PDBFile Class Reference

PDBFile parses a Protein Data Bank (PDB) 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 PDB 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 PDB file containing a single model.
def	writeHeader
	Write out the header for a PDB file.
def	writeModel
	Write out a model to a PDB file.
def	writeFooter
	Write out the footer for a PDB file.
Public Attributes
	topology
	The Topology read from the PDB file.
	positions
	The atom positions read from the PDB file.

---

Detailed Description

PDBFile parses a Protein Data Bank (PDB) file and constructs a Topology and a set of atom positions from it.

This class also provides methods for creating PDB files. To write a file containing a single model, call writeFile(). You also can create files that contain multiple models. To do this, first call writeHeader(), then writeModel() once for each model in the file, and finally writeFooter() to complete the file.

---

Constructor & Destructor Documentation

def __init__	(		self,
			file
	)

Load a PDB file.

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

Parameters:

file	(string) the name of the file to load

---

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	(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

def getTopology

(

self

)

Get the Topology of the model.

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

Write a PDB 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 PDB format. Otherwise, the output file will be invalid.

def writeFooter	(		topology,
			file = sys.stdout
	)		[static]

Write out the footer for a PDB file.

Parameters:

topology	(Topology) The Topology defining the molecular system being written
file	(file=stdout) A file to write the file to

def writeHeader	(		topology,
			file = sys.stdout
	)		[static]

Write out the header for a PDB file.

Parameters:

topology	(Topology) The Topology defining the molecular system being written
file	(file=stdout) A file to write the file to

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

Write out a model to a PDB 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=None) If not None, the model will be surrounded by MODEL/ENDMDL records with this index
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 PDB format. Otherwise, the output file will be invalid.

---

Member Data Documentation

positions

The atom positions read from the PDB file.

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

topology

The Topology read from the PDB file.

---

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

• pdbfile.py