Menu
▾
▴
[Cml-cvs] jumbo53/src/org/xmlcml/cml/element AbstractAbundance.java, 1.1, 1.2 AbstractAction.java, 1.2, 1.3 AbstractActionList.java, 1.2, 1.3 AbstractAlternative.java, 1.1, 1.2 AbstractAmount.java, 1.1, 1.2 AbstractAngle.java, 1.1, 1.2 AbstractAnnotation.java, 1.1, 1.2 AbstractAppinfo.java, 1.1, 1.2 AbstractArg.java, 1.2, 1.3 AbstractArray.java, 1.1, 1.2 AbstractAtom.java, 1.1, 1.2 AbstractAtomArray.java, 1.1, 1.2 AbstractAtomParity.java, 1.1, 1.2 AbstractAtomSet.java, 1.1, 1.2 AbstractAtomType.java, 1.1, 1.2 AbstractAtomTypeList.java, 1.1, 1.2 AbstractAtomicBasisFunction.java, 1.1, 1.2 AbstractBand.java, 1.1, 1.2 AbstractBandList.java, 1.1, 1.2 AbstractBasisSet.java, 1.1, 1.2 AbstractBond.java, 1.1, 1.2 AbstractBondArray.java, 1.1, 1.2 AbstractBondSet.java, 1.1, 1.2 AbstractBondStereo.java, 1.1, 1.2 AbstractBondType.java, 1.1, 1.2 AbstractBondTypeList.java, 1.1, 1.2 AbstractCellParameter.java, 1.1, 1.2 AbstractCml.java, 1.1, 1.2 AbstractComplexObject.java, 1.1, 1.2 AbstractConditionList.java, 1.1, 1.2 AbstractCopy.java, 1.1, 1.2 AbstractCrystal.java, 1.1, 1.2 AbstractDefinition.java, 1.1, 1.2 AbstractDescription.java, 1.1, 1.2 AbstractDictionary.java, 1.1, 1.2 AbstractDimension.java, 1.1, 1.2 AbstractDocumentation.java, 1.1, 1.2 AbstractEigen.java, 1.1, 1.2 AbstractElectron.java, 1.1, 1.2 AbstractEntry.java, 1.1, 1.2 AbstractEnumeration.java, 1.1, 1.2 AbstractExpression.java, 1.1, 1.2 AbstractFloat.java, 1.1, 1.2 AbstractFloatArray.java, 1.1, 1.2 AbstractFor.java, 1.1, 1.2 AbstractFormula.java, 1.1, 1.2 AbstractGradient.java, 1.1, 1.2 AbstractIdentifier.java, 1.1, 1.2 AbstractIf.java, 1.1, 1.2 AbstractInteger.java, 1.1, 1.2 AbstractIntegerArray.java, 1.1, 1.2 AbstractIsotope.java, 1.1, 1.2 AbstractIsotopeList.java, 1.1, 1.2 AbstractJoin.java, 1.2, 1.3 AbstractKpoint.java, 1.1, 1.2 AbstractKpointList.java, 1.1, 1.2 AbstractLabel.java, 1.1, 1.2 AbstractLattice.java, 1.1, 1.2 AbstractLatticeVector.java, 1.1, 1.2 AbstractLength.java, 1.1, 1.2 AbstractLine3.java, 1.1, 1.2 AbstractLink.java, 1.1, 1.2 AbstractList.java, 1.1, 1.2 AbstractMap.java, 1.1, 1.2 AbstractMatrix.java, 1.1, 1.2 AbstractMechanism.java, 1.1, 1.2 AbstractMechanismComponent.java, 1.1, 1.2 AbstractMetadata.java, 1.1, 1.2 AbstractMetadataList.java, 1.1, 1.2 AbstractModule.java, 1.1, 1.2 AbstractMolecule.java, 1.2, 1.3 AbstractName.java, 1.1, 1.2 AbstractObject.java, 1.1, 1.2 AbstractObservation.java, 1.1, 1.2 AbstractOperator.java, 1.1, 1.2 AbstractParameter.java, 1.1, 1.2 AbstractParameterList.java, 1.1, 1.2 AbstractParticle.java, 1.1, 1.2 AbstractPeak.java, 1.1, 1.2 AbstractPeakGroup.java, 1.1, 1.2 AbstractPeakList.java, 1.1, 1.2 AbstractPeakStructure.java, 1.1, 1.2 AbstractPlane3.java, 1.1, 1.2 AbstractPoint3.java, 1.1, 1.2 AbstractPotential.java, 1.1, 1.2 AbstractPotentialForm.java, 1.1, 1.2 AbstractPotentialList.java, 1.1, 1.2 AbstractProduct.java, 1.1, 1.2 AbstractProductList.java, 1.1, 1.2 AbstractProperty.java, 1.1, 1.2 AbstractPropertyList.java, 1.1, 1.2 AbstractReactant.java, 1.1, 1.2 AbstractReactantList.java, 1.1, 1.2 AbstractReaction.java, 1.1, 1.2 AbstractReactionList.java, 1.1, 1.2 AbstractReactionScheme.java, 1.1, 1.2 AbstractReactionStep.java, 1.1, 1.2 AbstractReactionStepList.java, 1.1, 1.2 AbstractReactiveCentre.java, 1.1, 1.2 AbstractRegion.java, 1.1, 1.2 AbstractRelatedEntry.java, 1.1, 1.2 AbstractSample.java, 1.1, 1.2 AbstractScalar.java, 1.1, 1.2 AbstractSpectator.java, 1.1, 1.2 AbstractSpectatorList.java, 1.1, 1.2 AbstractSpectrum.java, 1.1, 1.2 AbstractSpectrumData.java, 1.1, 1.2 AbstractSpectrumList.java, 1.1, 1.2 AbstractSphere3.java, 1.1, 1.2 AbstractStmml.java, 1.1, 1.2 AbstractString.java, 1.1, 1.2 AbstractStringArray.java, 1.1, 1.2 AbstractSubstance.java, 1.1, 1.2 AbstractSubstanceList.java, 1.1, 1.2 AbstractSymmetry.java, 1.1, 1.2 AbstractSystem.java, 1.1, 1.2 AbstractTable.java, 1.1, 1.2 AbstractTableContent.java, 1.1, 1.2 AbstractTableHeader.java, 1.1, 1.2 AbstractTableRow.java, 1.1, 1.2 AbstractTcell.java, 1.1, 1.2 AbstractTorsion.java, 1.1, 1.2 AbstractTransform3.java, 1.1, 1.2 AbstractTransitionState.java, 1.1, 1.2 AbstractTrow.java, 1.1, 1.2 AbstractUnit.java, 1.1, 1.2 AbstractUnitList.java, 1.1, 1.2 AbstractUnitType.java, 1.1, 1.2 AbstractUnitTypeList.java, 1.1, 1.2 AbstractVector3.java, 1.1, 1.2 AbstractXaxis.java, 1.1, 1.2 AbstractYaxis.java, 1.1, 1.2 AbstractZMatrix.java, 1.1, 1.2 CMLAtom.java, 1.2, 1.3 CMLAtomSet.java, 1.2, 1.3 CMLJoin.java, 1.3, 1.4 CMLMolecule.java, 1.2, 1.3 CMLNodeFactory.java, 1.2, 1.3 CMLTypeList.java, 1.1, 1.2
Update of /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element In directory sc8-pr-cvs4.sourceforge.net:/tmp/cvs-serv13136/src/org/xmlcml/cml/element Modified Files: AbstractAbundance.java AbstractAction.java AbstractActionList.java AbstractAlternative.java AbstractAmount.java AbstractAngle.java AbstractAnnotation.java AbstractAppinfo.java AbstractArg.java AbstractArray.java AbstractAtom.java AbstractAtomArray.java AbstractAtomParity.java AbstractAtomSet.java AbstractAtomType.java AbstractAtomTypeList.java AbstractAtomicBasisFunction.java AbstractBand.java AbstractBandList.java AbstractBasisSet.java AbstractBond.java AbstractBondArray.java AbstractBondSet.java AbstractBondStereo.java AbstractBondType.java AbstractBondTypeList.java AbstractCellParameter.java AbstractCml.java AbstractComplexObject.java AbstractConditionList.java AbstractCopy.java AbstractCrystal.java AbstractDefinition.java AbstractDescription.java AbstractDictionary.java AbstractDimension.java AbstractDocumentation.java AbstractEigen.java AbstractElectron.java AbstractEntry.java AbstractEnumeration.java AbstractExpression.java AbstractFloat.java AbstractFloatArray.java AbstractFor.java AbstractFormula.java AbstractGradient.java AbstractIdentifier.java AbstractIf.java AbstractInteger.java AbstractIntegerArray.java AbstractIsotope.java AbstractIsotopeList.java AbstractJoin.java AbstractKpoint.java AbstractKpointList.java AbstractLabel.java AbstractLattice.java AbstractLatticeVector.java AbstractLength.java AbstractLine3.java AbstractLink.java AbstractList.java AbstractMap.java AbstractMatrix.java AbstractMechanism.java AbstractMechanismComponent.java AbstractMetadata.java AbstractMetadataList.java AbstractModule.java AbstractMolecule.java AbstractName.java AbstractObject.java AbstractObservation.java AbstractOperator.java AbstractParameter.java AbstractParameterList.java AbstractParticle.java AbstractPeak.java AbstractPeakGroup.java AbstractPeakList.java AbstractPeakStructure.java AbstractPlane3.java AbstractPoint3.java AbstractPotential.java AbstractPotentialForm.java AbstractPotentialList.java AbstractProduct.java AbstractProductList.java AbstractProperty.java AbstractPropertyList.java AbstractReactant.java AbstractReactantList.java AbstractReaction.java AbstractReactionList.java AbstractReactionScheme.java AbstractReactionStep.java AbstractReactionStepList.java AbstractReactiveCentre.java AbstractRegion.java AbstractRelatedEntry.java AbstractSample.java AbstractScalar.java AbstractSpectator.java AbstractSpectatorList.java AbstractSpectrum.java AbstractSpectrumData.java AbstractSpectrumList.java AbstractSphere3.java AbstractStmml.java AbstractString.java AbstractStringArray.java AbstractSubstance.java AbstractSubstanceList.java AbstractSymmetry.java AbstractSystem.java AbstractTable.java AbstractTableContent.java AbstractTableHeader.java AbstractTableRow.java AbstractTcell.java AbstractTorsion.java AbstractTransform3.java AbstractTransitionState.java AbstractTrow.java AbstractUnit.java AbstractUnitList.java AbstractUnitType.java AbstractUnitTypeList.java AbstractVector3.java AbstractXaxis.java AbstractYaxis.java AbstractZMatrix.java CMLAtom.java CMLAtomSet.java CMLJoin.java CMLMolecule.java CMLNodeFactory.java CMLTypeList.java Log Message: Index: AbstractDescription.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractDescription.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractDescription.java 2 Jun 2006 15:47:45 -0000 1.1 --- AbstractDescription.java 23 Jun 2006 15:33:03 -0000 1.2 *************** *** 1,9 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; import java.util.HashMap; import java.util.Map; /** Descriptive information. * --- 1,15 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; + import nu.xom.Attribute; + + import org.xmlcml.cml.base.CMLAttribute; + import org.xmlcml.cml.base.CMLElement; + import org.xmlcml.cml.base.CMLException; + import org.xmlcml.cml.base.CMLRuntime; + import org.xmlcml.cml.base.StringAttribute; + /** Descriptive information. * Index: AbstractString.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractString.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractString.java 2 Jun 2006 15:47:48 -0000 1.1 --- AbstractString.java 23 Jun 2006 15:33:04 -0000 1.2 *************** *** 2,10 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; import java.util.HashMap; import java.util.Map; /** CML-1 dataType (DEPRECATED). * --- 2,16 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; + import nu.xom.Attribute; + + import org.xmlcml.cml.base.CMLAttribute; + import org.xmlcml.cml.base.CMLElement; + import org.xmlcml.cml.base.CMLException; + import org.xmlcml.cml.base.CMLRuntime; + import org.xmlcml.cml.base.StringAttribute; + /** CML-1 dataType (DEPRECATED). * Index: AbstractObservation.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractObservation.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractObservation.java 2 Jun 2006 15:47:46 -0000 1.1 --- AbstractObservation.java 23 Jun 2006 15:33:04 -0000 1.2 *************** *** 1,9 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; import java.util.HashMap; import java.util.Map; /** An observation or occurrence. * --- 1,16 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; + import nu.xom.Attribute; + + import org.xmlcml.cml.base.CMLAttribute; + import org.xmlcml.cml.base.CMLElement; + import org.xmlcml.cml.base.CMLException; + import org.xmlcml.cml.base.CMLRuntime; + import org.xmlcml.cml.base.DoubleAttribute; + import org.xmlcml.cml.base.StringAttribute; + /** An observation or occurrence. * Index: AbstractReactionStepList.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractReactionStepList.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractReactionStepList.java 2 Jun 2006 15:47:47 -0000 1.1 --- AbstractReactionStepList.java 23 Jun 2006 15:33:04 -0000 1.2 *************** *** 1,13 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; - import nu.xom.Elements; import java.util.HashMap; import java.util.Map; ! import org.xmlcml.cml.element.CMLMetadataList; ! import org.xmlcml.cml.element.CMLLabel; ! import org.xmlcml.cml.element.CMLName; ! import org.xmlcml.cml.element.CMLReactionStep; /** A container for one or more related reactionSteps. --- 1,16 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; ! ! import nu.xom.Attribute; ! import nu.xom.Elements; ! ! import org.xmlcml.cml.base.CMLAttribute; ! import org.xmlcml.cml.base.CMLElement; ! import org.xmlcml.cml.base.CMLElements; ! import org.xmlcml.cml.base.CMLException; ! import org.xmlcml.cml.base.CMLRuntime; ! import org.xmlcml.cml.base.StringAttribute; /** A container for one or more related reactionSteps. Index: AbstractFormula.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractFormula.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractFormula.java 2 Jun 2006 15:47:45 -0000 1.1 --- AbstractFormula.java 23 Jun 2006 15:33:03 -0000 1.2 *************** *** 1,11 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; - import nu.xom.Elements; import java.util.HashMap; import java.util.Map; ! import org.xmlcml.cml.element.CMLFormula; ! import org.xmlcml.cml.element.CMLAtomArray; /** A molecular formula. --- 1,18 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; ! ! import nu.xom.Attribute; ! import nu.xom.Elements; ! ! import org.xmlcml.cml.base.CMLAttribute; ! import org.xmlcml.cml.base.CMLElement; ! import org.xmlcml.cml.base.CMLElements; ! import org.xmlcml.cml.base.CMLException; ! import org.xmlcml.cml.base.CMLRuntime; ! import org.xmlcml.cml.base.DoubleAttribute; ! import org.xmlcml.cml.base.IntAttribute; ! import org.xmlcml.cml.base.StringAttribute; /** A molecular formula. Index: AbstractEigen.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractEigen.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractEigen.java 2 Jun 2006 15:47:45 -0000 1.1 --- AbstractEigen.java 23 Jun 2006 15:33:03 -0000 1.2 *************** *** 1,11 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; - import nu.xom.Elements; import java.util.HashMap; import java.util.Map; ! import org.xmlcml.cml.element.CMLMatrix; ! import org.xmlcml.cml.element.CMLArray; /** No current semantics. --- 1,16 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; ! ! import nu.xom.Attribute; ! import nu.xom.Elements; ! ! import org.xmlcml.cml.base.CMLAttribute; ! import org.xmlcml.cml.base.CMLElement; ! import org.xmlcml.cml.base.CMLElements; ! import org.xmlcml.cml.base.CMLException; ! import org.xmlcml.cml.base.CMLRuntime; ! import org.xmlcml.cml.base.StringAttribute; /** No current semantics. Index: AbstractAlternative.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractAlternative.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractAlternative.java 2 Jun 2006 15:47:43 -0000 1.1 --- AbstractAlternative.java 23 Jun 2006 15:33:03 -0000 1.2 *************** *** 2,10 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; import java.util.HashMap; import java.util.Map; /** An alternative name for an entry. * --- 2,16 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; + import nu.xom.Attribute; + + import org.xmlcml.cml.base.CMLAttribute; + import org.xmlcml.cml.base.CMLElement; + import org.xmlcml.cml.base.CMLException; + import org.xmlcml.cml.base.CMLRuntime; + import org.xmlcml.cml.base.StringAttribute; + /** An alternative name for an entry. * Index: AbstractPotentialForm.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractPotentialForm.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractPotentialForm.java 2 Jun 2006 15:47:46 -0000 1.1 --- AbstractPotentialForm.java 23 Jun 2006 15:33:04 -0000 1.2 *************** *** 1,12 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; - import nu.xom.Elements; import java.util.HashMap; import java.util.Map; ! import org.xmlcml.cml.element.CMLArg; ! import org.xmlcml.cml.element.CMLExpression; ! import org.xmlcml.cml.element.CMLParameter; /** The functional form of a potential. --- 1,16 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; ! ! import nu.xom.Attribute; ! import nu.xom.Elements; ! ! import org.xmlcml.cml.base.CMLAttribute; ! import org.xmlcml.cml.base.CMLElement; ! import org.xmlcml.cml.base.CMLElements; ! import org.xmlcml.cml.base.CMLException; ! import org.xmlcml.cml.base.CMLRuntime; ! import org.xmlcml.cml.base.StringAttribute; /** The functional form of a potential. Index: AbstractModule.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractModule.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractModule.java 2 Jun 2006 15:47:46 -0000 1.1 --- AbstractModule.java 23 Jun 2006 15:33:04 -0000 1.2 *************** *** 1,9 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; import java.util.HashMap; import java.util.Map; /** A module in a calculation. * --- 1,15 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; + import nu.xom.Attribute; + + import org.xmlcml.cml.base.CMLAttribute; + import org.xmlcml.cml.base.CMLElement; + import org.xmlcml.cml.base.CMLException; + import org.xmlcml.cml.base.CMLRuntime; + import org.xmlcml.cml.base.StringAttribute; + /** A module in a calculation. * Index: AbstractStringArray.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractStringArray.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractStringArray.java 2 Jun 2006 15:47:48 -0000 1.1 --- AbstractStringArray.java 23 Jun 2006 15:33:04 -0000 1.2 *************** *** 2,10 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; import java.util.HashMap; import java.util.Map; /** CML-1 dataType DEPRECATED. * --- 2,17 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; + import nu.xom.Attribute; + + import org.xmlcml.cml.base.CMLAttribute; + import org.xmlcml.cml.base.CMLElement; + import org.xmlcml.cml.base.CMLException; + import org.xmlcml.cml.base.CMLRuntime; + import org.xmlcml.cml.base.IntAttribute; + import org.xmlcml.cml.base.StringAttribute; + /** CML-1 dataType DEPRECATED. * Index: AbstractBondSet.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractBondSet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractBondSet.java 2 Jun 2006 15:47:44 -0000 1.1 --- AbstractBondSet.java 23 Jun 2006 15:33:03 -0000 1.2 *************** *** 2,10 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; import java.util.HashMap; import java.util.Map; /** A set of references to bonds. * --- 2,18 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; + import nu.xom.Attribute; + + import org.xmlcml.cml.base.CMLAttribute; + import org.xmlcml.cml.base.CMLElement; + import org.xmlcml.cml.base.CMLException; + import org.xmlcml.cml.base.CMLRuntime; + import org.xmlcml.cml.base.IntAttribute; + import org.xmlcml.cml.base.StringArrayAttribute; + import org.xmlcml.cml.base.StringAttribute; + /** A set of references to bonds. * Index: AbstractUnit.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractUnit.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractUnit.java 2 Jun 2006 15:47:50 -0000 1.1 --- AbstractUnit.java 23 Jun 2006 15:33:04 -0000 1.2 *************** *** 1,16 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; - import nu.xom.Elements; import java.util.HashMap; import java.util.Map; ! import org.xmlcml.cml.element.CMLUnitType; ! import org.xmlcml.cml.element.CMLAnnotation; ! import org.xmlcml.cml.element.CMLMetadataList; ! import org.xmlcml.cml.element.CMLUnit; ! import org.xmlcml.cml.element.CMLDefinition; ! import org.xmlcml.cml.element.CMLDescription; ! import org.xmlcml.cml.element.CMLMetadata; /** Power of unit used to create new one. --- 1,17 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; ! ! import nu.xom.Attribute; ! import nu.xom.Elements; ! ! import org.xmlcml.cml.base.CMLAttribute; ! import org.xmlcml.cml.base.CMLElement; ! import org.xmlcml.cml.base.CMLElements; ! import org.xmlcml.cml.base.CMLException; ! import org.xmlcml.cml.base.CMLRuntime; ! import org.xmlcml.cml.base.DoubleAttribute; ! import org.xmlcml.cml.base.StringAttribute; /** Power of unit used to create new one. Index: AbstractBondArray.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractBondArray.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractBondArray.java 2 Jun 2006 15:47:44 -0000 1.1 --- AbstractBondArray.java 23 Jun 2006 15:33:03 -0000 1.2 *************** *** 1,11 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; - import nu.xom.Elements; import java.util.HashMap; import java.util.Map; ! import org.xmlcml.cml.element.CMLBond; ! import org.xmlcml.cml.element.CMLArray; /** A container for a number of bonds. --- 1,17 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; ! ! import nu.xom.Attribute; ! import nu.xom.Elements; ! ! import org.xmlcml.cml.base.CMLAttribute; ! import org.xmlcml.cml.base.CMLElement; ! import org.xmlcml.cml.base.CMLElements; ! import org.xmlcml.cml.base.CMLException; ! import org.xmlcml.cml.base.CMLRuntime; ! import org.xmlcml.cml.base.StringArrayAttribute; ! import org.xmlcml.cml.base.StringAttribute; /** A container for a number of bonds. Index: CMLAtomSet.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/CMLAtomSet.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** CMLAtomSet.java 12 Jun 2006 22:09:32 -0000 1.2 --- CMLAtomSet.java 23 Jun 2006 15:33:05 -0000 1.3 *************** *** 1111,1114 **** --- 1111,1127 ---- /** + * transform fractional and 3D coordinates. does NOT alter 2D coordinates + * transforms fractionals then applies orthogonalisation to result + * @param transform + * the fractional symmetry transformation + * @param orthTransform + * orthogonalisation transform + */ + public void transformFractionalsAndCartesians(CMLTransform3 transform, Transform3 orthTransform) { + for (CMLAtom atom : getAtoms()) { + atom.transformFractionalsAndCartesians(transform, orthTransform); + } + } + /** * translate centroid of atomSet2 to centroid of this. * Index: AbstractYaxis.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractYaxis.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractYaxis.java 2 Jun 2006 15:47:51 -0000 1.1 --- AbstractYaxis.java 23 Jun 2006 15:33:05 -0000 1.2 *************** *** 1,10 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; - import nu.xom.Elements; import java.util.HashMap; import java.util.Map; ! import org.xmlcml.cml.element.CMLArray; /** The y-axis. --- 1,17 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; ! ! import nu.xom.Attribute; ! import nu.xom.Elements; ! ! import org.xmlcml.cml.base.CMLAttribute; ! import org.xmlcml.cml.base.CMLElement; ! import org.xmlcml.cml.base.CMLElements; ! import org.xmlcml.cml.base.CMLException; ! import org.xmlcml.cml.base.CMLRuntime; ! import org.xmlcml.cml.base.DoubleAttribute; ! import org.xmlcml.cml.base.StringAttribute; /** The y-axis. Index: AbstractBond.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractBond.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractBond.java 2 Jun 2006 15:47:44 -0000 1.1 --- AbstractBond.java 23 Jun 2006 15:33:03 -0000 1.2 *************** *** 1,12 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; - import nu.xom.Elements; import java.util.HashMap; import java.util.Map; ! import org.xmlcml.cml.element.CMLElectron; ! import org.xmlcml.cml.element.CMLBondStereo; ! import org.xmlcml.cml.element.CMLBondType; /** A bond between atoms, or between atoms and bonds. --- 1,17 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; ! ! import nu.xom.Attribute; ! import nu.xom.Elements; ! ! import org.xmlcml.cml.base.CMLAttribute; ! import org.xmlcml.cml.base.CMLElement; ! import org.xmlcml.cml.base.CMLElements; ! import org.xmlcml.cml.base.CMLException; ! import org.xmlcml.cml.base.CMLRuntime; ! import org.xmlcml.cml.base.StringArrayAttribute; ! import org.xmlcml.cml.base.StringAttribute; /** A bond between atoms, or between atoms and bonds. Index: AbstractParameterList.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractParameterList.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractParameterList.java 2 Jun 2006 15:47:46 -0000 1.1 --- AbstractParameterList.java 23 Jun 2006 15:33:04 -0000 1.2 *************** *** 1,13 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; - import nu.xom.Elements; import java.util.HashMap; import java.util.Map; ! import org.xmlcml.cml.element.CMLParameterList; ! import org.xmlcml.cml.element.CMLMetadataList; ! import org.xmlcml.cml.element.CMLParameter; ! import org.xmlcml.cml.element.CMLName; /** A container for one or more parameters. --- 1,16 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; ! ! import nu.xom.Attribute; ! import nu.xom.Elements; ! ! import org.xmlcml.cml.base.CMLAttribute; ! import org.xmlcml.cml.base.CMLElement; ! import org.xmlcml.cml.base.CMLElements; ! import org.xmlcml.cml.base.CMLException; ! import org.xmlcml.cml.base.CMLRuntime; ! import org.xmlcml.cml.base.StringAttribute; /** A container for one or more parameters. Index: AbstractReaction.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractReaction.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractReaction.java 2 Jun 2006 15:47:47 -0000 1.1 --- AbstractReaction.java 23 Jun 2006 15:33:04 -0000 1.2 *************** *** 1,24 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; - import nu.xom.Elements; import java.util.HashMap; import java.util.Map; ! import org.xmlcml.cml.element.CMLMetadataList; ! import org.xmlcml.cml.element.CMLMechanism; ! import org.xmlcml.cml.element.CMLReactiveCentre; ! import org.xmlcml.cml.element.CMLPropertyList; ! import org.xmlcml.cml.element.CMLReactantList; ! import org.xmlcml.cml.element.CMLSubstanceList; ! import org.xmlcml.cml.element.CMLObject; ! import org.xmlcml.cml.element.CMLConditionList; ! import org.xmlcml.cml.element.CMLLabel; ! import org.xmlcml.cml.element.CMLTransitionState; ! import org.xmlcml.cml.element.CMLSpectatorList; ! import org.xmlcml.cml.element.CMLMap; ! import org.xmlcml.cml.element.CMLIdentifier; ! import org.xmlcml.cml.element.CMLProductList; ! import org.xmlcml.cml.element.CMLName; /** A chemical reaction or reaction step. --- 1,17 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; ! ! import nu.xom.Attribute; ! import nu.xom.Elements; ! ! import org.xmlcml.cml.base.CMLAttribute; ! import org.xmlcml.cml.base.CMLElement; ! import org.xmlcml.cml.base.CMLElements; ! import org.xmlcml.cml.base.CMLException; ! import org.xmlcml.cml.base.CMLRuntime; ! import org.xmlcml.cml.base.DoubleAttribute; ! import org.xmlcml.cml.base.StringAttribute; /** A chemical reaction or reaction step. Index: AbstractSpectator.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractSpectator.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractSpectator.java 2 Jun 2006 15:47:47 -0000 1.1 --- AbstractSpectator.java 23 Jun 2006 15:33:04 -0000 1.2 *************** *** 1,13 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; - import nu.xom.Elements; import java.util.HashMap; import java.util.Map; ! import org.xmlcml.cml.element.CMLObject; ! import org.xmlcml.cml.element.CMLMetadataList; ! import org.xmlcml.cml.element.CMLLabel; ! import org.xmlcml.cml.element.CMLMolecule; /** A spectator object in a reaction. --- 1,16 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; ! ! import nu.xom.Attribute; ! import nu.xom.Elements; ! ! import org.xmlcml.cml.base.CMLAttribute; ! import org.xmlcml.cml.base.CMLElement; ! import org.xmlcml.cml.base.CMLElements; ! import org.xmlcml.cml.base.CMLException; ! import org.xmlcml.cml.base.CMLRuntime; ! import org.xmlcml.cml.base.StringAttribute; /** A spectator object in a reaction. Index: AbstractXaxis.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractXaxis.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractXaxis.java 2 Jun 2006 15:47:51 -0000 1.1 --- AbstractXaxis.java 23 Jun 2006 15:33:05 -0000 1.2 *************** *** 1,10 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; - import nu.xom.Elements; import java.util.HashMap; import java.util.Map; ! import org.xmlcml.cml.element.CMLArray; /** The x-axis. --- 1,17 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; ! ! import nu.xom.Attribute; ! import nu.xom.Elements; ! ! import org.xmlcml.cml.base.CMLAttribute; ! import org.xmlcml.cml.base.CMLElement; ! import org.xmlcml.cml.base.CMLElements; ! import org.xmlcml.cml.base.CMLException; ! import org.xmlcml.cml.base.CMLRuntime; ! import org.xmlcml.cml.base.DoubleAttribute; ! import org.xmlcml.cml.base.StringAttribute; /** The x-axis. Index: AbstractOperator.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractOperator.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractOperator.java 2 Jun 2006 15:47:46 -0000 1.1 --- AbstractOperator.java 23 Jun 2006 15:33:04 -0000 1.2 *************** *** 1,9 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; import java.util.HashMap; import java.util.Map; /** An operator within an expression. * --- 1,15 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; + import nu.xom.Attribute; + + import org.xmlcml.cml.base.CMLAttribute; + import org.xmlcml.cml.base.CMLElement; + import org.xmlcml.cml.base.CMLException; + import org.xmlcml.cml.base.CMLRuntime; + import org.xmlcml.cml.base.StringAttribute; + /** An operator within an expression. * Index: AbstractBondStereo.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractBondStereo.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractBondStereo.java 2 Jun 2006 15:47:44 -0000 1.1 --- AbstractBondStereo.java 23 Jun 2006 15:33:03 -0000 1.2 *************** *** 2,10 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; import java.util.HashMap; import java.util.Map; /** A container supporting cis trans wedge hatch and other stereochemistry. * --- 2,17 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; + import nu.xom.Attribute; + + import org.xmlcml.cml.base.CMLAttribute; + import org.xmlcml.cml.base.CMLElement; + import org.xmlcml.cml.base.CMLException; + import org.xmlcml.cml.base.CMLRuntime; + import org.xmlcml.cml.base.StringArrayAttribute; + import org.xmlcml.cml.base.StringAttribute; + /** A container supporting cis trans wedge hatch and other stereochemistry. * Index: AbstractProductList.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractProductList.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractProductList.java 2 Jun 2006 15:47:47 -0000 1.1 --- AbstractProductList.java 23 Jun 2006 15:33:04 -0000 1.2 *************** *** 1,13 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; - import nu.xom.Elements; import java.util.HashMap; import java.util.Map; ! import org.xmlcml.cml.element.CMLProduct; ! import org.xmlcml.cml.element.CMLMetadataList; ! import org.xmlcml.cml.element.CMLProductList; ! import org.xmlcml.cml.element.CMLName; /** A container for one or more products. --- 1,17 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; ! ! import nu.xom.Attribute; ! import nu.xom.Elements; ! ! import org.xmlcml.cml.base.CMLAttribute; ! import org.xmlcml.cml.base.CMLElement; ! import org.xmlcml.cml.base.CMLElements; ! import org.xmlcml.cml.base.CMLException; ! import org.xmlcml.cml.base.CMLRuntime; ! import org.xmlcml.cml.base.DoubleAttribute; ! import org.xmlcml.cml.base.StringAttribute; /** A container for one or more products. Index: AbstractGradient.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractGradient.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractGradient.java 2 Jun 2006 15:47:45 -0000 1.1 --- AbstractGradient.java 23 Jun 2006 15:33:03 -0000 1.2 *************** *** 1,13 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; - import nu.xom.Elements; import java.util.HashMap; import java.util.Map; ! import org.xmlcml.cml.element.CMLMatrix; ! import org.xmlcml.cml.element.CMLProperty; ! import org.xmlcml.cml.element.CMLArray; ! import org.xmlcml.cml.element.CMLScalar; /** A gradient. --- 1,16 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; ! ! import nu.xom.Attribute; ! import nu.xom.Elements; ! ! import org.xmlcml.cml.base.CMLAttribute; ! import org.xmlcml.cml.base.CMLElement; ! import org.xmlcml.cml.base.CMLElements; ! import org.xmlcml.cml.base.CMLException; ! import org.xmlcml.cml.base.CMLRuntime; ! import org.xmlcml.cml.base.StringAttribute; /** A gradient. Index: AbstractTorsion.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractTorsion.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractTorsion.java 2 Jun 2006 15:47:50 -0000 1.1 --- AbstractTorsion.java 23 Jun 2006 15:33:04 -0000 1.2 *************** *** 2,10 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; import java.util.HashMap; import java.util.Map; /** A torsion angle ("dihedral") between 4 distinct atoms. * --- 2,18 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; + import nu.xom.Attribute; + + import org.xmlcml.cml.base.CMLAttribute; + import org.xmlcml.cml.base.CMLElement; + import org.xmlcml.cml.base.CMLException; + import org.xmlcml.cml.base.CMLRuntime; + import org.xmlcml.cml.base.DoubleAttribute; + import org.xmlcml.cml.base.StringArrayAttribute; + import org.xmlcml.cml.base.StringAttribute; + /** A torsion angle ("dihedral") between 4 distinct atoms. * Index: AbstractSubstanceList.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractSubstanceList.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractSubstanceList.java 2 Jun 2006 15:47:49 -0000 1.1 --- AbstractSubstanceList.java 23 Jun 2006 15:33:04 -0000 1.2 *************** *** 1,13 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; - import nu.xom.Elements; import java.util.HashMap; import java.util.Map; ! import org.xmlcml.cml.element.CMLAmount; ! import org.xmlcml.cml.element.CMLMetadataList; ! import org.xmlcml.cml.element.CMLPropertyList; ! import org.xmlcml.cml.element.CMLSubstance; /** A list of chemical substances. --- 1,16 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; ! ! import nu.xom.Attribute; ! import nu.xom.Elements; ! ! import org.xmlcml.cml.base.CMLAttribute; ! import org.xmlcml.cml.base.CMLElement; ! import org.xmlcml.cml.base.CMLElements; ! import org.xmlcml.cml.base.CMLException; ! import org.xmlcml.cml.base.CMLRuntime; ! import org.xmlcml.cml.base.StringAttribute; /** A list of chemical substances. Index: AbstractSymmetry.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractSymmetry.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractSymmetry.java 2 Jun 2006 15:47:49 -0000 1.1 --- AbstractSymmetry.java 23 Jun 2006 15:33:04 -0000 1.2 *************** *** 1,11 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; - import nu.xom.Elements; import java.util.HashMap; import java.util.Map; ! import org.xmlcml.cml.element.CMLMatrix; ! import org.xmlcml.cml.element.CMLTransform3; /** Molecular, crystallographic or other symmetry. --- 1,17 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; ! ! import nu.xom.Attribute; ! import nu.xom.Elements; ! ! import org.xmlcml.cml.base.CMLAttribute; ! import org.xmlcml.cml.base.CMLElement; ! import org.xmlcml.cml.base.CMLElements; ! import org.xmlcml.cml.base.CMLException; ! import org.xmlcml.cml.base.CMLRuntime; ! import org.xmlcml.cml.base.IntAttribute; ! import org.xmlcml.cml.base.StringAttribute; /** Molecular, crystallographic or other symmetry. Index: AbstractTableRow.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractTableRow.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractTableRow.java 2 Jun 2006 15:47:49 -0000 1.1 --- AbstractTableRow.java 23 Jun 2006 15:33:04 -0000 1.2 *************** *** 2,10 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; import java.util.HashMap; import java.util.Map; /** Explicit row of a table. * --- 2,16 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; + import nu.xom.Attribute; + + import org.xmlcml.cml.base.CMLAttribute; + import org.xmlcml.cml.base.CMLElement; + import org.xmlcml.cml.base.CMLException; + import org.xmlcml.cml.base.CMLRuntime; + import org.xmlcml.cml.base.StringAttribute; + /** Explicit row of a table. * Index: AbstractAtomSet.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractAtomSet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractAtomSet.java 2 Jun 2006 15:47:44 -0000 1.1 --- AbstractAtomSet.java 23 Jun 2006 15:33:03 -0000 1.2 *************** *** 2,10 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; import java.util.HashMap; import java.util.Map; /** A set of references to atoms. * --- 2,18 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; + import nu.xom.Attribute; + + import org.xmlcml.cml.base.CMLAttribute; + import org.xmlcml.cml.base.CMLElement; + import org.xmlcml.cml.base.CMLException; + import org.xmlcml.cml.base.CMLRuntime; + import org.xmlcml.cml.base.IntAttribute; + import org.xmlcml.cml.base.StringArrayAttribute; + import org.xmlcml.cml.base.StringAttribute; + /** A set of references to atoms. * Index: AbstractDimension.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractDimension.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractDimension.java 2 Jun 2006 15:47:45 -0000 1.1 --- AbstractDimension.java 23 Jun 2006 15:33:03 -0000 1.2 *************** *** 1,9 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; import java.util.HashMap; import java.util.Map; /** A dimension supporting scientific unit. * --- 1,16 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; + import nu.xom.Attribute; + + import org.xmlcml.cml.base.CMLAttribute; + import org.xmlcml.cml.base.CMLElement; + import org.xmlcml.cml.base.CMLException; + import org.xmlcml.cml.base.CMLRuntime; + import org.xmlcml.cml.base.DoubleAttribute; + import org.xmlcml.cml.base.StringAttribute; + /** A dimension supporting scientific unit. * Index: CMLAtom.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/CMLAtom.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** CMLAtom.java 12 Jun 2006 22:09:32 -0000 1.2 --- CMLAtom.java 23 Jun 2006 15:33:05 -0000 1.3 *************** *** 306,309 **** --- 306,327 ---- /** + * transform fractional and 3D coordinates. does NOT alter 2D coordinates + * transforms fractionals then applies orthogonalisation to result + * @param transform + * the fractional symmetry transformation + * @param orthTransform + * orthogonalisation transform + */ + public void transformFractionalsAndCartesians(CMLTransform3 transform, Transform3 orthTransform) { + Point3 point = this.getXYZFract(); + point = point.transform(transform.getEuclidTransform3()); + this.setXYZFract(point); + point = point.transform(orthTransform); + this.setXYZ3(point); + // this.debug(); + // System.out.println("@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"); + } + + /** * gets Point3 for xFract, yFract, zFract. * *************** *** 677,681 **** } - /** * simple atom comparison based on atomic mass (not recursive). --- 695,698 ---- Index: AbstractMap.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractMap.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractMap.java 2 Jun 2006 15:47:46 -0000 1.1 --- AbstractMap.java 23 Jun 2006 15:33:04 -0000 1.2 *************** *** 1,10 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; - import nu.xom.Elements; import java.util.HashMap; import java.util.Map; ! import org.xmlcml.cml.element.CMLLink; /** A container for links. --- 1,16 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; ! ! import nu.xom.Attribute; ! import nu.xom.Elements; ! ! import org.xmlcml.cml.base.CMLAttribute; ! import org.xmlcml.cml.base.CMLElement; ! import org.xmlcml.cml.base.CMLElements; ! import org.xmlcml.cml.base.CMLException; ! import org.xmlcml.cml.base.CMLRuntime; ! import org.xmlcml.cml.base.StringAttribute; /** A container for links. Index: AbstractFloat.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractFloat.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractFloat.java 2 Jun 2006 15:47:45 -0000 1.1 --- AbstractFloat.java 23 Jun 2006 15:33:03 -0000 1.2 *************** *** 2,10 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; import java.util.HashMap; import java.util.Map; /** CML-1 dataType DEPRECATED. * --- 2,17 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; + import nu.xom.Attribute; + + import org.xmlcml.cml.base.CMLAttribute; + import org.xmlcml.cml.base.CMLElement; + import org.xmlcml.cml.base.CMLException; + import org.xmlcml.cml.base.CMLRuntime; + import org.xmlcml.cml.base.DoubleAttribute; + import org.xmlcml.cml.base.StringAttribute; + /** CML-1 dataType DEPRECATED. * Index: AbstractTrow.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractTrow.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractTrow.java 2 Jun 2006 15:47:50 -0000 1.1 --- AbstractTrow.java 23 Jun 2006 15:33:04 -0000 1.2 *************** *** 1,10 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; - import nu.xom.Elements; import java.util.HashMap; import java.util.Map; ! import org.xmlcml.cml.element.CMLTcell; /** A row in a table. --- 1,16 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; ! ! import nu.xom.Attribute; ! import nu.xom.Elements; ! ! import org.xmlcml.cml.base.CMLAttribute; ! import org.xmlcml.cml.base.CMLElement; ! import org.xmlcml.cml.base.CMLElements; ! import org.xmlcml.cml.base.CMLException; ! import org.xmlcml.cml.base.CMLRuntime; ! import org.xmlcml.cml.base.StringAttribute; /** A row in a table. Index: AbstractZMatrix.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractZMatrix.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractZMatrix.java 2 Jun 2006 15:47:51 -0000 1.1 --- AbstractZMatrix.java 23 Jun 2006 15:33:05 -0000 1.2 *************** *** 1,12 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; - import nu.xom.Elements; import java.util.HashMap; import java.util.Map; ! import org.xmlcml.cml.element.CMLLength; ! import org.xmlcml.cml.element.CMLAngle; ! import org.xmlcml.cml.element.CMLTorsion; /** A zMatrix. --- 1,16 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; ! ! import nu.xom.Attribute; ! import nu.xom.Elements; ! ! import org.xmlcml.cml.base.CMLAttribute; ! import org.xmlcml.cml.base.CMLElement; ! import org.xmlcml.cml.base.CMLElements; ! import org.xmlcml.cml.base.CMLException; ! import org.xmlcml.cml.base.CMLRuntime; ! import org.xmlcml.cml.base.StringAttribute; /** A zMatrix. Index: AbstractIdentifier.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractIdentifier.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractIdentifier.java 2 Jun 2006 15:47:45 -0000 1.1 --- AbstractIdentifier.java 23 Jun 2006 15:33:03 -0000 1.2 *************** *** 1,9 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; import java.util.HashMap; import java.util.Map; /** A structured identifier. * --- 1,15 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; + import nu.xom.Attribute; + + import org.xmlcml.cml.base.CMLAttribute; + import org.xmlcml.cml.base.CMLElement; + import org.xmlcml.cml.base.CMLException; + import org.xmlcml.cml.base.CMLRuntime; + import org.xmlcml.cml.base.StringAttribute; + /** A structured identifier. * Index: AbstractPeak.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractPeak.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractPeak.java 2 Jun 2006 15:47:46 -0000 1.1 --- AbstractPeak.java 23 Jun 2006 15:33:04 -0000 1.2 *************** *** 1,14 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; - import nu.xom.Elements; import java.util.HashMap; import java.util.Map; ! import org.xmlcml.cml.element.CMLMetadataList; ! import org.xmlcml.cml.element.CMLAtom; ! import org.xmlcml.cml.element.CMLPeakStructure; ! import org.xmlcml.cml.element.CMLBond; ! import org.xmlcml.cml.element.CMLMolecule; /** Molecule(s) contributing to this peak. --- 1,18 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; ! ! import nu.xom.Attribute; ! import nu.xom.Elements; ! ! import org.xmlcml.cml.base.CMLAttribute; ! import org.xmlcml.cml.base.CMLElement; ! import org.xmlcml.cml.base.CMLElements; ! import org.xmlcml.cml.base.CMLException; ! import org.xmlcml.cml.base.CMLRuntime; ! import org.xmlcml.cml.base.DoubleAttribute; ! import org.xmlcml.cml.base.StringArrayAttribute; ! import org.xmlcml.cml.base.StringAttribute; /** Molecule(s) contributing to this peak. Index: AbstractMechanismComponent.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractMechanismComponent.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractMechanismComponent.java 2 Jun 2006 15:47:46 -0000 1.1 --- AbstractMechanismComponent.java 23 Jun 2006 15:33:04 -0000 1.2 *************** *** 1,9 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; import java.util.HashMap; import java.util.Map; /** An information component within a reaction mechanism. * --- 1,15 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; + import nu.xom.Attribute; + + import org.xmlcml.cml.base.CMLAttribute; + import org.xmlcml.cml.base.CMLElement; + import org.xmlcml.cml.base.CMLException; + import org.xmlcml.cml.base.CMLRuntime; + import org.xmlcml.cml.base.StringAttribute; + /** An information component within a reaction mechanism. * Index: AbstractLabel.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractLabel.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractLabel.java 2 Jun 2006 15:47:45 -0000 1.1 --- AbstractLabel.java 23 Jun 2006 15:33:03 -0000 1.2 *************** *** 1,9 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; import java.util.HashMap; import java.util.Map; /** A text string qualifying an object. * --- 1,15 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; + import nu.xom.Attribute; + + import org.xmlcml.cml.base.CMLAttribute; + import org.xmlcml.cml.base.CMLElement; + import org.xmlcml.cml.base.CMLException; + import org.xmlcml.cml.base.CMLRuntime; + import org.xmlcml.cml.base.StringAttribute; + /** A text string qualifying an object. * Index: AbstractAngle.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractAngle.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractAngle.java 2 Jun 2006 15:47:43 -0000 1.1 --- AbstractAngle.java 23 Jun 2006 15:33:03 -0000 1.2 *************** *** 2,10 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; import java.util.HashMap; import java.util.Map; /** An angle between three atoms. * --- 2,18 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; + import nu.xom.Attribute; + + import org.xmlcml.cml.base.CMLAttribute; + import org.xmlcml.cml.base.CMLElement; + import org.xmlcml.cml.base.CMLException; + import org.xmlcml.cml.base.CMLRuntime; + import org.xmlcml.cml.base.DoubleAttribute; + import org.xmlcml.cml.base.StringArrayAttribute; + import org.xmlcml.cml.base.StringAttribute; + /** An angle between three atoms. * Index: CMLMolecule.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/CMLMolecule.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** CMLMolecule.java 12 Jun 2006 22:09:33 -0000 1.2 --- CMLMolecule.java 23 Jun 2006 15:33:05 -0000 1.3 *************** *** 764,768 **** countEx = countEx.substring("gaussian".length()); int[] counts = parseCount(countEx); ! if (counts[0] <= 3 || counts[1] < 1 || counts[0] / counts[1] < 3) { throw new CMLRuntime("Bad gaussian: "+countEx); --- 764,768 ---- countEx = countEx.substring("gaussian".length()); int[] counts = parseCount(countEx); ! if (counts.length != 2 || counts[0] <= 3 || counts[1] < 1 || counts[0] / counts[1] < 3) { throw new CMLRuntime("Bad gaussian: "+countEx); *************** *** 772,776 **** countEx = countEx.substring("range".length()); int[] counts = parseCount(countEx); ! if (counts[0] <= 0 || counts[0] >= counts[1]) { throw new CMLRuntime("Bad range: "+countEx); } --- 772,776 ---- countEx = countEx.substring("range".length()); int[] counts = parseCount(countEx); ! if (counts.length != 2 || counts[0] <= 0 || counts[0] >= counts[1]) { throw new CMLRuntime("Bad range: "+countEx); } *************** *** 779,792 **** double dd = mid2 + delta2 * (0.5 - Math.random()); count = (int) Math.round(dd); ! } else { ! try { ! count = Integer.parseInt(countEx); ! } catch (NumberFormatException e) { ! throw new CMLRuntime("Cannot parse integer: "+countEx); ! } ! if (count < 1) { ! System.out.println("WARNING count < 1: "+count); ! count = 1; } } } --- 779,790 ---- double dd = mid2 + delta2 * (0.5 - Math.random()); count = (int) Math.round(dd); ! } else if (countEx.startsWith(S_STAR)) { ! countEx = countEx.substring(S_STAR.length()); ! int[] counts = parseCount(countEx); ! if (counts.length != 1) { ! throw new CMLRuntime("Bad range: "+countEx); } + count = counts[0]; + } else { } } *************** *** 795,799 **** private int[] parseCount(String countEx) { - int[] counts = new int[2]; if (!countEx.startsWith(S_LBRAK) || !countEx.endsWith(S_RBRAK)) { --- 793,796 ---- *************** *** 802,809 **** countEx = countEx.substring(1, countEx.length()-1).trim(); String[] countStrings = countEx.split(S_COMMA); ! if (countStrings.length != 2) { ! throw new CMLRuntime("Bad range: "+countEx); ! } ! for (int i = 0; i < 2; i++) { try { counts[i] = Integer.parseInt(countStrings[i]); --- 799,804 ---- countEx = countEx.substring(1, countEx.length()-1).trim(); String[] countStrings = countEx.split(S_COMMA); ! int[] counts = new int[countStrings.length]; ! for (int i = 0; i < countStrings.length; i++) { try { counts[i] = Integer.parseInt(countStrings[i]); *************** *** 1363,1366 **** --- 1358,1375 ---- /** + * transform fractional and 3D coordinates. does NOT alter 2D coordinates + * transforms fractionals then applies orthogonalisation to result + * @param transform + * the fractional symmetry transformation + * @param orthMat + * orthogonalisation matrix + */ + public void transformFractionalsAndCartesians(CMLTransform3 transform, Transform3 orthMat) { + CMLAtomSet atomSet = this.getAtomSet(); + if (atomSet != null) { + atomSet.transformFractionalsAndCartesians(transform, orthMat); + } + } + /** * translate molecule in 2D. * Index: AbstractBondType.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractBondType.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractBondType.java 2 Jun 2006 15:47:44 -0000 1.1 --- AbstractBondType.java 23 Jun 2006 15:33:03 -0000 1.2 *************** *** 1,16 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; - import nu.xom.Elements; import java.util.HashMap; import java.util.Map; ! import org.xmlcml.cml.element.CMLMatrix; ! import org.xmlcml.cml.element.CMLLabel; ! import org.xmlcml.cml.element.CMLProperty; ! import org.xmlcml.cml.element.CMLBond; ! import org.xmlcml.cml.element.CMLMolecule; ! import org.xmlcml.cml.element.CMLArray; ! import org.xmlcml.cml.element.CMLScalar; /** The type of a bond. --- 1,16 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; ! ! import nu.xom.Attribute; ! import nu.xom.Elements; ! ! import org.xmlcml.cml.base.CMLAttribute; ! import org.xmlcml.cml.base.CMLElement; ! import org.xmlcml.cml.base.CMLElements; ! import org.xmlcml.cml.base.CMLException; ! import org.xmlcml.cml.base.CMLRuntime; ! import org.xmlcml.cml.base.StringAttribute; /** The type of a bond. Index: AbstractLink.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractLink.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractLink.java 2 Jun 2006 15:47:46 -0000 1.1 --- AbstractLink.java 23 Jun 2006 15:33:04 -0000 1.2 *************** *** 1,9 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; import java.util.HashMap; import java.util.Map; /** An internal or external link to other objects. * --- 1,16 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; + import nu.xom.Attribute; + + import org.xmlcml.cml.base.CMLAttribute; + import org.xmlcml.cml.base.CMLElement; + import org.xmlcml.cml.base.CMLException; + import org.xmlcml.cml.base.CMLRuntime; + import org.xmlcml.cml.base.StringArrayAttribute; + import org.xmlcml.cml.base.StringAttribute; + /** An internal or external link to other objects. * Index: AbstractTcell.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractTcell.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractTcell.java 2 Jun 2006 15:47:50 -0000 1.1 --- AbstractTcell.java 23 Jun 2006 15:33:04 -0000 1.2 *************** *** 1,9 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; import java.util.HashMap; import java.util.Map; /** A cell in a row of a table. * --- 1,15 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; + import nu.xom.Attribute; + + import org.xmlcml.cml.base.CMLAttribute; + import org.xmlcml.cml.base.CMLElement; + import org.xmlcml.cml.base.CMLException; + import org.xmlcml.cml.base.CMLRuntime; + import org.xmlcml.cml.base.StringAttribute; + /** A cell in a row of a table. * Index: AbstractMechanism.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractMechanism.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractMechanism.java 2 Jun 2006 15:47:46 -0000 1.1 --- AbstractMechanism.java 23 Jun 2006 15:33:04 -0000 1.2 *************** *** 1,13 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; - import nu.xom.Elements; import java.util.HashMap; import java.util.Map; ! import org.xmlcml.cml.element.CMLLabel; ! import org.xmlcml.cml.element.CMLDescription; ! import org.xmlcml.cml.element.CMLMechanismComponent; ! import org.xmlcml.cml.element.CMLName; /** The mechanism of a reaction. --- 1,16 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; ! ! import nu.xom.Attribute; ! import nu.xom.Elements; ! ! import org.xmlcml.cml.base.CMLAttribute; ! import org.xmlcml.cml.base.CMLElement; ! import org.xmlcml.cml.base.CMLElements; ! import org.xmlcml.cml.base.CMLException; ! import org.xmlcml.cml.base.CMLRuntime; ! import org.xmlcml.cml.base.StringAttribute; /** The mechanism of a reaction. Index: AbstractMetadata.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractMetadata.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractMetadata.java 2 Jun 2006 15:47:46 -0000 1.1 --- AbstractMetadata.java 23 Jun 2006 15:33:04 -0000 1.2 *************** *** 2,10 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; import java.util.HashMap; import java.util.Map; /** A general container for metadata. * --- 2,16 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; + import nu.xom.Attribute; + + import org.xmlcml.cml.base.CMLAttribute; + import org.xmlcml.cml.base.CMLElement; + import org.xmlcml.cml.base.CMLException; + import org.xmlcml.cml.base.CMLRuntime; + import org.xmlcml.cml.base.StringAttribute; + /** A general container for metadata. * Index: AbstractTableHeader.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractTableHeader.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** AbstractTableHeader.java 2 Jun 2006 15:47:49 -0000 1.1 --- AbstractTableHeader.java 23 Jun 2006 15:33:04 -0000 1.2 *************** *** 1,10 **** package org.xmlcml.cml.element; - import nu.xom.Attribute; - import org.xmlcml.cml.base.*; - import nu.xom.Elements; import java.util.HashMap; import java.util.Map; ! import org.xmlcml.cml.element.CMLTrow; /** Header for a table. --- 1,16 ---- package org.xmlcml.cml.element; import java.util.HashMap; import java.util.Map; ! ! import nu.xom.Attribute; ! import nu.xom.Elements; ! ! import org.xmlcml.cml.base.CMLAttribute; ! import org.xmlcml.cml.base.CMLElement; ! import org.xmlcml.cml.base.CMLElements; ! import org.xmlcml.cml.base.CMLException; ! import org.xmlcml.cml.base.CMLRuntime; ! import org.xmlcml.cml.base.StringAttribute; /** Header for a table. Index: AbstractSpectrumData.java =================================================================== RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/AbstractSp... [truncated message content] |