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Interfaces Interface Description org.openscience.cdk.smiles.smarts.parser.Node 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.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.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.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.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.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.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.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.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.
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Classes Class Description org.openscience.cdk.aromaticity.AromaticityCalculator useAromaticityorg.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector useAromaticitywith theElectronDonation.cdk()modelorg.openscience.cdk.aromaticity.DoubleBondAcceptingAromaticityDetector useAromaticitywith theElectronDonation.cdkAllowingExocyclic()modelorg.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.formula.MassToFormulaTool Please use MolecularFormulaGeneratororg.openscience.cdk.geometry.GeometryTools useGeometryUtilmoved for dependency reorganisationorg.openscience.cdk.graph.BFSShortestPath UseShortestPathsorg.openscience.cdk.graph.BiconnectivityInspector org.openscience.cdk.graph.invariant.CanonicalLabeler this labeller uses slow data structures and has been replaced -Canonorg.openscience.cdk.graph.MinimalPathIterator useShortestPathsorg.openscience.cdk.graph.MoleculeGraphs org.openscience.cdk.io.inchi.INChIContentProcessorTool org.openscience.cdk.io.inchi.INChIHandler 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 theMDLV2000Readershould 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 V3000org.openscience.cdk.isomorphism.matchers.CTFileQueryBond UseExpr.Type.SINGLE_OR_AROMATICetc.org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom org.openscience.cdk.isomorphism.matchers.OrderQueryBond org.openscience.cdk.isomorphism.matchers.OrderQueryBondOrderOnly Usenew QueryBond(beg, end, ORDER, bord)org.openscience.cdk.isomorphism.matchers.smarts.AliphaticAtom org.openscience.cdk.isomorphism.matchers.smarts.AliphaticSymbolAtom org.openscience.cdk.isomorphism.matchers.smarts.AnyAtom org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond org.openscience.cdk.isomorphism.matchers.smarts.AromaticAtom org.openscience.cdk.isomorphism.matchers.smarts.AromaticOrSingleQueryBond org.openscience.cdk.isomorphism.matchers.smarts.AromaticQueryBond org.openscience.cdk.isomorphism.matchers.smarts.AromaticSymbolAtom org.openscience.cdk.isomorphism.matchers.smarts.AtomicNumberAtom org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom org.openscience.cdk.isomorphism.matchers.smarts.ExplicitConnectionAtom org.openscience.cdk.isomorphism.matchers.smarts.FormalChargeAtom org.openscience.cdk.isomorphism.matchers.smarts.HybridizationNumberAtom org.openscience.cdk.isomorphism.matchers.smarts.HydrogenAtom org.openscience.cdk.isomorphism.matchers.smarts.ImplicitHCountAtom org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond org.openscience.cdk.isomorphism.matchers.smarts.MassAtom org.openscience.cdk.isomorphism.matchers.smarts.NonCHHeavyAtom org.openscience.cdk.isomorphism.matchers.smarts.OrderQueryBond org.openscience.cdk.isomorphism.matchers.smarts.PeriodicGroupNumberAtom org.openscience.cdk.isomorphism.matchers.smarts.ReactionRoleQueryAtom org.openscience.cdk.isomorphism.matchers.smarts.RecursiveSmartsAtom org.openscience.cdk.isomorphism.matchers.smarts.RingBond org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom org.openscience.cdk.isomorphism.matchers.smarts.RingMembershipAtom org.openscience.cdk.isomorphism.matchers.smarts.SmallestRingAtom org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom org.openscience.cdk.isomorphism.matchers.smarts.SMARTSBond org.openscience.cdk.isomorphism.matchers.smarts.SmartsMatchers org.openscience.cdk.isomorphism.matchers.smarts.StereoBond org.openscience.cdk.isomorphism.matchers.smarts.TotalConnectionAtom org.openscience.cdk.isomorphism.matchers.smarts.TotalHCountAtom org.openscience.cdk.isomorphism.matchers.smarts.TotalRingConnectionAtom org.openscience.cdk.isomorphism.matchers.smarts.TotalValencyAtom org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom Usenew Expr(Element, 6).and(new Expr(Element, 8))etcorg.openscience.cdk.isomorphism.SmartsStereoMatch use QueryStereoFilterorg.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.layout.OverlapResolver does not resolve overlaps correctlyorg.openscience.cdk.math.Primes org.openscience.cdk.modeling.builder3d.MMFF94BasedAtomTypePattern Mmffis faster more robust and fully validatedorg.openscience.cdk.normalize.Normalizer The functionality provided by with class is better suited to SMIRKSorg.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.qsar.descriptors.atomic.IPAtomicLearningDescriptor org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor org.openscience.cdk.renderer.color.CDKAtomColors JmolColorsprovides more comprehensive color pallet for 3Dorg.openscience.cdk.renderer.color.CPKAtomColors JmolColorsprovides more comprehensive CPK color palletorg.openscience.cdk.ringsearch.cyclebasis.CycleBasis internal implemenation detail from SSSRFinder, do not useorg.openscience.cdk.ringsearch.cyclebasis.SimpleCycle internal implemenation detail from SSSRFinder, do not useorg.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis internal implemenation detail from SSSRFinder, do not useorg.openscience.cdk.ringsearch.FiguerasSSSRFinder Use SSSRFinder instead (exact algorithm).org.openscience.cdk.ringsearch.Queue internal implemenation detail from SSSRFinder, do not useorg.openscience.cdk.ringsearch.SSSRFinder Use theCyclesAPICycles.sssr(IAtomContainer)org.openscience.cdk.smiles.DeduceBondSystemTool Use the newerKekulizationorg.openscience.cdk.smiles.FixBondOrdersTool useKekulizationorg.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor org.openscience.cdk.smiles.smarts.SmartsPattern org.openscience.cdk.smiles.smarts.SMARTSQueryTool useSmartsPatternorg.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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.smsd.Isomorphism A more recent version of SMSD is available at http://github.com/asad/smsdorg.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.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.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.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.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.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.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.smsd.ring.HanserRingFinder Use CDK AllRingsFinder. A more recent version of SMSD is available at http://github.com/asad/smsd.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.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.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.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.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.tools.MolHandler A more recent version of SMSD is available at http://github.com/asad/smsdorg.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.templates.MoleculeFactory Old CDK class primarily for testing, for CDK Tests please use TestMoleculeFactory in cdk-data (testjar).org.openscience.cdk.tools.CDKUtilities better accomplished with SMARTS patterns or simple REGEXorg.openscience.cdk.tools.DeAromatizationTool the newerKekulizationprovides a faster, more generic and comprehensive algorithm.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.tools.SwissArmyKnife org.openscience.cdk.tools.SystemOutLoggingTool should not be used directly
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Enums Enum 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.
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Fields Field Description org.openscience.cdk.CDKConstants.BONDORDER_DOUBLE UseIBond.OrderDOUBLE directly.org.openscience.cdk.CDKConstants.BONDORDER_QUADRUPLE UseIBond.OrderQUADRUPLE directly.org.openscience.cdk.CDKConstants.BONDORDER_SINGLE UseIBond.OrderSINGLE directly.org.openscience.cdk.CDKConstants.BONDORDER_TRIPLE UseIBond.OrderTRIPLE directly.org.openscience.cdk.config.Elements.PLUTOMNIUM org.openscience.cdk.smiles.SmiFlavor.AtomicMassStrict no longer needed, default CDK behaviour is now to pass through mass numbers if non-null
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Constructors Constructor Description org.openscience.cdk.inchi.InChIGenerator(IAtomContainer, List<INCHI_OPTION>, boolean) org.openscience.cdk.ringsearch.AllRingsFinder(boolean) turn logging off by setting the level in the logger implementationorg.openscience.cdk.smiles.SmilesGenerator() useSmilesGenerator(int)configuring withSmiFlavor.