Package org.openscience.cdk.smsd.algorithm.vflib.builder

Class VFQueryBuilder

java.lang.Object

org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder

All Implemented Interfaces:

IQuery

@Deprecated
public class VFQueryBuilder
extends Object
implements IQuery

Deprecated.

SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.

Class for parsing and generating query graph.

Author:

Syed Asad Rahman <asad@ebi.ac.uk>

Source code:

main

Belongs to CDK module:

smsd

Constructor Summary

Constructors

Constructor	Description
VFQueryBuilder()	Deprecated. Constructor for VF Query Builder

Method Summary

Modifier and Type	Method	Description
INode	addNode(VFAtomMatcher matcher, IAtom atom)	Deprecated. Add and return a node for a query atom
IEdge	connect(INode source, INode target, VFBondMatcher matcher)	Deprecated. Construct and return an edge for a given query and target node
int	countEdges()	Deprecated. Returns edge count.
int	countNodes()	Deprecated. Returns node count.
Iterable<IEdge>	edges()	Deprecated. Returns edges of the query.
IAtom	getAtom(INode node)	Deprecated. Returns an atom associated with this node.
IEdge	getEdge(int index)	Deprecated. Returns an edge of the query mol at a given position.
IEdge	getEdge(INode source, INode target)	Deprecated. Returns an edge associated between two nodes.
INode	getNode(int index)	Deprecated. Returns a node of the query mol at a given position.
INode	getNode(IAtom atom)	Deprecated. Return a node for a given atom else return null
Iterable<INode>	nodes()	Deprecated. Returns nodes of the query.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

VFQueryBuilder

public VFQueryBuilder()

Deprecated.

Constructor for VF Query Builder

Method Detail

edges

public Iterable<IEdge> edges()

Deprecated.

Returns edges of the query.

Specified by:

edges in interface IQuery

Returns:

edge Iterable.

nodes

public Iterable<INode> nodes()

Deprecated.

Returns nodes of the query.

Specified by:

nodes in interface IQuery

Returns:

node Iterable.

getNode

public INode getNode(int index)

Deprecated.

Returns a node of the query mol at a given position.

Specified by:

getNode in interface IQuery

Parameters:

index - at position.

Returns:

node.

getNode

public INode getNode(IAtom atom)

Deprecated.

Return a node for a given atom else return null

Parameters:

atom -

Returns:

Node in the graph for a given atom

getEdge

public IEdge getEdge(int index)

Deprecated.

Returns an edge of the query mol at a given position.

Specified by:

getEdge in interface IQuery

Parameters:

index - at position.

Returns:

edge

getEdge

public IEdge getEdge(INode source,
                     INode target)

Deprecated.

Returns an edge associated between two nodes.

Specified by:

getEdge in interface IQuery

Parameters:

source - get an between source.

target - and target.

Returns:

IEdge egde between source and target.

addNode

public INode addNode(VFAtomMatcher matcher,
                     IAtom atom)

Deprecated.

Add and return a node for a query atom

Parameters:

matcher -

atom -

Returns:

added Node

getAtom

public IAtom getAtom(INode node)

Deprecated.

Returns an atom associated with this node.

Specified by:

getAtom in interface IQuery

Parameters:

node - get Atom of this node.

Returns:

atom of this node

countNodes

public int countNodes()

Deprecated.

Returns node count.

Specified by:

countNodes in interface IQuery

Returns:

node count.

countEdges

public int countEdges()

Deprecated.

Returns edge count.

Specified by:

countEdges in interface IQuery

Returns:

edge count.

connect

public IEdge connect(INode source,
                     INode target,
                     VFBondMatcher matcher)

Deprecated.

Construct and return an edge for a given query and target node

Parameters:

source -

target -

matcher -

Returns:

connected edges