HDF5Trajectory¶

class narupatools.frame.hdf5.trajectory.HDF5Trajectory(file: tables.file.File)¶

Reader for the NarupaTools HDF5 format.

Inheritance

Methods

`__init__`	Initialize self.
`create_from_object`	Attempt to convert an arbitrary object to a trajectory source.
`get_frame`	Create a FrameData representation, with the given fields present if available.
`load_file`	Load a trajectory that conforms to the narupatools HDF5 format.

__init__(file: tables.file.File)¶: Initialize self. See help(type(self)) for accurate signature.

static create_from_object(obj: Any) → Optional[narupatools.frame.frame_source.TrajectorySource]¶: Attempt to convert an arbitrary object to a trajectory source.

get_frame(*, index: int, fields: infinite_sets.infinite_sets.InfiniteSet[str]) → narupa.trajectory.frame_data.FrameData ¶

Create a FrameData representation, with the given fields present if available.

Parameters

index – Index of frame to get.
fields – Collection of fields that should be added to FrameData if available.

Load a trajectory that conforms to the narupatools HDF5 format.

Attributes

`forces`	Forces on the particles for each frame, in nanometers per picoseconds.
`interactions`	Interactions applied during this trajectory.
`kinetic_energies`	Kinetic energy of each frame, in kilojoules per mole.
`positions`	Positions of the particles for each frame, in nanometers.
`potential_energies`	Potential energy of each frame, in kilojoules per mole.
`times`	Time of each frame, in picoseconds.
`topology`	Topology stored with the trajectory.
`velocities`	Velocities of the particles for each frame, in nanometers per picoseconds.

forces¶: Forces on the particles for each frame, in nanometers per picoseconds.

potential_energies¶: Potential energy of each frame, in kilojoules per mole.

velocities¶: Velocities of the particles for each frame, in nanometers per picoseconds.

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