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	__repr__
def	getNumAtoms
	Return the number of atoms in the Topology.
def	getNumResidues
	Return the number of residues in the Topology.
def	getNumChains
	Return the number of chains in the Topology.
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	getPeriodicBoxVectors
	Get the vectors defining the periodic box.
def	setPeriodicBoxVectors
	Set the vectors defining the periodic box.
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.
Static Public Member Functions
def	loadBondDefinitions
	Load an XML file containing definitions of bonds that should be used by createStandardBonds().

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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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Constructor & Destructor Documentation

def __init__

(

self

)

Create a new Topology object.

---

Member Function Documentation

def __repr__

(

self

)

def addAtom	(		self,
			name,
			element,
			residue,
			id = None
	)

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
id	(string=None) An optional identifier for the atom. If this is omitted, an id is generated based on the atom index.

Returns:

(Atom) 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,
			id = None
	)

Create a new Chain and add it to the Topology.

Parameters:

id	(string=None) An optional identifier for the chain. If this is omitted, an id is generated based on the chain index.

Returns:

(Chain) the newly created Chain

def addResidue	(		self,
			name,
			chain,
			id = None
	)

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
id	(string=None) An optional identifier for the residue. If this is omitted, an id is generated based on the residue index.

Returns:

(Residue) 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.

Definitions for standard amino acids and nucleotides are built in. You can call loadBondDefinitions() to load additional definitions for other residue types.

def getNumAtoms

(

self

)

Return the number of atoms in the Topology.

def getNumChains

(

self

)

Return the number of chains in the Topology.

def getNumResidues

(

self

)

Return the number of residues in the Topology.

def getPeriodicBoxVectors

(

self

)

Get the vectors defining the periodic box.

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

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 loadBondDefinitions

(

file

)

[static]

Load an XML file containing definitions of bonds that should be used by createStandardBonds().

The built in residues.xml file containing definitions for standard amino acids and nucleotides is loaded automatically. This method can be used to load additional definitions for other residue types. They will then be used in subsequent calls to createStandardBonds(). This is a static method, so it affects subsequent calls on all Topology objects. Also note that PDBFile calls createStandardBonds() automatically when a file is loaded, so the newly loaded definitions will be used for any PDB file loaded after this is called.

def residues

(

self

)

Iterate over all Residues in the Topology.

def setPeriodicBoxVectors	(		self,
			vectors
	)

Set the vectors defining the periodic box.

def setUnitCellDimensions	(		self,
			dimensions
	)

Set the dimensions of the crystallographic unit cell.

This method is an alternative to setPeriodicBoxVectors() for the case of a rectangular box. It sets the box vectors to be orthogonal to each other and to have the specified lengths.

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

• topology.py