OpenMM
 All Classes Namespaces Functions Variables Pages
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, PDBxFile.positions, GromacsGroFile.positions, PDBFile.positions, and CharmmRstFile.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

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