org.openscience.cdk.graph

Class SpanningTree

java.lang.Object

org.openscience.cdk.graph.SpanningTree

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

Dictionary pointer(s):

graphSpanningTree in the Blue Obelisk Chemoinformatics Dictionary [blue-obelisk:graphSpanningTree]

Source code:

master

Belongs to CDK module:

core

Keywords:

spanning tree, ring finding

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean[]	bondsInTree

Constructor Summary

Constructors

Constructor and Description
SpanningTree(IAtomContainer atomContainer) Create a new spanning tree for the provided molecule.

Method Summary

Modifier and Type	Method and Description
IRingSet	getAllRings() All basic rings and the all pairs of basic rings share at least one edge combined.
IRingSet	getBasicRings() The basic rings of the spanning tree.
int	getBondsAcyclicCount() Number of acyclic bonds.
int	getBondsCyclicCount() Number of cyclic bonds.
IAtomContainer	getCyclicFragmentsContainer() Returns an IAtomContainer which contains all the atoms and bonds which are involved in ring systems.
IAtomContainer	getPath(IAtomContainer spt, IAtom atom1, IAtom atom2) Find a path connected a1 and a2 in the tree.
IAtomContainer	getSpanningTree() Access the computed spanning tree of the input molecule.
int	getSpanningTreeSize() Size of the spanning tree specified as the number of edges in the tree.
boolean	isDisconnected() Is the molecule disconnected and has more then one component.

Methods inherited from class java.lang.Object

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

Field Detail

bondsInTree

protected boolean[] bondsInTree

Constructor Detail

SpanningTree

public SpanningTree(IAtomContainer atomContainer)

Create a new spanning tree for the provided molecule.

Parameters:

atomContainer - molecule to make a spanning tree for.

Method Detail

isDisconnected

public boolean isDisconnected()

Is the molecule disconnected and has more then one component.

Returns:

the molecule is disconnected

getSpanningTree

public IAtomContainer getSpanningTree()

Access the computed spanning tree of the input molecule.

Returns:

acyclic tree of the input molecule

getPath

public IAtomContainer getPath(IAtomContainer spt,
                              IAtom atom1,
                              IAtom atom2)
                       throws NoSuchAtomException

Find a path connected a1 and a2 in the tree. If there was an edge between a1 and a2 this path is a cycle.

Parameters:

spt - spanning tree

atom1 - start of path (source)

atom2 - end of path (target)

Returns:

a path through the spanning tree from the source to the target

Throws:

NoSuchAtomException - thrown if the atom is not in the spanning tree

getBasicRings

public IRingSet getBasicRings()
                       throws NoSuchAtomException

The basic rings of the spanning tree. Using the pruned edges, return any path which connects the end points of the pruned edge in the tree. These paths form cycles.

Returns:

basic rings

Throws:

NoSuchAtomException - atoms not found in the molecule

getCyclicFragmentsContainer

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

public IRingSet getAllRings()
                     throws NoSuchAtomException

All basic rings and the all pairs of basic rings share at least one edge combined.

Returns:

subset of all rings

Throws:

NoSuchAtomException - atom was not found in the molecule

See Also:

getBasicRings()

getSpanningTreeSize

public int getSpanningTreeSize()

Size of the spanning tree specified as the number of edges in the tree.

Returns:

number of edges in the spanning tree

getBondsAcyclicCount

public int getBondsAcyclicCount()

Number of acyclic bonds.

Returns:

Returns the bondsAcyclicCount.

getBondsCyclicCount

public int getBondsCyclicCount()

Number of cyclic bonds.

Returns:

Returns the bondsCyclicCount.