8.5. OpenMM topology parser MDAnalysis.converters.OpenMMParser

Added in version 2.0.0.

Changed in version 2.8.0: Removed type and mass guessing (attributes guessing takes place now through universe.guess_TopologyAttrs() API)

Converts an OpenMM topology openmm.app.topology.Topology into a MDAnalysis.core.Topology.

Also converts some objects within the OpenMM Application layer

The OpenMMTopologyParser generates a topology from an OpenMM Topology object.

8.5.1. Classes

class MDAnalysis.converters.OpenMMParser.OpenMMTopologyParser(filename)[source]
close()

Close the trajectory file.

convert_forces_from_native(force, inplace=True)

Conversion of forces array force from native to base units

Parameters:

  • force (array_like) – Forces to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input force is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Added in version 0.7.7.

convert_forces_to_native(force, inplace=True)

Conversion of force array force from base to native units.

Parameters:

  • force (array_like) – Forces to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input force is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Added in version 0.7.7.

convert_pos_from_native(x, inplace=True)

Conversion of coordinate array x from native units to base units.

Parameters:

  • x (array_like) – Positions to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input x is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_pos_to_native(x, inplace=True)

Conversion of coordinate array x from base units to native units.

Parameters:

  • x (array_like) – Positions to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input x is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_time_from_native(t, inplace=True)

Convert time t from native units to base units.

Parameters:

  • t (array_like) – Time values to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input t is modified in place and also returned (although note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.) In-place operations improve performance because allocating new arrays is avoided.

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_time_to_native(t, inplace=True)

Convert time t from base units to native units.

Parameters:

  • t (array_like) – Time values to transform

  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input t is modified in place and also returned. (Also note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.)

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_velocities_from_native(v, inplace=True)

Conversion of velocities array v from native to base units

Parameters:

  • v (array_like) – Velocities to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input v is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Added in version 0.7.5.

convert_velocities_to_native(v, inplace=True)

Conversion of coordinate array v from base to native units

Parameters:

  • v (array_like) – Velocities to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input v is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Added in version 0.7.5.

units = {'length': None, 'time': None, 'velocity': None}

dict with units of of time and length (and velocity, force, … for formats that support it)

class MDAnalysis.converters.OpenMMParser.OpenMMAppTopologyParser(filename)[source]
close()

Close the trajectory file.

convert_forces_from_native(force, inplace=True)

Conversion of forces array force from native to base units

Parameters:

  • force (array_like) – Forces to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input force is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Added in version 0.7.7.

convert_forces_to_native(force, inplace=True)

Conversion of force array force from base to native units.

Parameters:

  • force (array_like) – Forces to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input force is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Added in version 0.7.7.

convert_pos_from_native(x, inplace=True)

Conversion of coordinate array x from native units to base units.

Parameters:

  • x (array_like) – Positions to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input x is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_pos_to_native(x, inplace=True)

Conversion of coordinate array x from base units to native units.

Parameters:

  • x (array_like) – Positions to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input x is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_time_from_native(t, inplace=True)

Convert time t from native units to base units.

Parameters:

  • t (array_like) – Time values to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input t is modified in place and also returned (although note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.) In-place operations improve performance because allocating new arrays is avoided.

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_time_to_native(t, inplace=True)

Convert time t from base units to native units.

Parameters:

  • t (array_like) – Time values to transform

  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input t is modified in place and also returned. (Also note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.)

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_velocities_from_native(v, inplace=True)

Conversion of velocities array v from native to base units

Parameters:

  • v (array_like) – Velocities to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input v is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Added in version 0.7.5.

convert_velocities_to_native(v, inplace=True)

Conversion of coordinate array v from base to native units

Parameters:

  • v (array_like) – Velocities to transform

  • inplace (bool (optional)) – Whether to modify the array inplace, overwriting previous data

Note

By default, the input v is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided.

Added in version 0.7.5.

units = {'length': None, 'time': None, 'velocity': None}

dict with units of of time and length (and velocity, force, … for formats that support it)

8.6. OpenMM structure I/O — MDAnalysis.converters.OpenMM

Read coordinates data from a OpenMM openmm.app.simulation.Simulation with OpenMMReader into a MDAnalysis Universe.

Also converts other objects within the OpenMM Application Layer:

Example

OpenMM can read various file formats into OpenMM objects. MDAnalysis can then convert some of these OpenMM objects into MDAnalysis Universe objects.

>>> import 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>

8.6.1. Classes

class MDAnalysis.converters.OpenMM.OpenMMSimulationReader(filename, convert_units=True, n_atoms=None, **kwargs)[source]

Reader for OpenMM Simulation objects

Added in version 2.0.0.

units = {'energy': 'kJ/mol', 'force': 'kJ/(mol*nm)', 'length': 'nm', 'time': 'ps', 'velocity': 'nm/ps'}

dict with units of of time and length (and velocity, force, … for formats that support it)

class MDAnalysis.converters.OpenMM.OpenMMAppReader(filename, convert_units=True, n_atoms=None, **kwargs)[source]

Reader for OpenMM Application layer objects

See also the object definition in the OpenMM Application layer

Added in version 2.0.0.

units = {'length': 'nm', 'time': 'ps'}

dict with units of of time and length (and velocity, force, … for formats that support it)