Class ConjugatedPiSystemsDetector
java.lang.Object
org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector
- 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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic IAtomContainerSet
detect
(IAtomContainer ac) Detect all conjugated pi systems in an AtomContainer.
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Constructor Details
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ConjugatedPiSystemsDetector
public ConjugatedPiSystemsDetector()
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Method Details
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detect
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
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