-
Notifications
You must be signed in to change notification settings - Fork 661
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* Topology from omm topology and simulation objects. Coordinates from omm simulation * Remove debug lines * Move omm topology parsing code outside class for re-use in multiple omm reader objects * Change openmm trajectory reader into single frame reader * Add coordinates conversions for openmm modeller and pdbfile classes * Add topology parsing for openmm pdbfile and modeller objects * Tests for openmmtopology parser * Revert init * Test openmm topology parsing on pdb file with connections, add atomtypes * Use guesser for guessing atomtypes from atomnames * Off by one errors for 1-indexed resids * Set frame to 0 for first timestep * Unwrap simtk quantity for time * Coordinates tests for openmm pdbfile, modeller, simulation objects * update error messsage * Update documentation * Try updating some yaml files * Include datafiles and tests for pdbx files * More documentation for pdbx * Typo in format * Blacken code * Refactor so generic application objects share the same readers and functions * Adjust line length * Revert datafiles without black formatting * Add pdbx file to datafiles, update changelog * Update docstring with proper versionadded tag * Missing comma in list * Add pytest importorskip for testing openmm topology c onversion * Merge conflict * Remove unnecessary imports, more documentation for openmm application layer objects, additional openmm test from a basic openmm simulation made from scratch * Example usage in documentation * Convert simtk quanitties into default internal units * Update travis with extra variables for openmm, installing only on py37 tests * Revert back to atomtype guessing * Use proper openmm atom naming conventions for unit test * Modify appveyor config to specify openmm on py36 vs py38 * Correct syntax for appveyor env vars * Change appveyor var syntax * Empty string for conda openmm var * Merge conflict * Update GHA conda min dependencies for openmm on conda-forge * Remove inplace flag for converting energies, not used anywhere in openmm conversions * Update appveyor to pull openmm from conda-forge * Use simtk syntax for unit conversions * - Sanitize box angles when converting from OpenMM unitcell to MDA unitcell - Add xfail to pickle single frame reader for openmm tests - Use elements to specify atomtypes from OpenMM topology * Make sure OpenMM appears in the documentation * Add the stubs to trigger the build and link to the documentation of the new modules * Fix issues with references in the docstrings * PEP8 fixes for OpenMM reader and parser Co-authored-by: Oliver Beckstein <[email protected]> Co-authored-by: Jonathan Barnoud <[email protected]>
- Loading branch information
3 people
authored
May 5, 2021
1 parent
79183bf
commit 7f2ce3d
Showing
16 changed files
with
873 additions
and
6 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,198 @@ | ||
| # -*- 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.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 | ||
|
|
||
|
|
||
| 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) | ||
| 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) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.