def attempt_to_load_top_from_simtk(topology):
"""
Load topology from SIMTK.
Parameters
----------
topology : str or Path
Returns
-------
topology from mdtraj.Topology.from_openmm`
Raises
------
Dependency error from :func:`_log_simtkimport_error`, program
halts.
"""
topp = Path(topology)
if topp.suffix == '.cif' and SIMTK:
mol = app.PDBxFile(topp.str())
return mdtraj.Topology.from_openmm(mol.topology)
elif topp.suffix == '.cif' and not SIMTK:
_log_simtkimport_error()
else:
return topp.str()
def load_traj(topology, trajectory):
"""
Load trajectory with `MDTraj <http://mdtraj.org/1.9.3/index.html>`_.
Uses `mdtraj.load <http://mdtraj.org/1.9.3/api/generated/mdtraj.load.html?highlight=load#mdtraj.load>`_.
Example
-------
>>> libmdt.load_traj('bigtopology.cif', 'trajectory.dcd')
Parameters
----------
topology : str or Path
Path to the topology file. Accepts MDTraj compatible `topology files <http://mdtraj.org/1.9.3/load_functions.html#trajectory-reference>`_. mmCIF format is loaded using `OpenMM <http://mdtraj.org/1.9.3/api/generated/mdtraj.Topology.html?highlight=from_openmm#mdtraj.Topology.from_openmm>`_.
trajectory : str or Path
Path to the trajectory file. Accepts MDTraj compatible `files <http://mdtraj.org/1.9.3/load_functions.html#trajectory-reference>`_
Returns
-------
MDTraj trajectory
`Trajectory object <http://mdtraj.org/1.9.3/api/generated/mdtraj.Trajectory.html#mdtraj-trajectory>`_.
""" # noqa: E501
libio.report_input(topology, trajectory)
topp = Path(topology)
if topp.suffix == '.cif' and SIMTK:
mol = app.PDBxFile(topp.str())
top = mdtraj.Topology.from_openmm(mol.topology)
elif topp.suffix == '.cif' and not SIMTK:
_log_simtkimport_error()
else:
top = topp.str()
mdtrajectory = mdtraj.load(Path(trajectory).str(), top=top)
return mdtrajectory
def main(
topology,
trajectories,
insort=None,
start=None,
stop=None,
step=None,
selection='all',
traj_output='traj_out.dcd',
top_output=None,
unwrap=False,
unwrap_reference=None,
unwrap_compound='fragments',
align=False,
**kwargs,
):
"""Execute main client logic."""
log.info(T('editing trajectory'))
topology = Path(topology)
trajectories = [Path(t) for t in trajectories]
if insort:
trajectories = libio.sort_numbered_input(*trajectories)
u = libmda.load_universe(topology, *trajectories)
if unwrap:
log.info(T('unwrapping'))
log.info(S('set to: {}', unwrap))
log.info(S('reference: {}', unwrap_reference))
log.info(S('compound: {}', unwrap_compound))
if align:
log.info(T('Alignment'))
log.info(S('trajectory selection will be aligned to subselection:'))
log.info(S('- {}', align, indent=2))
align_reference = mda.Universe(Path(topology).str())
log.info(T('transformation'))
sliceObj = libio.frame_slice(start, stop, step)
log.info(S('selecting: {}', selection))
atom_selection = u.select_atoms(selection)
log.info(S('with {} atoms', atom_selection.n_atoms, indent=2))
log.info(T('saving trajectory'))
traj_output = Path(traj_output)
log.info(S('destination: {}', traj_output.resolve().str()))
with mda.Writer(traj_output.str(), atom_selection.n_atoms) as W:
for i, _ts in zip(
range(len(u.trajectory))[sliceObj],
u.trajectory[sliceObj],
):
log.info(S('working on frame: {}', i))
if unwrap:
log.debug(S('unwrapping', indent=2))
atom_selection.unwrap(
reference=unwrap_reference,
compound=unwrap_compound,
)
if align:
try:
libmda.mdaalignto(u, align_reference, selection=align)
except ZeroDivisionError:
_controlled_exit()
W.write(atom_selection)
log.info(S('trajectory saved'))
if top_output:
log.info(T('saving topology'))
fout = libio.parse_top_output(top_output, traj_output)
log.info(S('saving frame 0 to: {}', fout.resolve()))
with mda.Writer(fout.str(), atom_selection.n_atoms) as W:
for _ts in u.trajectory[sliceObj][0:1]:
if unwrap:
log.debug(S('unwrapping for topology', indent=2))
atom_selection.unwrap(
reference=unwrap_reference,
compound=unwrap_compound,
)
W.write(atom_selection)
log.info(S('Done'))
return