From: <eg...@us...> - 2007-11-03 08:14:43
|
Revision: 9353 http://cdk.svn.sourceforge.net/cdk/?rev=9353&view=rev Author: egonw Date: 2007-11-03 01:14:40 -0700 (Sat, 03 Nov 2007) Log Message: ----------- Down to about 500 compile errors Modified Paths: -------------- branches/egonw/ibondorder/src/org/openscience/cdk/Ring.java branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugAminoAcid.java branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugAtomContainer.java branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugBioPolymer.java branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugBond.java branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugCrystal.java branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugMolecule.java branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugMonomer.java branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugPolymer.java branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugRing.java branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugStrand.java branches/egonw/ibondorder/src/org/openscience/cdk/graph/invariant/ConjugatedPiSystemsDetector.java branches/egonw/ibondorder/src/org/openscience/cdk/isomorphism/matchers/QueryAtomContainerCreator.java branches/egonw/ibondorder/src/org/openscience/cdk/isomorphism/matchers/smarts/AnyOrderQueryBond.java branches/egonw/ibondorder/src/org/openscience/cdk/isomorphism/matchers/smarts/AromaticQueryBond.java branches/egonw/ibondorder/src/org/openscience/cdk/iupac/parser/MoleculeBuilder.java branches/egonw/ibondorder/src/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java branches/egonw/ibondorder/src/org/openscience/cdk/nonotify/NNBond.java branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptor.java branches/egonw/ibondorder/src/org/openscience/cdk/renderer/progz/TestRenderer.java branches/egonw/ibondorder/src/org/openscience/cdk/templates/MoleculeFactory.java branches/egonw/ibondorder/src/org/openscience/cdk/templates/saturatedhydrocarbons/IsoAlkanes.java branches/egonw/ibondorder/src/org/openscience/cdk/test/AtomContainerTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/atomtype/HybridizationStateATMatcherTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/charges/InductivePartialChargesTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/controller/ControllerTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/fingerprint/FingerprinterTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/graph/invariant/EquivalentClassPartitionerTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/gui/smiles/SmilesGeneratorTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/isomorphism/IsomorphismTesterTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/isomorphism/SMARTSTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/isomorphism/UniversalIsomorphismTesterTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/libio/cml/ConvertorTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/libio/joelib/JOELibIOTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/libio/md/MDMoleculeTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/qsar/descriptors/atomic/AtomHybridizationVSEPRDescriptorTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/qsar/descriptors/atomic/DistanceToAtomDescriptorTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/qsar/descriptors/atomic/InductiveAtomicHardnessDescriptorTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/qsar/descriptors/atomic/InductiveAtomicSoftnessDescriptorTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/reaction/type/BreakingBondReactionTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/reaction/type/DisplacementChargeFromAcceptorReactionTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/reaction/type/DisplacementChargeFromDonorReactionTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/reaction/type/HyperconjugationReactionTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/renderer/DrawPolygonTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/tools/LonePairElectronCheckerTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/tools/SaturationCheckerTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/tools/StructureResonanceGeneratorTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/tools/manipulator/AtomContainerManipulatorTest.java branches/egonw/ibondorder/src/org/openscience/cdk/test/tools/manipulator/RingSetManipulatorTest.java branches/egonw/ibondorder/src/org/openscience/cdk/tools/HOSECodeGenerator.java branches/egonw/ibondorder/src/org/openscience/cdk/tools/ProteinBuilderTool.java Modified: branches/egonw/ibondorder/src/org/openscience/cdk/Ring.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/Ring.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/Ring.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -23,6 +23,8 @@ */ package org.openscience.cdk; +import org.openscience.cdk.interfaces.IBond; + /** * Class representing a ring structure in a molecule. * A ring is a linear sequence of @@ -78,9 +80,9 @@ atoms[0] = new Atom(elementSymbol); for (int i = 1; i < ringSize; i++) { atoms[i] = new Atom(elementSymbol); - super.bonds[i-1] = new Bond(atoms[i - 1], atoms[i], 1); + super.bonds[i-1] = new Bond(atoms[i - 1], atoms[i], IBond.Order.SINGLE); } - super.bonds[ringSize-1] = new Bond(atoms[ringSize - 1], atoms[0], 1); + super.bonds[ringSize-1] = new Bond(atoms[ringSize - 1], atoms[0], IBond.Order.SINGLE); } Modified: branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugAminoAcid.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugAminoAcid.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugAminoAcid.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -392,12 +392,12 @@ super.removeAllBonds(); } - public void addBond(int atom1, int atom2, double order, int stereo) { + public void addBond(int atom1, int atom2, IBond.Order order, int stereo) { logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order + " stereo=" + stereo); super.addBond(atom1, atom2, order, stereo); } - public void addBond(int atom1, int atom2, double order) { + public void addBond(int atom1, int atom2, IBond.Order order) { logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order); super.addBond(atom1, atom2, order); } Modified: branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugAtomContainer.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugAtomContainer.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugAtomContainer.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -403,12 +403,12 @@ super.removeAllBonds(); } - public void addBond(int atom1, int atom2, double order, int stereo) { + public void addBond(int atom1, int atom2, IBond.Order order, int stereo) { logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order + " stereo=" + stereo); super.addBond(atom1, atom2, order, stereo); } - public void addBond(int atom1, int atom2, double order) { + public void addBond(int atom1, int atom2, IBond.Order order) { logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order); super.addBond(atom1, atom2, order); } Modified: branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugBioPolymer.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugBioPolymer.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugBioPolymer.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -396,12 +396,12 @@ super.removeAllBonds(); } - public void addBond(int atom1, int atom2, double order, int stereo) { + public void addBond(int atom1, int atom2, IBond.Order order, int stereo) { logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order + " stereo=" + stereo); super.addBond(atom1, atom2, order, stereo); } - public void addBond(int atom1, int atom2, double order) { + public void addBond(int atom1, int atom2, IBond.Order order) { logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order); super.addBond(atom1, atom2, order); } Modified: branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugBond.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugBond.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugBond.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -55,11 +55,11 @@ super(atom1, atom2); } - public DebugBond(org.openscience.cdk.interfaces.IAtom atom1, org.openscience.cdk.interfaces.IAtom atom2, double order) { + public DebugBond(IAtom atom1, IAtom atom2, IBond.Order order) { super(atom1, atom2, order); } - public DebugBond(org.openscience.cdk.interfaces.IAtom atom1, org.openscience.cdk.interfaces.IAtom atom2, double order, int stereo) { + public DebugBond(IAtom atom1, IAtom atom2, IBond.Order order, int stereo) { super(atom1, atom2, order, stereo); } Modified: branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugCrystal.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugCrystal.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugCrystal.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -404,12 +404,12 @@ super.removeAllBonds(); } - public void addBond(int atom1, int atom2, double order, int stereo) { + public void addBond(int atom1, int atom2, IBond.Order order, int stereo) { logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order + " stereo=" + stereo); super.addBond(atom1, atom2, order, stereo); } - public void addBond(int atom1, int atom2, double order) { + public void addBond(int atom1, int atom2, IBond.Order order) { logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order); super.addBond(atom1, atom2, order); } Modified: branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugMolecule.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugMolecule.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugMolecule.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -404,12 +404,12 @@ super.removeAllBonds(); } - public void addBond(int atom1, int atom2, double order, int stereo) { + public void addBond(int atom1, int atom2, IBond.Order order, int stereo) { logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order + " stereo=" + stereo); super.addBond(atom1, atom2, order, stereo); } - public void addBond(int atom1, int atom2, double order) { + public void addBond(int atom1, int atom2, IBond.Order order) { logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order); super.addBond(atom1, atom2, order); } Modified: branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugMonomer.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugMonomer.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugMonomer.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -392,12 +392,12 @@ super.removeAllBonds(); } - public void addBond(int atom1, int atom2, double order, int stereo) { + public void addBond(int atom1, int atom2, IBond.Order order, int stereo) { logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order + " stereo=" + stereo); super.addBond(atom1, atom2, order, stereo); } - public void addBond(int atom1, int atom2, double order) { + public void addBond(int atom1, int atom2, IBond.Order order) { logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order); super.addBond(atom1, atom2, order); } Modified: branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugPolymer.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugPolymer.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugPolymer.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -394,12 +394,12 @@ super.removeAllBonds(); } - public void addBond(int atom1, int atom2, double order, int stereo) { + public void addBond(int atom1, int atom2, IBond.Order order, int stereo) { logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order + " stereo=" + stereo); super.addBond(atom1, atom2, order, stereo); } - public void addBond(int atom1, int atom2, double order) { + public void addBond(int atom1, int atom2, IBond.Order order) { logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order); super.addBond(atom1, atom2, order); } Modified: branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugRing.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugRing.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugRing.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -63,9 +63,9 @@ atoms[0] = new DebugAtom(elementSymbol); for (int i = 1; i < ringSize; i++) { atoms[i] = new DebugAtom(elementSymbol); - super.bonds[i-1] = new Bond(atoms[i - 1], atoms[i], 1); + super.bonds[i-1] = new Bond(atoms[i - 1], atoms[i], IBond.Order.SINGLE); } - super.bonds[ringSize-1] = new Bond(atoms[ringSize - 1], atoms[0], 1); + super.bonds[ringSize-1] = new Bond(atoms[ringSize - 1], atoms[0], IBond.Order.SINGLE); } public DebugRing(int ringSize) { @@ -417,12 +417,12 @@ super.removeAllBonds(); } - public void addBond(int atom1, int atom2, double order, int stereo) { + public void addBond(int atom1, int atom2, IBond.Order order, int stereo) { logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order + " stereo=" + stereo); super.addBond(atom1, atom2, order, stereo); } - public void addBond(int atom1, int atom2, double order) { + public void addBond(int atom1, int atom2, IBond.Order order) { logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order); super.addBond(atom1, atom2, order); } Modified: branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugStrand.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugStrand.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/debug/DebugStrand.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -394,12 +394,12 @@ super.removeAllBonds(); } - public void addBond(int atom1, int atom2, double order, int stereo) { + public void addBond(int atom1, int atom2, IBond.Order order, int stereo) { logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order + " stereo=" + stereo); super.addBond(atom1, atom2, order, stereo); } - public void addBond(int atom1, int atom2, double order) { + public void addBond(int atom1, int atom2, IBond.Order order) { logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order); super.addBond(atom1, atom2, order); } Modified: branches/egonw/ibondorder/src/org/openscience/cdk/graph/invariant/ConjugatedPiSystemsDetector.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/graph/invariant/ConjugatedPiSystemsDetector.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/graph/invariant/ConjugatedPiSystemsDetector.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -60,13 +60,13 @@ * 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, 2); - * mol.addBond(1, 2, 1); - * mol.addBond(0, 3, 1); - * mol.addBond(0, 4, 1); - * mol.addBond(1, 5, 1); - * mol.addBond(2, 6, 1); - * mol.addBond(2, 7, 1); + * 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); * </pre> Modified: branches/egonw/ibondorder/src/org/openscience/cdk/isomorphism/matchers/QueryAtomContainerCreator.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/isomorphism/matchers/QueryAtomContainerCreator.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/isomorphism/matchers/QueryAtomContainerCreator.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -61,7 +61,7 @@ if (bond.getFlag(CDKConstants.ISAROMATIC)) { queryContainer.addBond(new AromaticQueryBond((IQueryAtom) queryContainer.getAtom(index1), (IQueryAtom) queryContainer.getAtom(index2), - 1.5)); + IBond.Order.SINGLE)); } else { queryContainer.addBond(new OrderQueryBond((IQueryAtom) queryContainer.getAtom(index1), (IQueryAtom) queryContainer.getAtom(index2), @@ -92,7 +92,7 @@ if (bond.getFlag(CDKConstants.ISAROMATIC)) { queryContainer.addBond(new AromaticQueryBond((IQueryAtom) queryContainer.getAtom(index1), (IQueryAtom) queryContainer.getAtom(index2), - 1.5)); + IBond.Order.SINGLE)); } else { queryContainer.addBond(new OrderQueryBond((IQueryAtom) queryContainer.getAtom(index1), (IQueryAtom) queryContainer.getAtom(index2), @@ -115,7 +115,7 @@ if (bond.getFlag(CDKConstants.ISAROMATIC)) { queryContainer.addBond(new AromaticQueryBond((IQueryAtom) queryContainer.getAtom(index1), (IQueryAtom) queryContainer.getAtom(index2), - 1.5)); + IBond.Order.SINGLE)); } else { queryContainer.addBond(new OrderQueryBond((IQueryAtom) queryContainer.getAtom(index1), (IQueryAtom) queryContainer.getAtom(index2), @@ -152,7 +152,7 @@ if (aromaticity && bond.getFlag(CDKConstants.ISAROMATIC)) { queryContainer.addBond(new AromaticQueryBond((IQueryAtom) queryContainer.getAtom(index1), (IQueryAtom) queryContainer.getAtom(index2), - 1.5)); + IBond.Order.SINGLE)); } else { queryContainer.addBond(new OrderQueryBond((IQueryAtom) queryContainer.getAtom(index1), (IQueryAtom) queryContainer.getAtom(index2), @@ -190,7 +190,7 @@ int index2 = container.getAtomNumber(bond.getAtom(1)); queryContainer.addBond(new AnyOrderQueryBond((IQueryAtom) queryContainer.getAtom(index1), (IQueryAtom) queryContainer.getAtom(index2), - bond.getOrder().ordinal()+1)); + bond.getOrder())); } return queryContainer; } @@ -222,7 +222,7 @@ if (bond.getFlag(CDKConstants.ISAROMATIC)) { queryContainer.addBond(new AromaticQueryBond((IQueryAtom) queryContainer.getAtom(index1), (IQueryAtom) queryContainer.getAtom(index2), - 1.5)); + IBond.Order.SINGLE)); } else { queryContainer.addBond(new OrderQueryBond((IQueryAtom) queryContainer.getAtom(index1), (IQueryAtom) queryContainer.getAtom(index2), Modified: branches/egonw/ibondorder/src/org/openscience/cdk/isomorphism/matchers/smarts/AnyOrderQueryBond.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/isomorphism/matchers/smarts/AnyOrderQueryBond.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/isomorphism/matchers/smarts/AnyOrderQueryBond.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -47,7 +47,7 @@ * @param atom1 * @param atom2 */ - public AnyOrderQueryBond(IQueryAtom atom1, IQueryAtom atom2, double order) { + public AnyOrderQueryBond(IQueryAtom atom1, IQueryAtom atom2, IBond.Order order) { super(atom1, atom2, order); } Modified: branches/egonw/ibondorder/src/org/openscience/cdk/isomorphism/matchers/smarts/AromaticQueryBond.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/isomorphism/matchers/smarts/AromaticQueryBond.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/isomorphism/matchers/smarts/AromaticQueryBond.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -51,7 +51,7 @@ * Creates a new instance * */ - public AromaticQueryBond(IQueryAtom atom1, IQueryAtom atom2, double order) { + public AromaticQueryBond(IQueryAtom atom1, IQueryAtom atom2, IBond.Order order) { super(atom1, atom2, order); setFlag(CDKConstants.ISAROMATIC, true); } Modified: branches/egonw/ibondorder/src/org/openscience/cdk/iupac/parser/MoleculeBuilder.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/iupac/parser/MoleculeBuilder.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/iupac/parser/MoleculeBuilder.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -37,6 +37,7 @@ import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomType; import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IBond.Order; import org.openscience.cdk.templates.MoleculeFactory; import org.openscience.cdk.tools.CDKHydrogenAdder; import org.openscience.cdk.tools.manipulator.AtomTypeManipulator; @@ -151,12 +152,12 @@ if (addPos < 0) { //Set the first bond to an order of 3 (i.e. a tripple bond) - currentMolecule.getBond(0).setOrder(3.0); + currentMolecule.getBond(0).setOrder(IBond.Order.TRIPLE); } else { //Set the addPos'th bond to an order of 3 (i.e. a tripple bond) - currentMolecule.getBond(addPos).setOrder(3.0); + currentMolecule.getBond(addPos).setOrder(IBond.Order.TRIPLE); } } //FUNCTIONAL GROUP SUFFIXES @@ -172,29 +173,29 @@ //If functional group hasn't had a location specified: if (addPos < 0) { - addAtom("O", endOfChain, 1.0, 1); + addAtom("O", endOfChain, IBond.Order.SINGLE, 1); } else { - addAtom("O", currentMolecule.getAtom(addPos), 1.0, 1); + addAtom("O", currentMolecule.getAtom(addPos), IBond.Order.SINGLE, 1); } } //Aldehydes else if (funGroupToken == "al") { - addAtom("O", endOfChain, 2.0, 0); + addAtom("O", endOfChain, IBond.Order.DOUBLE, 0); } //Carboxylic acid else if (funGroupToken == "oic acid") { - addAtom("O", endOfChain, 2.0, 0); - addAtom("O", endOfChain, 1.0, 1); + addAtom("O", endOfChain, IBond.Order.DOUBLE, 0); + addAtom("O", endOfChain, IBond.Order.SINGLE, 1); } //Carboxylic Acid Chloride else if (funGroupToken == "oyl chloride") { - addAtom("O", endOfChain, 2.0, 0); - addAtom("Cl", endOfChain, 1.0, 0); + addAtom("O", endOfChain, IBond.Order.DOUBLE, 0); + addAtom("Cl", endOfChain, IBond.Order.SINGLE, 0); } //PREFIXES //Halogens @@ -204,11 +205,11 @@ //If functional group hasn't had a location specified: if (addPos < 0) { - addAtom("Cl", currentMolecule.getFirstAtom(), 1.0, 0); + addAtom("Cl", currentMolecule.getFirstAtom(), IBond.Order.SINGLE, 0); } else { - addAtom("Cl", currentMolecule.getAtom(addPos), 1.0, 0); + addAtom("Cl", currentMolecule.getAtom(addPos), IBond.Order.SINGLE, 0); } } //Fluorine @@ -217,11 +218,11 @@ //If functional group hasn't had a location specified: if (addPos < 0) { - addAtom("F", currentMolecule.getFirstAtom(), 1.0, 0); + addAtom("F", currentMolecule.getFirstAtom(), IBond.Order.SINGLE, 0); } else { - addAtom("F", currentMolecule.getAtom(addPos), 1.0, 0); + addAtom("F", currentMolecule.getAtom(addPos), IBond.Order.SINGLE, 0); } } //Bromine @@ -230,11 +231,11 @@ //If functional group hasn't had a location specified: if (addPos < 0) { - addAtom("Br", currentMolecule.getFirstAtom(), 1.0, 0); + addAtom("Br", currentMolecule.getFirstAtom(), IBond.Order.SINGLE, 0); } else { - addAtom("Br", currentMolecule.getAtom(addPos), 1.0, 0); + addAtom("Br", currentMolecule.getAtom(addPos), IBond.Order.SINGLE, 0); } } //Iodine @@ -243,11 +244,11 @@ //If functional group hasn't had a location specified: if (addPos < 0) { - addAtom("I", currentMolecule.getFirstAtom(), 1.0, 0); + addAtom("I", currentMolecule.getFirstAtom(), IBond.Order.SINGLE, 0); } else { - addAtom("I", currentMolecule.getAtom(addPos), 1.0, 0); + addAtom("I", currentMolecule.getAtom(addPos), IBond.Order.SINGLE, 0); } } //Nitro @@ -256,19 +257,19 @@ //If functional group hasn't had a location specified: if (addPos < 0) { - addAtom("N", currentMolecule.getFirstAtom(), 1.0, 0); + addAtom("N", currentMolecule.getFirstAtom(), IBond.Order.SINGLE, 0); } else { - addAtom("N", currentMolecule.getAtom(addPos), 1.0, 0); + addAtom("N", currentMolecule.getAtom(addPos), IBond.Order.SINGLE, 0); } //Stuff which applied no matter where the N atom is: org.openscience.cdk.interfaces.IAtom nitrogenAtom = currentMolecule.getLastAtom(); nitrogenAtom.setFormalCharge(+1); - addAtom("O", nitrogenAtom, 1.0, 0); + addAtom("O", nitrogenAtom, IBond.Order.SINGLE, 0); currentMolecule.getLastAtom().setFormalCharge(-1); - addAtom("O", nitrogenAtom, 2.0, 0); + addAtom("O", nitrogenAtom, IBond.Order.DOUBLE, 0); } //Oxo else if (funGroupToken == "oxo") @@ -276,17 +277,17 @@ //If functional group hasn't had a location specified: if (addPos < 0) { - addAtom("O", currentMolecule.getFirstAtom(), 2.0, 0); + addAtom("O", currentMolecule.getFirstAtom(), IBond.Order.DOUBLE, 0); } else { - addAtom("O", currentMolecule.getAtom(addPos), 2.0, 0); + addAtom("O", currentMolecule.getAtom(addPos), IBond.Order.DOUBLE, 0); } } //Nitrile else if (funGroupToken == "nitrile" ) { - addAtom("N", currentMolecule.getFirstAtom(), 3.0, 0); + addAtom("N", currentMolecule.getFirstAtom(), IBond.Order.TRIPLE, 0); } //Benzene else if (funGroupToken == "phenyl" ) @@ -320,11 +321,11 @@ //If functional group hasn't had a location specified: if (addPos < 0) { - addAtom("N", currentMolecule.getFirstAtom(), 1.0, 2); + addAtom("N", currentMolecule.getFirstAtom(), IBond.Order.SINGLE, 2); } else { - addAtom("N", currentMolecule.getAtom(addPos), 1.0, 2); + addAtom("N", currentMolecule.getAtom(addPos), IBond.Order.SINGLE, 2); } } //ORGANO METALLICS ADDED AS PREFIXES @@ -333,11 +334,11 @@ //If functional group hasn't had a location specified: if (addPos < 0) { - addAtom("Al", currentMolecule.getFirstAtom(), 1.0, 2); + addAtom("Al", currentMolecule.getFirstAtom(), IBond.Order.SINGLE, 2); } else { - addAtom("Al", currentMolecule.getAtom(addPos), 1.0, 2); + addAtom("Al", currentMolecule.getAtom(addPos), IBond.Order.SINGLE, 2); } } else if (funGroupToken == "litho" ) @@ -345,11 +346,11 @@ //If functional group hasn't had a location specified: if (addPos < 0) { - addAtom("Li", currentMolecule.getFirstAtom(), 1.0, 2); + addAtom("Li", currentMolecule.getFirstAtom(), IBond.Order.SINGLE, 2); } else { - addAtom("Li", currentMolecule.getAtom(addPos), 1.0, 2); + addAtom("Li", currentMolecule.getAtom(addPos), IBond.Order.SINGLE, 2); } } //PRIORITY SUBSTITUENTS @@ -358,30 +359,30 @@ //Esters ("...oate") else if (funGroupToken == "oate") { - addAtom("O", endOfChain, 2.0, 0); - addAtom("O", endOfChain, 1.0, 0); + addAtom("O", endOfChain, IBond.Order.DOUBLE, 0); + addAtom("O", endOfChain, IBond.Order.SINGLE, 0); //Set the end of the chain to be built on for unspecified substituents. endOfChain = currentMolecule.getLastAtom(); } //Amines else if (funGroupToken == "amine") { - addAtom("N", endOfChain, 1.0, 1); + addAtom("N", endOfChain, IBond.Order.SINGLE, 1); //Set the end of the chain to be built on for unspecified substituents. endOfChain = currentMolecule.getLastAtom(); } //Amides else if (funGroupToken =="amide") { - addAtom("O", endOfChain, 2.0, 0); - addAtom("N", endOfChain, 1.0, 1); + addAtom("O", endOfChain, IBond.Order.DOUBLE, 0); + addAtom("N", endOfChain, IBond.Order.SINGLE, 1); //Set the end of the chain to be built on for unspecified substituents. endOfChain = currentMolecule.getLastAtom(); } //Ketones else if (funGroupToken == "one") { - addAtom("O", endOfChain, 2.0, 2); + addAtom("O", endOfChain, IBond.Order.DOUBLE, 2); //End of chain doesn't change in this case } //Organometals @@ -462,7 +463,7 @@ * @param bondOrder The order of the bond to use to join the two atoms. * @param hydrogenCount The number of hydrogen atoms connected to this atom. */ - private void addAtom(String newAtomType, org.openscience.cdk.interfaces.IAtom otherConnectingAtom, double bondOrder, int hydrogenCount) + private void addAtom(String newAtomType, IAtom otherConnectingAtom, Order bondOrder, int hydrogenCount) { //Create the new atom and bond. Atom newAtom = new Atom(newAtomType); Modified: branches/egonw/ibondorder/src/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -268,7 +268,7 @@ atom.setFlag(CDKConstants.ISINRING, false); isInHeteroRing = false; } - atom.setProperty("MAX_BOND_ORDER", new Double(molecule.getMaximumBondOrder(atom))); + atom.setProperty("MAX_BOND_ORDER", new Double(molecule.getMaximumBondOrder(atom).ordinal()+1)); try { hoseCode = hcg.getHOSECode(molecule, atom, 3); Modified: branches/egonw/ibondorder/src/org/openscience/cdk/nonotify/NNBond.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/nonotify/NNBond.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/nonotify/NNBond.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -27,6 +27,7 @@ import org.openscience.cdk.Bond; import org.openscience.cdk.CDKConstants; import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IChemObjectListener; @@ -39,18 +40,18 @@ private static final long serialVersionUID = -6286559199533034379L; public NNBond() { - this(null, null, 0.0, CDKConstants.STEREO_BOND_NONE); + this(null, null, null, CDKConstants.STEREO_BOND_NONE); } public NNBond(IAtom atom1, IAtom atom2) { - this(atom1, atom2, 1.0, CDKConstants.STEREO_BOND_NONE); + this(atom1, atom2, IBond.Order.SINGLE, CDKConstants.STEREO_BOND_NONE); } - public NNBond(IAtom atom1, IAtom atom2, double order) { + public NNBond(IAtom atom1, IAtom atom2, IBond.Order order) { this(atom1, atom2, order, CDKConstants.STEREO_BOND_NONE); } - public NNBond(IAtom atom1, IAtom atom2, double order, int stereo) { + public NNBond(IAtom atom1, IAtom atom2, IBond.Order order, int stereo) { super(atom1, atom2, order, stereo); setNotification(false); } Modified: branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptor.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptor.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptor.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -859,7 +859,7 @@ bondAtom1=bond.getAtom(1); if ((bondAtom0.getSymbol().equals("C") && bondAtom1.getSymbol().equals("N")) || (bondAtom0.getSymbol().equals("N") && bondAtom1.getSymbol().equals("C"))&& bond.getOrder() == IBond.Order.SINGLE){ aminoAcid.removeBond(bondAtom0,bondAtom1); - aminoAcid.addBond(new AnyOrderQueryBond((IQueryAtom)bondAtom0,(IQueryAtom)bondAtom1,1)); + aminoAcid.addBond(new AnyOrderQueryBond((IQueryAtom)bondAtom0,(IQueryAtom)bondAtom1,IBond.Order.SINGLE)); break; } } @@ -913,9 +913,9 @@ atom3.setSymbol("O"); SymbolQueryAtom atom4=new SymbolQueryAtom(); atom4.setSymbol("O"); - orthopair.addBond(new AromaticQueryBond(atom1,atom2,1.5)); - orthopair.addBond(new OrderQueryBond(atom1,atom3,1)); - orthopair.addBond(new OrderQueryBond(atom2,atom4,1)); + orthopair.addBond(new AromaticQueryBond(atom1,atom2,IBond.Order.SINGLE)); + orthopair.addBond(new OrderQueryBond(atom1,atom3,IBond.Order.SINGLE)); + orthopair.addBond(new OrderQueryBond(atom2,atom4,IBond.Order.SINGLE)); if (UniversalIsomorphismTester.isSubgraph((org.openscience.cdk.AtomContainer)ac, orthopair)) { xlogP -= 0.268; Modified: branches/egonw/ibondorder/src/org/openscience/cdk/renderer/progz/TestRenderer.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/renderer/progz/TestRenderer.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/renderer/progz/TestRenderer.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -240,12 +240,12 @@ atom = new Atom("C"); atom.setHydrogenCount(2); currentChain.addAtom(atom); - currentChain.addBond(atomCount, atomCount - 1, 1); + currentChain.addBond(atomCount, atomCount - 1, IBond.Order.SINGLE); } atom = new Atom("C"); atom.setHydrogenCount(3); currentChain.addAtom(atom); - currentChain.addBond(atomCount, atomCount - 1, 1); + currentChain.addBond(atomCount, atomCount - 1, IBond.Order.SINGLE); return currentChain; } Modified: branches/egonw/ibondorder/src/org/openscience/cdk/templates/MoleculeFactory.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/templates/MoleculeFactory.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/templates/MoleculeFactory.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -100,7 +100,7 @@ //Add further atoms and bonds as needed, a pair at a time. for (int atomCount = 1; atomCount < chainLength; atomCount ++) { currentChain.addAtom(new Atom("C")); - currentChain.addBond(atomCount, atomCount - 1, 1); + currentChain.addBond(atomCount, atomCount - 1, IBond.Order.SINGLE); } return currentChain; Modified: branches/egonw/ibondorder/src/org/openscience/cdk/templates/saturatedhydrocarbons/IsoAlkanes.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/templates/saturatedhydrocarbons/IsoAlkanes.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/templates/saturatedhydrocarbons/IsoAlkanes.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -25,6 +25,7 @@ import org.openscience.cdk.Atom; import org.openscience.cdk.Molecule; +import org.openscience.cdk.interfaces.IBond; /** * This class contains methods for generating simple organic alkanes. @@ -41,9 +42,9 @@ mol.addAtom(new Atom("C")); mol.addAtom(new Atom("C")); - mol.addBond(0, 1, 1); - mol.addBond(0, 2, 1); - mol.addBond(0, 3, 1); + mol.addBond(0, 1, IBond.Order.SINGLE); + mol.addBond(0, 2, IBond.Order.SINGLE); + mol.addBond(0, 3, IBond.Order.SINGLE); return mol; } @@ -55,10 +56,10 @@ mol.addAtom(new Atom("C")); mol.addAtom(new Atom("C")); - mol.addBond(0, 1, 1); - mol.addBond(0, 2, 1); - mol.addBond(0, 3, 1); - mol.addBond(3, 4, 1); + mol.addBond(0, 1, IBond.Order.SINGLE); + mol.addBond(0, 2, IBond.Order.SINGLE); + mol.addBond(0, 3, IBond.Order.SINGLE); + mol.addBond(3, 4, IBond.Order.SINGLE); return mol; } @@ -71,11 +72,11 @@ mol.addAtom(new Atom("C")); mol.addAtom(new Atom("C")); - mol.addBond(0, 1, 1); - mol.addBond(0, 2, 1); - mol.addBond(0, 3, 1); - mol.addBond(3, 4, 1); - mol.addBond(4, 5, 1); + mol.addBond(0, 1, IBond.Order.SINGLE); + mol.addBond(0, 2, IBond.Order.SINGLE); + mol.addBond(0, 3, IBond.Order.SINGLE); + mol.addBond(3, 4, IBond.Order.SINGLE); + mol.addBond(4, 5, IBond.Order.SINGLE); return mol; } Modified: branches/egonw/ibondorder/src/org/openscience/cdk/test/AtomContainerTest.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/test/AtomContainerTest.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/test/AtomContainerTest.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -1283,9 +1283,9 @@ acetone.addAtom(c2); acetone.addAtom(c3); acetone.addAtom(o); - acetone.addBond(0, 1, 1); - acetone.addBond(1, 3, 2); - acetone.addBond(1, 2, 1); + acetone.addBond(0, 1, IBond.Order.SINGLE); + acetone.addBond(1, 3, IBond.Order.DOUBLE); + acetone.addBond(1, 2, IBond.Order.SINGLE); assertEquals(3, acetone.getBondCount()); Iterator bonds = acetone.bonds(); Modified: branches/egonw/ibondorder/src/org/openscience/cdk/test/atomtype/HybridizationStateATMatcherTest.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/test/atomtype/HybridizationStateATMatcherTest.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/test/atomtype/HybridizationStateATMatcherTest.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -26,12 +26,14 @@ import junit.framework.Test; import junit.framework.TestSuite; + import org.openscience.cdk.Atom; import org.openscience.cdk.Molecule; import org.openscience.cdk.atomtype.HybridizationStateATMatcher; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomType; +import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.test.CDKTestCase; /** @@ -66,19 +68,19 @@ mol.addAtom(new Atom("C")); mol.addBond(0,1,3); mol.addAtom(new Atom("C")); - mol.addBond(1,2,1); + mol.addBond(1, 2, IBond.Order.SINGLE); mol.addAtom(new Atom("C")); - mol.addBond(2,3,1); + mol.addBond(2, 3, IBond.Order.SINGLE); mol.addAtom(new Atom("O")); - mol.addBond(3,4,2); + mol.addBond(3, 4, IBond.Order.DOUBLE); mol.addAtom(new Atom("H")); - mol.addBond(5,0,1); + mol.addBond(5, 0, IBond.Order.SINGLE); mol.addAtom(new Atom("H")); - mol.addBond(6,2,1); + mol.addBond(6, 2, IBond.Order.SINGLE); mol.addAtom(new Atom("H")); - mol.addBond(7,2,1); + mol.addBond(7, 2, IBond.Order.SINGLE); mol.addAtom(new Atom("H")); - mol.addBond(8,3,1); + mol.addBond(8, 3, IBond.Order.SINGLE); IAtom atom = mol.getAtom(0); Modified: branches/egonw/ibondorder/src/org/openscience/cdk/test/charges/InductivePartialChargesTest.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/test/charges/InductivePartialChargesTest.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/test/charges/InductivePartialChargesTest.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -33,6 +33,7 @@ import org.openscience.cdk.Molecule; import org.openscience.cdk.charges.InductivePartialCharges; import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.test.CDKTestCase; /** @@ -99,10 +100,10 @@ mol.addAtom(h3); h3.setPoint3d(h3_coord); - mol.addBond(0, 1, 1); // 1 - mol.addBond(0, 2, 1); // 1 - mol.addBond(0, 3, 1); // 1 - mol.addBond(0, 4, 1); // 1 + mol.addBond(0, 1, IBond.Order.SINGLE); // 1 + mol.addBond(0, 2, IBond.Order.SINGLE); // 1 + mol.addBond(0, 3, IBond.Order.SINGLE); // 1 + mol.addBond(0, 4, IBond.Order.SINGLE); // 1 InductivePartialCharges ipc = new InductivePartialCharges(); ipc.assignInductivePartialCharges(mol); for (int i = 0; i < mol.getAtomCount(); i++) { Modified: branches/egonw/ibondorder/src/org/openscience/cdk/test/controller/ControllerTest.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/test/controller/ControllerTest.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/test/controller/ControllerTest.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -35,6 +35,7 @@ import org.openscience.cdk.applications.swing.MoleculeViewer2D; import org.openscience.cdk.controller.Controller2DModel; import org.openscience.cdk.controller.PopupController2D; +import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.MDLReader; import org.openscience.cdk.renderer.Renderer2DModel; @@ -100,16 +101,16 @@ mol.addAtom(new Atom("C")); // 5 mol.addAtom(new Atom("C")); // 6 - mol.addBond(0, 1, 1); // 1 - mol.addBond(1, 2, 1); // 2 - mol.addBond(2, 3, 1); // 3 - mol.addBond(3, 4, 1); // 4 - mol.addBond(4, 5, 1); // 5 - mol.addBond(5, 6, 1); // 6 - mol.addBond(2, 0, 1); // 7 - mol.addBond(1, 3, 1); // 8 - mol.addBond(4, 2, 1); // 9 - mol.addBond(6, 4, 1); // 9 + mol.addBond(0, 1, IBond.Order.SINGLE); // 1 + mol.addBond(1, 2, IBond.Order.SINGLE); // 2 + mol.addBond(2, 3, IBond.Order.SINGLE); // 3 + mol.addBond(3, 4, IBond.Order.SINGLE); // 4 + mol.addBond(4, 5, IBond.Order.SINGLE); // 5 + mol.addBond(5, 6, IBond.Order.SINGLE); // 6 + mol.addBond(2, 0, IBond.Order.SINGLE); // 7 + mol.addBond(1, 3, IBond.Order.SINGLE); // 8 + mol.addBond(4, 2, IBond.Order.SINGLE); // 9 + mol.addBond(6, 4, IBond.Order.SINGLE); // 9 return mol; } @@ -122,11 +123,11 @@ mol.addAtom(new Atom("C")); // 2 mol.addAtom(new Atom("C")); // 3 - mol.addBond(0, 1, 1); // 1 - mol.addBond(1, 2, 1); // 2 - mol.addBond(2, 0, 1); // 3 - mol.addBond(2, 3, 1); // 7 - mol.addBond(1, 3, 1); // 8 + mol.addBond(0, 1, IBond.Order.SINGLE); // 1 + mol.addBond(1, 2, IBond.Order.SINGLE); // 2 + mol.addBond(2, 0, IBond.Order.SINGLE); // 3 + mol.addBond(2, 3, IBond.Order.SINGLE); // 7 + mol.addBond(1, 3, IBond.Order.SINGLE); // 8 return mol; } @@ -141,13 +142,13 @@ mol.addAtom(new Atom("C")); // 2 mol.addAtom(new Atom("C")); // 3 - mol.addBond(0, 1, 1); // 1 - mol.addBond(1, 2, 1); // 2 - mol.addBond(2, 3, 1); // 3 - mol.addBond(3, 0, 1); // 7 - mol.addBond(1, 4, 1); // 8 - mol.addBond(4, 5, 1); // 7 - mol.addBond(5, 2, 1); // 8 + mol.addBond(0, 1, IBond.Order.SINGLE); // 1 + mol.addBond(1, 2, IBond.Order.SINGLE); // 2 + mol.addBond(2, 3, IBond.Order.SINGLE); // 3 + mol.addBond(3, 0, IBond.Order.SINGLE); // 7 + mol.addBond(1, 4, IBond.Order.SINGLE); // 8 + mol.addBond(4, 5, IBond.Order.SINGLE); // 7 + mol.addBond(5, 2, IBond.Order.SINGLE); // 8 return mol; } @@ -166,18 +167,18 @@ mol.addAtom(new Atom("C")); // 8 mol.addAtom(new Atom("C")); // 9 - mol.addBond(0, 1, 1); // 1 - mol.addBond(1, 2, 1); // 2 - mol.addBond(2, 3, 1); // 3 - mol.addBond(3, 4, 1); // 4 - mol.addBond(4, 5, 1); // 5 - mol.addBond(5, 0, 1); // 6 - mol.addBond(5, 6, 1); // 7 - mol.addBond(6, 7, 1); // 8 - mol.addBond(7, 4, 1); // 9 - mol.addBond(8, 0, 1); // 10 - mol.addBond(9, 1, 1); // 11 - mol.addBond(9, 8, 1); // 11 + mol.addBond(0, 1, IBond.Order.SINGLE); // 1 + mol.addBond(1, 2, IBond.Order.SINGLE); // 2 + mol.addBond(2, 3, IBond.Order.SINGLE); // 3 + mol.addBond(3, 4, IBond.Order.SINGLE); // 4 + mol.addBond(4, 5, IBond.Order.SINGLE); // 5 + mol.addBond(5, 0, IBond.Order.SINGLE); // 6 + mol.addBond(5, 6, IBond.Order.SINGLE); // 7 + mol.addBond(6, 7, IBond.Order.SINGLE); // 8 + mol.addBond(7, 4, IBond.Order.SINGLE); // 9 + mol.addBond(8, 0, IBond.Order.SINGLE); // 10 + mol.addBond(9, 1, IBond.Order.SINGLE); // 11 + mol.addBond(9, 8, IBond.Order.SINGLE); // 11 return mol; @@ -199,17 +200,17 @@ - mol.addBond(0, 1, 1); // 1 - mol.addBond(1, 2, 1); // 2 - mol.addBond(2, 3, 1); // 3 - mol.addBond(3, 4, 1); // 4 - mol.addBond(4, 5, 1); // 5 - mol.addBond(5, 6, 1); // 6 - mol.addBond(6, 0, 1); // 7 - mol.addBond(6, 7, 1); // 8 - mol.addBond(7, 8, 1); // 9 - mol.addBond(8, 9, 1); // 10 - mol.addBond(9, 6, 1); // 11 + mol.addBond(0, 1, IBond.Order.SINGLE); // 1 + mol.addBond(1, 2, IBond.Order.SINGLE); // 2 + mol.addBond(2, 3, IBond.Order.SINGLE); // 3 + mol.addBond(3, 4, IBond.Order.SINGLE); // 4 + mol.addBond(4, 5, IBond.Order.SINGLE); // 5 + mol.addBond(5, 6, IBond.Order.SINGLE); // 6 + mol.addBond(6, 0, IBond.Order.SINGLE); // 7 + mol.addBond(6, 7, IBond.Order.SINGLE); // 8 + mol.addBond(7, 8, IBond.Order.SINGLE); // 9 + mol.addBond(8, 9, IBond.Order.SINGLE); // 10 + mol.addBond(9, 6, IBond.Order.SINGLE); // 11 return mol; } @@ -228,17 +229,17 @@ // mol.addAtom(new Atom("C")); // 8 // mol.addAtom(new Atom("C")); // 9 - mol.addBond(0, 1, 1); // 1 - mol.addBond(1, 2, 1); // 2 - mol.addBond(2, 3, 1); // 3 - mol.addBond(3, 4, 1); // 4 - mol.addBond(4, 5, 1); // 5 - mol.addBond(5, 0, 1); // 6 -// mol.addBond(5, 6, 1); // 7 -// mol.addBond(6, 7, 1); // 8 -// mol.addBond(7, 4, 1); // 9 -// mol.addBond(8, 0, 1); // 10 -// mol.addBond(9, 1, 1); // 11 + mol.addBond(0, 1, IBond.Order.SINGLE); // 1 + mol.addBond(1, 2, IBond.Order.SINGLE); // 2 + mol.addBond(2, 3, IBond.Order.SINGLE); // 3 + mol.addBond(3, 4, IBond.Order.SINGLE); // 4 + mol.addBond(4, 5, IBond.Order.SINGLE); // 5 + mol.addBond(5, 0, IBond.Order.SINGLE); // 6 +// mol.addBond(5, 6, IBond.Order.SINGLE); // 7 +// mol.addBond(6, 7, IBond.Order.SINGLE); // 8 +// mol.addBond(7, 4, IBond.Order.SINGLE); // 9 +// mol.addBond(8, 0, IBond.Order.SINGLE); // 10 +// mol.addBond(9, 1, IBond.Order.SINGLE); // 11 return mol; Modified: branches/egonw/ibondorder/src/org/openscience/cdk/test/fingerprint/FingerprinterTest.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/test/fingerprint/FingerprinterTest.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/test/fingerprint/FingerprinterTest.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -38,6 +38,7 @@ import org.openscience.cdk.fingerprint.Fingerprinter; import org.openscience.cdk.fingerprint.FingerprinterTool; import org.openscience.cdk.fingerprint.IFingerprinter; +import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.MDLReader; import org.openscience.cdk.templates.MoleculeFactory; @@ -360,12 +361,12 @@ mol.addAtom(new Atom("C")); // 5 mol.addAtom(new Atom("C")); // 6 - mol.addBond(0, 1, 1); // 1 - mol.addBond(0, 2, 1); // 2 - mol.addBond(0, 3, 1); // 3 - mol.addBond(0, 4, 1); // 4 - mol.addBond(3, 5, 1); // 5 - mol.addBond(5, 6, 2); // 6 + mol.addBond(0, 1, IBond.Order.SINGLE); // 1 + mol.addBond(0, 2, IBond.Order.SINGLE); // 2 + mol.addBond(0, 3, IBond.Order.SINGLE); // 3 + mol.addBond(0, 4, IBond.Order.SINGLE); // 4 + mol.addBond(3, 5, IBond.Order.SINGLE); // 5 + mol.addBond(5, 6, IBond.Order.DOUBLE); // 6 return mol; } @@ -376,7 +377,7 @@ mol.addAtom(new Atom("C")); // 0 mol.addAtom(new Atom("C")); // 1 - mol.addBond(0, 1, 1); // 1 + mol.addBond(0, 1, IBond.Order.SINGLE); // 1 return mol; } @@ -391,13 +392,13 @@ mol.addAtom(new Atom("C")); // 5 mol.addAtom(new Atom("C")); // 6 - mol.addBond(0, 1, 2); // 1 - mol.addBond(0, 2, 1); // 2 - mol.addBond(0, 3, 1); // 3 - mol.addBond(0, 4, 1); // 4 - mol.addBond(3, 5, 1); // 5 - mol.addBond(5, 6, 2); // 6 - mol.addBond(5, 6, 2); // 7 + mol.addBond(0, 1, IBond.Order.DOUBLE); // 1 + mol.addBond(0, 2, IBond.Order.SINGLE); // 2 + mol.addBond(0, 3, IBond.Order.SINGLE); // 3 + mol.addBond(0, 4, IBond.Order.SINGLE); // 4 + mol.addBond(3, 5, IBond.Order.SINGLE); // 5 + mol.addBond(5, 6, IBond.Order.DOUBLE); // 6 + mol.addBond(5, 6, IBond.Order.DOUBLE); // 7 return mol; } @@ -412,12 +413,12 @@ mol.addAtom(new Atom("C")); // 5 mol.addAtom(new Atom("C")); // 6 - mol.addBond(0, 1, 1); // 1 - mol.addBond(0, 2, 1); // 2 - mol.addBond(0, 3, 1); // 3 - mol.addBond(0, 4, 1); // 4 - mol.addBond(3, 5, 2); // 5 - mol.addBond(5, 6, 1); // 6 + mol.addBond(0, 1, IBond.Order.SINGLE); // 1 + mol.addBond(0, 2, IBond.Order.SINGLE); // 2 + mol.addBond(0, 3, IBond.Order.SINGLE); // 3 + mol.addBond(0, 4, IBond.Order.SINGLE); // 4 + mol.addBond(3, 5, IBond.Order.DOUBLE); // 5 + mol.addBond(5, 6, IBond.Order.SINGLE); // 6 return mol; } Modified: branches/egonw/ibondorder/src/org/openscience/cdk/test/graph/invariant/EquivalentClassPartitionerTest.java =================================================================== --- branches/egonw/ibondorder/src/org/openscience/cdk/test/graph/invariant/EquivalentClassPartitionerTest.java 2007-11-03 08:12:30 UTC (rev 9352) +++ branches/egonw/ibondorder/src/org/openscience/cdk/test/graph/invariant/EquivalentClassPartitionerTest.java 2007-11-03 08:14:40 UTC (rev 9353) @@ -26,6 +26,7 @@ import org.openscience.cdk.Atom; import org.openscience.cdk.AtomContainer; import org.openscience.cdk.graph.invariant.EquivalentClassPartitioner; +import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.test.CDKTestCase; /** @@ -95,66 +96,66 @@ C40C3V.addAtom(new Atom("C")); // 39 C40C3V.addAtom(new Atom("C")); // 40 - C40C3V.addBond(0, 1, 1); // 1 - C40C3V.addBond(0, 5, 1); // 2 - C40C3V.addBond(0, 8, 1); // 3 - C40C3V.addBond(1, 2, 1); // 4 - C40C3V.addBond(1, 25, 1); // 5 - C40C3V.addBond(2, 3, 1); // 6 - C40C3V.addBond(2, 6, 1); // 7 - C40C3V.addBond(3, 4, 1); // 8 - C40C3V.addBond(3, 24, 1); // 9 - C40C3V.addBond(4, 7, 1); // 10 - C40C3V.addBond(4, 8, 1); // 11 - C40C3V.addBond(5, 21, 1); // 12 - C40C3V.addBond(5, 28, 1); // 13 - C40C3V.addBond(6, 22, 1); // 14 - C40C3V.addBond(6, 27, 1); // 15 - C40C3V.addBond(7, 20, 1); // 16 - C40C3V.addBond(7, 23, 1); // 17 - C40C3V.addBond(8, 26, 1); // 18 - C40C3V.addBond(9, 12, 1); // 19 - C40C3V.addBond(9, 37, 1); // 20 - C40C3V.addBond(9, 39, 1); // 21 - C40C3V.addBond(10, 14, 1); // 22 - C40C3V.addBond(10, 38, 1); // 23 - C40C3V.addBond(10, 39, 1); // 24 - C40C3V.addBond(11, 13, 1); // 25 - C40C3V.addBond(11, 36, 1); // 26 - C40C3V.addBond(11, 39, 1); // 27 - C40C3V.addBond(12, 35, 1); // 28 - C40C3V.addBond(12, 38, 1); // 29 - C40C3V.addBond(13, 34, 1); // 30 - C40C3V.addBond(13, 37, 1); // 31 - C40C3V.addBond(14, 33, 1); // 32 - C40C3V.addBond(14, 36, 1); // 33 - C40C3V.addBond(15, 29, 1); // 34 - C40C3V.addBond(15, 17, 1); // 35 - C40C3V.addBond(15, 37, 1); // 36 - C40C3V.addBond(16, 19, 1); // 37 - C40C3V.addBond(16, 30, 1); // 38 - C40C3V.addBond(16, 36, 1); // 39 - C40C3V.addBond(17, 20, 1); // 40 - C40C3V.addBond(17, 35, 1); // 41 - C40C3V.addBond(18, 22, 1); // 42 - C40C3V.addBond(18, 32, 1); // 43 - C40C3V.addBond(18, 33, 1); // 44 - C40C3V.addBond(19, 28, 1); // 45 - C40C3V.addBond(19, 34, 1); // 46 - C40C3V.addBond(20, 26, 1); // 47 - C40C3V.addBond(21, 26, 1); // 48 - C40C3V.addBond(21, 29, 1); // 49 - C40C3V.addBond(22, 24, 1); // 50 - C40C3V.addBond(23, 24, 1); // 51 - C40C3V.addBond(23, 31, 1); // 52 - C40C3V.addBond(25, 27, 1); // 53 - C40C3V.addBond(25, 28, 1); // 54 - C40C3V.addBond(27, 30, 1); // 55 - C40C3V.addBond(29, 34, 1); // 56 - C40C3V.addBond(30, 33, 1); // 57 - C40C3V.addBond(31, 32, 1); // 58 - C40C3V.addBond(31, 35, 1); // 59 - C40C3V.addBond(32, 38, 1); // 60 + C40C3V.addBond(0, 1, IBond.Order.SINGLE); // 1 + C40C3V.addBond(0, 5, IBond.Order.SINGLE); // 2 + C40C3V.addBond(0, 8, IBond.Order.SINGLE); // 3 + C40C3V.addBond(1, 2, IBond.Order.SINGLE); // 4 + C40C3V.addBond(1, 25, IBond.Order.SINGLE); // 5 + C40C3V.addBond(2, 3, IBond.Order.SINGLE); // 6 + C40C3V.addBond(2, 6, IBond.Order.SINGLE); // 7 + C40C3V.addBond(3, 4, IBond.Order.SINGLE); // 8 + C40C3V.addBond(3, 24, IBond.Order.SINGLE); // 9 + C40C3V.addBond(4, 7, IBond.Order.SINGLE); // 10 + C40C3V.addBond(4, 8, IBond.Order.SINGLE); // 11 + C40C3V.addBond(5, 21, IBond.Order.SINGLE); // 12 + C40C3V.addBond(5, 28, IBond.Order.SINGLE); // 13 + C40C3V.addBond(6, 22, IBond.Order.SINGLE); // 14 + C40C3V.addBond(6, 27, IBond.Order.SINGLE); // 15 + C40C3V.addBond(7, 20, IBond.Order.SINGLE); // 16 + C40C3V.addBond(7, 23, IBond.Order.SINGLE); // 17 + C40C3V.addBond(8, 26, IBond.Order.SINGLE); // 18 + C40C3V.addBond(9, 12, IBond.Order.SINGLE); // 19 + C40C3V.addBond(9, 37, IBond.Order.SINGLE); // 20 + C40C3V.addBond(9, 39, IBond.Order.SINGLE); // 21 + C40C3V.addBond(10, 14, IBond.Order.SINGLE); // 22 + C40C3V.addBond(10, 38, IBond.Order.SINGLE); // 23 + C40C3V.addBond(10, 39, IBond.Order.SINGLE); // 24 + C40C3V.addBond(11, 13, IBond.Order.SINGLE); // 25 + C40C3V.addBond(11, 36, IBond.Order.SINGLE); // 26 + C40C3V.addBond(11, 39, IBond.Order.SINGLE); // 27 + C40C3V.addBond(12, 35, IBond.Order.SINGLE); // 28 + C40C3V.addBond(12, 38, IBond.Order.SINGLE); // 29 + C40C3V.addBond(13, 34, IBond.Order.SINGLE); // 30 + C40C3V.addBond(13, 37, IBond.Order.SINGLE); // 31 + C40C3V.addBond(14, 33, IBond.Order.SINGLE); // 32 + C40C3V.addBond(14, 36, IBond.Order.SINGLE); // 33 + C40C3V.addBond(15, 29, IBond.Order.SINGLE); // 34 + C40C3V.addBond(15, 17, IBond.Order.SINGLE); // 35 + C40C3V.addBond(15, 37, IBond.Order.SINGLE); // 36 + C40C3V.addBond(16, 19, IBond.Order.SINGLE); // 37 + C40C3V.addBond(16, 30, IBond.Order.SINGLE); // 38 + C40C3V.addBond(16, 36, IBond.Order.SINGLE); // 39 + C40C3V.addBond(17, 20, IBond.Order.SINGLE); // 40 + C40C3V.addBond(17, 35, IBond.Order.SINGLE); // 41 + C40C3V.addBond(18, 22, IBond.Order.SINGLE); // 42 + C40C3V.addBond(18, 32, IBond.Order.SINGLE); // 43 + C40C3V.addBond(18, 33, IBond.Order.SINGLE); // 44 + C40C3V.addBond(19, 28, IBond.Order.SINGLE); // 45 + C40C3V.addBond(19, 34, IBond.Order.SINGLE); // 46 + C40C3V.addBond(20, 26, IBond.Order.SINGLE); // 47 + C40C3V.addBond(21, 26, IBond.Order.SINGLE); // 48 + C40C3V.addBond(21, 29, IBond.Order.SINGLE); // 49 + C40C3V.addBond(22, 24, IBond.Order.SINGLE); // 50 + C40C3V.addBond(23, 24, IBond.Order.SINGLE); // 51 + C40C3V.addBond(23, 31, IBond.Order.SINGLE); // 52 + C40C3V.addBond(25, 27, IBond.Order.SINGLE); // 53 + C40C3V.addBond(25, 28, IBond.Order.SINGLE); // 54 + C40C3V.addBond(27, 30, IBond.Order.SINGLE); // 55 + C40C3V.addBond(29, 34, IBond.Order.SINGLE); // 56 + C40C3V.addBond(30, 33, IBond.Order.SINGLE); // 57 + C40C3V.addBond(31, 32, IBond.Order.SINGLE); // 58 + C40C3V.addBond(31, 35, IBond.Order.SINGLE); // 59 + C40C3V.addBond(32, 38, IBond.Order.SINGLE); // 60 EquivalentClassPartitioner it = new EquivalentClassPartitioner(C40C3V); int equivalentClass[]=it.getTopoEquivClassbyHuXu(C40C3V); char[] arrEquivalent=new char[39]; @@ -196,42 +197,42 @@ C24D6D.addAtom(new Atom("C")); // 24 - C24D6D.addBond(0, 1, 1); // 1 - C24D6D.addBond(0, 5, 1); // 2 - C24D6D.addBond(0, 11, 1); // 3 - C24D6D.addBond(1, 2, 1); // 4 - C24D6D.addBond(1, 10, 1); // 5 - C24D6D.addBond(2... [truncated message content] |