Binary compatibility report for the CDK library between 1.4.14 and 1.4.15 versions
Test Info
| Library Name | CDK |
|---|
| Version #1 | 1.4.14 |
|---|
| Version #2 | 1.4.15 |
|---|
Test Results
| Total Java ARchives | 1 |
|---|
| Total Methods / Classes | 32167 / 3523 |
|---|
| Verdict | Incompatible
(1.5%) |
|---|
Problem Summary
| Severity | Count |
|---|
| Added Methods | - | 308 |
|---|
| Removed Methods | High | 0 |
|---|
Problems with
Data Types | High | 0 |
|---|
| Medium | 2 |
| Low | 42 |
Problems with
Methods | High | 0 |
|---|
| Medium | 0 |
| Low | 0 |
Other Changes
in Data Types | - | 19 |
|---|
Added Methods (308)
cdk-1.4.15.jar, AminoAcid.class
package org.openscience.cdk
AminoAcid.clone ( ) : IAminoAcid
[mangled: org/openscience/cdk/AminoAcid.clone:()Lorg/openscience/cdk/interfaces/IAminoAcid;]
AminoAcid.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/AminoAcid.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
AminoAcid.clone ( ) : IMonomer
[mangled: org/openscience/cdk/AminoAcid.clone:()Lorg/openscience/cdk/interfaces/IMonomer;]
package org.openscience.cdk.silent
AminoAcid.clone ( ) : IAminoAcid
[mangled: org/openscience/cdk/silent/AminoAcid.clone:()Lorg/openscience/cdk/interfaces/IAminoAcid;]
AminoAcid.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/silent/AminoAcid.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
AminoAcid.clone ( ) : IMonomer
[mangled: org/openscience/cdk/silent/AminoAcid.clone:()Lorg/openscience/cdk/interfaces/IMonomer;]
cdk-1.4.15.jar, ArrowHeadWidth.class
package org.openscience.cdk.renderer.generators
ReactionSceneGenerator.ArrowHeadWidth.getDefault ( ) : Double
[mangled: org/openscience/cdk/renderer/generators/ReactionSceneGenerator.ArrowHeadWidth.getDefault:()Ljava/lang/Double;]
ReactionSceneGenerator.ArrowHeadWidth.getDefault ( ) : Object
[mangled: org/openscience/cdk/renderer/generators/ReactionSceneGenerator.ArrowHeadWidth.getDefault:()Ljava/lang/Object;]
ReactionSceneGenerator.ArrowHeadWidth.ReactionSceneGenerator.ArrowHeadWidth ( )
[mangled: org/openscience/cdk/renderer/generators/ReactionSceneGenerator.ArrowHeadWidth."<init>":()V]
cdk-1.4.15.jar, AtomAtomMappingLineColor.class
package org.openscience.cdk.renderer.generators
MappingGenerator.AtomAtomMappingLineColor.getDefault ( ) : Color
[mangled: org/openscience/cdk/renderer/generators/MappingGenerator.AtomAtomMappingLineColor.getDefault:()Ljava/awt/Color;]
MappingGenerator.AtomAtomMappingLineColor.getDefault ( ) : Object
[mangled: org/openscience/cdk/renderer/generators/MappingGenerator.AtomAtomMappingLineColor.getDefault:()Ljava/lang/Object;]
MappingGenerator.AtomAtomMappingLineColor.MappingGenerator.AtomAtomMappingLineColor ( )
[mangled: org/openscience/cdk/renderer/generators/MappingGenerator.AtomAtomMappingLineColor."<init>":()V]
cdk-1.4.15.jar, AtomColorer.class
package org.openscience.cdk.renderer.generators
AtomNumberGenerator.AtomColorer.AtomNumberGenerator.AtomColorer ( )
[mangled: org/openscience/cdk/renderer/generators/AtomNumberGenerator.AtomColorer."<init>":()V]
AtomNumberGenerator.AtomColorer.getDefault ( ) : IAtomColorer
[mangled: org/openscience/cdk/renderer/generators/AtomNumberGenerator.AtomColorer.getDefault:()Lorg/openscience/cdk/renderer/color/IAtomColorer;]
AtomNumberGenerator.AtomColorer.getDefault ( ) : Object
[mangled: org/openscience/cdk/renderer/generators/AtomNumberGenerator.AtomColorer.getDefault:()Ljava/lang/Object;]
cdk-1.4.15.jar, AtomContainer.class
package org.openscience.cdk
AtomContainer.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/AtomContainer.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
AtomContainer.isEmpty ( ) : boolean
[mangled: org/openscience/cdk/AtomContainer.isEmpty:()Z]
AtomContainer.setStereoElements ( List elements ) : void
[mangled: org/openscience/cdk/AtomContainer.setStereoElements:(Ljava/util/List;)V]
package org.openscience.cdk.silent
AtomContainer.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/silent/AtomContainer.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
AtomContainer.isEmpty ( ) : boolean
[mangled: org/openscience/cdk/silent/AtomContainer.isEmpty:()Z]
AtomContainer.setStereoElements ( List elements ) : void
[mangled: org/openscience/cdk/silent/AtomContainer.setStereoElements:(Ljava/util/List;)V]
cdk-1.4.15.jar, AtomContainerBoundsGenerator.class
package org.openscience.cdk.renderer.generators
AtomContainerBoundsGenerator.AtomContainerBoundsGenerator ( )
[mangled: org/openscience/cdk/renderer/generators/AtomContainerBoundsGenerator."<init>":()V]
AtomContainerBoundsGenerator.generate ( IAtomContainer container, RendererModel model ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/generators/AtomContainerBoundsGenerator.generate:(Lorg/openscience/cdk/interfaces/IAtomContainer;Lorg/openscience/cdk/renderer/RendererModel;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
AtomContainerBoundsGenerator.generate ( IChemObject x0, RendererModel x1 ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/generators/AtomContainerBoundsGenerator.generate:(Lorg/openscience/cdk/interfaces/IChemObject;Lorg/openscience/cdk/renderer/RendererModel;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
AtomContainerBoundsGenerator.getParameters ( ) : List
[mangled: org/openscience/cdk/renderer/generators/AtomContainerBoundsGenerator.getParameters:()Ljava/util/List;]
cdk-1.4.15.jar, AtomContainerSet.class
package org.openscience.cdk
AtomContainerSet.isEmpty ( ) : boolean
[mangled: org/openscience/cdk/AtomContainerSet.isEmpty:()Z]
package org.openscience.cdk.silent
AtomContainerSet.isEmpty ( ) : boolean
[mangled: org/openscience/cdk/silent/AtomContainerSet.isEmpty:()Z]
cdk-1.4.15.jar, AtomMassGenerator.class
package org.openscience.cdk.renderer.generators
AtomMassGenerator.AtomMassGenerator ( )
[mangled: org/openscience/cdk/renderer/generators/AtomMassGenerator."<init>":()V]
AtomMassGenerator.showCarbon ( IAtom atom, IAtomContainer container, RendererModel model ) : boolean
[mangled: org/openscience/cdk/renderer/generators/AtomMassGenerator.showCarbon:(Lorg/openscience/cdk/interfaces/IAtom;Lorg/openscience/cdk/interfaces/IAtomContainer;Lorg/openscience/cdk/renderer/RendererModel;)Z]
cdk-1.4.15.jar, AtomMassSymbolElement.class
package org.openscience.cdk.renderer.elements
AtomMassSymbolElement.AtomMassSymbolElement ( double xCoord, double yCoord, String symbol, Integer formalCharge, Integer hydrogenCount, int alignment, Integer atomMass, Color color )
[mangled: org/openscience/cdk/renderer/elements/AtomMassSymbolElement."<init>":(DDLjava/lang/String;Ljava/lang/Integer;Ljava/lang/Integer;ILjava/lang/Integer;Ljava/awt/Color;)V]
cdk-1.4.15.jar, AtomNumberGenerator.class
package org.openscience.cdk.renderer.generators
AtomNumberGenerator.AtomNumberGenerator ( )
[mangled: org/openscience/cdk/renderer/generators/AtomNumberGenerator."<init>":()V]
AtomNumberGenerator.generate ( IAtomContainer container, RendererModel model ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/generators/AtomNumberGenerator.generate:(Lorg/openscience/cdk/interfaces/IAtomContainer;Lorg/openscience/cdk/renderer/RendererModel;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
AtomNumberGenerator.generate ( IChemObject x0, RendererModel x1 ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/generators/AtomNumberGenerator.generate:(Lorg/openscience/cdk/interfaces/IChemObject;Lorg/openscience/cdk/renderer/RendererModel;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
AtomNumberGenerator.getParameters ( ) : List
[mangled: org/openscience/cdk/renderer/generators/AtomNumberGenerator.getParameters:()Ljava/util/List;]
cdk-1.4.15.jar, AtomNumberTextColor.class
package org.openscience.cdk.renderer.generators
AtomNumberGenerator.AtomNumberTextColor.AtomNumberGenerator.AtomNumberTextColor ( )
[mangled: org/openscience/cdk/renderer/generators/AtomNumberGenerator.AtomNumberTextColor."<init>":()V]
AtomNumberGenerator.AtomNumberTextColor.getDefault ( ) : Color
[mangled: org/openscience/cdk/renderer/generators/AtomNumberGenerator.AtomNumberTextColor.getDefault:()Ljava/awt/Color;]
AtomNumberGenerator.AtomNumberTextColor.getDefault ( ) : Object
[mangled: org/openscience/cdk/renderer/generators/AtomNumberGenerator.AtomNumberTextColor.getDefault:()Ljava/lang/Object;]
cdk-1.4.15.jar, AtomParity.class
package org.openscience.cdk
AtomParity.map ( Map atoms, Map bonds ) : IAtomParity
[mangled: org/openscience/cdk/AtomParity.map:(Ljava/util/Map;Ljava/util/Map;)Lorg/openscience/cdk/interfaces/IAtomParity;]
AtomParity.map ( Map x0, Map x1 ) : IStereoElement
[mangled: org/openscience/cdk/AtomParity.map:(Ljava/util/Map;Ljava/util/Map;)Lorg/openscience/cdk/interfaces/IStereoElement;]
package org.openscience.cdk.silent
AtomParity.map ( Map atoms, Map bonds ) : IAtomParity
[mangled: org/openscience/cdk/silent/AtomParity.map:(Ljava/util/Map;Ljava/util/Map;)Lorg/openscience/cdk/interfaces/IAtomParity;]
AtomParity.map ( Map x0, Map x1 ) : IStereoElement
[mangled: org/openscience/cdk/silent/AtomParity.map:(Ljava/util/Map;Ljava/util/Map;)Lorg/openscience/cdk/interfaces/IStereoElement;]
cdk-1.4.15.jar, BioPolymer.class
package org.openscience.cdk
BioPolymer.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/BioPolymer.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
BioPolymer.clone ( ) : IBioPolymer
[mangled: org/openscience/cdk/BioPolymer.clone:()Lorg/openscience/cdk/interfaces/IBioPolymer;]
BioPolymer.clone ( ) : IMolecule
[mangled: org/openscience/cdk/BioPolymer.clone:()Lorg/openscience/cdk/interfaces/IMolecule;]
BioPolymer.clone ( ) : IPolymer
[mangled: org/openscience/cdk/BioPolymer.clone:()Lorg/openscience/cdk/interfaces/IPolymer;]
package org.openscience.cdk.silent
BioPolymer.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/silent/BioPolymer.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
BioPolymer.clone ( ) : IBioPolymer
[mangled: org/openscience/cdk/silent/BioPolymer.clone:()Lorg/openscience/cdk/interfaces/IBioPolymer;]
BioPolymer.clone ( ) : IMolecule
[mangled: org/openscience/cdk/silent/BioPolymer.clone:()Lorg/openscience/cdk/interfaces/IMolecule;]
BioPolymer.clone ( ) : IPolymer
[mangled: org/openscience/cdk/silent/BioPolymer.clone:()Lorg/openscience/cdk/interfaces/IPolymer;]
cdk-1.4.15.jar, BoundsColor.class
package org.openscience.cdk.renderer.generators
BoundsGenerator.BoundsColor.BoundsGenerator.BoundsColor ( )
[mangled: org/openscience/cdk/renderer/generators/BoundsGenerator.BoundsColor."<init>":()V]
BoundsGenerator.BoundsColor.getDefault ( ) : Color
[mangled: org/openscience/cdk/renderer/generators/BoundsGenerator.BoundsColor.getDefault:()Ljava/awt/Color;]
BoundsGenerator.BoundsColor.getDefault ( ) : Object
[mangled: org/openscience/cdk/renderer/generators/BoundsGenerator.BoundsColor.getDefault:()Ljava/lang/Object;]
cdk-1.4.15.jar, BoundsGenerator.class
package org.openscience.cdk.renderer.generators
BoundsGenerator.BoundsGenerator ( )
[mangled: org/openscience/cdk/renderer/generators/BoundsGenerator."<init>":()V]
BoundsGenerator.generate ( IChemObject x0, RendererModel x1 ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/generators/BoundsGenerator.generate:(Lorg/openscience/cdk/interfaces/IChemObject;Lorg/openscience/cdk/renderer/RendererModel;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
BoundsGenerator.generate ( IReaction reaction, RendererModel model ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/generators/BoundsGenerator.generate:(Lorg/openscience/cdk/interfaces/IReaction;Lorg/openscience/cdk/renderer/RendererModel;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
BoundsGenerator.getParameters ( ) : List
[mangled: org/openscience/cdk/renderer/generators/BoundsGenerator.getParameters:()Ljava/util/List;]
cdk-1.4.15.jar, ChemModel.class
package org.openscience.cdk
ChemModel.isEmpty ( ) : boolean
[mangled: org/openscience/cdk/ChemModel.isEmpty:()Z]
package org.openscience.cdk.silent
ChemModel.isEmpty ( ) : boolean
[mangled: org/openscience/cdk/silent/ChemModel.isEmpty:()Z]
cdk-1.4.15.jar, ChemModelRenderer.class
package org.openscience.cdk.renderer
ChemModelRenderer.calculateDiagramBounds ( IChemModel model ) : Rectangle
[mangled: org/openscience/cdk/renderer/ChemModelRenderer.calculateDiagramBounds:(Lorg/openscience/cdk/interfaces/IChemModel;)Ljava/awt/Rectangle;]
ChemModelRenderer.calculateDiagramBounds ( IChemObject x0 ) : Rectangle
[mangled: org/openscience/cdk/renderer/ChemModelRenderer.calculateDiagramBounds:(Lorg/openscience/cdk/interfaces/IChemObject;)Ljava/awt/Rectangle;]
ChemModelRenderer.calculateScaleForBondLength ( double modelBondLength ) : double
[mangled: org/openscience/cdk/renderer/ChemModelRenderer.calculateScaleForBondLength:(D)D]
ChemModelRenderer.ChemModelRenderer ( List generators, IFontManager fontManager )
[mangled: org/openscience/cdk/renderer/ChemModelRenderer."<init>":(Ljava/util/List;Lorg/openscience/cdk/renderer/font/IFontManager;)V]
ChemModelRenderer.ChemModelRenderer ( List generators, List reactionGenerators, IFontManager fontManager )
[mangled: org/openscience/cdk/renderer/ChemModelRenderer."<init>":(Ljava/util/List;Ljava/util/List;Lorg/openscience/cdk/renderer/font/IFontManager;)V]
ChemModelRenderer.getGenerators ( ) : List
[mangled: org/openscience/cdk/renderer/ChemModelRenderer.getGenerators:()Ljava/util/List;]
ChemModelRenderer.paint ( IChemModel chemModel, IDrawVisitor drawVisitor ) : Rectangle
[mangled: org/openscience/cdk/renderer/ChemModelRenderer.paint:(Lorg/openscience/cdk/interfaces/IChemModel;Lorg/openscience/cdk/renderer/visitor/IDrawVisitor;)Ljava/awt/Rectangle;]
ChemModelRenderer.paint ( IChemModel chemModel, IDrawVisitor drawVisitor, Rectangle2D bounds, boolean resetCenter ) : void
[mangled: org/openscience/cdk/renderer/ChemModelRenderer.paint:(Lorg/openscience/cdk/interfaces/IChemModel;Lorg/openscience/cdk/renderer/visitor/IDrawVisitor;Ljava/awt/geom/Rectangle2D;Z)V]
ChemModelRenderer.paint ( IChemObject x0, IDrawVisitor x1 ) : Rectangle
[mangled: org/openscience/cdk/renderer/ChemModelRenderer.paint:(Lorg/openscience/cdk/interfaces/IChemObject;Lorg/openscience/cdk/renderer/visitor/IDrawVisitor;)Ljava/awt/Rectangle;]
ChemModelRenderer.paint ( IChemObject x0, IDrawVisitor x1, Rectangle2D x2, boolean x3 ) : void
[mangled: org/openscience/cdk/renderer/ChemModelRenderer.paint:(Lorg/openscience/cdk/interfaces/IChemObject;Lorg/openscience/cdk/renderer/visitor/IDrawVisitor;Ljava/awt/geom/Rectangle2D;Z)V]
ChemModelRenderer.repaint ( IDrawVisitor drawVisitor ) : void
[mangled: org/openscience/cdk/renderer/ChemModelRenderer.repaint:(Lorg/openscience/cdk/renderer/visitor/IDrawVisitor;)V]
ChemModelRenderer.setScale ( IChemModel chemModel ) : void
[mangled: org/openscience/cdk/renderer/ChemModelRenderer.setScale:(Lorg/openscience/cdk/interfaces/IChemModel;)V]
ChemModelRenderer.setScale ( IChemObject x0 ) : void
[mangled: org/openscience/cdk/renderer/ChemModelRenderer.setScale:(Lorg/openscience/cdk/interfaces/IChemObject;)V]
ChemModelRenderer.setup ( IChemModel chemModel, Rectangle screen ) : void
[mangled: org/openscience/cdk/renderer/ChemModelRenderer.setup:(Lorg/openscience/cdk/interfaces/IChemModel;Ljava/awt/Rectangle;)V]
ChemModelRenderer.setup ( IChemObject x0, Rectangle x1 ) : void
[mangled: org/openscience/cdk/renderer/ChemModelRenderer.setup:(Lorg/openscience/cdk/interfaces/IChemObject;Ljava/awt/Rectangle;)V]
cdk-1.4.15.jar, ColorByType.class
package org.openscience.cdk.renderer.generators
AtomNumberGenerator.ColorByType.AtomNumberGenerator.ColorByType ( )
[mangled: org/openscience/cdk/renderer/generators/AtomNumberGenerator.ColorByType."<init>":()V]
AtomNumberGenerator.ColorByType.getDefault ( ) : Boolean
[mangled: org/openscience/cdk/renderer/generators/AtomNumberGenerator.ColorByType.getDefault:()Ljava/lang/Boolean;]
AtomNumberGenerator.ColorByType.getDefault ( ) : Object
[mangled: org/openscience/cdk/renderer/generators/AtomNumberGenerator.ColorByType.getDefault:()Ljava/lang/Object;]
cdk-1.4.15.jar, Conformation.class
package org.openscience.cdk.interfaces
IDoubleBondStereochemistry.Conformation.valueOf ( String name ) [static] : IDoubleBondStereochemistry.Conformation
[mangled: org/openscience/cdk/interfaces/IDoubleBondStereochemistry.Conformation.valueOf:(Ljava/lang/String;)Lorg/openscience/cdk/interfaces/IDoubleBondStereochemistry$Conformation;]
IDoubleBondStereochemistry.Conformation.values ( ) [static] : IDoubleBondStereochemistry.Conformation[ ]
[mangled: org/openscience/cdk/interfaces/IDoubleBondStereochemistry.Conformation.values:()[Lorg/openscience/cdk/interfaces/IDoubleBondStereochemistry$Conformation;]
cdk-1.4.15.jar, Crystal.class
package org.openscience.cdk
Crystal.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/Crystal.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
Crystal.clone ( ) : ICrystal
[mangled: org/openscience/cdk/Crystal.clone:()Lorg/openscience/cdk/interfaces/ICrystal;]
package org.openscience.cdk.silent
Crystal.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/silent/Crystal.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
Crystal.clone ( ) : ICrystal
[mangled: org/openscience/cdk/silent/Crystal.clone:()Lorg/openscience/cdk/interfaces/ICrystal;]
cdk-1.4.15.jar, DebugAminoAcid.class
package org.openscience.cdk.debug
DebugAminoAcid.clone ( ) : IAminoAcid
[mangled: org/openscience/cdk/debug/DebugAminoAcid.clone:()Lorg/openscience/cdk/interfaces/IAminoAcid;]
DebugAminoAcid.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/debug/DebugAminoAcid.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
DebugAminoAcid.clone ( ) : IMonomer
[mangled: org/openscience/cdk/debug/DebugAminoAcid.clone:()Lorg/openscience/cdk/interfaces/IMonomer;]
cdk-1.4.15.jar, DebugAtomContainer.class
package org.openscience.cdk.debug
DebugAtomContainer.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/debug/DebugAtomContainer.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
DebugAtomContainer.isEmpty ( ) : boolean
[mangled: org/openscience/cdk/debug/DebugAtomContainer.isEmpty:()Z]
DebugAtomContainer.setStereoElements ( List elements ) : void
[mangled: org/openscience/cdk/debug/DebugAtomContainer.setStereoElements:(Ljava/util/List;)V]
cdk-1.4.15.jar, DebugAtomContainerSet.class
package org.openscience.cdk.debug
DebugAtomContainerSet.isEmpty ( ) : boolean
[mangled: org/openscience/cdk/debug/DebugAtomContainerSet.isEmpty:()Z]
cdk-1.4.15.jar, DebugAtomParity.class
package org.openscience.cdk.debug
DebugAtomParity.map ( Map atoms, Map bonds ) : IAtomParity
[mangled: org/openscience/cdk/debug/DebugAtomParity.map:(Ljava/util/Map;Ljava/util/Map;)Lorg/openscience/cdk/interfaces/IAtomParity;]
DebugAtomParity.map ( Map x0, Map x1 ) : IStereoElement
[mangled: org/openscience/cdk/debug/DebugAtomParity.map:(Ljava/util/Map;Ljava/util/Map;)Lorg/openscience/cdk/interfaces/IStereoElement;]
cdk-1.4.15.jar, DebugBioPolymer.class
package org.openscience.cdk.debug
DebugBioPolymer.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/debug/DebugBioPolymer.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
DebugBioPolymer.clone ( ) : IBioPolymer
[mangled: org/openscience/cdk/debug/DebugBioPolymer.clone:()Lorg/openscience/cdk/interfaces/IBioPolymer;]
DebugBioPolymer.clone ( ) : IMolecule
[mangled: org/openscience/cdk/debug/DebugBioPolymer.clone:()Lorg/openscience/cdk/interfaces/IMolecule;]
DebugBioPolymer.clone ( ) : IPolymer
[mangled: org/openscience/cdk/debug/DebugBioPolymer.clone:()Lorg/openscience/cdk/interfaces/IPolymer;]
cdk-1.4.15.jar, DebugChemModel.class
package org.openscience.cdk.debug
DebugChemModel.isEmpty ( ) : boolean
[mangled: org/openscience/cdk/debug/DebugChemModel.isEmpty:()Z]
cdk-1.4.15.jar, DebugCrystal.class
package org.openscience.cdk.debug
DebugCrystal.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/debug/DebugCrystal.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
DebugCrystal.clone ( ) : ICrystal
[mangled: org/openscience/cdk/debug/DebugCrystal.clone:()Lorg/openscience/cdk/interfaces/ICrystal;]
DebugCrystal.isEmpty ( ) : boolean
[mangled: org/openscience/cdk/debug/DebugCrystal.isEmpty:()Z]
cdk-1.4.15.jar, DebugMolecule.class
package org.openscience.cdk.debug
DebugMolecule.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/debug/DebugMolecule.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
DebugMolecule.clone ( ) : IMolecule
[mangled: org/openscience/cdk/debug/DebugMolecule.clone:()Lorg/openscience/cdk/interfaces/IMolecule;]
cdk-1.4.15.jar, DebugMonomer.class
package org.openscience.cdk.debug
DebugMonomer.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/debug/DebugMonomer.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
DebugMonomer.clone ( ) : IMonomer
[mangled: org/openscience/cdk/debug/DebugMonomer.clone:()Lorg/openscience/cdk/interfaces/IMonomer;]
cdk-1.4.15.jar, DebugPolymer.class
package org.openscience.cdk.debug
DebugPolymer.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/debug/DebugPolymer.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
DebugPolymer.clone ( ) : IMolecule
[mangled: org/openscience/cdk/debug/DebugPolymer.clone:()Lorg/openscience/cdk/interfaces/IMolecule;]
DebugPolymer.clone ( ) : IPolymer
[mangled: org/openscience/cdk/debug/DebugPolymer.clone:()Lorg/openscience/cdk/interfaces/IPolymer;]
cdk-1.4.15.jar, DebugReactionSet.class
package org.openscience.cdk.debug
DebugReactionSet.isEmpty ( ) : boolean
[mangled: org/openscience/cdk/debug/DebugReactionSet.isEmpty:()Z]
cdk-1.4.15.jar, DebugRing.class
package org.openscience.cdk.debug
DebugRing.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/debug/DebugRing.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
DebugRing.clone ( ) : IRing
[mangled: org/openscience/cdk/debug/DebugRing.clone:()Lorg/openscience/cdk/interfaces/IRing;]
cdk-1.4.15.jar, DebugStrand.class
package org.openscience.cdk.debug
DebugStrand.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/debug/DebugStrand.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
DebugStrand.clone ( ) : IStrand
[mangled: org/openscience/cdk/debug/DebugStrand.clone:()Lorg/openscience/cdk/interfaces/IStrand;]
cdk-1.4.15.jar, DoubleBondAcceptingAromaticityDetector.class
package org.openscience.cdk.aromaticity
DoubleBondAcceptingAromaticityDetector.detectAromaticity ( IAtomContainer atomContainer ) [static] : boolean
[mangled: org/openscience/cdk/aromaticity/DoubleBondAcceptingAromaticityDetector.detectAromaticity:(Lorg/openscience/cdk/interfaces/IAtomContainer;)Z]
DoubleBondAcceptingAromaticityDetector.DoubleBondAcceptingAromaticityDetector ( )
[mangled: org/openscience/cdk/aromaticity/DoubleBondAcceptingAromaticityDetector."<init>":()V]
cdk-1.4.15.jar, DoubleBondStereochemistry.class
package org.openscience.cdk.stereo
DoubleBondStereochemistry.DoubleBondStereochemistry ( IBond stereoBond, IBond[ ] ligandBonds, IDoubleBondStereochemistry.Conformation stereo )
[mangled: org/openscience/cdk/stereo/DoubleBondStereochemistry."<init>":(Lorg/openscience/cdk/interfaces/IBond;[Lorg/openscience/cdk/interfaces/IBond;Lorg/openscience/cdk/interfaces/IDoubleBondStereochemistry$Conformation;)V]
DoubleBondStereochemistry.getBonds ( ) : IBond[ ]
[mangled: org/openscience/cdk/stereo/DoubleBondStereochemistry.getBonds:()[Lorg/openscience/cdk/interfaces/IBond;]
DoubleBondStereochemistry.getBuilder ( ) : IChemObjectBuilder
[mangled: org/openscience/cdk/stereo/DoubleBondStereochemistry.getBuilder:()Lorg/openscience/cdk/interfaces/IChemObjectBuilder;]
DoubleBondStereochemistry.getStereo ( ) : IDoubleBondStereochemistry.Conformation
[mangled: org/openscience/cdk/stereo/DoubleBondStereochemistry.getStereo:()Lorg/openscience/cdk/interfaces/IDoubleBondStereochemistry$Conformation;]
DoubleBondStereochemistry.getStereoBond ( ) : IBond
[mangled: org/openscience/cdk/stereo/DoubleBondStereochemistry.getStereoBond:()Lorg/openscience/cdk/interfaces/IBond;]
DoubleBondStereochemistry.map ( Map atoms, Map bonds ) : IDoubleBondStereochemistry
[mangled: org/openscience/cdk/stereo/DoubleBondStereochemistry.map:(Ljava/util/Map;Ljava/util/Map;)Lorg/openscience/cdk/interfaces/IDoubleBondStereochemistry;]
DoubleBondStereochemistry.map ( Map x0, Map x1 ) : IStereoElement
[mangled: org/openscience/cdk/stereo/DoubleBondStereochemistry.map:(Ljava/util/Map;Ljava/util/Map;)Lorg/openscience/cdk/interfaces/IStereoElement;]
DoubleBondStereochemistry.setBuilder ( IChemObjectBuilder builder ) : void
[mangled: org/openscience/cdk/stereo/DoubleBondStereochemistry.setBuilder:(Lorg/openscience/cdk/interfaces/IChemObjectBuilder;)V]
cdk-1.4.15.jar, ExtendedAtomGenerator.class
package org.openscience.cdk.renderer.generators
ExtendedAtomGenerator.ExtendedAtomGenerator ( )
[mangled: org/openscience/cdk/renderer/generators/ExtendedAtomGenerator."<init>":()V]
ExtendedAtomGenerator.generate ( IAtomContainer container, IAtom atom, RendererModel model ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.generate:(Lorg/openscience/cdk/interfaces/IAtomContainer;Lorg/openscience/cdk/interfaces/IAtom;Lorg/openscience/cdk/renderer/RendererModel;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
ExtendedAtomGenerator.getParameters ( ) : List
[mangled: org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.getParameters:()Ljava/util/List;]
cdk-1.4.15.jar, IAminoAcid.class
package org.openscience.cdk.interfaces
IAminoAcid.clone ( ) [abstract] : IAminoAcid
[mangled: org/openscience/cdk/interfaces/IAminoAcid.clone:()Lorg/openscience/cdk/interfaces/IAminoAcid;]
cdk-1.4.15.jar, IAtomContainer.class
package org.openscience.cdk.interfaces
IAtomContainer.clone ( ) [abstract] : IAtomContainer
[mangled: org/openscience/cdk/interfaces/IAtomContainer.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
IAtomContainer.isEmpty ( ) [abstract] : boolean
[mangled: org/openscience/cdk/interfaces/IAtomContainer.isEmpty:()Z]
IAtomContainer.setStereoElements ( List p1 ) [abstract] : void
[mangled: org/openscience/cdk/interfaces/IAtomContainer.setStereoElements:(Ljava/util/List;)V]
cdk-1.4.15.jar, IAtomContainerSet.class
package org.openscience.cdk.interfaces
IAtomContainerSet.isEmpty ( ) [abstract] : boolean
[mangled: org/openscience/cdk/interfaces/IAtomContainerSet.isEmpty:()Z]
cdk-1.4.15.jar, IAtomParity.class
package org.openscience.cdk.interfaces
IAtomParity.map ( Map p1, Map p2 ) [abstract] : IAtomParity
[mangled: org/openscience/cdk/interfaces/IAtomParity.map:(Ljava/util/Map;Ljava/util/Map;)Lorg/openscience/cdk/interfaces/IAtomParity;]
cdk-1.4.15.jar, IBioPolymer.class
package org.openscience.cdk.interfaces
IBioPolymer.clone ( ) [abstract] : IBioPolymer
[mangled: org/openscience/cdk/interfaces/IBioPolymer.clone:()Lorg/openscience/cdk/interfaces/IBioPolymer;]
cdk-1.4.15.jar, IChemModel.class
package org.openscience.cdk.interfaces
IChemModel.isEmpty ( ) [abstract] : boolean
[mangled: org/openscience/cdk/interfaces/IChemModel.isEmpty:()Z]
cdk-1.4.15.jar, ICrystal.class
package org.openscience.cdk.interfaces
ICrystal.clone ( ) [abstract] : ICrystal
[mangled: org/openscience/cdk/interfaces/ICrystal.clone:()Lorg/openscience/cdk/interfaces/ICrystal;]
cdk-1.4.15.jar, IDoubleBondStereochemistry.class
package org.openscience.cdk.interfaces
IDoubleBondStereochemistry.getBonds ( ) [abstract] : IBond[ ]
[mangled: org/openscience/cdk/interfaces/IDoubleBondStereochemistry.getBonds:()[Lorg/openscience/cdk/interfaces/IBond;]
IDoubleBondStereochemistry.getStereo ( ) [abstract] : IDoubleBondStereochemistry.Conformation
[mangled: org/openscience/cdk/interfaces/IDoubleBondStereochemistry.getStereo:()Lorg/openscience/cdk/interfaces/IDoubleBondStereochemistry$Conformation;]
IDoubleBondStereochemistry.getStereoBond ( ) [abstract] : IBond
[mangled: org/openscience/cdk/interfaces/IDoubleBondStereochemistry.getStereoBond:()Lorg/openscience/cdk/interfaces/IBond;]
IDoubleBondStereochemistry.map ( Map p1, Map p2 ) [abstract] : IDoubleBondStereochemistry
[mangled: org/openscience/cdk/interfaces/IDoubleBondStereochemistry.map:(Ljava/util/Map;Ljava/util/Map;)Lorg/openscience/cdk/interfaces/IDoubleBondStereochemistry;]
cdk-1.4.15.jar, IMolecule.class
package org.openscience.cdk.interfaces
IMolecule.clone ( ) [abstract] : IMolecule
[mangled: org/openscience/cdk/interfaces/IMolecule.clone:()Lorg/openscience/cdk/interfaces/IMolecule;]
cdk-1.4.15.jar, IMonomer.class
package org.openscience.cdk.interfaces
IMonomer.clone ( ) [abstract] : IMonomer
[mangled: org/openscience/cdk/interfaces/IMonomer.clone:()Lorg/openscience/cdk/interfaces/IMonomer;]
cdk-1.4.15.jar, IPDBMonomer.class
package org.openscience.cdk.interfaces
IPDBMonomer.clone ( ) [abstract] : IPDBMonomer
[mangled: org/openscience/cdk/interfaces/IPDBMonomer.clone:()Lorg/openscience/cdk/interfaces/IPDBMonomer;]
cdk-1.4.15.jar, IPDBPolymer.class
package org.openscience.cdk.interfaces
IPDBPolymer.clone ( ) [abstract] : IPDBPolymer
[mangled: org/openscience/cdk/interfaces/IPDBPolymer.clone:()Lorg/openscience/cdk/interfaces/IPDBPolymer;]
cdk-1.4.15.jar, IPolymer.class
package org.openscience.cdk.interfaces
IPolymer.clone ( ) [abstract] : IPolymer
[mangled: org/openscience/cdk/interfaces/IPolymer.clone:()Lorg/openscience/cdk/interfaces/IPolymer;]
cdk-1.4.15.jar, IReactionSet.class
package org.openscience.cdk.interfaces
IReactionSet.isEmpty ( ) [abstract] : boolean
[mangled: org/openscience/cdk/interfaces/IReactionSet.isEmpty:()Z]
cdk-1.4.15.jar, IRing.class
package org.openscience.cdk.interfaces
IRing.clone ( ) [abstract] : IRing
[mangled: org/openscience/cdk/interfaces/IRing.clone:()Lorg/openscience/cdk/interfaces/IRing;]
cdk-1.4.15.jar, IRingSet.class
package org.openscience.cdk.interfaces
IRingSet.isEmpty ( ) [abstract] : boolean
[mangled: org/openscience/cdk/interfaces/IRingSet.isEmpty:()Z]
cdk-1.4.15.jar, IStereoElement.class
package org.openscience.cdk.interfaces
IStereoElement.map ( Map p1, Map p2 ) [abstract] : IStereoElement
[mangled: org/openscience/cdk/interfaces/IStereoElement.map:(Ljava/util/Map;Ljava/util/Map;)Lorg/openscience/cdk/interfaces/IStereoElement;]
cdk-1.4.15.jar, IStrand.class
package org.openscience.cdk.interfaces
IStrand.clone ( ) [abstract] : IStrand
[mangled: org/openscience/cdk/interfaces/IStrand.clone:()Lorg/openscience/cdk/interfaces/IStrand;]
cdk-1.4.15.jar, ITetrahedralChirality.class
package org.openscience.cdk.interfaces
ITetrahedralChirality.map ( Map p1, Map p2 ) [abstract] : ITetrahedralChirality
[mangled: org/openscience/cdk/interfaces/ITetrahedralChirality.map:(Ljava/util/Map;Ljava/util/Map;)Lorg/openscience/cdk/interfaces/ITetrahedralChirality;]
cdk-1.4.15.jar, LonePairGenerator.class
package org.openscience.cdk.renderer.generators
LonePairGenerator.generate ( IAtomContainer container, RendererModel model ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/generators/LonePairGenerator.generate:(Lorg/openscience/cdk/interfaces/IAtomContainer;Lorg/openscience/cdk/renderer/RendererModel;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
LonePairGenerator.generate ( IChemObject x0, RendererModel x1 ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/generators/LonePairGenerator.generate:(Lorg/openscience/cdk/interfaces/IChemObject;Lorg/openscience/cdk/renderer/RendererModel;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
LonePairGenerator.getParameters ( ) : List
[mangled: org/openscience/cdk/renderer/generators/LonePairGenerator.getParameters:()Ljava/util/List;]
LonePairGenerator.LonePairGenerator ( )
[mangled: org/openscience/cdk/renderer/generators/LonePairGenerator."<init>":()V]
cdk-1.4.15.jar, MappingGenerator.class
package org.openscience.cdk.renderer.generators
MappingGenerator.generate ( IChemObject x0, RendererModel x1 ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/generators/MappingGenerator.generate:(Lorg/openscience/cdk/interfaces/IChemObject;Lorg/openscience/cdk/renderer/RendererModel;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
MappingGenerator.generate ( IReaction reaction, RendererModel model ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/generators/MappingGenerator.generate:(Lorg/openscience/cdk/interfaces/IReaction;Lorg/openscience/cdk/renderer/RendererModel;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
MappingGenerator.getParameters ( ) : List
[mangled: org/openscience/cdk/renderer/generators/MappingGenerator.getParameters:()Ljava/util/List;]
MappingGenerator.MappingGenerator ( )
[mangled: org/openscience/cdk/renderer/generators/MappingGenerator."<init>":()V]
cdk-1.4.15.jar, MappingLineWidth.class
package org.openscience.cdk.renderer.generators
MappingGenerator.MappingLineWidth.getDefault ( ) : Double
[mangled: org/openscience/cdk/renderer/generators/MappingGenerator.MappingLineWidth.getDefault:()Ljava/lang/Double;]
MappingGenerator.MappingLineWidth.getDefault ( ) : Object
[mangled: org/openscience/cdk/renderer/generators/MappingGenerator.MappingLineWidth.getDefault:()Ljava/lang/Object;]
MappingGenerator.MappingLineWidth.MappingGenerator.MappingLineWidth ( )
[mangled: org/openscience/cdk/renderer/generators/MappingGenerator.MappingLineWidth."<init>":()V]
cdk-1.4.15.jar, Molecule.class
package org.openscience.cdk
Molecule.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/Molecule.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
Molecule.clone ( ) : IMolecule
[mangled: org/openscience/cdk/Molecule.clone:()Lorg/openscience/cdk/interfaces/IMolecule;]
package org.openscience.cdk.silent
Molecule.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/silent/Molecule.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
Molecule.clone ( ) : IMolecule
[mangled: org/openscience/cdk/silent/Molecule.clone:()Lorg/openscience/cdk/interfaces/IMolecule;]
cdk-1.4.15.jar, MoleculeSetRenderer.class
package org.openscience.cdk.renderer
MoleculeSetRenderer.calculateDiagramBounds ( IChemObject x0 ) : Rectangle
[mangled: org/openscience/cdk/renderer/MoleculeSetRenderer.calculateDiagramBounds:(Lorg/openscience/cdk/interfaces/IChemObject;)Ljava/awt/Rectangle;]
MoleculeSetRenderer.calculateDiagramBounds ( IMoleculeSet moleculeSet ) : Rectangle
[mangled: org/openscience/cdk/renderer/MoleculeSetRenderer.calculateDiagramBounds:(Lorg/openscience/cdk/interfaces/IMoleculeSet;)Ljava/awt/Rectangle;]
MoleculeSetRenderer.calculateScaleForBondLength ( double modelBondLength ) : double
[mangled: org/openscience/cdk/renderer/MoleculeSetRenderer.calculateScaleForBondLength:(D)D]
MoleculeSetRenderer.generateDiagram ( IChemObject x0 ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/MoleculeSetRenderer.generateDiagram:(Lorg/openscience/cdk/interfaces/IChemObject;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
MoleculeSetRenderer.generateDiagram ( IMoleculeSet molecules ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/MoleculeSetRenderer.generateDiagram:(Lorg/openscience/cdk/interfaces/IMoleculeSet;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
MoleculeSetRenderer.getGenerators ( ) : List
[mangled: org/openscience/cdk/renderer/MoleculeSetRenderer.getGenerators:()Ljava/util/List;]
MoleculeSetRenderer.MoleculeSetRenderer ( List generators, IFontManager fontManager )
[mangled: org/openscience/cdk/renderer/MoleculeSetRenderer."<init>":(Ljava/util/List;Lorg/openscience/cdk/renderer/font/IFontManager;)V]
MoleculeSetRenderer.MoleculeSetRenderer ( RendererModel rendererModel, List generators, IFontManager fontManager )
[mangled: org/openscience/cdk/renderer/MoleculeSetRenderer."<init>":(Lorg/openscience/cdk/renderer/RendererModel;Ljava/util/List;Lorg/openscience/cdk/renderer/font/IFontManager;)V]
MoleculeSetRenderer.paint ( IChemObject x0, IDrawVisitor x1 ) : Rectangle
[mangled: org/openscience/cdk/renderer/MoleculeSetRenderer.paint:(Lorg/openscience/cdk/interfaces/IChemObject;Lorg/openscience/cdk/renderer/visitor/IDrawVisitor;)Ljava/awt/Rectangle;]
MoleculeSetRenderer.paint ( IChemObject x0, IDrawVisitor x1, Rectangle2D x2, boolean x3 ) : void
[mangled: org/openscience/cdk/renderer/MoleculeSetRenderer.paint:(Lorg/openscience/cdk/interfaces/IChemObject;Lorg/openscience/cdk/renderer/visitor/IDrawVisitor;Ljava/awt/geom/Rectangle2D;Z)V]
MoleculeSetRenderer.paint ( IMoleculeSet molecules, IDrawVisitor drawVisitor, Rectangle2D bounds, boolean resetCenter ) : void
[mangled: org/openscience/cdk/renderer/MoleculeSetRenderer.paint:(Lorg/openscience/cdk/interfaces/IMoleculeSet;Lorg/openscience/cdk/renderer/visitor/IDrawVisitor;Ljava/awt/geom/Rectangle2D;Z)V]
MoleculeSetRenderer.paint ( IMoleculeSet moleculeSet, IDrawVisitor drawVisitor ) : Rectangle
[mangled: org/openscience/cdk/renderer/MoleculeSetRenderer.paint:(Lorg/openscience/cdk/interfaces/IMoleculeSet;Lorg/openscience/cdk/renderer/visitor/IDrawVisitor;)Ljava/awt/Rectangle;]
MoleculeSetRenderer.setScale ( IChemObject x0 ) : void
[mangled: org/openscience/cdk/renderer/MoleculeSetRenderer.setScale:(Lorg/openscience/cdk/interfaces/IChemObject;)V]
MoleculeSetRenderer.setScale ( IMoleculeSet moleculeSet ) : void
[mangled: org/openscience/cdk/renderer/MoleculeSetRenderer.setScale:(Lorg/openscience/cdk/interfaces/IMoleculeSet;)V]
MoleculeSetRenderer.setup ( IChemObject x0, Rectangle x1 ) : void
[mangled: org/openscience/cdk/renderer/MoleculeSetRenderer.setup:(Lorg/openscience/cdk/interfaces/IChemObject;Ljava/awt/Rectangle;)V]
MoleculeSetRenderer.setup ( IMoleculeSet moleculeSet, Rectangle screen ) : void
[mangled: org/openscience/cdk/renderer/MoleculeSetRenderer.setup:(Lorg/openscience/cdk/interfaces/IMoleculeSet;Ljava/awt/Rectangle;)V]
MoleculeSetRenderer.shift ( Rectangle screenBounds, Rectangle diagramBounds ) : Rectangle
[mangled: org/openscience/cdk/renderer/MoleculeSetRenderer.shift:(Ljava/awt/Rectangle;Ljava/awt/Rectangle;)Ljava/awt/Rectangle;]
cdk-1.4.15.jar, Monomer.class
package org.openscience.cdk
Monomer.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/Monomer.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
Monomer.clone ( ) : IMonomer
[mangled: org/openscience/cdk/Monomer.clone:()Lorg/openscience/cdk/interfaces/IMonomer;]
Monomer.clone ( ) : Object
[mangled: org/openscience/cdk/Monomer.clone:()Ljava/lang/Object;]
package org.openscience.cdk.silent
Monomer.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/silent/Monomer.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
Monomer.clone ( ) : IMonomer
[mangled: org/openscience/cdk/silent/Monomer.clone:()Lorg/openscience/cdk/interfaces/IMonomer;]
Monomer.clone ( ) : Object
[mangled: org/openscience/cdk/silent/Monomer.clone:()Ljava/lang/Object;]
cdk-1.4.15.jar, NNAtomParity.class
package org.openscience.cdk.nonotify
NNAtomParity.map ( Map atoms, Map bonds ) : IAtomParity
[mangled: org/openscience/cdk/nonotify/NNAtomParity.map:(Ljava/util/Map;Ljava/util/Map;)Lorg/openscience/cdk/interfaces/IAtomParity;]
NNAtomParity.map ( Map x0, Map x1 ) : IStereoElement
[mangled: org/openscience/cdk/nonotify/NNAtomParity.map:(Ljava/util/Map;Ljava/util/Map;)Lorg/openscience/cdk/interfaces/IStereoElement;]
cdk-1.4.15.jar, Offset.class
package org.openscience.cdk.renderer.generators
AtomNumberGenerator.Offset.AtomNumberGenerator.Offset ( )
[mangled: org/openscience/cdk/renderer/generators/AtomNumberGenerator.Offset."<init>":()V]
AtomNumberGenerator.Offset.getDefault ( ) : Object
[mangled: org/openscience/cdk/renderer/generators/AtomNumberGenerator.Offset.getDefault:()Ljava/lang/Object;]
AtomNumberGenerator.Offset.getDefault ( ) : Vector2d
[mangled: org/openscience/cdk/renderer/generators/AtomNumberGenerator.Offset.getDefault:()Ljavax/vecmath/Vector2d;]
cdk-1.4.15.jar, PDBMonomer.class
package org.openscience.cdk.protein.data
PDBMonomer.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/protein/data/PDBMonomer.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
PDBMonomer.clone ( ) : IMonomer
[mangled: org/openscience/cdk/protein/data/PDBMonomer.clone:()Lorg/openscience/cdk/interfaces/IMonomer;]
PDBMonomer.clone ( ) : IPDBMonomer
[mangled: org/openscience/cdk/protein/data/PDBMonomer.clone:()Lorg/openscience/cdk/interfaces/IPDBMonomer;]
PDBMonomer.clone ( ) : Object
[mangled: org/openscience/cdk/protein/data/PDBMonomer.clone:()Ljava/lang/Object;]
package org.openscience.cdk.silent
PDBMonomer.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/silent/PDBMonomer.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
PDBMonomer.clone ( ) : IMonomer
[mangled: org/openscience/cdk/silent/PDBMonomer.clone:()Lorg/openscience/cdk/interfaces/IMonomer;]
PDBMonomer.clone ( ) : IPDBMonomer
[mangled: org/openscience/cdk/silent/PDBMonomer.clone:()Lorg/openscience/cdk/interfaces/IPDBMonomer;]
PDBMonomer.clone ( ) : Object
[mangled: org/openscience/cdk/silent/PDBMonomer.clone:()Ljava/lang/Object;]
cdk-1.4.15.jar, PDBPolymer.class
package org.openscience.cdk.protein.data
PDBPolymer.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/protein/data/PDBPolymer.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
PDBPolymer.clone ( ) : IBioPolymer
[mangled: org/openscience/cdk/protein/data/PDBPolymer.clone:()Lorg/openscience/cdk/interfaces/IBioPolymer;]
PDBPolymer.clone ( ) : IMolecule
[mangled: org/openscience/cdk/protein/data/PDBPolymer.clone:()Lorg/openscience/cdk/interfaces/IMolecule;]
PDBPolymer.clone ( ) : IPDBPolymer
[mangled: org/openscience/cdk/protein/data/PDBPolymer.clone:()Lorg/openscience/cdk/interfaces/IPDBPolymer;]
PDBPolymer.clone ( ) : IPolymer
[mangled: org/openscience/cdk/protein/data/PDBPolymer.clone:()Lorg/openscience/cdk/interfaces/IPolymer;]
PDBPolymer.clone ( ) : Object
[mangled: org/openscience/cdk/protein/data/PDBPolymer.clone:()Ljava/lang/Object;]
package org.openscience.cdk.silent
PDBPolymer.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/silent/PDBPolymer.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
PDBPolymer.clone ( ) : IBioPolymer
[mangled: org/openscience/cdk/silent/PDBPolymer.clone:()Lorg/openscience/cdk/interfaces/IBioPolymer;]
PDBPolymer.clone ( ) : IMolecule
[mangled: org/openscience/cdk/silent/PDBPolymer.clone:()Lorg/openscience/cdk/interfaces/IMolecule;]
PDBPolymer.clone ( ) : IPDBPolymer
[mangled: org/openscience/cdk/silent/PDBPolymer.clone:()Lorg/openscience/cdk/interfaces/IPDBPolymer;]
PDBPolymer.clone ( ) : IPolymer
[mangled: org/openscience/cdk/silent/PDBPolymer.clone:()Lorg/openscience/cdk/interfaces/IPolymer;]
PDBPolymer.clone ( ) : Object
[mangled: org/openscience/cdk/silent/PDBPolymer.clone:()Ljava/lang/Object;]
cdk-1.4.15.jar, Polymer.class
package org.openscience.cdk
Polymer.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/Polymer.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
Polymer.clone ( ) : IMolecule
[mangled: org/openscience/cdk/Polymer.clone:()Lorg/openscience/cdk/interfaces/IMolecule;]
Polymer.clone ( ) : IPolymer
[mangled: org/openscience/cdk/Polymer.clone:()Lorg/openscience/cdk/interfaces/IPolymer;]
package org.openscience.cdk.silent
Polymer.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/silent/Polymer.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
Polymer.clone ( ) : IMolecule
[mangled: org/openscience/cdk/silent/Polymer.clone:()Lorg/openscience/cdk/interfaces/IMolecule;]
Polymer.clone ( ) : IPolymer
[mangled: org/openscience/cdk/silent/Polymer.clone:()Lorg/openscience/cdk/interfaces/IPolymer;]
cdk-1.4.15.jar, ProductsBoxGenerator.class
package org.openscience.cdk.renderer.generators
ProductsBoxGenerator.generate ( IChemObject x0, RendererModel x1 ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/generators/ProductsBoxGenerator.generate:(Lorg/openscience/cdk/interfaces/IChemObject;Lorg/openscience/cdk/renderer/RendererModel;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
ProductsBoxGenerator.generate ( IReaction reaction, RendererModel model ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/generators/ProductsBoxGenerator.generate:(Lorg/openscience/cdk/interfaces/IReaction;Lorg/openscience/cdk/renderer/RendererModel;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
ProductsBoxGenerator.getParameters ( ) : List
[mangled: org/openscience/cdk/renderer/generators/ProductsBoxGenerator.getParameters:()Ljava/util/List;]
ProductsBoxGenerator.ProductsBoxGenerator ( )
[mangled: org/openscience/cdk/renderer/generators/ProductsBoxGenerator."<init>":()V]
cdk-1.4.15.jar, RadicalGenerator.class
package org.openscience.cdk.renderer.generators
RadicalGenerator.generate ( IAtomContainer container, RendererModel model ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/generators/RadicalGenerator.generate:(Lorg/openscience/cdk/interfaces/IAtomContainer;Lorg/openscience/cdk/renderer/RendererModel;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
RadicalGenerator.generate ( IChemObject x0, RendererModel x1 ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/generators/RadicalGenerator.generate:(Lorg/openscience/cdk/interfaces/IChemObject;Lorg/openscience/cdk/renderer/RendererModel;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
RadicalGenerator.getParameters ( ) : List
[mangled: org/openscience/cdk/renderer/generators/RadicalGenerator.getParameters:()Ljava/util/List;]
RadicalGenerator.RadicalGenerator ( )
[mangled: org/openscience/cdk/renderer/generators/RadicalGenerator."<init>":()V]
cdk-1.4.15.jar, ReactantsBoxGenerator.class
package org.openscience.cdk.renderer.generators
ReactantsBoxGenerator.generate ( IChemObject x0, RendererModel x1 ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.generate:(Lorg/openscience/cdk/interfaces/IChemObject;Lorg/openscience/cdk/renderer/RendererModel;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
ReactantsBoxGenerator.generate ( IReaction reaction, RendererModel model ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.generate:(Lorg/openscience/cdk/interfaces/IReaction;Lorg/openscience/cdk/renderer/RendererModel;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
ReactantsBoxGenerator.getParameters ( ) : List
[mangled: org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.getParameters:()Ljava/util/List;]
ReactantsBoxGenerator.ReactantsBoxGenerator ( )
[mangled: org/openscience/cdk/renderer/generators/ReactantsBoxGenerator."<init>":()V]
cdk-1.4.15.jar, ReactionArrowGenerator.class
package org.openscience.cdk.renderer.generators
ReactionArrowGenerator.generate ( IChemObject x0, RendererModel x1 ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/generators/ReactionArrowGenerator.generate:(Lorg/openscience/cdk/interfaces/IChemObject;Lorg/openscience/cdk/renderer/RendererModel;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
ReactionArrowGenerator.generate ( IReaction reaction, RendererModel model ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/generators/ReactionArrowGenerator.generate:(Lorg/openscience/cdk/interfaces/IReaction;Lorg/openscience/cdk/renderer/RendererModel;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
ReactionArrowGenerator.getParameters ( ) : List
[mangled: org/openscience/cdk/renderer/generators/ReactionArrowGenerator.getParameters:()Ljava/util/List;]
ReactionArrowGenerator.ReactionArrowGenerator ( )
[mangled: org/openscience/cdk/renderer/generators/ReactionArrowGenerator."<init>":()V]
cdk-1.4.15.jar, ReactionBoxGenerator.class
package org.openscience.cdk.renderer.generators
ReactionBoxGenerator.generate ( IChemObject x0, RendererModel x1 ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/generators/ReactionBoxGenerator.generate:(Lorg/openscience/cdk/interfaces/IChemObject;Lorg/openscience/cdk/renderer/RendererModel;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
ReactionBoxGenerator.generate ( IReaction reaction, RendererModel model ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/generators/ReactionBoxGenerator.generate:(Lorg/openscience/cdk/interfaces/IReaction;Lorg/openscience/cdk/renderer/RendererModel;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
ReactionBoxGenerator.getParameters ( ) : List
[mangled: org/openscience/cdk/renderer/generators/ReactionBoxGenerator.getParameters:()Ljava/util/List;]
ReactionBoxGenerator.ReactionBoxGenerator ( )
[mangled: org/openscience/cdk/renderer/generators/ReactionBoxGenerator."<init>":()V]
cdk-1.4.15.jar, ReactionPlusGenerator.class
package org.openscience.cdk.renderer.generators
ReactionPlusGenerator.generate ( IChemObject x0, RendererModel x1 ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/generators/ReactionPlusGenerator.generate:(Lorg/openscience/cdk/interfaces/IChemObject;Lorg/openscience/cdk/renderer/RendererModel;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
ReactionPlusGenerator.generate ( IReaction reaction, RendererModel model ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/generators/ReactionPlusGenerator.generate:(Lorg/openscience/cdk/interfaces/IReaction;Lorg/openscience/cdk/renderer/RendererModel;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
ReactionPlusGenerator.getParameters ( ) : List
[mangled: org/openscience/cdk/renderer/generators/ReactionPlusGenerator.getParameters:()Ljava/util/List;]
ReactionPlusGenerator.ReactionPlusGenerator ( )
[mangled: org/openscience/cdk/renderer/generators/ReactionPlusGenerator."<init>":()V]
cdk-1.4.15.jar, ReactionRenderer.class
package org.openscience.cdk.renderer
ReactionRenderer.calculateDiagramBounds ( IChemObject x0 ) : Rectangle
[mangled: org/openscience/cdk/renderer/ReactionRenderer.calculateDiagramBounds:(Lorg/openscience/cdk/interfaces/IChemObject;)Ljava/awt/Rectangle;]
ReactionRenderer.calculateDiagramBounds ( IReaction reaction ) : Rectangle
[mangled: org/openscience/cdk/renderer/ReactionRenderer.calculateDiagramBounds:(Lorg/openscience/cdk/interfaces/IReaction;)Ljava/awt/Rectangle;]
ReactionRenderer.calculateScaleForBondLength ( double modelBondLength ) : double
[mangled: org/openscience/cdk/renderer/ReactionRenderer.calculateScaleForBondLength:(D)D]
ReactionRenderer.generateDiagram ( IChemObject x0 ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/ReactionRenderer.generateDiagram:(Lorg/openscience/cdk/interfaces/IChemObject;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
ReactionRenderer.generateDiagram ( IReaction reaction ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/ReactionRenderer.generateDiagram:(Lorg/openscience/cdk/interfaces/IReaction;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
ReactionRenderer.getGenerators ( ) : List
[mangled: org/openscience/cdk/renderer/ReactionRenderer.getGenerators:()Ljava/util/List;]
ReactionRenderer.paint ( IChemObject x0, IDrawVisitor x1 ) : Rectangle
[mangled: org/openscience/cdk/renderer/ReactionRenderer.paint:(Lorg/openscience/cdk/interfaces/IChemObject;Lorg/openscience/cdk/renderer/visitor/IDrawVisitor;)Ljava/awt/Rectangle;]
ReactionRenderer.paint ( IChemObject x0, IDrawVisitor x1, Rectangle2D x2, boolean x3 ) : void
[mangled: org/openscience/cdk/renderer/ReactionRenderer.paint:(Lorg/openscience/cdk/interfaces/IChemObject;Lorg/openscience/cdk/renderer/visitor/IDrawVisitor;Ljava/awt/geom/Rectangle2D;Z)V]
ReactionRenderer.paint ( IReaction reaction, IDrawVisitor drawVisitor ) : Rectangle
[mangled: org/openscience/cdk/renderer/ReactionRenderer.paint:(Lorg/openscience/cdk/interfaces/IReaction;Lorg/openscience/cdk/renderer/visitor/IDrawVisitor;)Ljava/awt/Rectangle;]
ReactionRenderer.paint ( IReaction reaction, IDrawVisitor drawVisitor, Rectangle2D bounds, boolean resetCenter ) : void
[mangled: org/openscience/cdk/renderer/ReactionRenderer.paint:(Lorg/openscience/cdk/interfaces/IReaction;Lorg/openscience/cdk/renderer/visitor/IDrawVisitor;Ljava/awt/geom/Rectangle2D;Z)V]
ReactionRenderer.ReactionRenderer ( List generators, IFontManager fontManager )
[mangled: org/openscience/cdk/renderer/ReactionRenderer."<init>":(Ljava/util/List;Lorg/openscience/cdk/renderer/font/IFontManager;)V]
ReactionRenderer.ReactionRenderer ( List generators, List reactionGenerators, IFontManager fontManager )
[mangled: org/openscience/cdk/renderer/ReactionRenderer."<init>":(Ljava/util/List;Ljava/util/List;Lorg/openscience/cdk/renderer/font/IFontManager;)V]
ReactionRenderer.ReactionRenderer ( RendererModel rendererModel, List generators, IFontManager fontManager )
[mangled: org/openscience/cdk/renderer/ReactionRenderer."<init>":(Lorg/openscience/cdk/renderer/RendererModel;Ljava/util/List;Lorg/openscience/cdk/renderer/font/IFontManager;)V]
ReactionRenderer.setScale ( IChemObject x0 ) : void
[mangled: org/openscience/cdk/renderer/ReactionRenderer.setScale:(Lorg/openscience/cdk/interfaces/IChemObject;)V]
ReactionRenderer.setScale ( IReaction reaction ) : void
[mangled: org/openscience/cdk/renderer/ReactionRenderer.setScale:(Lorg/openscience/cdk/interfaces/IReaction;)V]
ReactionRenderer.setup ( IChemObject x0, Rectangle x1 ) : void
[mangled: org/openscience/cdk/renderer/ReactionRenderer.setup:(Lorg/openscience/cdk/interfaces/IChemObject;Ljava/awt/Rectangle;)V]
ReactionRenderer.setup ( IReaction reaction, Rectangle screen ) : void
[mangled: org/openscience/cdk/renderer/ReactionRenderer.setup:(Lorg/openscience/cdk/interfaces/IReaction;Ljava/awt/Rectangle;)V]
cdk-1.4.15.jar, ReactionSceneGenerator.class
package org.openscience.cdk.renderer.generators
ReactionSceneGenerator.generate ( IChemObject x0, RendererModel x1 ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/generators/ReactionSceneGenerator.generate:(Lorg/openscience/cdk/interfaces/IChemObject;Lorg/openscience/cdk/renderer/RendererModel;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
ReactionSceneGenerator.generate ( IReaction reaction, RendererModel model ) : IRenderingElement
[mangled: org/openscience/cdk/renderer/generators/ReactionSceneGenerator.generate:(Lorg/openscience/cdk/interfaces/IReaction;Lorg/openscience/cdk/renderer/RendererModel;)Lorg/openscience/cdk/renderer/elements/IRenderingElement;]
ReactionSceneGenerator.getParameters ( ) : List
[mangled: org/openscience/cdk/renderer/generators/ReactionSceneGenerator.getParameters:()Ljava/util/List;]
ReactionSceneGenerator.ReactionSceneGenerator ( )
[mangled: org/openscience/cdk/renderer/generators/ReactionSceneGenerator."<init>":()V]
cdk-1.4.15.jar, ReactionSet.class
package org.openscience.cdk
ReactionSet.isEmpty ( ) : boolean
[mangled: org/openscience/cdk/ReactionSet.isEmpty:()Z]
package org.openscience.cdk.silent
ReactionSet.isEmpty ( ) : boolean
[mangled: org/openscience/cdk/silent/ReactionSet.isEmpty:()Z]
cdk-1.4.15.jar, ReactionSetRenderer.class
package org.openscience.cdk.renderer
ReactionSetRenderer.calculateDiagramBounds ( IChemObject x0 ) : Rectangle
[mangled: org/openscience/cdk/renderer/ReactionSetRenderer.calculateDiagramBounds:(Lorg/openscience/cdk/interfaces/IChemObject;)Ljava/awt/Rectangle;]
ReactionSetRenderer.calculateDiagramBounds ( IReactionSet reactionSet ) : Rectangle
[mangled: org/openscience/cdk/renderer/ReactionSetRenderer.calculateDiagramBounds:(Lorg/openscience/cdk/interfaces/IReactionSet;)Ljava/awt/Rectangle;]
ReactionSetRenderer.calculateScaleForBondLength ( double modelBondLength ) : double
[mangled: org/openscience/cdk/renderer/ReactionSetRenderer.calculateScaleForBondLength:(D)D]
ReactionSetRenderer.getGenerators ( ) : List
[mangled: org/openscience/cdk/renderer/ReactionSetRenderer.getGenerators:()Ljava/util/List;]
ReactionSetRenderer.paint ( IChemObject x0, IDrawVisitor x1 ) : Rectangle
[mangled: org/openscience/cdk/renderer/ReactionSetRenderer.paint:(Lorg/openscience/cdk/interfaces/IChemObject;Lorg/openscience/cdk/renderer/visitor/IDrawVisitor;)Ljava/awt/Rectangle;]
ReactionSetRenderer.paint ( IChemObject x0, IDrawVisitor x1, Rectangle2D x2, boolean x3 ) : void
[mangled: org/openscience/cdk/renderer/ReactionSetRenderer.paint:(Lorg/openscience/cdk/interfaces/IChemObject;Lorg/openscience/cdk/renderer/visitor/IDrawVisitor;Ljava/awt/geom/Rectangle2D;Z)V]
ReactionSetRenderer.paint ( IReactionSet reactionSet, IDrawVisitor drawVisitor ) : Rectangle
[mangled: org/openscience/cdk/renderer/ReactionSetRenderer.paint:(Lorg/openscience/cdk/interfaces/IReactionSet;Lorg/openscience/cdk/renderer/visitor/IDrawVisitor;)Ljava/awt/Rectangle;]
ReactionSetRenderer.paint ( IReactionSet reactionSet, IDrawVisitor drawVisitor, Rectangle2D bounds, boolean resetCenter ) : void
[mangled: org/openscience/cdk/renderer/ReactionSetRenderer.paint:(Lorg/openscience/cdk/interfaces/IReactionSet;Lorg/openscience/cdk/renderer/visitor/IDrawVisitor;Ljava/awt/geom/Rectangle2D;Z)V]
ReactionSetRenderer.ReactionSetRenderer ( List generators, IFontManager fontManager )
[mangled: org/openscience/cdk/renderer/ReactionSetRenderer."<init>":(Ljava/util/List;Lorg/openscience/cdk/renderer/font/IFontManager;)V]
ReactionSetRenderer.ReactionSetRenderer ( List generators, List reactionGenerators, IFontManager fontManager )
[mangled: org/openscience/cdk/renderer/ReactionSetRenderer."<init>":(Ljava/util/List;Ljava/util/List;Lorg/openscience/cdk/renderer/font/IFontManager;)V]
ReactionSetRenderer.ReactionSetRenderer ( RendererModel rendererModel, List generators, IFontManager fontManager )
[mangled: org/openscience/cdk/renderer/ReactionSetRenderer."<init>":(Lorg/openscience/cdk/renderer/RendererModel;Ljava/util/List;Lorg/openscience/cdk/renderer/font/IFontManager;)V]
ReactionSetRenderer.ReactionSetRenderer ( RendererModel rendererModel, List generators, List reactionGenerators, IFontManager fontManager )
[mangled: org/openscience/cdk/renderer/ReactionSetRenderer."<init>":(Lorg/openscience/cdk/renderer/RendererModel;Ljava/util/List;Ljava/util/List;Lorg/openscience/cdk/renderer/font/IFontManager;)V]
ReactionSetRenderer.setScale ( IChemObject x0 ) : void
[mangled: org/openscience/cdk/renderer/ReactionSetRenderer.setScale:(Lorg/openscience/cdk/interfaces/IChemObject;)V]
ReactionSetRenderer.setScale ( IReactionSet reactionSet ) : void
[mangled: org/openscience/cdk/renderer/ReactionSetRenderer.setScale:(Lorg/openscience/cdk/interfaces/IReactionSet;)V]
ReactionSetRenderer.setup ( IChemObject x0, Rectangle x1 ) : void
[mangled: org/openscience/cdk/renderer/ReactionSetRenderer.setup:(Lorg/openscience/cdk/interfaces/IChemObject;Ljava/awt/Rectangle;)V]
ReactionSetRenderer.setup ( IReactionSet reactionSet, Rectangle screen ) : void
[mangled: org/openscience/cdk/renderer/ReactionSetRenderer.setup:(Lorg/openscience/cdk/interfaces/IReactionSet;Ljava/awt/Rectangle;)V]
cdk-1.4.15.jar, Ring.class
package org.openscience.cdk
Ring.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/Ring.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
Ring.clone ( ) : IRing
[mangled: org/openscience/cdk/Ring.clone:()Lorg/openscience/cdk/interfaces/IRing;]
Ring.clone ( ) : Object
[mangled: org/openscience/cdk/Ring.clone:()Ljava/lang/Object;]
package org.openscience.cdk.silent
Ring.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/silent/Ring.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
Ring.clone ( ) : IRing
[mangled: org/openscience/cdk/silent/Ring.clone:()Lorg/openscience/cdk/interfaces/IRing;]
Ring.clone ( ) : Object
[mangled: org/openscience/cdk/silent/Ring.clone:()Ljava/lang/Object;]
cdk-1.4.15.jar, ShowAtomAtomMapping.class
package org.openscience.cdk.renderer.generators
MappingGenerator.ShowAtomAtomMapping.getDefault ( ) : Boolean
[mangled: org/openscience/cdk/renderer/generators/MappingGenerator.ShowAtomAtomMapping.getDefault:()Ljava/lang/Boolean;]
MappingGenerator.ShowAtomAtomMapping.getDefault ( ) : Object
[mangled: org/openscience/cdk/renderer/generators/MappingGenerator.ShowAtomAtomMapping.getDefault:()Ljava/lang/Object;]
MappingGenerator.ShowAtomAtomMapping.MappingGenerator.ShowAtomAtomMapping ( )
[mangled: org/openscience/cdk/renderer/generators/MappingGenerator.ShowAtomAtomMapping."<init>":()V]
cdk-1.4.15.jar, ShowAtomTypeNames.class
package org.openscience.cdk.renderer.generators
ExtendedAtomGenerator.ShowAtomTypeNames.ExtendedAtomGenerator.ShowAtomTypeNames ( )
[mangled: org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.ShowAtomTypeNames."<init>":()V]
ExtendedAtomGenerator.ShowAtomTypeNames.getDefault ( ) : Boolean
[mangled: org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.ShowAtomTypeNames.getDefault:()Ljava/lang/Boolean;]
ExtendedAtomGenerator.ShowAtomTypeNames.getDefault ( ) : Object
[mangled: org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.ShowAtomTypeNames.getDefault:()Ljava/lang/Object;]
cdk-1.4.15.jar, ShowImplicitHydrogens.class
package org.openscience.cdk.renderer.generators
ExtendedAtomGenerator.ShowImplicitHydrogens.ExtendedAtomGenerator.ShowImplicitHydrogens ( )
[mangled: org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.ShowImplicitHydrogens."<init>":()V]
ExtendedAtomGenerator.ShowImplicitHydrogens.getDefault ( ) : Boolean
[mangled: org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.ShowImplicitHydrogens.getDefault:()Ljava/lang/Boolean;]
ExtendedAtomGenerator.ShowImplicitHydrogens.getDefault ( ) : Object
[mangled: org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.ShowImplicitHydrogens.getDefault:()Ljava/lang/Object;]
cdk-1.4.15.jar, ShowReactionBoxes.class
package org.openscience.cdk.renderer.generators
ReactionSceneGenerator.ShowReactionBoxes.getDefault ( ) : Boolean
[mangled: org/openscience/cdk/renderer/generators/ReactionSceneGenerator.ShowReactionBoxes.getDefault:()Ljava/lang/Boolean;]
ReactionSceneGenerator.ShowReactionBoxes.getDefault ( ) : Object
[mangled: org/openscience/cdk/renderer/generators/ReactionSceneGenerator.ShowReactionBoxes.getDefault:()Ljava/lang/Object;]
ReactionSceneGenerator.ShowReactionBoxes.ReactionSceneGenerator.ShowReactionBoxes ( )
[mangled: org/openscience/cdk/renderer/generators/ReactionSceneGenerator.ShowReactionBoxes."<init>":()V]
cdk-1.4.15.jar, Strand.class
package org.openscience.cdk
Strand.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/Strand.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
Strand.clone ( ) : IStrand
[mangled: org/openscience/cdk/Strand.clone:()Lorg/openscience/cdk/interfaces/IStrand;]
package org.openscience.cdk.silent
Strand.clone ( ) : IAtomContainer
[mangled: org/openscience/cdk/silent/Strand.clone:()Lorg/openscience/cdk/interfaces/IAtomContainer;]
Strand.clone ( ) : IStrand
[mangled: org/openscience/cdk/silent/Strand.clone:()Lorg/openscience/cdk/interfaces/IStrand;]
cdk-1.4.15.jar, TetrahedralChirality.class
package org.openscience.cdk.stereo
TetrahedralChirality.map ( Map atoms, Map bonds ) : ITetrahedralChirality
[mangled: org/openscience/cdk/stereo/TetrahedralChirality.map:(Ljava/util/Map;Ljava/util/Map;)Lorg/openscience/cdk/interfaces/ITetrahedralChirality;]
TetrahedralChirality.map ( Map x0, Map x1 ) : IStereoElement
[mangled: org/openscience/cdk/stereo/TetrahedralChirality.map:(Ljava/util/Map;Ljava/util/Map;)Lorg/openscience/cdk/interfaces/IStereoElement;]
TetrahedralChirality.setBuilder ( IChemObjectBuilder builder ) : void
[mangled: org/openscience/cdk/stereo/TetrahedralChirality.setBuilder:(Lorg/openscience/cdk/interfaces/IChemObjectBuilder;)V]
cdk-1.4.15.jar, WillDrawAtomNumbers.class
package org.openscience.cdk.renderer.generators
AtomNumberGenerator.WillDrawAtomNumbers.AtomNumberGenerator.WillDrawAtomNumbers ( )
[mangled: org/openscience/cdk/renderer/generators/AtomNumberGenerator.WillDrawAtomNumbers."<init>":()V]
AtomNumberGenerator.WillDrawAtomNumbers.getDefault ( ) : Boolean
[mangled: org/openscience/cdk/renderer/generators/AtomNumberGenerator.WillDrawAtomNumbers.getDefault:()Ljava/lang/Boolean;]
AtomNumberGenerator.WillDrawAtomNumbers.getDefault ( ) : Object
[mangled: org/openscience/cdk/renderer/generators/AtomNumberGenerator.WillDrawAtomNumbers.getDefault:()Ljava/lang/Object;]
to the top
Problems with Data Types, Medium Severity (2)
cdk-1.4.14.jar
package org.openscience.cdk.interfaces
[+] IAtomContainer (1)
| Change | Effect |
|---|
| 1 | Abstract method clone ( ) has been added to this interface. | A client program may be interrupted by AbstractMethodError exception. Added abstract method is called in 2nd library version by the method calculate ( IAtom, IAtomContainer, IRingSet ) and may not be implemented by old clients. |
|---|
[+] affected methods (871)
isAromatic ( IRing, IAtomContainer )2nd parameter 'atomContainer' of this method has type 'IAtomContainer'.
detectAromaticity ( IAtomContainer )1st parameter 'atomContainer' of this method has type 'IAtomContainer'.
AtomContainer ( IAtomContainer )1st parameter 'container' of this method has type 'IAtomContainer'.
add ( IAtomContainer )1st parameter 'atomContainer' of this method has type 'IAtomContainer'.
remove ( IAtomContainer )1st parameter 'atomContainer' of this method has type 'IAtomContainer'.
addAtomContainer ( IAtomContainer )1st parameter 'atomContainer' of this method has type 'IAtomContainer'.
addAtomContainer ( IAtomContainer, double )1st parameter 'atomContainer' of this method has type 'IAtomContainer'.
getAtomContainer ( int )Return value of this method has type 'IAtomContainer'.
getMultiplier ( IAtomContainer )1st parameter 'container' of this method has type 'IAtomContainer'.
removeAtomContainer ( IAtomContainer )1st parameter 'atomContainer' of this method has type 'IAtomContainer'.
replaceAtomContainer ( int, IAtomContainer )2nd parameter 'container' of this method has type 'IAtomContainer'.
setMultiplier ( IAtomContainer, Double )1st parameter 'container' of this method has type 'IAtomContainer'.
...
[+] IMolecule (1)
| Change | Effect |
|---|
| 1 | Abstract method clone ( ) has been added to this interface. | A client program may be interrupted by AbstractMethodError exception. Added abstract method is called in 2nd library version by the method initiate ( IMoleculeSet, ArrayList, ArrayList ) and may not be implemented by old clients. |
|---|
[+] affected methods (115)
addMolecule ( IMolecule )1st parameter 'molecule' of this method has type 'IMolecule'.
getMolecule ( int )Return value of this method has type 'IMolecule'.
addAgent ( IMolecule )1st parameter 'agent' of this method has type 'IMolecule'.
addProduct ( IMolecule )1st parameter 'product' of this method has type 'IMolecule'.
addProduct ( IMolecule, Double )1st parameter 'product' of this method has type 'IMolecule'.
addReactant ( IMolecule )1st parameter 'reactant' of this method has type 'IMolecule'.
addReactant ( IMolecule, Double )1st parameter 'reactant' of this method has type 'IMolecule'.
getProductCoefficient ( IMolecule )1st parameter 'product' of this method has type 'IMolecule'.
getReactantCoefficient ( IMolecule )1st parameter 'reactant' of this method has type 'IMolecule'.
setProductCoefficient ( IMolecule, Double )1st parameter 'product' of this method has type 'IMolecule'.
setReactantCoefficient ( IMolecule, Double )1st parameter 'reactant' of this method has type 'IMolecule'.
calculate ( IMolecule )1st parameter 'molecule' of this method has type 'IMolecule'.
...
to the top
Problems with Data Types, Low Severity (42)
cdk-1.4.14.jar
package org.openscience.cdk
[+] AtomContainer (1)
| Change | Effect |
|---|
| 1 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
[+] affected methods (1)
clone ( )Method 'clone ( )' will be called instead of this method in a client program.
[+] BioPolymer (4)
| Change | Effect |
|---|
| 1 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 2 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 3 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 4 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
[+] affected methods (1)
clone ( )Method 'clone ( )' will be called instead of this method in a client program.
[+] Polymer (3)
| Change | Effect |
|---|
| 1 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 2 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 3 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
[+] affected methods (1)
clone ( )Method 'clone ( )' will be called instead of this method in a client program.
package org.openscience.cdk.debug
[+] DebugAminoAcid (3)
| Change | Effect |
|---|
| 1 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 2 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 3 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
[+] affected methods (1)
clone ( )Method 'clone ( )' will be called instead of this method in a client program.
[+] DebugCrystal (2)
| Change | Effect |
|---|
| 1 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 2 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
[+] affected methods (1)
clone ( )Method 'clone ( )' will be called instead of this method in a client program.
[+] DebugMolecule (2)
| Change | Effect |
|---|
| 1 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 2 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
[+] affected methods (1)
clone ( )Method 'clone ( )' will be called instead of this method in a client program.
[+] DebugPolymer (3)
| Change | Effect |
|---|
| 1 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 2 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 3 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
[+] affected methods (1)
clone ( )Method 'clone ( )' will be called instead of this method in a client program.
[+] DebugStrand (2)
| Change | Effect |
|---|
| 1 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 2 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
[+] affected methods (1)
clone ( )Method 'clone ( )' will be called instead of this method in a client program.
package org.openscience.cdk.silent
[+] AtomContainer (1)
| Change | Effect |
|---|
| 1 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
[+] affected methods (1)
clone ( )Method 'clone ( )' will be called instead of this method in a client program.
[+] Crystal (2)
| Change | Effect |
|---|
| 1 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 2 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
[+] affected methods (1)
clone ( )Method 'clone ( )' will be called instead of this method in a client program.
[+] Molecule (2)
| Change | Effect |
|---|
| 1 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 2 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
[+] affected methods (1)
clone ( )Method 'clone ( )' will be called instead of this method in a client program.
[+] Monomer (3)
| Change | Effect |
|---|
| 1 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 2 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 3 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
[+] affected methods (1)
clone ( )Method 'clone ( )' will be called instead of this method in a client program.
[+] PDBPolymer (6)
| Change | Effect |
|---|
| 1 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 2 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 3 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 4 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 5 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 6 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
[+] affected methods (1)
clone ( )Method 'clone ( )' will be called instead of this method in a client program.
[+] Polymer (3)
| Change | Effect |
|---|
| 1 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 2 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 3 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
[+] affected methods (1)
clone ( )Method 'clone ( )' will be called instead of this method in a client program.
[+] Ring (3)
| Change | Effect |
|---|
| 1 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 2 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 3 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
[+] affected methods (1)
clone ( )Method 'clone ( )' will be called instead of this method in a client program.
[+] Strand (2)
| Change | Effect |
|---|
| 1 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
| 2 | Method clone ( ) has been overridden by clone ( ) | Method clone ( ) will be called instead of clone ( ) in a client program. |
|---|
[+] affected methods (1)
clone ( )Method 'clone ( )' will be called instead of this method in a client program.
to the top
Other Changes in Data Types (19)
cdk-1.4.14.jar
package org.openscience.cdk.interfaces
[+] IAminoAcid (1)
| Change | Effect |
|---|
| 1 | Abstract method clone ( ) has been added to this interface. | No effect. |
|---|
[+] affected methods (6)
addCTerminus ( IAtom )This abstract method is from 'IAminoAcid' interface.
addNTerminus ( IAtom )This abstract method is from 'IAminoAcid' interface.
getCTerminus ( )This abstract method is from 'IAminoAcid' interface.
getNTerminus ( )This abstract method is from 'IAminoAcid' interface.
addAcidicOxygen ( IAminoAcid )1st parameter 'acid' of this method has type 'IAminoAcid'.
removeAcidicOxygen ( IAminoAcid )1st parameter 'acid' of this method has type 'IAminoAcid'.
[+] IAtomContainer (2)
| Change | Effect |
|---|
| 1 | Abstract method isEmpty ( ) has been added to this interface. | No effect. |
|---|
| 2 | Abstract method setStereoElements ( List ) has been added to this interface. | No effect. |
|---|
[+] affected methods (871)
isAromatic ( IRing, IAtomContainer )2nd parameter 'atomContainer' of this method has type 'IAtomContainer'.
detectAromaticity ( IAtomContainer )1st parameter 'atomContainer' of this method has type 'IAtomContainer'.
AtomContainer ( IAtomContainer )1st parameter 'container' of this method has type 'IAtomContainer'.
add ( IAtomContainer )1st parameter 'atomContainer' of this method has type 'IAtomContainer'.
remove ( IAtomContainer )1st parameter 'atomContainer' of this method has type 'IAtomContainer'.
addAtomContainer ( IAtomContainer )1st parameter 'atomContainer' of this method has type 'IAtomContainer'.
addAtomContainer ( IAtomContainer, double )1st parameter 'atomContainer' of this method has type 'IAtomContainer'.
getAtomContainer ( int )Return value of this method has type 'IAtomContainer'.
getMultiplier ( IAtomContainer )1st parameter 'container' of this method has type 'IAtomContainer'.
removeAtomContainer ( IAtomContainer )1st parameter 'atomContainer' of this method has type 'IAtomContainer'.
replaceAtomContainer ( int, IAtomContainer )2nd parameter 'container' of this method has type 'IAtomContainer'.
setMultiplier ( IAtomContainer, Double )1st parameter 'container' of this method has type 'IAtomContainer'.
...
[+] IAtomContainerSet (1)
| Change | Effect |
|---|
| 1 | Abstract method isEmpty ( ) has been added to this interface. | No effect. |
|---|
[+] affected methods (43)
add ( IAtomContainerSet )1st parameter 'atomContainerSet' of this method has type 'IAtomContainerSet'.
assignrPiMarsilliFactors ( IAtomContainerSet )1st parameter 'setAc' of this method has type 'IAtomContainerSet'.
add ( IAtomContainerSet )1st parameter 'atomContainerSet' of this method has type 'IAtomContainerSet'.
add ( IAtomContainerSet )1st parameter 'atomContainerSet' of this method has type 'IAtomContainerSet'.
detect ( IAtomContainer )Return value of this method has type 'IAtomContainerSet'.
add ( IAtomContainerSet )1st parameter 'p1' of this abstract method has type 'IAtomContainerSet'.
addAtomContainer ( IAtomContainer )This abstract method is from 'IAtomContainerSet' interface.
addAtomContainer ( IAtomContainer, double )This abstract method is from 'IAtomContainerSet' interface.
atomContainers ( )This abstract method is from 'IAtomContainerSet' interface.
getAtomContainer ( int )This abstract method is from 'IAtomContainerSet' interface.
getAtomContainerCount ( )This abstract method is from 'IAtomContainerSet' interface.
getMultiplier ( int )This abstract method is from 'IAtomContainerSet' interface.
...
[+] IAtomParity (1)
| Change | Effect |
|---|
| 1 | Abstract method map ( Map, Map ) has been added to this interface. | No effect. |
|---|
[+] affected methods (4)
getAtom ( )This abstract method is from 'IAtomParity' interface.
getParity ( )This abstract method is from 'IAtomParity' interface.
getSurroundingAtoms ( )This abstract method is from 'IAtomParity' interface.
getAtomParity ( IAtomContainer, IAtom )Return value of this method has type 'IAtomParity'.
[+] IBioPolymer (1)
| Change | Effect |
|---|
| 1 | Abstract method clone ( ) has been added to this interface. | No effect. |
|---|
[+] affected methods (14)
addAtom ( IAtom )This abstract method is from 'IBioPolymer' interface.
addAtom ( IAtom, IMonomer, IStrand )This abstract method is from 'IBioPolymer' interface.
addAtom ( IAtom, IStrand )This abstract method is from 'IBioPolymer' interface.
getMonomer ( String, String )This abstract method is from 'IBioPolymer' interface.
getMonomerCount ( )This abstract method is from 'IBioPolymer' interface.
getMonomerNames ( )This abstract method is from 'IBioPolymer' interface.
getStrand ( String )This abstract method is from 'IBioPolymer' interface.
getStrandCount ( )This abstract method is from 'IBioPolymer' interface.
getStrandNames ( )This abstract method is from 'IBioPolymer' interface.
getStrands ( )This abstract method is from 'IBioPolymer' interface.
removeStrand ( String )This abstract method is from 'IBioPolymer' interface.
ProteinPocketFinder ( IBioPolymer, double[ ][ ][ ] )1st parameter 'protein' of this method has type 'IBioPolymer'.
...
[+] IChemModel (1)
| Change | Effect |
|---|
| 1 | Abstract method isEmpty ( ) has been added to this interface. | No effect. |
|---|
[+] affected methods (60)
addChemModel ( IChemModel )1st parameter 'chemModel' of this method has type 'IChemModel'.
getChemModel ( int )Return value of this method has type 'IChemModel'.
addChemModel ( IChemModel )1st parameter 'chemModel' of this method has type 'IChemModel'.
getChemModel ( int )Return value of this method has type 'IChemModel'.
has3DCoordinates ( IChemModel )1st parameter 'chemModel' of this method has type 'IChemModel'.
getCrystal ( )This abstract method is from 'IChemModel' interface.
getMoleculeSet ( )This abstract method is from 'IChemModel' interface.
getReactionSet ( )This abstract method is from 'IChemModel' interface.
getRingSet ( )This abstract method is from 'IChemModel' interface.
setCrystal ( ICrystal )This abstract method is from 'IChemModel' interface.
setMoleculeSet ( IMoleculeSet )This abstract method is from 'IChemModel' interface.
setReactionSet ( IReactionSet )This abstract method is from 'IChemModel' interface.
...
[+] ICrystal (1)
| Change | Effect |
|---|
| 1 | Abstract method clone ( ) has been added to this interface. | No effect. |
|---|
[+] affected methods (46)
ChemModel ( )Field 'this.crystal' in the object of this method has type 'ICrystal'.
clone ( )Field 'this.crystal' in the object of this method has type 'ICrystal'.
getCrystal ( )Field 'this.crystal' in the object of this method has type 'ICrystal'.
getMoleculeSet ( )Field 'this.crystal' in the object of this method has type 'ICrystal'.
getReactionSet ( )Field 'this.crystal' in the object of this method has type 'ICrystal'.
getRingSet ( )Field 'this.crystal' in the object of this method has type 'ICrystal'.
setCrystal ( ICrystal )1st parameter 'crystal' of this method has type 'ICrystal'.
setMoleculeSet ( IMoleculeSet )Field 'this.crystal' in the object of this method has type 'ICrystal'.
setReactionSet ( IReactionSet )Field 'this.crystal' in the object of this method has type 'ICrystal'.
setRingSet ( IRingSet )Field 'this.crystal' in the object of this method has type 'ICrystal'.
stateChanged ( IChemObjectChangeEvent )Field 'this.crystal' in the object of this method has type 'ICrystal'.
toString ( )Field 'this.crystal' in the object of this method has type 'ICrystal'.
...
[+] IMonomer (1)
| Change | Effect |
|---|
| 1 | Abstract method clone ( ) has been added to this interface. | No effect. |
|---|
[+] affected methods (57)
addAtom ( IAtom, IMonomer, IStrand )2nd parameter 'oMonomer' of this method has type 'IMonomer'.
getMonomer ( String, String )Return value of this method has type 'IMonomer'.
addAtom ( IAtom, IMonomer )2nd parameter 'oMonomer' of this method has type 'IMonomer'.
addAtom ( IAtom, IMonomer, IStrand )2nd parameter 'oMonomer' of this method has type 'IMonomer'.
getMonomer ( String )Return value of this method has type 'IMonomer'.
getMonomer ( String, String )Return value of this method has type 'IMonomer'.
addAtom ( IAtom, IMonomer )2nd parameter 'oMonomer' of this method has type 'IMonomer'.
getMonomer ( String )Return value of this method has type 'IMonomer'.
addAtom ( IAtom, IMonomer )2nd parameter 'oMonomer' of this method has type 'IMonomer'.
getMonomer ( String )Return value of this method has type 'IMonomer'.
addAtom ( IAtom, IMonomer, IStrand )2nd parameter 'p2' of this abstract method has type 'IMonomer'.
getMonomer ( String, String )Return value of this abstract method has type 'IMonomer'.
...
[+] IPDBMonomer (1)
| Change | Effect |
|---|
| 1 | Abstract method clone ( ) has been added to this interface. | No effect. |
|---|
[+] affected methods (6)
getChainID ( )This abstract method is from 'IPDBMonomer' interface.
getICode ( )This abstract method is from 'IPDBMonomer' interface.
getResSeq ( )This abstract method is from 'IPDBMonomer' interface.
setChainID ( String )This abstract method is from 'IPDBMonomer' interface.
setICode ( String )This abstract method is from 'IPDBMonomer' interface.
setResSeq ( String )This abstract method is from 'IPDBMonomer' interface.
[+] IPDBPolymer (1)
| Change | Effect |
|---|
| 1 | Abstract method clone ( ) has been added to this interface. | No effect. |
|---|
[+] affected methods (5)
addAtom ( IPDBAtom )This abstract method is from 'IPDBPolymer' interface.
addAtom ( IPDBAtom, IMonomer, IStrand )This abstract method is from 'IPDBPolymer' interface.
addStructure ( IPDBStructure )This abstract method is from 'IPDBPolymer' interface.
getStructures ( )This abstract method is from 'IPDBPolymer' interface.
cdkPDBPolymerToCMLMolecule ( IPDBPolymer )1st parameter 'pdbPolymer' of this method has type 'IPDBPolymer'.
[+] IPolymer (1)
| Change | Effect |
|---|
| 1 | Abstract method clone ( ) has been added to this interface. | No effect. |
|---|
[+] affected methods (6)
addAtom ( IAtom )This abstract method is from 'IPolymer' interface.
addAtom ( IAtom, IMonomer )This abstract method is from 'IPolymer' interface.
getMonomer ( String )This abstract method is from 'IPolymer' interface.
getMonomerCount ( )This abstract method is from 'IPolymer' interface.
getMonomerNames ( )This abstract method is from 'IPolymer' interface.
removeMonomer ( String )This abstract method is from 'IPolymer' interface.
[+] IReactionSet (1)
| Change | Effect |
|---|
| 1 | Abstract method isEmpty ( ) has been added to this interface. | No effect. |
|---|
[+] affected methods (116)
ChemModel ( )Field 'this.setOfReactions' in the object of this method has type 'IReactionSet'.
clone ( )Field 'this.setOfReactions' in the object of this method has type 'IReactionSet'.
getCrystal ( )Field 'this.setOfReactions' in the object of this method has type 'IReactionSet'.
getMoleculeSet ( )Field 'this.setOfReactions' in the object of this method has type 'IReactionSet'.
getReactionSet ( )Field 'this.setOfReactions' in the object of this method has type 'IReactionSet'.
getRingSet ( )Field 'this.setOfReactions' in the object of this method has type 'IReactionSet'.
setCrystal ( ICrystal )Field 'this.setOfReactions' in the object of this method has type 'IReactionSet'.
setMoleculeSet ( IMoleculeSet )Field 'this.setOfReactions' in the object of this method has type 'IReactionSet'.
setReactionSet ( IReactionSet )1st parameter 'sor' of this method has type 'IReactionSet'.
setRingSet ( IRingSet )Field 'this.setOfReactions' in the object of this method has type 'IReactionSet'.
stateChanged ( IChemObjectChangeEvent )Field 'this.setOfReactions' in the object of this method has type 'IReactionSet'.
toString ( )Field 'this.setOfReactions' in the object of this method has type 'IReactionSet'.
...
[+] IRing (1)
| Change | Effect |
|---|
| 1 | Abstract method clone ( ) has been added to this interface. | No effect. |
|---|
[+] affected methods (24)
isAromatic ( IRing, IAtomContainer )1st parameter 'ring' of this method has type 'IRing'.
getConnectedRings ( IRing )1st parameter 'ring' of this method has type 'IRing'.
getBondOrderSum ( )This abstract method is from 'IRing' interface.
getNextBond ( IBond, IAtom )This abstract method is from 'IRing' interface.
getRingSize ( )This abstract method is from 'IRing' interface.
getConnectedRings ( IRing )1st parameter 'p1' of this abstract method has type 'IRing'.
getNativeRingRadius ( IRing, double )1st parameter 'ring' of this method has type 'IRing'.
partitionNonRingPartners ( IAtom, IRing, IAtomContainer, IAtomContainer )2nd parameter 'ring' of this method has type 'IRing'.
placeFusedRing ( IRing, IAtomContainer, Point2d, Vector2d, double )1st parameter 'ring' of this method has type 'IRing'.
placeRing ( IRing, Point2d, double )1st parameter 'ring' of this method has type 'IRing'.
placeRing ( IRing, Point2d, double, Map )1st parameter 'ring' of this method has type 'IRing'.
placeRing ( IRing, IAtomContainer, Point2d, Vector2d, double )1st parameter 'ring' of this method has type 'IRing'.
...
[+] IRingSet (1)
| Change | Effect |
|---|
| 1 | Abstract method isEmpty ( ) has been added to this interface. | No effect. |
|---|
[+] affected methods (104)
inSameAromaticRing ( IAtomContainer, IAtom, IAtom, IRingSet )4th parameter 'rs' of this method has type 'IRingSet'.
setRingSet ( IRingSet )1st parameter 'rs' of this method has type 'IRingSet'.
ChemModel ( )Field 'this.ringSet' in the object of this method has type 'IRingSet'.
clone ( )Field 'this.ringSet' in the object of this method has type 'IRingSet'.
getCrystal ( )Field 'this.ringSet' in the object of this method has type 'IRingSet'.
getMoleculeSet ( )Field 'this.ringSet' in the object of this method has type 'IRingSet'.
getReactionSet ( )Field 'this.ringSet' in the object of this method has type 'IRingSet'.
getRingSet ( )Field 'this.ringSet' in the object of this method has type 'IRingSet'.
setCrystal ( ICrystal )Field 'this.ringSet' in the object of this method has type 'IRingSet'.
setMoleculeSet ( IMoleculeSet )Field 'this.ringSet' in the object of this method has type 'IRingSet'.
setReactionSet ( IReactionSet )Field 'this.ringSet' in the object of this method has type 'IRingSet'.
setRingSet ( IRingSet )1st parameter 'ringSet' of this method has type 'IRingSet'.
...
[+] IStereoElement (1)
| Change | Effect |
|---|
| 1 | Abstract method map ( Map, Map ) has been added to this interface. | No effect. |
|---|
[+] affected methods (12)
addStereoElement ( IStereoElement )1st parameter 'element' of this method has type 'IStereoElement'.
addStereoElement ( IStereoElement )1st parameter 'parity' of this method has type 'IStereoElement'.
addStereoElement ( IStereoElement )1st parameter 'parity' of this method has type 'IStereoElement'.
addStereoElement ( IStereoElement )1st parameter 'parity' of this method has type 'IStereoElement'.
addStereoElement ( IStereoElement )1st parameter 'parity' of this method has type 'IStereoElement'.
addStereoElement ( IStereoElement )1st parameter 'parity' of this method has type 'IStereoElement'.
addStereoElement ( IStereoElement )1st parameter 'parity' of this method has type 'IStereoElement'.
addStereoElement ( IStereoElement )1st parameter 'parity' of this method has type 'IStereoElement'.
addStereoElement ( IStereoElement )1st parameter 'parity' of this method has type 'IStereoElement'.
addStereoElement ( IStereoElement )1st parameter 'parity' of this method has type 'IStereoElement'.
addStereoElement ( IStereoElement )1st parameter 'p1' of this abstract method has type 'IStereoElement'.
addStereoElement ( IStereoElement )1st parameter 'element' of this method has type 'IStereoElement'.
...
[+] IStrand (1)
| Change | Effect |
|---|
| 1 | Abstract method clone ( ) has been added to this interface. | No effect. |
|---|
[+] affected methods (46)
addAtom ( IAtom, IMonomer, IStrand )3rd parameter 'oStrand' of this method has type 'IStrand'.
addAtom ( IAtom, IStrand )2nd parameter 'oStrand' of this method has type 'IStrand'.
getStrand ( String )Return value of this method has type 'IStrand'.
addAtom ( IAtom, IMonomer, IStrand )3rd parameter 'oStrand' of this method has type 'IStrand'.
addAtom ( IAtom, IStrand )2nd parameter 'oStrand' of this method has type 'IStrand'.
getStrand ( String )Return value of this method has type 'IStrand'.
addAtom ( IAtom, IMonomer, IStrand )3rd parameter 'p3' of this abstract method has type 'IStrand'.
addAtom ( IAtom, IStrand )2nd parameter 'p2' of this abstract method has type 'IStrand'.
getStrand ( String )Return value of this abstract method has type 'IStrand'.
addAtom ( IPDBAtom, IMonomer, IStrand )3rd parameter 'p3' of this abstract method has type 'IStrand'.
addAtom ( IAtom )This abstract method is from 'IStrand' interface.
addAtom ( IAtom, IMonomer )This abstract method is from 'IStrand' interface.
...
[+] ITetrahedralChirality (1)
| Change | Effect |
|---|
| 1 | Abstract method map ( Map, Map ) has been added to this interface. | No effect. |
|---|
[+] affected methods (4)
getCIPChirality ( IAtomContainer, ITetrahedralChirality )2nd parameter 'stereoCenter' of this method has type 'ITetrahedralChirality'.
getChiralAtom ( )This abstract method is from 'ITetrahedralChirality' interface.
getLigands ( )This abstract method is from 'ITetrahedralChirality' interface.
getStereo ( )This abstract method is from 'ITetrahedralChirality' interface.
package org.openscience.cdk.qsar
[+] DescriptorEngine (1)
| Change | Effect |
|---|
| 1 | Field ATOMPAIR has been added to this class. | No effect.
NOTE: A static field from a super-interface of a client class may hide an added field (with the same name) inherited from the super-class of a client class and cause IncompatibleClassChangeError exception. |
|---|
[+] affected methods (22)
DescriptorEngine ( int )This constructor is from 'DescriptorEngine' class.
DescriptorEngine ( int, String[ ] )This constructor is from 'DescriptorEngine' class.
DescriptorEngine ( List )This constructor is from 'DescriptorEngine' class.
getAvailableDictionaryClasses ( )This method is from 'DescriptorEngine' class.
getDescriptorClassNameByInterface ( String, String[ ] )This method is from 'DescriptorEngine' class.
getDescriptorClassNameByPackage ( String, String[ ] )This method is from 'DescriptorEngine' class.
getDescriptorClassNames ( )This method is from 'DescriptorEngine' class.
getDescriptorInstances ( )This method is from 'DescriptorEngine' class.
getDescriptorSpecifications ( )This method is from 'DescriptorEngine' class.
getDictionaryClass ( String )This method is from 'DescriptorEngine' class.
getDictionaryClass ( DescriptorSpecification )This method is from 'DescriptorEngine' class.
getDictionaryDefinition ( String )This method is from 'DescriptorEngine' class.
...
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Java ARchives (1)
cdk-1.4.14.jar
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