nanover.mdanalysis.converter module

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

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

Bases: tuple

key

Alias for field number 0

required

Alias for field number 1

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

Bases: tuple

converter

Alias for field number 1

key

Alias for field number 0

nanover.mdanalysis.converter.add_frame_positions_to_mda(u: Universe, frame: FrameData)

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

Parameters:

  • u – MDAnalysis Universe to set positions of.

  • frame – NanoVer FrameData from which to extract positions.

nanover.mdanalysis.converter.add_frame_topology_to_mda(u: Universe, frame: FrameData)
nanover.mdanalysis.converter.add_mda_positions_to_frame_data(u: Universe, frame_data: FrameData)

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

Parameters:

  • u – MDAnalysis Universe.

  • frame_data – NanoVer FrameData to add to.

Raises:

MissingDataError – if no positions exist in the universe.

nanover.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.

nanover.mdanalysis.converter.frame_data_to_mdanalysis(frame: FrameData) → Universe

Converts from a NanoVer FrameData object to an MDAnalysis universe.

Parameters:

frame – NanoVer FrameData object.

Returns:

MDAnalysis Universe constructed from the given FrameData.

nanover.mdanalysis.converter.mdanalysis_to_frame_data(u: Universe, topology=True, positions=True) → FrameData

Converts from an MDAnalysis universe to NanoVer 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

nanover.mdanalysis.converter.nullable_int(value)