narupatools.mdtraj.converter

Conversion methods for converting between MDTraj and Narupa.

Functions

mdtraj_topology_to_frame

Convert an MDTraj topology into a FrameData.

mdtraj_trajectory_to_frame

Convert an MDTraj trajectory into a FrameData.
narupatools.mdtraj.converter.mdtraj_topology_to_frame(topology: mdtraj.core.topology.Topology, *, fields: infinite_sets.infinite_sets.InfiniteSet[str] = frozenset({'bond.count', 'bond.pairs', 'chain.count', 'particle.count', 'particle.elements', 'particle.names', 'particle.positions', 'particle.residues', 'residue.chains', 'residue.count', 'residue.names', 'system.box.vectors'}), frame: Optional[narupa.trajectory.frame_data.FrameData] = None) → narupa.trajectory.frame_data.FrameData

Convert an MDTraj topology into a FrameData.

Parameters

  • topology – Topology to convert.

  • fields – Set of fields to add to the FrameData.

  • frame – Prexisting FrameData to add fields to.

Returns

FrameData with fields requested added from the topology.

narupatools.mdtraj.converter.mdtraj_trajectory_to_frame(trajectory: mdtraj.core.trajectory.Trajectory, *, frame_index: int = 0, fields: infinite_sets.infinite_sets.InfiniteSet[str] = frozenset({'bond.count', 'bond.pairs', 'chain.count', 'particle.count', 'particle.elements', 'particle.names', 'particle.positions', 'particle.residues', 'residue.chains', 'residue.count', 'residue.names', 'system.box.vectors'}), frame: Optional[narupa.trajectory.frame_data.FrameData] = None) → narupa.trajectory.frame_data.FrameData

Convert an MDTraj trajectory into a FrameData.

Parameters

  • trajectory – Trajectory to convert.

  • frame_index – Index of the frame in the trajectory to convert.

  • fields – Set of fields to add to the FrameData.

  • frame – Prexisting FrameData to add fields to.

Returns

FrameData with fields requested added from the trajectory.

Classes

MDTrajConverter()

FrameConverter for the mdtraj package.