AmberInpcrdFile Class Reference

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

Inheritance diagram for AmberInpcrdFile:

Public Member Functions
def	__init__
	Load an inpcrd file. More...
def	getPositions
	Get the atomic positions. More...
def	getVelocities
	Get the atomic velocities. More...
def	getBoxVectors
	Get the periodic box vectors. More...

Public Attributes
	file
	boxVectors

Detailed Description

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

Constructor & Destructor Documentation

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	(string) the name of the file to load
loadVelocities	(boolean=None) deprecated. Velocities are loaded automatically if present
loadBoxVectors	(boolean=None) deprecated. Box vectors are loaded automatically if present

Member Function Documentation

def getBoxVectors	(		self,
			asNumpy = False
	)

Get the periodic box vectors.

Parameters

asNumpy

(boolean=False) if true, the values are returned as a numpy array instead of a list of Vec3s

References AmberInpcrdFile._numpyBoxVectors, AmberInpcrdFile.boxVectors, and AmberInpcrdFile.file.

def getPositions	(		self,
			asNumpy = False
	)

Get the atomic positions.

Parameters

asNumpy

(boolean=False) if true, the values are returned as a numpy array instead of a list of Vec3s

References AmberInpcrdFile._numpyPositions, CharmmCrdFile.positions, Modeller.positions, DesmondDMSFile.positions, CharmmRstFile.positions, PDBxFile.positions, PDBFile.positions, and GromacsGroFile.positions.

def getVelocities	(		self,
			asNumpy = False
	)

Get the atomic velocities.

Parameters

asNumpy

(boolean=False) if true, the vectors are returned as numpy arrays instead of Vec3s

References AmberInpcrdFile._numpyVelocities, AmberInpcrdFile.file, and CharmmRstFile.velocities.

Member Data Documentation

boxVectors

Referenced by AmberInpcrdFile.getBoxVectors().

file

Referenced by AmberInpcrdFile.getBoxVectors(), and AmberInpcrdFile.getVelocities().

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The documentation for this class was generated from the following file:

• amberinpcrdfile.py