molsysmt.thirds.openmm.reporters package#

Submodules#

molsysmt.thirds.openmm.reporters.MolSys module#

class molsysmt.thirds.openmm.reporters.MolSys.MolSysReporter(reportInterval, topology, selection='all', syntax='MolSysMT', id=True, time=True, coordinates=True, boxVectors=True, potentialEnergy=False, kineticEnergy=False, temperature=False, runningTime=False)[source]#

Bases: object

OpenMM reporter that writes trajectories as MolSysMT MolSys objects.

end()[source]#
report(simulation, state)[source]#

molsysmt.thirds.openmm.reporters.StructuresDict module#

class molsysmt.thirds.openmm.reporters.StructuresDict.StructuresDictReporter(reportInterval, time=True, coordinates=True, velocities=False, potentialEnergy=False, kineticEnergy=False, totalEnergy=False, temperature=False, box=False, includeInitialContext=True)[source]#

Bases: object

OpenMM reporter emitting data into MolSysMT StructuresDict objects.

describeNextReport(simulation)[source]#
finalize()[source]#
report(simulation, state)[source]#

molsysmt.thirds.openmm.reporters.h5msm module#

class molsysmt.thirds.openmm.reporters.h5msm.H5MSMReporter(file, reportInterval, steps, selection='all', topology=True, time=True, box=True, coordinates=True, velocities=False, potentialEnergy=False, kineticEnergy=False, temperature=False, includeInitialContext=True, constantReportInterval=True, constantStepSize=True, constantBox=True, compression='lzf', compression_opts=None, int_precision='single', float_precision='single', auto_close=False, syntax='MolSysMT')[source]#

Bases: object

OpenMM reporter that writes trajectories to h5msm files.

close()[source]#
describeNextReport(simulation)[source]#
report(simulation, state)[source]#

molsysmt.thirds.openmm.reporters.tqdm module#

class molsysmt.thirds.openmm.reporters.tqdm.TQDMReporter(reportInterval, total_n_steps, potential_energy=True, temperature=True, volume=False)[source]#

Bases: object

OpenMM reporter that displays progress via tqdm.

describeNextReport(simulation)[source]#
finalize(state)[source]#
report(simulation, state)[source]#

Module contents#