PDBxFile Class Reference

PDBxFile parses a PDBx/mmCIF file and constructs a Topology and a set of atom positions from it. More...

Inheritance diagram for PDBxFile:

Public Member Functions
def	__init__
	Load a PDBx/mmCIF file. More...
def	getTopology
	Get the Topology of the model. More...
def	getNumFrames
	Get the number of frames stored in the file. More...
def	getPositions
	Get the atomic positions. More...

Public Attributes
	topology
	The Topology read from the PDBx/mmCIF file. More...
	positions
	The atom positions read from the PDBx/mmCIF file. More...

Detailed Description

PDBxFile parses a PDBx/mmCIF file and constructs a Topology and a set of atom positions from it.

Constructor & Destructor Documentation

def __init__	(		self,
			file
	)

Load a PDBx/mmCIF file.

The atom positions and Topology can be retrieved by calling getPositions() and getTopology().

Parameters

file	(string) the name of the file to load. Alternatively you can pass an open file object.

Member Function Documentation

def getNumFrames

(

self

)

Get the number of frames stored in the file.

References PDBxFile._positions, PDBFile._positions, and GromacsGroFile._positions.

def getPositions	(		self,
			asNumpy = False,
			frame = 0
	)

Get the atomic positions.

Parameters

asNumpy	(boolean=False) if true, the values are returned as a numpy array instead of a list of Vec3s
frame	(int=0) the index of the frame for which to get positions

References AmberInpcrdFile._numpyPositions, PDBxFile._numpyPositions, PDBFile._numpyPositions, GromacsGroFile._numpyPositions, PDBxFile._positions, PDBFile._positions, and GromacsGroFile._positions.

def getTopology

(

self

)

Get the Topology of the model.

References PDBxFile.topology, Modeller.topology, PDBFile.topology, AmberPrmtopFile.topology, and GromacsTopFile.topology.

Member Data Documentation

positions

The atom positions read from the PDBx/mmCIF file.

If the file contains multiple frames, these are the positions in the first frame.

Referenced by AmberInpcrdFile.getPositions().

topology

The Topology read from the PDBx/mmCIF file.

Referenced by DesmondDMSFile.getTopology(), and PDBxFile.getTopology().

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

• pdbxfile.py