AmberInpcrdFile¶
- class 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