PDBReporter¶
- class openmm.app.pdbreporter.PDBReporter(file, reportInterval, enforcePeriodicBox=None, atomSubset=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, atomSubset=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.
atomSubset (list) – Atom indices (zero indexed) of the particles to output. if None (the default), all particles will be output.
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 dictionary describing the required information for the next report
- Return type
dict
- report(simulation, state)¶
Generate a report.
- Parameters
simulation (Simulation) – The Simulation to generate a report for
state (State) – The current state of the simulation