Deprecated List (cdk 2.2 API)

Deprecated Classes
Class and Description
org.openscience.cdk.graph.invariant.CanonicalLabeler this labeller uses slow data structures and has been replaced - `Canon`
org.openscience.cdk.renderer.color.CDKAtomColors `JmolColors` provides more comprehensive color pallet for 3D
org.openscience.cdk.renderer.color.CPKAtomColors `JmolColors` provides more comprehensive CPK color pallet
org.openscience.cdk.io.MDLReader This reader is only for molfiles without a version tag, typically the most common molfile now encountered is V2000 and the `MDLV2000Reader` should be used instead. The V2000 reader can actually read files missing the version tag when in relaxed mode.
org.openscience.cdk.io.MDLRXNReader Use V2000 or V3000
org.openscience.cdk.layout.OverlapResolver does not resolve overlaps correctly
org.openscience.cdk.math.Primes

Deprecated Fields
Field and Description
org.openscience.cdk.smiles.SmiFlavor.AtomicMassStrict no longer needed, default CDK behaviour is now to pass through mass numbers if non-null
org.openscience.cdk.CDKConstants.BONDORDER_DOUBLE Use `IBond.Order` DOUBLE directly.
org.openscience.cdk.CDKConstants.BONDORDER_QUADRUPLE Use `IBond.Order` QUADRUPLE directly.
org.openscience.cdk.CDKConstants.BONDORDER_SINGLE Use `IBond.Order` SINGLE directly.
org.openscience.cdk.CDKConstants.BONDORDER_TRIPLE Use `IBond.Order` TRIPLE directly.
org.openscience.cdk.config.Elements.PLUTOMNIUM

Deprecated Methods
Method and Description
org.openscience.cdk.graph.Cycles.allOrVertexShort() use `Cycles.or(org.openscience.cdk.graph.CycleFinder, org.openscience.cdk.graph.CycleFinder)` to define a custom fall-back
org.openscience.cdk.smiles.SmilesGenerator.aromatic() configure with `SmiFlavor`
org.openscience.cdk.ringsearch.AllRingsFinder.checkTimeout() timeout not used
org.openscience.cdk.tools.manipulator.AtomContainerManipulator.createAllCarbonAllSingleNonAromaticBondAtomContainer(IAtomContainer) not all attributes are removed producing unexpected results, use `AtomContainerManipulator.anonymise(org.openscience.cdk.interfaces.IAtomContainer)`
org.openscience.cdk.smiles.SmilesGenerator.createReactionSMILES(IReaction) use `SmilesGenerator.create(IAtomContainer)`
org.openscience.cdk.smiles.SmilesGenerator.createSMILES(IAtomContainer) use #create
org.openscience.cdk.smiles.SmilesGenerator.createSMILES(IReaction) use #createReactionSMILES
org.openscience.cdk.tools.manipulator.BondManipulator.destroyBondOrder(IBond.Order) use `IBond.Order.numeric().doubleValue()` instead
org.openscience.cdk.fingerprint.Fingerprinter.findPathes(IAtomContainer, int) Use `Fingerprinter.encodePaths(IAtomContainer, int, BitSet, int)`
org.openscience.cdk.layout.StructureDiagramGenerator.generateExperimentalCoordinates() use `StructureDiagramGenerator.generateCoordinates()`
org.openscience.cdk.layout.StructureDiagramGenerator.generateExperimentalCoordinates(Vector2d) use `StructureDiagramGenerator.generateCoordinates()`
org.openscience.cdk.interfaces.IAtomContainer.getAtomNumber(IAtom) use `IAtomContainer.indexOf(IAtom)`
org.openscience.cdk.interfaces.IAtomContainer.getBondNumber(IAtom, IAtom) use `IAtomContainer.indexOf(IBond)`
org.openscience.cdk.interfaces.IAtomContainer.getBondNumber(IBond) use `IAtomContainer.indexOf(IBond)`
org.openscience.cdk.isomorphism.matchers.QueryAtomContainer.getBondOrderSum(IAtom) Replaced by `AtomContainerManipulator#getBondOrderSum(IAtomContainer, IAtom)`
org.openscience.cdk.interfaces.IBond.getConnectedAtom(IAtom) use the method `IBond.getOther(IAtom)`
org.openscience.cdk.interfaces.IAtomContainer.getConnectedAtomsCount(IAtom) use `IAtomContainer.getConnectedBondsCount(IAtom)`
org.openscience.cdk.interfaces.IAtomContainer.getFirstAtom() use `IAtomContainer.getAtom(int)`
org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator.getHillString(IMolecularFormula) Use `MolecularFormulaManipulator.getString(org.openscience.cdk.interfaces.IMolecularFormula)`
org.openscience.cdk.inchi.InChIGeneratorFactory.getIgnoreAromaticBonds()
org.openscience.cdk.interfaces.IAtomContainer.getLastAtom() use `IAtomContainer.getAtom(int)`
org.openscience.cdk.interfaces.IAtomContainer.getLonePairNumber(ILonePair) use `IAtomContainer.indexOf(ILonePair)`
org.openscience.cdk.graph.PathTools.getShortestPath(IAtomContainer, IAtom, IAtom) This implementation recalculates all shortest paths from the start atom for each method call and does not indicate if there are equally short paths from the start to the end. Replaced by `ShortestPaths.atomsTo(IAtom)`
org.openscience.cdk.interfaces.IAtomContainer.getSingleElectronNumber(ISingleElectron) use `IAtomContainer.indexOf(ISingleElectron)`
org.openscience.cdk.interfaces.IAtom.getStereoParity() use `IStereoElement`s for storing stereochemistry
org.openscience.cdk.tautomers.InChITautomerGenerator.getTautomers(IAtomContainer, String) use `InChITautomerGenerator.getTautomers(IAtomContainer)` directly
org.openscience.cdk.layout.StructureDiagramGenerator.getTemplateHandler() always null, substructure templates are not used anymore
org.openscience.cdk.ringsearch.AllRingsFinder.getTimeout() timeout not used
org.openscience.cdk.layout.StructureDiagramGenerator.getUseTemplates() always false, substructure templates are not used anymore
org.openscience.cdk.geometry.GeometryUtil.has2DCoordinatesNew(IAtomContainer) use `GeometryUtil.get2DCoordinateCoverage(org.openscience.cdk.interfaces.IAtomContainer)` for determining partial coordinates
org.openscience.cdk.smiles.SmilesParser.isPreservingAromaticity()
org.openscience.cdk.isomorphism.UniversalIsomorphismTester.isSubgraph(IAtomContainer, IAtomContainer) Use the Pattern APIs from the cdk-isomorphism module
org.openscience.cdk.modeling.builder3d.TemplateHandler3D.mapTemplates(IAtomContainer, double) Use `TemplateHandler3D.mapTemplates(org.openscience.cdk.interfaces.IAtomContainer, int)`
org.openscience.cdk.renderer.elements.path.PathElement.points()
org.openscience.cdk.isomorphism.matchers.QueryAtomContainer.removeAtomAndConnectedElectronContainers(IAtom)
org.openscience.cdk.AtomContainer.removeAtomAndConnectedElectronContainers(IAtom)
org.openscience.cdk.interfaces.IAtomContainer.removeAtomAndConnectedElectronContainers(IAtom) Method has be renamed `IAtomContainer.removeAtom(IAtom)`.
org.openscience.cdk.silent.AtomContainer.removeAtomAndConnectedElectronContainers(IAtom)
org.openscience.cdk.tools.manipulator.AtomContainerManipulator.removeHydrogensPreserveMultiplyBonded(IAtomContainer) `AtomContainerManipulator.suppressHydrogens(org.openscience.cdk.interfaces.IAtomContainer)` will now not removed bridging hydrogens by default
org.openscience.cdk.layout.StructureDiagramGenerator.setBondLength(double) use `GeometryUtil.scaleMolecule(IAtomContainer, double)`
org.openscience.cdk.formula.AdductFormula.setCharge(Integer)
org.openscience.cdk.silent.AdductFormula.setCharge(Integer)
org.openscience.cdk.tools.SystemOutLoggingTool.setDebugEnabled(boolean) use `SystemOutLoggingTool.setLevel(int)`
org.openscience.cdk.inchi.InChIGeneratorFactory.setIgnoreAromaticBonds(boolean) "the use of aromatic bonds is strongly discouraged" - InChI FAQ, the InChI will fail for many compounds if ignore aromatic bonds is not enabled and the compound have aromatic flags.
org.openscience.cdk.smiles.SmilesParser.setPreservingAromaticity(boolean)
org.openscience.cdk.io.rdf.CDKOWLReader.setReader(Reader)
org.openscience.cdk.interfaces.IAtom.setStereoParity(Integer) use `IStereoElement`s for storing stereochemistry
org.openscience.cdk.layout.StructureDiagramGenerator.setTemplateHandler(TemplateHandler) substructure templates are no longer used for layout but those provided here will be converted to identity templates
org.openscience.cdk.ringsearch.AllRingsFinder.setTimeout(long) use the new threshold (during construction)
org.openscience.cdk.smiles.SmilesGenerator.setUseAromaticityFlag(boolean) since 1.5.6, use `SmilesGenerator.aromatic()` - invoking this method does nothing
org.openscience.cdk.layout.StructureDiagramGenerator.setUseTemplates(boolean) always false, substructure templates are not used anymore
org.openscience.cdk.layout.AtomPlacer.shouldBeLinear(IAtom, IAtomContainer)
org.openscience.cdk.isomorphism.Mappings.stereochemistry() Results now automatically consider stereo if it's present, to match without stereochemistry remove the stereo features.
org.openscience.cdk.smiles.SmilesGenerator.withAtomClasses() configure with `SmiFlavor`

Deprecated Constructors
Constructor and Description
org.openscience.cdk.ringsearch.AllRingsFinder(boolean) turn logging off by setting the level in the logger implementation
org.openscience.cdk.smiles.SmilesGenerator() use `SmilesGenerator.SmilesGenerator(int)` configuring with `SmiFlavor`.

Deprecated Enum Constants
Enum Constant and Description
org.openscience.cdk.config.Elements.Ununoctium
org.openscience.cdk.config.Elements.Ununpentium
org.openscience.cdk.config.Elements.Ununseptium
org.openscience.cdk.config.Elements.Ununtrium

Deprecated API

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