Topology Class Reference

Topology stores the topological information about a system. More...

List of all members.

Public Member Functions
def	__init__
	Create a new Topology object.
def	addChain
	Create a new Chain and add it to the Topology.
def	addResidue
	Create a new Residue and add it to the Topology.
def	addAtom
	Create a new Atom and add it to the Topology.
def	addBond
	Create a new bond and add it to the Topology.
def	chains
	Iterate over all Chains in the Topology.
def	residues
	Iterate over all Residues in the Topology.
def	atoms
	Iterate over all Atoms in the Topology.
def	bonds
	Iterate over all bonds (each represented as a tuple of two Atoms) in the Topology.
def	getUnitCellDimensions
	Get the dimensions of the crystallographic unit cell.
def	setUnitCellDimensions
	Set the dimensions of the crystallographic unit cell.
def	createStandardBonds
	Create bonds based on the atom and residue names for all standard residue types.
def	createDisulfideBonds
	Identify disulfide bonds based on proximity and add them to the Topology.

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Detailed Description

Topology stores the topological information about a system.

The structure of a Topology object is similar to that of a PDB file. It consists of a set of Chains (often but not always corresponding to polymer chains). Each Chain contains a set of Residues, and each Residue contains a set of Atoms. In addition, the Topology stores a list of which atom pairs are bonded to each other, and the dimensions of the crystallographic unit cell.

Atom and residue names should follow the PDB 3.0 nomenclature for all molecules for which one exists.

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Member Function Documentation

def __init__

(

self

)

Create a new Topology object.

def addAtom	(		self,
			name,
			element,
			residue
	)

Create a new Atom and add it to the Topology.

Parameters:

	name	(string) The name of the atom to add
	element	(Element) The element of the atom to add
	residue	(Residue) The Residue to add it to

Returns:

the newly created Atom

def addBond	(		self,
			atom1,
			atom2
	)

Create a new bond and add it to the Topology.

Parameters:

	atom1	(Atom) The first Atom connected by the bond
	atom2	(Atom) The second Atom connected by the bond

def addChain

(

self

)

Create a new Chain and add it to the Topology.

Returns:

the newly created Chain

def addResidue	(		self,
			name,
			chain
	)

Create a new Residue and add it to the Topology.

Parameters:

	name	(string) The name of the residue to add
	chain	(Chain) The Chain to add it to

Returns:

the newly created Residue

def atoms

(

self

)

Iterate over all Atoms in the Topology.

def bonds

(

self

)

Iterate over all bonds (each represented as a tuple of two Atoms) in the Topology.

def chains

(

self

)

Iterate over all Chains in the Topology.

def createDisulfideBonds	(		self,
			positions
	)

Identify disulfide bonds based on proximity and add them to the Topology.

Parameters:

positions

(list) The list of atomic positions based on which to identify bonded atoms

def createStandardBonds

(

self

)

Create bonds based on the atom and residue names for all standard residue types.

def getUnitCellDimensions

(

self

)

Get the dimensions of the crystallographic unit cell.

The return value may be None if this Topology does not represent a periodic structure.

def residues

(

self

)

Iterate over all Residues in the Topology.

def setUnitCellDimensions	(		self,
			dimensions
	)

Set the dimensions of the crystallographic unit cell.

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

• topology.py