narupa.mdanalysis.converter module

Module for performing conversions between MDAnalysis universes and Narupa FrameData objects.

class narupa.mdanalysis.converter.FrameDataField(key, required)

Bases: tuple

key

Alias for field number 0

required

Alias for field number 1

class narupa.mdanalysis.converter.FrameDataFieldConversion(key, converter)

Bases: tuple

converter

Alias for field number 1

key

Alias for field number 0

narupa.mdanalysis.converter.add_frame_positions_to_mda(u: MDAnalysis.core.universe.Universe, frame: narupa.trajectory.frame_data.FrameData)

Updates the positions in an MDAnalysis Universe with those from the given frame.

Parameters:

• u – MDAnalysis Universe to set positions of.
• frame – Narupa FrameData from which to extract positions.

narupa.mdanalysis.converter.add_frame_topology_to_mda(u: MDAnalysis.core.universe.Universe, frame: narupa.trajectory.frame_data.FrameData)

narupa.mdanalysis.converter.add_mda_positions_to_frame_data(u: MDAnalysis.core.universe.Universe, frame_data: narupa.trajectory.frame_data.FrameData)

Adds the positions in a MDAnalysis universe to the frame data, if they exist.

Parameters:

• u – MDAnalysis Universe.
• frame_data – Narupa FrameData to add to.

Raises:

MissingDataError – if no positions exist in the universe.

narupa.mdanalysis.converter.add_mda_topology_to_frame_data(u, frame_data)

Adds available topology information from an MDAnalysis Universe to a FrameData.

Parameters:

• u – MDAnalysis Universe.
• frame_data – FrameData to add to.

narupa.mdanalysis.converter.frame_data_to_mdanalysis(frame: narupa.trajectory.frame_data.FrameData) → MDAnalysis.core.universe.Universe

Converts from a Narupa FrameData object to an MDAnalysis universe.

Parameters:frame – Narupa FrameData object. Returns:MDAnalysis Universe constructed from the given FrameData.

narupa.mdanalysis.converter.mdanalysis_to_frame_data(u: MDAnalysis.core.universe.Universe, topology=True, positions=True) → narupa.trajectory.frame_data.FrameData

Converts from an MDAnalysis universe to Narupa FrameData object.

Parameters:

• u – MDAnalysis Universe.
• topology – Whether to include topology.
• positions – Whether to include positions.

Returns:

FrameData constructed from MDAnalysis universe.

Raises:

MissingDataError – if no positions exist in the MDAnalysis universe, and positions are specified.

Topological information consists any available information such as bonds, residue names, residue ids, atom names, chain names, residue index and chain indexes

narupa.mdanalysis.converter.nullable_int(value)