this topology will be used to construct the mdtraj
objects otherwise the topology object will be taken from the
configurations in the trajectory snapshots.
Returns
-------
:class:`mdtraj.Trajectory`
the trajectory
Notes
-----
If the OPS trajectory is zero-length (has no snapshots), then this
fails. OPS cannot currently convert zero-length trajectories to
MDTraj, because an OPS zero-length trajectory cannot determine its
MDTraj topology.
"""
error_if_no_mdtraj("Converting to mdtraj")
try:
snap = self[0]
except IndexError:
raise ValueError("Cannot convert zero-length trajectory " +
"to MDTraj")
if topology is None:
# TODO: maybe add better error output?
# if AttributeError here, engine doesn't support mdtraj
topology = snap.engine.mdtraj_topology
output = self.xyz
traj = md.Trajectory(output, topology)
box_vectors = self.box_vectors
# box_vectors is a list with an entry for each frame of the traj
# if they're all None, we return None, not [None, None, ..., None]
if not np.any(box_vectors):
box_vectors = None
traj.unitcell_vectors = box_vectors
return traj
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 ops_load_trajectory(filename, **kwargs):
error_if_no_mdtraj("ops_load_trajectory")
return trajectory_from_mdtraj(md.load(filename, **kwargs))