Class GenerateCompatibilityGraph
java.lang.Object
org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent
version of SMSD is available at http://github.com/asad/smsd.
This class generates compatibility graph between query and target molecule.
It also markes edges in the compatibility graph as c-edges or d-edges.
- Author:
- Syed Asad Rahman <asad@ebi.ac.uk>
- Source code:
- main
- Belongs to CDK module:
- smsd
-
Constructor Summary
ConstructorsConstructorDescriptionDeprecated.Default constructor addedGenerateCompatibilityGraph
(IAtomContainer source, IAtomContainer target, boolean shouldMatchBonds) Deprecated.Generates a compatibility graph between two molecules -
Method Summary
Modifier and TypeMethodDescriptionvoid
clear()
Deprecated.protected void
Deprecated.protected void
Deprecated.protected void
Deprecated.protected void
Deprecated.protected int
Deprecated.Generate Compatibility Graph Nodes Bond Insensitiveprotected int
Deprecated.compatibilityGraphCEdgeZero is used to build up of the edges of the compatibility graph BISprotected int
Deprecated.Generate Compatibility Graph Nodesprotected Integer
Deprecated.compGraphNodesCZero is used to build up of the edges of the compatibility graphprotected int
Deprecated.Deprecated.Deprecated.Deprecated.protected int
Deprecated.Deprecated.boolean
Deprecated.protected void
Deprecated.protected void
Deprecated.void
setMatchBond
(boolean shouldMatchBonds) Deprecated.
-
Constructor Details
-
GenerateCompatibilityGraph
public GenerateCompatibilityGraph()Deprecated.Default constructor added -
GenerateCompatibilityGraph
public GenerateCompatibilityGraph(IAtomContainer source, IAtomContainer target, boolean shouldMatchBonds) throws IOException Deprecated.Generates a compatibility graph between two molecules- Parameters:
source
-target
-shouldMatchBonds
-- Throws:
IOException
-
-
Method Details
-
compatibilityGraphNodes
Deprecated.Generate Compatibility Graph Nodes- Returns:
- Throws:
IOException
-
compatibilityGraph
Deprecated.Generate Compatibility Graph Nodes Bond Insensitive- Returns:
- Throws:
IOException
-
compatibilityGraphNodesIfCEdgeIsZero
Deprecated.compGraphNodesCZero is used to build up of the edges of the compatibility graph- Returns:
- Throws:
IOException
-
compatibilityGraphCEdgeZero
Deprecated.compatibilityGraphCEdgeZero is used to build up of the edges of the compatibility graph BIS- Returns:
- Throws:
IOException
-
getCEgdes
Deprecated. -
getDEgdes
Deprecated. -
getCompGraphNodes
Deprecated. -
getCEdgesSize
protected int getCEdgesSize()Deprecated. -
getDEdgesSize
protected int getDEdgesSize()Deprecated. -
getCompGraphNodesCZero
Deprecated. -
clearCEgdes
protected void clearCEgdes()Deprecated. -
clearDEgdes
protected void clearDEgdes()Deprecated. -
clearCompGraphNodes
protected void clearCompGraphNodes()Deprecated. -
clearCompGraphNodesCZero
protected void clearCompGraphNodesCZero()Deprecated. -
resetCEdgesSize
protected void resetCEdgesSize()Deprecated. -
resetDEdgesSize
protected void resetDEdgesSize()Deprecated. -
clear
public void clear()Deprecated. -
isMatchBond
public boolean isMatchBond()Deprecated.- Returns:
- the shouldMatchBonds
-
setMatchBond
public void setMatchBond(boolean shouldMatchBonds) Deprecated.- Parameters:
shouldMatchBonds
- the shouldMatchBonds to set
-