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 Details

    • VFQueryBuilder

      public VFQueryBuilder()
      Deprecated.
      Constructor for VF Query Builder
  • Method Details

    • 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