Converter for OpenMM

.disabled-travis.yml

@@ -30,7 +30,7 @@ env:
     - SETUP_CMD="${PYTEST_FLAGS}"
     - BUILD_CMD="pip install -e package/ && (cd testsuite/ && python setup.py build)"
     - CONDA_MIN_DEPENDENCIES="mmtf-python biopython networkx cython matplotlib scipy griddataformats hypothesis gsd codecov"
-    - CONDA_DEPENDENCIES="${CONDA_MIN_DEPENDENCIES} seaborn>=0.7.0 clustalw=2.1 netcdf4 scikit-learn joblib>=0.12 chemfiles tqdm>=4.43.0 tidynamics>=1.0.0 rdkit>=2020.03.1 h5py"
+    - CONDA_DEPENDENCIES="${CONDA_MIN_DEPENDENCIES} seaborn>=0.7.0 clustalw=2.1 netcdf4 scikit-learn joblib>=0.12 chemfiles tqdm>=4.43.0 tidynamics>=1.0.0 rdkit>=2020.03.1 h5py openmm"
     - CONDA_CHANNELS='biobuilds conda-forge'
     - CONDA_CHANNEL_PRIORITY=True
     - PIP_DEPENDENCIES="duecredit parmed"
@@ -43,7 +43,7 @@ env:
   matrix:
     # Run a coverage test for most versions
     - CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
-    - PYTHON_VERSION=3.8 CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
+    - PYTHON_VERSION=3.8 CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis" 
     - PYTHON_VERSION=3.7 CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
     - NUMPY_VERSION=1.16.0
     - NUMPY_VERSION=dev  EVENT_TYPE="cron"

.github/workflows/gh-ci.yaml

@@ -14,7 +14,7 @@ defaults:
     shell: bash -l {0}
 
 env:
-  MDA_CONDA_MIN_DEPS: "pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib-base scipy griddataformats hypothesis gsd codecov threadpoolctl"
+  MDA_CONDA_MIN_DEPS: "pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib-base scipy griddataformats hypothesis gsd codecov threadpoolctl openmm"
   MDA_CONDA_EXTRA_DEPS: "seaborn>=0.7.0 clustalw=2.1 netcdf4 scikit-learn joblib>=0.12 chemfiles tqdm>=4.43.0 tidynamics>=1.0.0 rdkit>=2020.03.1 h5py"
   MDA_PIP_MIN_DEPS: 'coveralls coverage<5 pytest-cov pytest-xdist'
   MDA_PIP_EXTRA_DEPS: 'duecredit parmed'

package/AUTHORS

@@ -165,6 +165,7 @@ Chronological list of authors
   - Henry Kobin
   - Kosuke Kudo
   - Sulay Shah
+  - Alexander Yang
 
 External code
 -------------

package/CHANGELOG

@@ -18,7 +18,7 @@ The rules for this file:
          calcraven，xiki-tempula, mieczyslaw, manuel.nuno.melo, PicoCentauri,
          hanatok, rmeli, aditya-kamath, tirkarthi, LeonardoBarneschi, hejamu,
          biogen98, orioncohen, z3y50n, hp115, ojeda-e, thadanipaarth, HenryKobin,
-         1ut, sulays
+         1ut, sulays, ahy3nz
 
   * 2.0.0
 
@@ -205,6 +205,7 @@ Changes
     ``analysis.helix_analysis`` (PR #2929)
   * Move water bridge analysis from hbonds to hydrogenbonds (Issue #2739 PR #2913)
   * `threadpoolctl` is required for installation (Issue #2860)
+  * Added OpenMM coordinate and topology converters (Issue #2863, PR #2917)
 
 Deprecations
 

package/MDAnalysis/coordinates/OpenMM.py

@@ -0,0 +1,186 @@
+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
+#
+# MDAnalysis --- https://www.mdanalysis.org
+# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
+# (see the file AUTHORS for the full list of names)
+#
+# Released under the GNU Public Licence, v2 or any higher version
+#
+# Please cite your use of MDAnalysis in published work:
+#
+# 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.
+# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
+# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
+# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
+# doi: 10.25080/majora-629e541a-00e
+#
+# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
+# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
+# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
+#
+
+"""OpenMM structure I/O --- :mod:`MDAnalysis.coordinates.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 . import base
+from .. import units
+
+
+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.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.positions = state.getPositions(asNumpy=True)._value
+        ts.velocities = state.getVelocities(asNumpy=True)._value
+        ts.forces = state.getForces(asNumpy=True)._value
+
+        return ts
+
+
+class OpenMMAppReader(base.SingleFrameReaderBase):
+    """Reader for OpenMM Application layer objects 
+
+    See also `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)
+            self.ts.triclinic_dimensions = self.convert_pos_from_native(
+                self.ts.triclinic_dimensions, inplace=False
+            )
+
+    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.positions = np.array(omm_object.getPositions()._value)
+
+        return ts
+
+

package/MDAnalysis/coordinates/__init__.py

@@ -732,6 +732,7 @@ class can choose an appropriate reader automatically.
 from . import INPCRD
 from . import LAMMPS
 from . import MOL2
+from . import OpenMM
 from . import ParmEd
 from . import PDB
 from . import PDBQT