InteractionsView

class narupatools.frame.hdf5.trajectory.InteractionsView(source: narupatools.frame.hdf5.trajectory.HDF5Trajectory, interactions: Optional[tables.group.Group] = None)

View of the interactions of a HDF5 trajectory.

Inheritance

Methods

__init__	Initialize self.
calculate_cumulative_work	Calculate the work done by all interactions, in kilojoules per mole.
calculate_per_particle_work	Calculate the work done by all interactions on each particle.
calculate_work	Calculate the work done by all interactions, in kilojoules per mole.
get
items
keys
values

__init__(source: narupatools.frame.hdf5.trajectory.HDF5Trajectory, interactions: Optional[tables.group.Group] = None)

Initialize self. See help(type(self)) for accurate signature.

calculate_cumulative_work() → numpy.ndarray[Any, numpy.dtype[numpy.float64]]

Calculate the work done by all interactions, in kilojoules per mole.

calculate_per_particle_work() → numpy.ndarray[Any, numpy.dtype[numpy.float64]]

Calculate the work done by all interactions on each particle.

The work is in kilojoules per mole.

Returns

NumPy array of shape (n_particles, ), giving the total work done by all interactions on each particle.

calculate_work() → float

Calculate the work done by all interactions, in kilojoules per mole.

get(k[, d]) → D[k] if k in D, else d.  d defaults to None.

items() → a set-like object providing a view on D’s items

keys() → a set-like object providing a view on D’s keys

values() → an object providing a view on D’s values

Attributes

forces	Forces on each particle for each frame due to all interactions.
potential_energies	Potential energies for each frame due to interactions.

forces

Forces on each particle for each frame due to all interactions.

These forces are in kilojoules per mole per nanometer.

potential_energies

Potential energies for each frame due to interactions.

These energies are in kilojoules per mole.