Class ConjugatedPiSystemsDetector

java.lang.Object
org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector

public class ConjugatedPiSystemsDetector extends Object
Author:
kaihartmann
Source code:
main
Belongs to CDK module:
reaction
Created on:
2004-09-17
To do:
add negatively charged atoms (e.g. O-) to the pi system
  • Constructor Details

    • ConjugatedPiSystemsDetector

      public ConjugatedPiSystemsDetector()
  • Method Details

    • detect

      public static IAtomContainerSet detect(IAtomContainer ac)
      Detect all conjugated pi systems in an AtomContainer. This method returns a AtomContainerSet with Atom and Bond objects from the original AtomContainer. The aromaticity has to be known before calling this method.

      An example for detection of Radical Allyl:

              Atom a0 = new Atom("C"); mol.addAtom(a0);
              Atom a1 = new Atom("C"); mol.addAtom(a1);
              Atom a2 = new Atom("C"); mol.addAtom(a2);
              Atom h1 = new Atom("H"); mol.addAtom(h1);
              Atom h2 = new Atom("H"); mol.addAtom(h2);
              Atom h3 = new Atom("H"); mol.addAtom(h3);
              Atom h4 = new Atom("H"); mol.addAtom(h4);
              Atom h5 = new Atom("H"); mol.addAtom(h5);
              mol.addBond(0, 1, IBond.Order.DOUBLE);
              mol.addBond(1, 2, IBond.Order.SINGLE);
              mol.addBond(0, 3, IBond.Order.SINGLE);
              mol.addBond(0, 4, IBond.Order.SINGLE);
              mol.addBond(1, 5, IBond.Order.SINGLE);
              mol.addBond(2, 6, IBond.Order.SINGLE);
              mol.addBond(2, 7, IBond.Order.SINGLE);
              SingleElectron se = new SingleElectron(a2);
              mol.addElectronContainer(se);
        
      Parameters:
      ac - The AtomContainer for which to detect conjugated pi systems
      Returns:
      The set of AtomContainers with conjugated pi systems