PDBReporter

class simtk.openmm.app.pdbreporter.PDBReporter(file, reportInterval, enforcePeriodicBox=None)

PDBReporter outputs a series of frames from a Simulation to a PDB file.

To use it, create a PDBReporter, then add it to the Simulation’s list of reporters.

__init__(file, reportInterval, enforcePeriodicBox=None)

Create a PDBReporter.

Parameters:
  • file (string) – The file to write to
  • reportInterval (int) – The interval (in time steps) at which to write frames
  • enforcePeriodicBox (bool) – Specifies whether particle positions should be translated so the center of every molecule lies in the same periodic box. If None (the default), it will automatically decide whether to translate molecules based on whether the system being simulated uses periodic boundary conditions.

Methods

__init__(file, reportInterval[, ...]) Create a PDBReporter.
describeNextReport(simulation) Get information about the next report this object will generate.
report(simulation, state) Generate a report.
describeNextReport(simulation)

Get information about the next report this object will generate.

Parameters:simulation (Simulation) – The Simulation to generate a report for
Returns:A six element tuple. The first element is the number of steps until the next report. The next four elements specify whether that report will require positions, velocities, forces, and energies respectively. The final element specifies whether positions should be wrapped to lie in a single periodic box.
Return type:tuple
report(simulation, state)

Generate a report.

Parameters:
  • simulation (Simulation) – The Simulation to generate a report for
  • state (State) – The current state of the simulation
__delattr__

x.__delattr__(‘name’) <==> del x.name

__format__()

default object formatter

__getattribute__

x.__getattribute__(‘name’) <==> x.name

__hash__
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__
__setattr__

x.__setattr__(‘name’, value) <==> x.name = value

__sizeof__() → int

size of object in memory, in bytes

__str__