org.openscience.cdk.graph

Class SpanningTree

java.lang.Object

org.openscience.cdk.graph.SpanningTree

@TestClass(value="org.openscience.cdk.graph.SpanningTreeTest")
public class SpanningTree
extends Object

Spanning tree of a molecule. Used to discover the number of cyclic bonds in order to prevent the inefficient AllRingsFinder to run for too long.

Author:

Nina Jeliazkova

Keywords:

spanning tree, ring finding

Constructor Summary

Constructors

Constructor and Description
SpanningTree(IAtomContainer atomContainer)

Method Summary

Methods

Modifier and Type	Method and Description
IRingSet	getAllRings()
IRingSet	getBasicRings()
int	getBondsAcyclicCount()
int	getBondsCyclicCount()
IAtomContainer	getCyclicFragmentsContainer() Returns an IAtomContainer which contains all the atoms and bonds which are involved in ring systems.
IAtomContainer	getPath(IAtomContainer spt, IAtom a1, IAtom a2)
IAtomContainer	getSpanningTree()
int	getSpanningTreeSize()
boolean	isDisconnected()

Methods inherited from class java.lang.Object

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

Constructor Detail

SpanningTree

@TestMethod(value="testSpanningTree_IAtomContainer")
public SpanningTree(IAtomContainer atomContainer)

Method Detail

isDisconnected

@TestMethod(value="testIsDisconnected")
public boolean isDisconnected()

getSpanningTree

@TestMethod(value="testGetSpanningTree")
public IAtomContainer getSpanningTree()

getPath

@TestMethod(value="testGetPath_IAtomContainer_IAtom_IAtom")
public IAtomContainer getPath(IAtomContainer spt,
                                     IAtom a1,
                                     IAtom a2)
                       throws NoSuchAtomException

Throws:

NoSuchAtomException

getBasicRings

@TestMethod(value="testGetBasicRings")
public IRingSet getBasicRings()
                       throws NoSuchAtomException

Throws:

NoSuchAtomException

getCyclicFragmentsContainer

@TestMethod(value="testGetCyclicFragmentsContainer")
public IAtomContainer getCyclicFragmentsContainer()

Returns an IAtomContainer which contains all the atoms and bonds which are involved in ring systems.

Returns:

the IAtomContainer as described above

See Also:

getAllRings(), getBasicRings()

getAllRings

@TestMethod(value="testGetAllRings")
public IRingSet getAllRings()
                     throws NoSuchAtomException

Throws:

NoSuchAtomException

getSpanningTreeSize

@TestMethod(value="testGetSpanningTreeSize")
public int getSpanningTreeSize()

getBondsAcyclicCount

@TestMethod(value="testGetBondsAcyclicCount")
public int getBondsAcyclicCount()

Returns:

Returns the bondsAcyclicCount.

getBondsCyclicCount

@TestMethod(value="testGetBondsCyclicCount")
public int getBondsCyclicCount()

Returns:

Returns the bondsCyclicCount.