narupatools.ase.converter

Conversion functions for converting ASE objects to Narupa objects.

Functions

ase_atoms_to_frame

Convert an ASE Atoms object to a Narupa FrameData.

frame_to_ase_atoms

Convert a Narupa FrameData to an ASE atoms object.
narupatools.ase.converter.ase_atoms_to_frame(atoms: ase.atoms.Atoms, *, fields: infinite_sets.infinite_sets.InfiniteSet[str] = frozenset({'particle.count', 'particle.elements', 'particle.names', 'particle.positions', 'particle.residues', 'residue.count', 'residue.names', 'system.box.vectors'}), frame: Optional[narupa.trajectory.frame_data.FrameData] = None) → narupa.trajectory.frame_data.FrameData

Convert an ASE Atoms object to a Narupa FrameData.

Parameters

  • atoms – ASE Atoms object to convert.

  • fields – A collection of keys that should be added to the frame if available.

  • frame – An optional preexisting FrameData to populate.

Returns

A FrameData populated with information available in the ASE atoms object whose keys are present in the properties parameter.

narupatools.ase.converter.frame_to_ase_atoms(frame: narupa.trajectory.frame_data.FrameData, *, fields: infinite_sets.infinite_sets.InfiniteSet[str] = everything()) → ase.atoms.Atoms

Convert a Narupa FrameData to an ASE atoms object.

Parameters

  • frame – Narupa FrameData to convert.

  • fields – Set of fields to convert.

Returns

ASE atoms objects with properties read from the frame.

Classes

ASEConverter()

Converters for the ASE package.