Package 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:
main
Belongs to CDK module:
core
Keywords:
spanning tree, ring finding

  • Field Details

    • bondsInTree

      protected boolean[] bondsInTree

  • Constructor Details

    • SpanningTree

      public SpanningTree(IAtomContainer atomContainer)
      Create a new spanning tree for the provided molecule.
      Parameters:
      atomContainer - molecule to make a spanning tree for.

  • Method Details

    • 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

      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:

    • 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.