htmd.membranebuilder.pdbreporter module

pdbreporter.py: Outputs simulation trajectories in PDB format

This is part of the OpenMM molecular simulation toolkit originating from Simbios, the NIH National Center for Physics-Based Simulation of Biological Structures at Stanford, funded under the NIH Roadmap for Medical Research, grant U54 GM072970. See https://simtk.org.

Portions copyright (c) 2012 Stanford University and the Authors. Authors: Peter Eastman Contributors:

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

class htmd.membranebuilder.pdbreporter.PDBReporter(file, reportInterval, enforcePeriodicBox=True)

Bases: object

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.

describeNextReport(simulation)

Get information about the next report this object will generate.

Parameters

simulation (Simulation) – The Simulation to generate a report for

Returns

A five element tuple. The first element is the number of steps until the next report. The remaining elements specify whether that report will require positions, velocities, forces, and energies respectively.

Return type

tuple

report(simulation, _)

Generate a report.

Parameters
  • simulation (Simulation) – The Simulation to generate a report for

  • _ (State) – The current state of the simulation

class htmd.membranebuilder.pdbreporter.PDBxReporter(file, reportInterval, enforcePeriodicBox=True)

Bases: htmd.membranebuilder.pdbreporter.PDBReporter

PDBxReporter outputs a series of frames from a Simulation to a PDBx/mmCIF file.

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

report(simulation, _)

Generate a report.

Parameters
  • simulation (Simulation) – The Simulation to generate a report for

  • _ (State) – The current state of the simulation