AmberInpcrdFile

class simtk.openmm.app.amberinpcrdfile.AmberInpcrdFile(file, loadVelocities=None, loadBoxVectors=None)

AmberInpcrdFile parses an AMBER inpcrd file and loads the data stored in it.

__init__(file, loadVelocities=None, loadBoxVectors=None)

Load an inpcrd file.

An inpcrd file contains atom positions and, optionally, velocities and periodic box dimensions.

Parameters:
  • file (str) – The name of the file to load
  • loadVelocities (bool) – Deprecated. Velocities are loaded automatically if present
  • loadBoxVectors (bool) – Deprecated. Box vectors are loaded automatically if present

Methods

__init__(file[, loadVelocities, loadBoxVectors]) Load an inpcrd file.
getBoxVectors([asNumpy]) Get the periodic box vectors.
getPositions([asNumpy]) Get the atomic positions.
getVelocities([asNumpy]) Get the atomic velocities.
getPositions(asNumpy=False)

Get the atomic positions.

Parameters:asNumpy (bool=False) – if true, the values are returned as a numpy array instead of a list of Vec3s
getVelocities(asNumpy=False)

Get the atomic velocities.

Parameters:asNumpy (bool=False) – if true, the vectors are returned as numpy arrays instead of Vec3s
getBoxVectors(asNumpy=False)

Get the periodic box vectors.

Parameters:asNumpy (bool=False) – if true, the values are returned as a numpy array instead of a list of Vec3s