narupatools.frame.fields

Standard fields and their getters/setters for Narupa frames.

Module Attributes

ParticlePositions

Array of particle positions in nanometers, as a NumPy N by 3 array of floats.

ParticleVelocities

Array of particle velocities in nanometers per picosecond, as a NumPy N by 3 array of floats.

ParticleForces

Array of particle forces in kilojoule per mole per nanometer, as a NumPy N by 3 array of floats.

ParticleElements

Array of particle elements, as a NumPy array of atomic number.

ParticleResidues

Array of particle residue indices, as a NumPy array of zero-based indices.

ParticleNames

Array of particle names, as a NumPy array of strings.

ParticleTypes

Array of particle types, as a NumPy array of strings.

ParticleMasses

Array of particle masses in atomic mass units, as a NumPy array of floats.

ParticleCharges

Array of particle charges in proton charges, as a NumPy array of floats.

ParticleCount

Number of particles in the system, as an integer.

PotentialEnergy

Potential energy of the system in kilojoules per mole, as a float.

KineticEnergy

Kinetic energy of the system in kilojoules per mole, as a float.

SimulationElapsedTime

Elapsed time in the simulation in picoseconds, as a float.

SimulationTotalTime

Total time in the simulation in picoseconds, as a float.

SimulationElapsedSteps

Elapsed steps in the simulation, as a integer.

SimulationTotalSteps

Total steps in the simulation, as a integer.

BondPairs

Array of bonds as pairs of particle indices, as a N by 2 NumPy array of integers.

BondOrders

Array of bond orders, as a NumPy array of integers.

BondCount

Number of bonds in the system, as an integer.

ResidueNames

Array of residue names, as a NumPy array of strings.

ResidueIds

Array of residue ids, as a NumPy array of strings.

ResidueChains

Array of residue chain indices, as a NumPy array of integers.

ResidueCount

Number of residues in the system, as an integer.

ChainNames

Array of chain names, as a NumPy array of strings.

ChainCount

Number of chains in the system, as an integer.

BoxVectors

Array of box vectors in nanometers indicating the simulation box, as a NumPy 3 by 3 or 4 x 3 array of floats.

Functions

get_frame_key

Get the defined FrameKey for a given string key.
narupatools.frame.fields.get_frame_key(key: str) → narupatools.frame.fields.FrameKey

Get the defined FrameKey for a given string key.

Parameters

key – Key as it appears in the frame data.

Classes

FrameKey(key)

Key that can be placed in a Narupa FrameData, such as positions or potential energy.