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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

 positions
 The atom positions read from the inpcrd file. More...
 
 boxVectors
 The periodic box vectors read from the inpcrd file. More...
 
 velocities
 The atom velocities read from the inpcrd file. More...
 

Detailed Description

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

Constructor & Destructor Documentation

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

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, and AmberInpcrdFile.boxVectors.

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, and AmberInpcrdFile.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, and AmberInpcrdFile.velocities.

Member Data Documentation

boxVectors

The periodic box vectors read from the inpcrd file.

Referenced by AmberInpcrdFile.getBoxVectors().

velocities

The atom velocities read from the inpcrd file.

Referenced by AmberInpcrdFile.getVelocities().


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