Source code for MDAnalysis.converters.OpenMM
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# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
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# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
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"""OpenMM structure I/O --- :mod:`MDAnalysis.converters.OpenMM`
================================================================
Read coordinates data from a
`OpenMM <http://docs.openmm.org/latest/api-python/generated/simtk.openmm.app.simulation.Simulation.html#simtk.openmm.app.simulation.Simulation>`_
:class:`simtk.openmm.app.simulation.Simulation` with :class:`OpenMMReader`
into a MDAnalysis Universe.
Also converts other objects within the
`OpenMM Application Layer <http://docs.openmm.org/latest/api-python/app.html>`_:
- `simtk.openmm.app.pdbfile.PDBFile <http://docs.openmm.org/latest/api-python/generated/simtk.openmm.app.pdbfile.PDBFile.html#simtk.openmm.app.pdbfile.PDBFile>`_
- `simtk.openmm.app.modeller.Modeller <http://docs.openmm.org/latest/api-python/generated/simtk.openmm.app.modeller.Modeller.html#simtk.openmm.app.modeller.Modeller>`_
- `simtk.openmm.app.pdbxfile.PDBxFile <http://docs.openmm.org/latest/api-python/generated/simtk.openmm.app.pdbxfile.PDBxFile.html#simtk.openmm.app.pdbxfile.PDBxFile>`_
Example
-------
OpenMM can read various file formats into OpenMM objects.
MDAnalysis can then convert some of these OpenMM objects into MDAnalysis Universe objects.
>>> import simtk.openmm.app as app
>>> import MDAnalysis as mda
>>> from MDAnalysis.tests.datafiles import PDBX
>>> pdbxfile = app.PDBxFile(PDBX)
>>> mda.Universe(pdbxfile)
<Universe with 60 atoms>
Classes
-------
.. autoclass:: OpenMMSimulationReader
:members:
.. autoclass:: OpenMMAppReader
:members:
"""
import numpy as np
from ..coordinates import base
[docs]class OpenMMSimulationReader(base.SingleFrameReaderBase):
"""Reader for OpenMM Simulation objects
.. versionadded:: 2.0.0
"""
format = "OPENMMSIMULATION"
units = {"time": "ps", "length": "nm", "velocity": "nm/ps",
"force": "kJ/(mol*nm)", "energy": "kJ/mol"}
@staticmethod
def _format_hint(thing):
"""Can this reader read *thing*?
"""
try:
from simtk.openmm.app import Simulation
except ImportError:
return False
else:
return isinstance(thing, Simulation)
def _read_first_frame(self):
self.n_atoms = self.filename.topology.getNumAtoms()
self.ts = self._mda_timestep_from_omm_context()
if self.convert_units:
self.convert_pos_from_native(self.ts._pos)
self.ts.triclinic_dimensions = self.convert_pos_from_native(
self.ts.triclinic_dimensions, inplace=False
)
self.ts.dimensions[3:] = _sanitize_box_angles(self.ts.dimensions[3:])
self.convert_velocities_from_native(self.ts._velocities)
self.convert_forces_from_native(self.ts._forces)
self.convert_time_from_native(self.ts.dt)
def _mda_timestep_from_omm_context(self):
""" Construct Timestep object from OpenMM context """
import simtk.unit as u
state = self.filename.context.getState(-1, getVelocities=True,
getForces=True, getEnergy=True)
n_atoms = self.filename.context.getSystem().getNumParticles()
ts = self._Timestep(n_atoms, **self._ts_kwargs)
ts.frame = 0
ts.data["time"] = state.getTime()._value
ts.data["potential_energy"] = (
state.getPotentialEnergy().in_units_of(u.kilojoule/u.mole)
)
ts.data["kinetic_energy"] = (
state.getKineticEnergy().in_units_of(u.kilojoule/u.mole)
)
ts.triclinic_dimensions = state.getPeriodicBoxVectors(
asNumpy=True)._value
ts.dimensions[3:] = _sanitize_box_angles(ts.dimensions[3:])
ts.positions = state.getPositions(asNumpy=True)._value
ts.velocities = state.getVelocities(asNumpy=True)._value
ts.forces = state.getForces(asNumpy=True)._value
return ts
[docs]class OpenMMAppReader(base.SingleFrameReaderBase):
"""Reader for OpenMM Application layer objects
See also `the object definition in the OpenMM Application layer <http://docs.openmm.org/latest/api-python/generated/simtk.openmm.app.simulation.Simulation.html#simtk.openmm.app.simulation.Simulation>`_
.. versionadded:: 2.0.0
"""
format = "OPENMMAPP"
units = {"time": "ps", "length": "nm"}
@staticmethod
def _format_hint(thing):
"""Can this reader read *thing*?
"""
try:
from simtk.openmm import app
except ImportError:
return False
else:
return isinstance(thing, (app.PDBFile, app.Modeller,
app.PDBxFile))
def _read_first_frame(self):
self.n_atoms = self.filename.topology.getNumAtoms()
self.ts = self._mda_timestep_from_omm_app()
if self.convert_units:
self.convert_pos_from_native(self.ts._pos)
if self.ts.dimensions is not None:
self.ts.triclinic_dimensions = self.convert_pos_from_native(
self.ts.triclinic_dimensions, inplace=False
)
self.ts.dimensions[3:] = _sanitize_box_angles(self.ts.dimensions[3:])
def _mda_timestep_from_omm_app(self):
""" Construct Timestep object from OpenMM Application object """
omm_object = self.filename
n_atoms = omm_object.topology.getNumAtoms()
ts = self._Timestep(n_atoms, **self._ts_kwargs)
ts.frame = 0
if omm_object.topology.getPeriodicBoxVectors() is not None:
ts.triclinic_dimensions = np.array(
omm_object.topology.getPeriodicBoxVectors()._value
)
ts.dimensions[3:] = _sanitize_box_angles(ts.dimensions[3:])
ts.positions = np.array(omm_object.getPositions()._value)
return ts
def _sanitize_box_angles(angles):
""" Ensure box angles correspond to first quadrant
See `discussion on unitcell angles <https://github.com/MDAnalysis/mdanalysis/pull/2917/files#r620558575>`_
"""
inverted = 180 - angles
return np.min(np.array([angles, inverted]), axis=0)