AmberInpcrdFile¶
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class
simtk.openmm.app.amberinpcrdfile.
AmberInpcrdFile
(file, loadVelocities=None, loadBoxVectors=None)¶ AmberInpcrdFile parses an AMBER inpcrd file and loads the data stored in it.
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__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
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getVelocities
(asNumpy=False)¶ Get the atomic velocities.
Parameters: asNumpy (bool=False) – if true, the vectors are returned as numpy arrays instead of Vec3s
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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
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