Deprecated API

Contents

• Deprecated Interfaces
• Deprecated Classes
• Deprecated Enums
• Deprecated Fields
• Deprecated Methods
• Deprecated Constructors
• Deprecated Enum Constants

Deprecated Interfaces

Interface and Description
org.openscience.cdk.smsd.algorithm.matchers.AtomMatcher This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.matchers.BondMatcher This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.labelling.ICanonicalMoleculeLabeller This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.labelling.ICanonicalReactionLabeller This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.vflib.interfaces.IEdge SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.interfaces.IFinalMapping SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.interfaces.IMCSBase SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQueryCompiler SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.vflib.interfaces.IState SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.ring.RingFinder This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.matchers.VFAtomMatcher This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.matchers.VFBondMatcher This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.

Deprecated Classes

Class and Description
org.openscience.cdk.smsd.interfaces.AbstractMCS SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.interfaces.AbstractMCSAlgorithm SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.labelling.AbstractReactionLabeller This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.interfaces.AbstractSubGraph SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.aromaticity.AromaticityCalculator use Aromaticity
org.openscience.cdk.smsd.labelling.AtomContainerAtomPermutor This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.labelling.AtomContainerPrinter This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.helper.BinaryTree SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.mcsplus.BKKCKCF SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.tools.BondEnergies SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.helper.BondEnergy SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.graph.invariant.CanonicalLabeler this labeller uses slow data structures and has been replaced - Canon
org.openscience.cdk.smsd.labelling.CanonicalLabellingAdaptor This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.renderer.color.CDKAtomColors JmolColors provides more comprehensive color pallet for 3D
org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector use Aromaticity with the ElectronDonation.cdk() model
org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.tools.CDKUtilities better accomplished with SMARTS patterns or simple REGEX
org.openscience.cdk.smsd.filters.ChemicalFilters SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.renderer.color.CPKAtomColors JmolColors provides more comprehensive CPK color pallet
org.openscience.cdk.ringsearch.cyclebasis.CycleBasis internal implemenation detail from SSSRFinder, do not use
org.openscience.cdk.tools.DeAromatizationTool the newer Kekulization provides a faster, more generic and comprehensive algorithm.
org.openscience.cdk.smiles.DeduceBondSystemTool Use the newer Kekulization
org.openscience.cdk.smsd.algorithm.matchers.DefaultBondMatcher This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.matchers.DefaultMatcher This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.matchers.DefaultVFBondMatcher This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.aromaticity.DoubleBondAcceptingAromaticityDetector use Aromaticity with the ElectronDonation.cdkAllowingExocyclic() model
org.openscience.cdk.smsd.algorithm.vflib.builder.EdgeBuilder SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.mcsplus.ExactMapping SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.ringsearch.FiguerasSSSRFinder Use SSSRFinder instead (exact algorithm).
org.openscience.cdk.smsd.helper.FinalMappings SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smiles.FixBondOrdersTool use Kekulization
org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.ring.HanserRingFinder Use CDK AllRingsFinder. A more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.tools.IonizationPotentialTool Results depend on the order of atoms in bonds, resolving this would require retraining the models which are not available.
org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor
org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor
org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
org.openscience.cdk.smsd.Isomorphism A more recent version of SMSD is available at http://github.com/asad/smsd
org.openscience.cdk.smsd.helper.LabelContainer SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.formula.MassToFormulaTool Please use MolecularFormulaGenerator
org.openscience.cdk.smsd.algorithm.vflib.map.Match SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.mcgregor.McGregor SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlus SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
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.atomtype.MM2AtomTypeMatcher Incomplete and error prone - use at your own risk.
org.openscience.cdk.atomtype.MMFF94AtomTypeMatcher use the newer Mmff.assignAtomTypes()
org.openscience.cdk.templates.MoleculeFactory Old CDK class primarily for testing, for CDK Tests please use TestMoleculeFactory in cdk-data (testjar).
org.openscience.cdk.smsd.tools.MoleculeSanityCheck SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.labelling.MoleculeSignatureLabellingAdaptor This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.tools.MolHandler A more recent version of SMSD is available at http://github.com/asad/smsd
org.openscience.cdk.smsd.algorithm.vflib.builder.NodeBuilder SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.iupac.parser.NomParser The OPSIN (http://opsin.ch.cam.ac.uk/) tool offers a more comprehensive alternative to this parsers functionality.
org.openscience.cdk.normalize.Normalizer The functionality provided by with class is better suited to SMIRKS
org.openscience.cdk.layout.OverlapResolver does not resolve overlaps correctly
org.openscience.cdk.smsd.ring.PathEdge This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK and a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.ring.PathGraph This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK and a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.labelling.Permutor This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.filters.PostFilter SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.math.Primes
org.openscience.cdk.smsd.algorithm.vflib.query.QueryCompiler SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.mcgregor.QueryProcessor SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.ringsearch.Queue internal implemenation detail from SSSRFinder, do not use
org.openscience.cdk.smsd.ring.RingFilter This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK and a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.labelling.SignatureReactionCanoniser This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle internal implemenation detail from SSSRFinder, do not use
org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis internal implemenation detail from SSSRFinder, do not use
org.openscience.cdk.smsd.algorithm.single.SingleMapping This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.labelling.SmilesReactionCanoniser This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.normalize.SMSDNormalizer This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.ringsearch.SSSRFinder Use the Cycles API Cycles.sssr(IAtomContainer)
org.openscience.cdk.tools.SwissArmyKnife
org.openscience.cdk.smsd.algorithm.mcgregor.TargetProcessor SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.tools.TimeManager SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.global.TimeOut SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
org.openscience.cdk.smsd.algorithm.vflib.map.VFState SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.

Deprecated Enums

Enum and Description
org.openscience.cdk.smsd.interfaces.Algorithm SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.

Deprecated Fields

Field and Description
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.AtomContainer.getBondOrderSum(IAtom) Replaced by AtomContainerManipulator#getBondOrderSum(IAtomContainer, IAtom)
org.openscience.cdk.silent.AtomContainer.getBondOrderSum(IAtom) Replaced by AtomContainerManipulator#getBondOrderSum(IAtomContainer, IAtom)
org.openscience.cdk.smiles.smarts.parser.SimpleCharStream.getColumn()
org.openscience.cdk.iupac.parser.SimpleCharStream.getColumn()
org.openscience.cdk.interfaces.IBond.getConnectedAtom(IAtom) use the method IBond.getOther(IAtom)
org.openscience.cdk.interfaces.IAtomContainer.getFirstAtom() use IAtomContainer.getAtom(int)
org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom.getFlag(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.isomorphism.matchers.smarts.LogicalOperatorAtom.getLeft()
org.openscience.cdk.smiles.smarts.parser.SimpleCharStream.getLine()
org.openscience.cdk.iupac.parser.SimpleCharStream.getLine()
org.openscience.cdk.interfaces.IAtomContainer.getLonePairNumber(ILonePair) use IAtomContainer.indexOf(ILonePair)
org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom.getOperator()
org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom.getRight()
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 IStereoElements 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.GeometryTools.has2DCoordinatesNew(IAtomContainer) use GeometryTools.get2DCoordinateCoverage(org.openscience.cdk.interfaces.IAtomContainer) for determining partial coordinates
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.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.tools.manipulator.AtomContainerManipulator.removeHydrogensPreserveMultiplyBonded(IAtomContainer) AtomContainerManipulator.suppressHydrogens(org.openscience.cdk.interfaces.IAtomContainer) will now not removed bridging hydrogens by default
org.openscience.cdk.formula.AdductFormula.setCharge(Integer)
org.openscience.cdk.silent.AdductFormula.setCharge(Integer)
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.isomorphism.matchers.smarts.LogicalOperatorAtom.setLeft(IQueryAtom)
org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom.setOperator(String) use static utility methods to create logical atom matcher, LogicalOperatorAtom.and(org.openscience.cdk.isomorphism.matchers.IQueryAtom, org.openscience.cdk.isomorphism.matchers.IQueryAtom), LogicalOperatorAtom.or(org.openscience.cdk.isomorphism.matchers.IQueryAtom, org.openscience.cdk.isomorphism.matchers.IQueryAtom) or LogicalOperatorAtom.not(org.openscience.cdk.isomorphism.matchers.IQueryAtom).
org.openscience.cdk.smiles.SmilesParser.setPreservingAromaticity(boolean)
org.openscience.cdk.io.rdf.CDKOWLReader.setReader(Reader)
org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom.setRight(IQueryAtom)
org.openscience.cdk.interfaces.IAtom.setStereoParity(Integer) use IStereoElements 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.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