PDBxFile Class Reference

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

List of all members.

Public Member Functions
def	__init__
	Load a PDBx/mmCIF file.
def	getTopology
	Get the Topology of the model.
def	getNumFrames
	Get the number of frames stored in the file.
def	getPositions
	Get the atomic positions.
Static Public Member Functions
def	writeFile
	Write a PDBx/mmCIF file containing a single model.
def	writeHeader
	Write out the header for a PDBx/mmCIF file.
def	writeModel
	Write out a model to a PDBx/mmCIF file.
Public Attributes
	topology
	The Topology read from the PDBx/mmCIF file.
	positions
	The atom positions read from the PDBx/mmCIF file.

---

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.

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

Get the atomic positions.

Parameters:

asNumpy	(bool=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

def getTopology

(

self

)

Get the Topology of the model.

def writeFile	(		topology,
			positions,
			file = sys.stdout,
			keepIds = False,
			entry = None
	)		[static]

Write a PDBx/mmCIF file containing a single model.

Parameters:

topology	(Topology) The Topology defining the model to write
positions	(list) The list of atomic positions to write
file	(file=stdout) A file to write to
keepIds	(bool=False) If True, keep the residue and chain IDs specified in the Topology rather than generating new ones. Warning: It is up to the caller to make sure these are valid IDs that satisfy the requirements of the PDBx/mmCIF format. Otherwise, the output file will be invalid.
entry	(str=None) The entry ID to assign to the CIF file

def writeHeader	(		topology,
			file = sys.stdout,
			entry = None
	)		[static]

Write out the header for a PDBx/mmCIF file.

Parameters:

topology	(Topology) The Topology defining the molecular system being written
file	(file=stdout) A file to write the file to
entry	(str=None) The entry ID to assign to the CIF file

def writeModel	(		topology,
			positions,
			file = sys.stdout,
			modelIndex = 1,
			keepIds = False
	)		[static]

Write out a model to a PDBx/mmCIF file.

Parameters:

topology	(Topology) The Topology defining the model to write
positions	(list) The list of atomic positions to write
file	(file=stdout) A file to write the model to
modelIndex	(int=1) The model number of this frame
keepIds	(bool=False) If True, keep the residue and chain IDs specified in the Topology rather than generating new ones. Warning: It is up to the caller to make sure these are valid IDs that satisfy the requirements of the PDBx/mmCIF format. Otherwise, the output file will be invalid.

---

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.

topology

The Topology read from the PDBx/mmCIF file.

---

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

• pdbxfile.py