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Deprecated InterfacesInterfaceDescriptionThis 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.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.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.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.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.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.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.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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Deprecated ClassesClassDescriptionuse
AromaticityuseAromaticitywith theElectronDonation.cdk()modeluseAromaticitywith theElectronDonation.cdkAllowingExocyclic()modelIncomplete and error prone - use at your own risk.use the newer Mmff.assignAtomTypes()Please use MolecularFormulaGeneratoruseGeometryUtilmoved for dependency reorganisationUseShortestPathsthis labeller uses slow data structures and has been replaced -CanonuseShortestPathsThis 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.Use V2000 or V3000UseExpr.Type.SINGLE_OR_AROMATICetc.Usenew QueryBond(beg, end, ORDER, bord)Usenew Expr(Element, 6).and(new Expr(Element, 8))etcuse QueryStereoFilterThe OPSIN (http://opsin.ch.cam.ac.uk/) tool offers a more comprehensive alternative to this parsers functionality.does not resolve overlaps correctlyMmffis faster more robust and fully validatedThe functionality provided by with class is better suited to SMIRKSThis 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.JmolColorsprovides more comprehensive color pallet for 3DJmolColorsprovides more comprehensive CPK color palletinternal implemenation detail from SSSRFinder, do not useinternal implemenation detail from SSSRFinder, do not useinternal implemenation detail from SSSRFinder, do not useUse SSSRFinder instead (exact algorithm).internal implemenation detail from SSSRFinder, do not useUse theCyclesAPICycles.sssr(IAtomContainer)Use the newerKekulizationuseKekulizationuseSmartsPatternThis 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.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.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.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.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.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.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.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.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.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.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.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.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.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.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.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.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.A more recent version of SMSD is available at http://github.com/asad/smsdThis 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.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.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.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.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.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.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.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.Use CDK AllRingsFinder. A more recent version of SMSD is available at http://github.com/asad/smsd.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.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.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.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.A more recent version of SMSD is available at http://github.com/asad/smsdSMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.Old CDK class primarily for testing, for CDK Tests please use TestMoleculeFactory in cdk-data (testjar).better accomplished with SMARTS patterns or simple REGEXthe newerKekulizationprovides a faster, more generic and comprehensive algorithm.Results depend on the order of atoms in bonds, resolving this would require retraining the models which are not available.should not be used directly
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Deprecated Enum ClassesEnum ClassDescriptionSMSD 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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Deprecated FieldsFieldDescriptionUse
IBond.OrderDOUBLE directly.UseIBond.OrderQUADRUPLE directly.UseIBond.OrderSINGLE directly.UseIBond.OrderTRIPLE directly.no longer needed, default CDK behaviour is now to pass through mass numbers if non-null
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Deprecated MethodsMethodDescriptionuse
GeometryTools.get2DCoordinateCoverage(org.openscience.cdk.interfaces.IAtomContainer)for determining partial coordinatesuseGeometryUtil.get2DCoordinateCoverage(org.openscience.cdk.interfaces.IAtomContainer)for determining partial coordinatesuseCycles.or(org.openscience.cdk.graph.CycleFinder, org.openscience.cdk.graph.CycleFinder)to define a custom fall-backThis 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 byShortestPaths.atomsTo(IAtom)use getStatus"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.use getStatususeIStereoElements for storing stereochemistryuseIStereoElements for storing stereochemistryMethod has be renamedIAtomContainer.removeAtom(IAtom).use the methodIBond.getOther(IAtom)Results now automatically consider stereo if it's present, to match without stereochemistry remove the stereo features.Replaced byAtomContainerManipulator#getBondOrderSum(IAtomContainer, IAtom)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)orLogicalOperatorAtom.not(org.openscience.cdk.isomorphism.matchers.IQueryAtom).Use the Pattern APIs from the cdk-isomorphism modulealways null, substructure templates are not used anymorealways false, substructure templates are not used anymoresubstructure templates are no longer used for layout but those provided here will be converted to identity templatesalways false, substructure templates are not used anymoretimeout not usedtimeout not useduse the new threshold (during construction)configure withSmiFlavoruse #createuse #createReactionSMILESsince 1.5.6, useSmilesGenerator.aromatic()- invoking this method does nothingconfigure withSmiFlavoruseInChITautomerGenerator.getTautomers(IAtomContainer)directlynot all attributes are removed producing unexpected results, useAtomContainerManipulator.anonymise(org.openscience.cdk.interfaces.IAtomContainer)AtomContainerManipulator.suppressHydrogens(org.openscience.cdk.interfaces.IAtomContainer)will now not removed bridging hydrogens by defaultuseIBond.Order.numeric().doubleValue()insteadcallsMolecularFormulaManipulator.getMass(IMolecularFormula, int)with optionMolecularFormulaManipulator.MonoIsotopicand adjusts for charge withMolecularFormulaManipulator.correctMass(double, Integer). These functions should be used directly.
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Deprecated ConstructorsConstructorDescriptionturn logging off by setting the level in the logger implementationuse
SmilesGenerator(int)configuring withSmiFlavor.
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Deprecated Enum Constants