Package org.openscience.cdk.graph.invariant

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 Summary

Constructors

Constructor	Description
ConjugatedPiSystemsDetector()

Method Summary

Modifier and Type	Method	Description
static IAtomContainerSet	detect(IAtomContainer ac)	Detect all conjugated pi systems in an AtomContainer.

Methods inherited from class java.lang.Object

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

Constructor Detail

ConjugatedPiSystemsDetector

public ConjugatedPiSystemsDetector()

Method Detail

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