def __init__(self, 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
"""
self.file = file
if loadVelocities is not None or loadBoxVectors is not None:
warnings.warn('loadVelocities and loadBoxVectors have been '
'deprecated. velocities and box information '
'is loaded automatically if the inpcrd file contains '
'them.', DeprecationWarning)
results = amber_file_parser.readAmberCoordinates(file)
self.positions, self.velocities, self.boxVectors = results
# Cached numpy arrays
self._numpyPositions = None
self._numpyVelocities = None
self._numpyBoxVectors = None
def __init__(self, file, loadVelocities=False, loadBoxVectors=False):
"""Load an inpcrd file.
An inpcrd file contains atom positions and, optionally, velocities and periodic box dimensions.
Unfortunately, it is sometimes impossible to determine from the file itself exactly what data
it contains. You therefore must specify in advance what data to load. It is stored into this
object's "positions", "velocities", and "boxVectors" fields.
Parameters:
- file (string) the name of the file to load
- loadVelocities (boolean=False) whether to load velocities from the file
- loadBoxVectors (boolean=False) whether to load the periodic box vectors
"""
results = amber_file_parser.readAmberCoordinates(file, read_velocities=loadVelocities, read_box=loadBoxVectors)
if loadVelocities:
## The atom positions read from the inpcrd file
self.positions = results[0]
if loadBoxVectors:
## The periodic box vectors read from the inpcrd file
self.boxVectors = results[1]
## The atom velocities read from the inpcrd file
self.velocities = results[2]
else:
self.velocities = results[1]
elif loadBoxVectors:
self.positions = results[0]
self.boxVectors = results[1]
else:
self.positions = results
self._numpyPositions = None
if loadVelocities:
self._numpyVelocities = None
if loadBoxVectors:
self._numpyBoxVectors = None
def __init__(self, file, loadVelocities=False, loadBoxVectors=False):
"""Load an inpcrd file.
An inpcrd file contains atom positions and, optionally, velocities and periodic box dimensions.
Unfortunately, it is sometimes impossible to determine from the file itself exactly what data
it contains. You therefore must specify in advance what data to load. It is stored into this
object's "positions", "velocities", and "boxVectors" fields.
Parameters:
- file (string) the name of the file to load
- loadVelocities (boolean=False) whether to load velocities from the file
- loadBoxVectors (boolean=False) whether to load the periodic box vectors
"""
results = amber_file_parser.readAmberCoordinates(
file, read_velocities=loadVelocities, read_box=loadBoxVectors)
if loadVelocities:
## The atom positions read from the inpcrd file
self.positions = results[0]
if loadBoxVectors:
## The periodic box vectors read from the inpcrd file
self.boxVectors = results[1]
## The atom velocities read from the inpcrd file
self.velocities = results[2]
else:
self.velocities = results[1]
elif loadBoxVectors:
self.positions = results[0]
self.boxVectors = results[1]
else:
self.positions = results
self._numpyPositions = None
if loadVelocities:
self._numpyVelocities = None
if loadBoxVectors:
self._numpyBoxVectors = None
