narupatools.mdanalysis.converter

Conversion methods between MDAnalysis and Narupa.

Functions

frame_to_mdanalysis_topology	Convert a Narupa frame to an MDAnalysis topology.
frame_to_mdanalysis_universe	Convert a Narupa frame to an MDAnlysis universe.
mdanalysis_atomgroup_to_frame	Convert an MDAnalysis AtomGroup into a Narupa FrameData.
mdanalysis_universe_to_frame	Convert an MDAnalysis Universe into a Narupa FrameData.

narupatools.mdanalysis.converter.frame_to_mdanalysis_topology(frame: narupa.trajectory.frame_data.FrameData, *, fields: infinite_sets.infinite_sets.InfiniteSet[str] = everything()) → MDAnalysis.core.topology.Topology

Convert a Narupa frame to an MDAnalysis topology.

Parameters

• frame – Narupa frame to convert.

• fields – Set of fields to copy.

Returns

MDAnalysis topology with the given fields copied over.

narupatools.mdanalysis.converter.frame_to_mdanalysis_universe(frame: narupa.trajectory.frame_data.FrameData, *, fields: infinite_sets.infinite_sets.InfiniteSet[str] = everything()) → MDAnalysis.core.universe.Universe

Convert a Narupa frame to an MDAnlysis universe.

Parameters

• frame – Narupa frame to convert.

• fields – Fields to copy from the frame data.

Returns

Universe with the given data included.

narupatools.mdanalysis.converter.mdanalysis_atomgroup_to_frame(group: MDAnalysis.core.groups.AtomGroup, *, fields: infinite_sets.infinite_sets.InfiniteSet[str] = frozenset({'bond.count', 'bond.pairs', 'chain.count', 'chain.names', 'particle.count', 'particle.elements', 'particle.names', 'particle.positions', 'particle.residues', 'particle.types', 'residue.chains', 'residue.count', 'residue.ids', 'residue.names', 'system.box.vectors'}), frame: Optional[narupa.trajectory.frame_data.FrameData] = None) → narupa.trajectory.frame_data.FrameData

Convert an MDAnalysis AtomGroup into a Narupa FrameData.

Parameters

• group – The MDAnalysis AtomGroup to convert.

• fields – Fields to add to FrameData.

• frame – Optional pre-existing FrameData to populate.

Returns

FrameData populated with requested fields.

narupatools.mdanalysis.converter.mdanalysis_universe_to_frame(universe: MDAnalysis.core.universe.Universe, *, fields: infinite_sets.infinite_sets.InfiniteSet[str] = frozenset({'bond.count', 'bond.pairs', 'chain.count', 'chain.names', 'particle.count', 'particle.elements', 'particle.names', 'particle.positions', 'particle.residues', 'particle.types', 'residue.chains', 'residue.count', 'residue.ids', 'residue.names', 'system.box.vectors'}), frame: Optional[narupa.trajectory.frame_data.FrameData] = None) → narupa.trajectory.frame_data.FrameData

Convert an MDAnalysis Universe into a Narupa FrameData.

Parameters

• universe – The MDAnalysis universe to convert.

• fields – Fields to add to FrameData.

• frame – Optional pre-existing FrameData to populate.

Returns

FrameData populated with requested fields.

Classes

MDAnalysisConverter()

Frame converter for the MDAnalysis package.