Index (cdk-standard 2.1.1 API)

A B C D E F G H I K L M N O P R S T U V W

A

AbstractFingerprinter - Class in org.openscience.cdk.fingerprint
AbstractFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.AbstractFingerprinter
add(double) - Method in class org.openscience.cdk.qsar.result.DoubleArrayResult
add(int) - Method in class org.openscience.cdk.qsar.result.IntegerArrayResult
addAcidicOxygen(IAminoAcid) - Static method in class org.openscience.cdk.tools.manipulator.AminoAcidManipulator: Adds the singly bonded oxygen from the acid group of the AminoAcid.
addNode(RNode) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Adds a new node to the RGraph.
addTuple(Bspt.Tuple) - Method in class org.openscience.cdk.graph.rebond.Bspt
allCoplanar(Vector3d, Point3d, Point3d...) - Static method in class org.openscience.cdk.stereo.StereoTool: Check that all the points in the list are coplanar (in the same plane) as the plane defined by the planeNormal and the pointInPlane.
AllRingsFinder - Class in org.openscience.cdk.ringsearch: Compute the set of all rings in a molecule.
AllRingsFinder(boolean) - Constructor for class org.openscience.cdk.ringsearch.AllRingsFinder: Deprecated.
turn logging off by setting the level in the logger implementation
AllRingsFinder() - Constructor for class org.openscience.cdk.ringsearch.AllRingsFinder: Default constructor using a threshold of AllRingsFinder.Threshold.PubChem_99.
AllRingsFinder.Threshold - Enum in org.openscience.cdk.ringsearch: The threshold values provide a limit at which the computation stops.
allSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.LonePairElectronChecker: Determines of all atoms on the AtomContainer have the right number the lone pair electrons.
AminoAcidManipulator - Class in org.openscience.cdk.tools.manipulator: Class with convenience methods that provide methods to manipulate AminoAcid's.
AminoAcidManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.AminoAcidManipulator
and(IBitFingerprint) - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
and(IBitFingerprint) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
and(IntArrayFingerprint) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
anonymise(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Anonymise the provided container to single-bonded carbon atoms.
apply(IAtomContainer) - Method in class org.openscience.cdk.aromaticity.Aromaticity: Apply this aromaticity model to a molecule.
Aromaticity - Class in org.openscience.cdk.aromaticity: A configurable model to perceive aromatic systems.
Aromaticity(ElectronDonation, CycleFinder) - Constructor for class org.openscience.cdk.aromaticity.Aromaticity: Create an aromaticity model using the specified electron donation model which is tested on the cycles.
asBitSet() - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
asBitSet() - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
atof(String) - Static method in class org.openscience.cdk.math.FortranFormat: Converts a string of digits to an double.
atomContainer - Variable in class org.openscience.cdk.graph.AtomContainerPermutor: The atom container that is permuted at each step.
atomContainer - Variable in class org.openscience.cdk.tools.HOSECodeGenerator: The molecular structure on which we work
AtomContainerAtomPermutor - Class in org.openscience.cdk.graph: An atom container atom permutor that uses ranking and unranking to calculate the next permutation in the series.
AtomContainerAtomPermutor(IAtomContainer) - Constructor for class org.openscience.cdk.graph.AtomContainerAtomPermutor: A permutor wraps the original atom container, and produces cloned (and permuted!) copies on demand.
AtomContainerBondPermutor - Class in org.openscience.cdk.graph: This class allows the user to iterate through the set of all possible permutations of the bond order in a given atom container.
AtomContainerBondPermutor(IAtomContainer) - Constructor for class org.openscience.cdk.graph.AtomContainerBondPermutor: A permutor wraps the original atom container, and produces cloned (and permuted!) copies on demand.
AtomContainerComparator - Class in org.openscience.cdk.tools.manipulator: Compares two IAtomContainers for order with the following criteria with decreasing priority:
AtomContainerComparator() - Constructor for class org.openscience.cdk.tools.manipulator.AtomContainerComparator: Creates a new instance of AtomContainerComparator
AtomContainerComparatorBy2DCenter - Class in org.openscience.cdk.tools.manipulator: Compares two IAtomContainers based on their 2D position.
AtomContainerComparatorBy2DCenter() - Constructor for class org.openscience.cdk.tools.manipulator.AtomContainerComparatorBy2DCenter
AtomContainerManipulator - Class in org.openscience.cdk.tools.manipulator: Class with convenience methods that provide methods to manipulate AtomContainer's.
AtomContainerManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
AtomContainerPermutor - Class in org.openscience.cdk.graph: The base class for permutors of atom containers, with a single abstract method containerFromPermutation that should be implemented in concrete derived classes.
AtomContainerPermutor(int, IAtomContainer) - Constructor for class org.openscience.cdk.graph.AtomContainerPermutor: Start the permutor off with an initial atom container, and the size of the permutation.
AtomContainerSetManipulator - Class in org.openscience.cdk.tools.manipulator
AtomContainerSetManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
AtomMappingTools - Class in org.openscience.cdk.isomorphism
AtomMappingTools() - Constructor for class org.openscience.cdk.isomorphism.AtomMappingTools
AtomTypeManipulator - Class in org.openscience.cdk.tools.manipulator: Class with utilities for the IAtomType class.
AtomTypeManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.AtomTypeManipulator
AtomValenceTool - Class in org.openscience.cdk.qsar: This class returns the valence of an atom.
AtomValenceTool() - Constructor for class org.openscience.cdk.qsar.AtomValenceTool

B

basicInvariants(IAtomContainer, int[][]) - Static method in class org.openscience.cdk.graph.invariant.Canon: Generate the initial invariants for each atom in the container.
BitSetFingerprint - Class in org.openscience.cdk.fingerprint
BitSetFingerprint(BitSet) - Constructor for class org.openscience.cdk.fingerprint.BitSetFingerprint
BitSetFingerprint() - Constructor for class org.openscience.cdk.fingerprint.BitSetFingerprint
BitSetFingerprint(int) - Constructor for class org.openscience.cdk.fingerprint.BitSetFingerprint
BitSetFingerprint(IBitFingerprint) - Constructor for class org.openscience.cdk.fingerprint.BitSetFingerprint
bitSetToRMap(BitSet) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Converts a RGraph bitset (set of RNode) to a list of RMap that represents the mapping between to substructures in G1 and G2 (the projection of the RGraph bitset on G1 and G2).
bondMap - Variable in class org.openscience.cdk.stereo.StereoElementFactory: A bond map for fast access to bond labels between two atom indices.
bondSymbols - Variable in class org.openscience.cdk.tools.HOSECodeGenerator: The bond symbols used for bond orders "single", "double", "triple" and "aromatic"
BondTools - Class in org.openscience.cdk.geometry: A set of static utility classes for geometric calculations on IBonds.
BondTools() - Constructor for class org.openscience.cdk.geometry.BondTools
BooleanResult - Class in org.openscience.cdk.qsar.result: Object that provides access to the calculated descriptor value.
BooleanResult(boolean) - Constructor for class org.openscience.cdk.qsar.result.BooleanResult
BooleanResultType - Class in org.openscience.cdk.qsar.result: IDescriptorResult type for boolean.
BooleanResultType() - Constructor for class org.openscience.cdk.qsar.result.BooleanResultType
booleanValue() - Method in class org.openscience.cdk.qsar.result.BooleanResult
Bspt - Class in org.openscience.cdk.graph.rebond: BSP-Tree stands for Binary Space Partitioning Tree.
Bspt(int) - Constructor for class org.openscience.cdk.graph.rebond.Bspt
Bspt.Tuple - Interface in org.openscience.cdk.graph.rebond
buildRGraph(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Builds the RGraph ( resolution graph ), from two atomContainer (description of the two molecules to compare) This is the interface point between the CDK model and the generic MCSS algorithm based on the RGRaph.

C

calcInvertedAxes(Vector3d, Vector3d, Vector3d) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools: Inverts three cell axes.
calculate(IAtomContainer) - Static method in class org.openscience.cdk.geometry.volume.VABCVolume: Calculates the volume for the given IAtomContainer.
calculateMaxRank() - Method in class org.openscience.cdk.graph.Permutor: Calculate the max possible rank for permutations of N numbers.
calculatePerpendicularUnitVector(Point2d, Point2d) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Determines the normalized vector orthogonal on the vector p1->p2.
Canon - Class in org.openscience.cdk.graph.invariant: An implementation based on the canon algorithm [Weininger, David and Weininger, Arthur and Weininger, Joseph L., SMILES 2. Algorithm for Generation of Unique SMILES Notation, Journal of Chemical Information and Computer Sciences, 1989, 29:97-101].
CANONICAL_LABEL - Static variable in class org.openscience.cdk.smiles.InvPair
CanonicalLabeler - Class in org.openscience.cdk.graph.invariant: Deprecated.
this labeller uses slow data structures and has been replaced - Canon
CanonicalLabeler() - Constructor for class org.openscience.cdk.graph.invariant.CanonicalLabeler: Deprecated.
canonLabel(IAtomContainer) - Method in class org.openscience.cdk.graph.invariant.CanonicalLabeler: Deprecated.

Canonically label the fragment.
cardinality() - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
cardinality() - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
cartesianToFractional(Vector3d, Vector3d, Vector3d, Point3d) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools
cartesianToNotional(Vector3d, Vector3d, Vector3d) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools
cdk() - Static method in class org.openscience.cdk.aromaticity.ElectronDonation: Use the preset CDK atom types to determine the electron contribution of atoms.
cdkAllowingExocyclic() - Static method in class org.openscience.cdk.aromaticity.ElectronDonation: Use the preset CDK atom types to determine the electron contribution of atoms.
cdkLegacy() - Static method in class org.openscience.cdk.aromaticity.Aromaticity: Access an aromaticity instance that replicates the previously utilised - CDKHueckelAromaticityDetector.
center(IAtomContainer, double[]) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Centers the molecule in the given area.
centerCode - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
checkSingleAtomCases(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Checks for single atom cases before doing subgraph/isomorphism search.
checkSymmetry(boolean) - Method in class org.openscience.cdk.stereo.StereoElementFactory
checkTimeout() - Method in class org.openscience.cdk.ringsearch.AllRingsFinder: Deprecated.
timeout not used
ChemFileManipulator - Class in org.openscience.cdk.tools.manipulator: Class with convenience methods that provide methods from methods from ChemObjects within the ChemFile.
ChemFileManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ChemFileManipulator
ChemModelManipulator - Class in org.openscience.cdk.tools.manipulator: Class with convenience methods that provide methods from methods from ChemObjects within the ChemModel.
ChemModelManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ChemModelManipulator
ChemSequenceManipulator - Class in org.openscience.cdk.tools.manipulator: Class with convenience methods that provide methods from methods from ChemObjects within the ChemSequence.
ChemSequenceManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator
clear() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Reinitialisation of the TGraph.
clearAtomConfigurations(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: This method will reset all atom configuration to UNSET.
closeEnoughToBond(IAtom, IAtom, double) - Static method in class org.openscience.cdk.geometry.BondTools: Returns true if the two atoms are within the distance fudge factor of each other.
commit() - Method in class org.openscience.cdk.smiles.InvPair
compare(String, String) - Method in class org.openscience.cdk.tools.ElementComparator: Returns a negative if o1 comes before o2 in a molecular formula, returns zero if they are identical, and positive if o1 comes after o2 in the formula.
compare(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.tools.manipulator.AtomContainerComparator
compare(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.tools.manipulator.AtomContainerComparatorBy2DCenter: Compare two AtomContainers based on their 2D position.
compare(IRing, IRing) - Method in class org.openscience.cdk.tools.manipulator.RingSizeComparator
configure(IAtom, IAtomType) - Static method in class org.openscience.cdk.tools.manipulator.AtomTypeManipulator: Method that assign properties to an atom given a particular atomType.
configureUnsetProperties(IAtom, IAtomType) - Static method in class org.openscience.cdk.tools.manipulator.AtomTypeManipulator: Method that assign properties to an atom given a particular atomType.
ConnectionMatrix - Class in org.openscience.cdk.graph.matrix: Calculator for a connection matrix representation of this AtomContainer.
ConnectionMatrix() - Constructor for class org.openscience.cdk.graph.matrix.ConnectionMatrix
ConnectivityChecker - Class in org.openscience.cdk.graph: Tool class for checking whether the (sub)structure in an AtomContainer is connected.
ConnectivityChecker() - Constructor for class org.openscience.cdk.graph.ConnectivityChecker
container - Variable in class org.openscience.cdk.stereo.StereoElementFactory: Native CDK structure representation.
containerFromPermutation(int[]) - Method in class org.openscience.cdk.graph.AtomContainerAtomPermutor: Generate the atom container with this permutation of the atoms.
containerFromPermutation(int[]) - Method in class org.openscience.cdk.graph.AtomContainerBondPermutor
containerFromPermutation(int[]) - Method in class org.openscience.cdk.graph.AtomContainerPermutor: Convert a permutation (expressed as a list of numbers) into a permuted atom container.
containsByID(IAtomContainerSet, String) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator: Tells if an AtomContainerSet contains at least one AtomContainer with the same ID as atomContainer.
convertImplicitToExplicitHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Adds explicit hydrogens (without coordinates) to the IAtomContainer, equaling the number of set implicit hydrogens.
convertToAtomContainer(IRingSet) - Static method in class org.openscience.cdk.ringsearch.RingPartitioner: Converts a RingSet to an AtomContainer.
copyAndSuppressedHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Copy the input container and suppress any explicit hydrogens.
countExplicitHydrogens(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Count explicit hydrogens.
countHydrogens(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
createAll() - Method in class org.openscience.cdk.stereo.StereoElementFactory: Creates all stereo elements found by Stereocenters using the or 2D/3D coordinates to specify the configuration (clockwise/anticlockwise).
createAllCarbonAllSingleNonAromaticBondAtomContainer(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Deprecated.
not all attributes are removed producing unexpected results, use AtomContainerManipulator.anonymise(org.openscience.cdk.interfaces.IAtomContainer)
createIDs(IChemObject) - Static method in class org.openscience.cdk.tools.IDCreator: Labels the Atom's and Bond's in the AtomContainer using the a1, a2, b1, b2 scheme often used in CML.
createNewMolecule(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator: Adds a new Molecule to the MoleculeSet inside a given ChemModel.
createReactionScheme(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator: Create a IReactionScheme give a IReactionSet object.
CrystalGeometryTools - Class in org.openscience.cdk.geometry: A set of static methods for working with crystal coordinates.
CrystalGeometryTools() - Constructor for class org.openscience.cdk.geometry.CrystalGeometryTools

D

daylight() - Static method in class org.openscience.cdk.aromaticity.ElectronDonation: Electron donation model closely mirroring the Daylight model for use in generating SMILES.
debug - Static variable in class org.openscience.cdk.ringsearch.RingPartitioner: Debugging on/off
DEFAULT_SEARCH_DEPTH - Static variable in class org.openscience.cdk.fingerprint.Fingerprinter: The default search depth used to create the fingerprints.
DEFAULT_SIZE - Static variable in class org.openscience.cdk.fingerprint.Fingerprinter: The default length of created fingerprints.
DescriptorSpecification - Class in org.openscience.cdk.qsar: Class that is used to distribute descriptor specifications.
DescriptorSpecification(String, String, String, String) - Constructor for class org.openscience.cdk.qsar.DescriptorSpecification: Container for specifying the type of descriptor.
DescriptorSpecification(String, String, String) - Constructor for class org.openscience.cdk.qsar.DescriptorSpecification: Container for specifying the type of descriptor.
DescriptorValue - Class in org.openscience.cdk.qsar: Class that is used to store descriptor values as IChemObject properties.
DescriptorValue(DescriptorSpecification, String[], Object[], IDescriptorResult, String[]) - Constructor for class org.openscience.cdk.qsar.DescriptorValue: Construct a descriptor value object, representing the numeric values as well as parameters and provenance.
DescriptorValue(DescriptorSpecification, String[], Object[], IDescriptorResult, String[], Exception) - Constructor for class org.openscience.cdk.qsar.DescriptorValue: Construct a descriptor value object, representing the numeric values as well as parameters and provenance.
differences(BitSet, BitSet) - Static method in class org.openscience.cdk.fingerprint.FingerprinterTool: List all differences between the two bit vectors.
DisjointSetForest - Class in org.openscience.cdk.group: Implementation of a union-find data structure, largely copied from code due to Derrick Stolee.
DisjointSetForest(int) - Constructor for class org.openscience.cdk.group.DisjointSetForest: Initialize a disjoint set forest with a number of elements.
distanceCalculator(int[], double) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Gets the coordinates of two points (that represent a bond) and calculates for each the coordinates of two new points that have the given distance vertical to the bond.
distanceCalculator(double[], double) - Static method in class org.openscience.cdk.geometry.GeometryUtil
DoubleArrayResult - Class in org.openscience.cdk.qsar.result
DoubleArrayResult() - Constructor for class org.openscience.cdk.qsar.result.DoubleArrayResult
DoubleArrayResult(int) - Constructor for class org.openscience.cdk.qsar.result.DoubleArrayResult
DoubleArrayResultType - Class in org.openscience.cdk.qsar.result: IDescriptorResult type for doubles.
DoubleArrayResultType(int) - Constructor for class org.openscience.cdk.qsar.result.DoubleArrayResultType
DoubleResult - Class in org.openscience.cdk.qsar.result
DoubleResult(double) - Constructor for class org.openscience.cdk.qsar.result.DoubleResult
DoubleResultType - Class in org.openscience.cdk.qsar.result: IDescriptorResult type for double.
DoubleResultType() - Constructor for class org.openscience.cdk.qsar.result.DoubleResultType
doubleValue() - Method in class org.openscience.cdk.qsar.result.DoubleResult
dump() - Method in class org.openscience.cdk.graph.rebond.Bspt

E

ElectronDonation - Class in org.openscience.cdk.aromaticity: Defines an electron donation model for perceiving aromatic systems.
ElectronDonation() - Constructor for class org.openscience.cdk.aromaticity.ElectronDonation
ElementComparator - Class in org.openscience.cdk.tools: Compares elements based on the order commonly used in molecular formula.
ElementComparator() - Constructor for class org.openscience.cdk.tools.ElementComparator
elementType(int) - Method in class org.openscience.cdk.stereo.Stereocenters: Obtain the type of stereo element support for atom at index v.
encodePaths(IAtomContainer, int, BitSet, int) - Method in class org.openscience.cdk.fingerprint.Fingerprinter
enumeration() - Method in class org.openscience.cdk.graph.rebond.Bspt
enumHemiSphere(Bspt.Tuple, double) - Method in class org.openscience.cdk.graph.rebond.Bspt
enumNear(Bspt.Tuple, double) - Method in class org.openscience.cdk.graph.rebond.Bspt
enumSphere(Bspt.Tuple, double) - Method in class org.openscience.cdk.graph.rebond.Bspt
equals(Object) - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
equals(Object) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
equals(Object) - Method in class org.openscience.cdk.isomorphism.mcss.RMap: The equals method.
equals(Object) - Method in class org.openscience.cdk.smiles.InvPair: Check whether this instance equals another instance.
ERROR_MARKER - Static variable in class org.openscience.cdk.validate.ProblemMarker
exponentialDouble(double) - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random double from an Exponential distribution with the specified mean value.
extractSubstructure(IAtomContainer, int...) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Extract a substructure from an atom container, in the form of a new cloned atom container with only the atoms with indices in atomIndices and bonds that connect these atoms.
extractTopReactions(IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator: Extract a set of Reactions which are in top of a IReactionScheme.

F

findAllRings(IAtomContainer) - Method in class org.openscience.cdk.ringsearch.AllRingsFinder: Compute all rings in the given IAtomContainer.
findAllRings(IAtomContainer, int) - Method in class org.openscience.cdk.ringsearch.AllRingsFinder: Compute all rings up to and including the maxRingSize.
findAllRingsInIsolatedRingSystem(IAtomContainer) - Method in class org.openscience.cdk.ringsearch.AllRingsFinder: Compute all rings in the given IAtomContainer.
findAllRingsInIsolatedRingSystem(IAtomContainer, int) - Method in class org.openscience.cdk.ringsearch.AllRingsFinder: Compute all rings up to an including the maxRingSize.
findBonds(IAtomContainer) - Method in class org.openscience.cdk.aromaticity.Aromaticity: Find the bonds of a molecule which this model determined were aromatic.
findClosestInSpace(IAtomContainer, IAtom, int) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the atoms which are closes to an atom in an AtomContainer by distance in 3d.
findMappedBonds(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: Collect the set of bonds that mapped in both a reactant and a product.
findPathes(IAtomContainer, int) - Method in class org.openscience.cdk.fingerprint.Fingerprinter: Deprecated.
Use Fingerprinter.encodePaths(IAtomContainer, int, BitSet, int)
Fingerprinter - Class in org.openscience.cdk.fingerprint: Generates a fingerprint for a given AtomContainer.
Fingerprinter() - Constructor for class org.openscience.cdk.fingerprint.Fingerprinter: Creates a fingerprint generator of length DEFAULT_SIZE and with a search depth of DEFAULT_SEARCH_DEPTH.
Fingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.Fingerprinter
Fingerprinter(int, int) - Constructor for class org.openscience.cdk.fingerprint.Fingerprinter: Constructs a fingerprint generator that creates fingerprints of the given size, using a generation algorithm with the given search depth.
FingerprinterTool - Class in org.openscience.cdk.fingerprint: Tool with helper methods for IFingerprint.
FingerprinterTool() - Constructor for class org.openscience.cdk.fingerprint.FingerprinterTool
flipCoin(double) - Static method in class org.openscience.cdk.math.RandomNumbersTool: Returns a boolean value based on a biased coin toss.
format(char) - Method in class org.openscience.cdk.tools.FormatStringBuffer: Format a char.
format(float) - Method in class org.openscience.cdk.tools.FormatStringBuffer: Format a float.
format(double) - Method in class org.openscience.cdk.tools.FormatStringBuffer: Format a double.
format(int) - Method in class org.openscience.cdk.tools.FormatStringBuffer: Format a float.
format(long) - Method in class org.openscience.cdk.tools.FormatStringBuffer: Format a float.
format(String) - Method in class org.openscience.cdk.tools.FormatStringBuffer: Format a String.
FormatStringBuffer - Class in org.openscience.cdk.tools: A class for formatting output similar to the C printf command.
FormatStringBuffer(String) - Constructor for class org.openscience.cdk.tools.FormatStringBuffer: Create a new FormatStringBuffer.
FortranFormat - Class in org.openscience.cdk.math: Converts a String representation of a Fortran double to a double.
FortranFormat() - Constructor for class org.openscience.cdk.math.FortranFormat
fractionalToCartesian(Vector3d, Vector3d, Vector3d, Point3d) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools
fractionalToCartesian(ICrystal) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools: Creates Cartesian coordinates for all Atoms in the Crystal.

G

gaussianDouble(double) - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random double from a Gaussian distribution with the specified deviation.
gaussianFloat(float) - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random float from a Gaussian distribution with the specified deviation.
GeometryUtil - Class in org.openscience.cdk.geometry: A set of static utility classes for geometric calculations and operations.
GeometryUtil.CoordinateCoverage - Enum in org.openscience.cdk.geometry: Provides the coverage of coordinates for this molecule.
get(int) - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
get(int) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
get(int) - Method in class org.openscience.cdk.group.DisjointSetForest: Get the value of the forest at this index - note that this will not necessarily give the set for that element : use DisjointSetForest.getSets() after union-ing elements.
get(int) - Method in class org.openscience.cdk.qsar.result.DoubleArrayResult: The first double is at index = 0;
get(int) - Method in class org.openscience.cdk.qsar.result.IntegerArrayResult: The first int is at index = 0.
get2DCenter(Iterable<IAtom>) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Calculates the center of the given atoms and returns it as a Point2d.
get2DCenter(Iterator<IAtom>) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Calculates the center of the given atoms and returns it as a Point2d.
get2DCenter(IRingSet) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the geometric center of all the rings in this ringset.
get2DCenter(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the geometric center of all the atoms in the atomContainer.
get2DCentreOfMass(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Calculates the center of mass for the Atoms in the AtomContainer for the 2D coordinates.
get2DCoordinateCoverage(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Determines the coverage of this IAtomContainer's 2D coordinates.
get2DDimension(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the dimension of a molecule (width/height).
get3DCenter(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the geometric center of all the atoms in this atomContainer.
get3DCentreOfMass(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Calculates the center of mass for the Atoms in the AtomContainer.
get3DCoordinateCoverage(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Determines the coverage of this IAtomContainer's 3D coordinates.
getAllAgents(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
getAllAtomContainers(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator: Returns all the AtomContainer's of a MoleculeSet.
getAllAtomContainers(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator: Returns all the AtomContainer's of a ChemFile.
getAllAtomContainers(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator: Returns all the AtomContainer's of a ChemModel.
getAllAtomContainers(IChemSequence) - Static method in class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator: Returns all the AtomContainer's of a ChemSequence.
getAllAtomContainers(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator: Returns all the AtomContainer's of a MoleculeSet.
getAllAtomContainers(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: Returns all the AtomContainer's of a Reaction.
getAllAtomContainers(IReactionScheme, IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator: Get all molecule objects from a set of Reactions given a IAtomContainerSet to add.
getAllAtomContainers(IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator: get all AtomContainers object from a set of Reactions.
getAllAtomContainers(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator: Returns all the AtomContainer's of a Reaction.
getAllAtomContainers(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator: Returns all the AtomContainer's in a RingSet.
getAllAtomRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Return the RMSD between the 2 aligned molecules.
getAllChemModels(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator: Get a list of all ChemModels inside an IChemFile.
getAllChemObjects(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator: Does not recursively return the contents of the AtomContainer.
getAllChemObjects(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator: Returns a List of all IChemObject inside a ChemFile.
getAllChemObjects(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator: Retrieve a List of all ChemObject objects within an IChemModel.
getAllChemObjects(IChemSequence) - Static method in class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator: Returns a List of all IChemObject inside a ChemSequence.
getAllChemObjects(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
getAllChemObjects(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
getAllChemObjects(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
getAllIDs(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
getAllIDs(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
getAllIDs(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator
getAllIDs(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
getAllIDs(IChemSequence) - Static method in class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator
getAllIDs(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
getAllIDs(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
getAllIDs(IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator: Get all ID of this IReactionSet.
getAllIDs(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
getAllInOneContainer(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator: Puts all rings of a ringSet in a single atomContainer
getAllMolecules(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: Get all molecule of a IReaction: reactants + products.
getAllMolecules(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator: get all Molecules object from a set of Reactions.
getAllProducts(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: get all products of a IReaction
getAllReactants(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: get all reactants of a IReaction
getAllReactions(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator: Get a list of all IReaction inside an IChemFile.
getAllReactions(IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator: Get all IReaction's object from a given IReactionScheme.
getAngle(double, double) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Gets the angle attribute of the GeometryTools class.
getAngleRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Return the variation of each angle value between the 2 aligned molecules.
getAtom() - Method in class org.openscience.cdk.smiles.InvPair
getAtomArray(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Constructs an array of Atom objects from an AtomContainer.
getAtomArray(List<IAtom>) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Constructs an array of Atom objects from a List of Atom objects.
getAtomById(IAtomContainer, String) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Returns an atom in an atomcontainer identified by id
getAtomContainerSet(IAtomContainer, IAtomContainer, IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator: Extract the list of AtomContainers taking part in the IReactionScheme to originate a product given a reactant.
getAtomCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
getAtomCount(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator: Get the total number of atoms inside an IChemFile.
getAtomCount(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator: Get the total number of atoms inside an IChemModel.
getAtomCount(IChemSequence) - Static method in class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator: Get the total number of atoms inside an IChemSequence.
getAtomCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
getAtomCount(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
getAtomCount(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
getAtomCount(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator: Return the total number of atoms over all the rings in the colllection.
getBestAlignmentForLabel(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Determines the best alignment for the label of an atom in 2D space.
getBestAlignmentForLabelXY(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Determines the best alignment for the label of an atom in 2D space.
getBitFingerprint(IAtomContainer, AllRingsFinder) - Method in class org.openscience.cdk.fingerprint.Fingerprinter: Generates a fingerprint of the default size for the given AtomContainer.
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.Fingerprinter: Generates a fingerprint of the default size for the given AtomContainer.
getBitFingerprint(IAtomContainer, int) - Method in class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter
getBitSet(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Transforms an AtomContainer into a BitSet (which's size = number of bond in the atomContainer, all the bit are set to true).
getBondArray(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Constructs an array of Bond objects from an AtomContainer.
getBondArray(List<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Constructs an array of Atom objects from a List of Atom objects.
getBondCoordinates(IBond) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Writes the coordinates of the atoms participating the given bond into an array.
getBondCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
getBondCount(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator: Get the total number of bonds inside an IChemFile.
getBondCount(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator: Get the total number of bonds inside an IChemModel.
getBondCount(IChemSequence) - Static method in class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator: Get the total number of bonds inside an IChemSequence.
getBondCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
getBondCount(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
getBondCount(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
getBondCount(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator: Return the total number of bonds over all the rings in the colllection.
getBondLengthAverage(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: An average of all 2D bond length values is produced.
getBondLengthAverage(IReaction) - Static method in class org.openscience.cdk.geometry.GeometryUtil
getBondLengthAverage3D(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: An average of all 3D bond length values is produced, using point3ds in atoms.
getBondLengthMedian(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Calculate the median bond length of an atom container.
getBondLengthRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Return the RMSD of bonds length between the 2 aligned molecules.
getBondOrderSum(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Returns the sum of the bond order equivalents for a given IAtom.
getBondSymbol(IBond) - Method in class org.openscience.cdk.fingerprint.Fingerprinter: Gets the bondSymbol attribute of the Fingerprinter class
getBondSymbol(IBond) - Method in class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter: Gets the bondSymbol attribute of the Fingerprinter class.
getBondSymbol(IBond) - Method in class org.openscience.cdk.fingerprint.HybridizationFingerprinter: Gets the bond Symbol attribute of the Fingerprinter class.
getClosestAtom(int, int, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the atom of the given molecule that is closest to the given coordinates.
getClosestAtom(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the atom of the given molecule that is closest to the given atom (excluding itself).
getClosestAtom(double, double, IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the atom of the given molecule that is closest to the given coordinates and is not the atom.
getClosestAtom(double, double, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the atom of the given molecule that is closest to the given coordinates.
getClosestBond(int, int, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the bond of the given molecule that is closest to the given coordinates.
getClosestBond(double, double, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the bond of the given molecule that is closest to the given coordinates.
getCount(int) - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.Fingerprinter
getCountForHash(int) - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
getCurr() - Method in class org.openscience.cdk.smiles.InvPair: Get the current seed.
getCurrentPermutation() - Method in class org.openscience.cdk.graph.Permutor: Get the permutation that is currently being used.
getDimValue(int) - Method in interface org.openscience.cdk.graph.rebond.Bspt.Tuple
getDimValue(int) - Method in class org.openscience.cdk.graph.rebond.Point
getElectronContainerArray(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Constructs an array of Bond objects from an AtomContainer.
getElectronContainerArray(List<IElectronContainer>) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Constructs an array of Atom objects from a List of Atom objects.
getException() - Method in class org.openscience.cdk.qsar.DescriptorValue
getExtension() - Method in class org.openscience.cdk.isomorphism.mcss.RNode: Gets the extension attribute of the RNode object.
getFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.AbstractFingerprinter
getFirstGraphSize() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Returns the size of the first of the two compared graphs.
getForbidden() - Method in class org.openscience.cdk.isomorphism.mcss.RNode: Gets the forbidden attribute of the RNode object.
getGraph() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Returns the graph object of this RGraph.
getHandedness(IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool: Gets the tetrahedral handedness of four atoms - three of which form the 'base' of the tetrahedron, and the other the apex.
getHash(int) - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
getHeaviestRing(IRingSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator: We define the heaviest ring as the one with the highest number of double bonds.
getHeavyAtomRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean, boolean) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Return the RMSD of the heavy atoms between the 2 aligned molecules.
getHeavyAtoms(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Returns a set of nodes excluding all the hydrogens.
getHOSECode(IAtomContainer, IAtom, int) - Method in class org.openscience.cdk.tools.HOSECodeGenerator: Produces a HOSE code for Atom root in the IAtomContainer ac.
getHOSECode(IAtomContainer, IAtom, int, boolean) - Method in class org.openscience.cdk.tools.HOSECodeGenerator: Produces a HOSE code for Atom root in the IAtomContainer ac.
getId1() - Method in class org.openscience.cdk.isomorphism.mcss.RMap: Gets the id1 attribute of the RMap object.
getId2() - Method in class org.openscience.cdk.isomorphism.mcss.RMap: Gets the id2 attribute of the RMap object.
getImplementationIdentifier() - Method in interface org.openscience.cdk.IImplementationSpecification: Identifier for this implementation which must include version information.
getImplementationIdentifier() - Method in class org.openscience.cdk.qsar.DescriptorSpecification
getImplementationTitle() - Method in interface org.openscience.cdk.IImplementationSpecification: Human-readable name for the implementation for the algorithm specified by the reference.
getImplementationTitle() - Method in class org.openscience.cdk.qsar.DescriptorSpecification
getImplementationVendor() - Method in interface org.openscience.cdk.IImplementationSpecification: Human-readable name for the vendor that holds copyright for this implementation.
getImplementationVendor() - Method in class org.openscience.cdk.qsar.DescriptorSpecification
getImplicitHydrogenCount(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Counts the number of implicit hydrogens on the provided IAtomContainer.
getIntersection(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Compares this AtomContainer with another given AtomContainer and returns the Intersection between them.
getIsomorphAtomsMap(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Returns the first isomorph 'atom mapping' found for g2 in g1.
getIsomorphMap(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Returns the first isomorph mapping found or null.
getIsomorphMaps(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Returns all the isomorph 'mappings' found between two atom containers.
getLargestRingSet(List<IRingSet>) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator: Returns the largest (number of atoms) ring set in a molecule
getLast() - Method in class org.openscience.cdk.smiles.InvPair
getLength2D(IBond) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the geometric length of this bond in 2D space.
getMappedChemObject(IReaction, IChemObject) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: get the IAtom which is mapped
getMatrix(IAtomContainer) - Static method in class org.openscience.cdk.graph.matrix.ConnectionMatrix: Returns the connection matrix representation of this AtomContainer.
getMaximumBondOrder(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
getMinMax(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the minimum and maximum X and Y coordinates of the atoms in the AtomContainer.
getMolecularWeight(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Calculate the molecular weight of a molecule.
getMorganNumbers(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.MorganNumbersTools: Makes an array containing the morgan numbers of the atoms of atomContainer.
getMorganNumbersWithElementSymbol(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.MorganNumbersTools: Makes an array containing the morgan numbers+element symbol of the atoms of atomContainer.
getMostComplexRing(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator: Returns the ring with the highest numbers of other rings attached to it.
getNames() - Method in class org.openscience.cdk.qsar.DescriptorValue: Returns an array of names for each descriptor value calculated.
getNaturalExactMass(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Returns the molecular mass of the IAtomContainer.
getNextPermutation() - Method in class org.openscience.cdk.graph.Permutor: Get the next permutation in the list.
getNodesInSphere(int) - Method in class org.openscience.cdk.tools.HOSECodeGenerator
getNormal(Point3d, Point3d, Point3d) - Static method in class org.openscience.cdk.stereo.StereoTool: Given three points (A, B, C), makes the vectors A-B and A-C, and makes the cross product of these two vectors; this has the effect of making a third vector at right angles to AB and AC.
getNormalizationFactor(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Calculates the normalization factor in order to get an average bond length of 1.5.
getOverlaps(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Returns all the maximal common substructure between two atom containers.
getParameterNames() - Method in class org.openscience.cdk.qsar.DescriptorValue
getParameters() - Method in class org.openscience.cdk.fingerprint.AbstractFingerprinter: Base classes should override this method to report the parameters they are configured with.
getParameters() - Method in class org.openscience.cdk.fingerprint.Fingerprinter
getParameters() - Method in class org.openscience.cdk.qsar.DescriptorValue
getPrime() - Method in class org.openscience.cdk.smiles.InvPair: Get the current prime number.
getPrimeAt(int) - Static method in class org.openscience.cdk.math.Primes: Deprecated.

Returns the i-th prime number in the sequence of all prime numbers below 19700.
getRandom() - Static method in class org.openscience.cdk.math.RandomNumbersTool: Returns the instance of Random used by this class.
getRandomNextPermutation() - Method in class org.openscience.cdk.graph.Permutor: Randomly skip ahead in the list of permutations.
getRandomSeed() - Static method in class org.openscience.cdk.math.RandomNumbersTool: Returns the seed being used by this random number generator.
getRank() - Method in class org.openscience.cdk.graph.Permutor: Get the current rank.
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.Fingerprinter
getReactionByAtomContainerID(IReactionSet, String) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator: Gets a reaction from a ReactionSet by ID of any product or reactant.
getReactionByReactionID(IReactionSet, String) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator: Gets a reaction from a ReactionSet by ID.
getRelevantAtomContainer(IAtomContainerSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
getRelevantAtomContainer(IAtomContainerSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
getRelevantAtomContainer(IChemModel, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator: This badly named methods tries to determine which AtomContainer in the ChemModel is best suited to contain added Atom's and Bond's.
getRelevantAtomContainer(IChemModel, IBond) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator: Retrieves the first IAtomContainer containing a given IBond from an IChemModel.
getRelevantAtomContainer(IAtomContainerSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
getRelevantAtomContainer(IAtomContainerSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
getRelevantAtomContainer(IReaction, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
getRelevantAtomContainer(IReaction, IBond) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
getRelevantAtomContainer(IReactionSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
getRelevantAtomContainer(IReactionSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
getRelevantReaction(IChemModel, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator: Retrieves the first IReaction containing a given IAtom from an IChemModel.
getRelevantReaction(IReactionSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
getRelevantReaction(IReactionSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
getRelevantReactions(IReactionSet, IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator: Get all Reactions object containing a Molecule from a set of Reactions.
getRelevantReactionsAsProduct(IReactionSet, IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator: Get all Reactions object containing a Molecule as a Product from a set of Reactions.
getRelevantReactionsAsReactant(IReactionSet, IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator: Get all Reactions object containing a Molecule as a Reactant from a set of Reactions.
getRMap() - Method in class org.openscience.cdk.isomorphism.mcss.RNode: Gets the rMap attribute of the RNode object.
getRoot(int) - Method in class org.openscience.cdk.group.DisjointSetForest: Travel up the tree that this element is in, until the root of the set is found, and return that root.
getScaleFactor(IAtomContainer, double) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Determines the scale factor for displaying a structure loaded from disk in a frame.
getSearchDepth() - Method in class org.openscience.cdk.fingerprint.Fingerprinter
getSecondGraphSize() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Returns the size of the second of the two compared graphs.
getSetbits() - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
getSetbits() - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
getSets() - Method in class org.openscience.cdk.group.DisjointSetForest: Retrieve the sets as 2D-array of ints.
getSingleBondEquivalentSum(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Returns the sum of bond orders, where a single bond counts as one single bond equivalent, a double as two, etc.
getSize() - Method in class org.openscience.cdk.fingerprint.Fingerprinter
getSolutions() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Returns the list of solutions.
getSpecification() - Method in class org.openscience.cdk.qsar.DescriptorValue
getSpecificationReference() - Method in interface org.openscience.cdk.IImplementationSpecification: Pointer to a dictionary or ontology describing a unique algorithm.
getSpecificationReference() - Method in class org.openscience.cdk.qsar.DescriptorSpecification
getSpheres(IAtomContainer, IAtom, int, boolean) - Method in class org.openscience.cdk.tools.HOSECodeGenerator: This method is intended to be used to get the atoms around an atom in spheres.
getSquarePlanarShape(IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool: Given four atoms (assumed to be in the same plane), returns the arrangement of those atoms in that plane.
getStereo(IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool: Take four atoms, and return Stereo.CLOCKWISE or Stereo.ANTI_CLOCKWISE.
getSubgraphAtomsMap(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Returns the first subgraph 'atom mapping' found for g2 in g1, where g2 must be a substructure of g1.
getSubgraphAtomsMaps(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Returns all subgraph 'atom mappings' found for g2 in g1, where g2 must be a substructure of g1.
getSubgraphMap(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Returns the first subgraph 'bond mapping' found for g2 in g1.
getSubgraphMaps(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Returns all the subgraph 'bond mappings' found for g2 in g1.
getTimeout() - Method in class org.openscience.cdk.ringsearch.AllRingsFinder: Deprecated.
timeout not used
getTotalCharge(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Get the summed charge of all atoms in an AtomContainer
getTotalCharge(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
getTotalCharge(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
getTotalExactMass(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Get the summed exact mass of all atoms in an AtomContainer.
getTotalFormalCharge(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Get the total formal charge on a molecule.
getTotalFormalCharge(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
getTotalFormalCharge(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
getTotalHydrogenCount(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Counts the number of hydrogens on the provided IAtomContainer.
getTotalHydrogenCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
getTotalHydrogenCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
getTotalNaturalAbundance(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Get the summed natural abundance of all atoms in an AtomContainer
getTotalNegativeFormalCharge(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Get the total formal negative charge on a molecule.
getTotalPositiveFormalCharge(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Get the total positive formal charge on a molecule.
getValence(IAtom) - Static method in class org.openscience.cdk.qsar.AtomValenceTool
getValue() - Method in class org.openscience.cdk.qsar.DescriptorValue
getVersionDescription() - Method in class org.openscience.cdk.fingerprint.AbstractFingerprinter
giveAngle(IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools: Calls giveAngleBothMethods with bool = true.
giveAngleBothMethods(IAtom, IAtom, IAtom, boolean) - Static method in class org.openscience.cdk.geometry.BondTools: Gives the angle between two lines starting at atom from and going to to1 and to2.
giveAngleBothMethods(Point2d, Point2d, Point2d, boolean) - Static method in class org.openscience.cdk.geometry.BondTools
giveAngleFromMiddle(IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools: Calls giveAngleBothMethods with bool = false.
graph - Variable in class org.openscience.cdk.stereo.StereoElementFactory: Adjacency list graph representation.
GraphOnlyFingerprinter - Class in org.openscience.cdk.fingerprint: Specialized version of the Fingerprinter which does not take bond orders into account.
GraphOnlyFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter: Creates a fingerprint generator of length defaultSize and with a search depth of defaultSearchDepth.
GraphOnlyFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter
GraphOnlyFingerprinter(int, int) - Constructor for class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter

H

has2DCoordinates(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Determines if all this IAtomContainer's atoms contain 2D coordinates.
has2DCoordinates(IReaction) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Determine if all parts of a reaction have coodinates
has2DCoordinates(IAtom) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Determines if this Atom contains 2D coordinates.
has2DCoordinates(IBond) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Determines if this Bond contains 2D coordinates.
has2DCoordinatesNew(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Deprecated.
use GeometryUtil.get2DCoordinateCoverage(org.openscience.cdk.interfaces.IAtomContainer) for determining partial coordinates
has3DCoordinates(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Determines if all this IAtomContainer's atoms contain 3D coordinates.
has3DCoordinates(IChemModel) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Determines if this model contains 3D coordinates for all atoms.
hasCrystalCoordinates(IAtomContainer) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools: Determines if this model contains fractional (crystal) coordinates.
hasHash(int) - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
hashCode() - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
hashCode() - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
hasNext() - Method in class org.openscience.cdk.graph.Permutor
HOSECode - Variable in class org.openscience.cdk.tools.HOSECodeGenerator: The HOSECode string that we assemble
HOSECodeGenerator - Class in org.openscience.cdk.tools: Generates HOSE codes [Bremser, W., HOSE - A Novel Substructure Code, Analytica Chimica Acta, 1978, 103:355-365].
HOSECodeGenerator() - Constructor for class org.openscience.cdk.tools.HOSECodeGenerator: Constructor for the HOSECodeGenerator.
HybridizationFingerprinter - Class in org.openscience.cdk.fingerprint: Generates a fingerprint for a given IAtomContainer.
HybridizationFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.HybridizationFingerprinter: Creates a fingerprint generator of length DEFAULT_SIZE and with a search depth of DEFAULT_SEARCH_DEPTH.
HybridizationFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.HybridizationFingerprinter
HybridizationFingerprinter(int, int) - Constructor for class org.openscience.cdk.fingerprint.HybridizationFingerprinter: Constructs a fingerprint generator that creates fingerprints of the given size, using a generation algorithm with the given search depth.

I

ICDKSelectionChangeListener - Interface in org.openscience.cdk.event: A ChangeListener for the CDK, to be independent from the Swing package.
IDCreator - Class in org.openscience.cdk.tools: Class that provides methods to give unique IDs to ChemObjects.
IDCreator() - Constructor for class org.openscience.cdk.tools.IDCreator
IDescriptorResult - Interface in org.openscience.cdk.qsar.result: Object that provides access to the calculated descriptor value.
IImplementationSpecification - Interface in org.openscience.cdk: Interface that is used to describe the specification of a certain implementation of an algorithm.
IntArrayCountFingerprint - Class in org.openscience.cdk.fingerprint
IntArrayCountFingerprint() - Constructor for class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
IntArrayCountFingerprint(Map<String, Integer>) - Constructor for class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
IntArrayCountFingerprint(Map<String, Integer>, boolean) - Constructor for class org.openscience.cdk.fingerprint.IntArrayCountFingerprint: Create an IntArrayCountFingerprint from a rawFingerprint and if behaveAsBitFingerprint make it only return 0 or 1 as count thus behaving like a bit finger print.
IntArrayFingerprint - Class in org.openscience.cdk.fingerprint
IntArrayFingerprint(Map<String, Integer>) - Constructor for class org.openscience.cdk.fingerprint.IntArrayFingerprint
IntArrayFingerprint(int[]) - Constructor for class org.openscience.cdk.fingerprint.IntArrayFingerprint
IntArrayFingerprint() - Constructor for class org.openscience.cdk.fingerprint.IntArrayFingerprint
IntArrayFingerprint(IBitFingerprint) - Constructor for class org.openscience.cdk.fingerprint.IntArrayFingerprint
IntegerArrayResult - Class in org.openscience.cdk.qsar.result
IntegerArrayResult() - Constructor for class org.openscience.cdk.qsar.result.IntegerArrayResult
IntegerArrayResult(int) - Constructor for class org.openscience.cdk.qsar.result.IntegerArrayResult
IntegerArrayResultType - Class in org.openscience.cdk.qsar.result: IDescriptorResult type for integers.
IntegerArrayResultType(int) - Constructor for class org.openscience.cdk.qsar.result.IntegerArrayResultType
IntegerResult - Class in org.openscience.cdk.qsar.result: Object that provides access to the calculated descriptor value.
IntegerResult(int) - Constructor for class org.openscience.cdk.qsar.result.IntegerResult
IntegerResultType - Class in org.openscience.cdk.qsar.result: IDescriptorResult type for integer.
IntegerResultType() - Constructor for class org.openscience.cdk.qsar.result.IntegerResultType
interpretProjections(Projection...) - Method in class org.openscience.cdk.stereo.StereoElementFactory: Indicate that stereochemistry drawn as a certain projection should be interpreted.
intValue() - Method in class org.openscience.cdk.qsar.result.IntegerResult
INVARIANCE_PAIR - Static variable in class org.openscience.cdk.smiles.InvPair: The description used to set the invariance numbers in the atom's property
InvPair - Class in org.openscience.cdk.smiles: This is used to hold the invariance numbers for the canonical labeling of IAtomContainers.
InvPair() - Constructor for class org.openscience.cdk.smiles.InvPair
InvPair(long, IAtom) - Constructor for class org.openscience.cdk.smiles.InvPair
isCisTrans(IAtom, IAtom, IAtom, IAtom, IAtomContainer) - Static method in class org.openscience.cdk.geometry.BondTools: Says if two atoms are in cis or trans position around a double bond.
isColinear(Point3d, Point3d, Point3d) - Static method in class org.openscience.cdk.stereo.StereoTool: Checks the three supplied points to see if they fall on the same line.
isConnected(IAtomContainer) - Static method in class org.openscience.cdk.graph.ConnectivityChecker: Check whether a set of atoms in an IAtomContainer is connected.
isIsomorph(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Tests if g1 and g2 are isomorph.
isIsomorphic(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.IsomorphismTester: Checks whether a given molecule is isomorphic with the one that has been assigned to this IsomorphismTester at construction time.
isIsomorphic(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.IsomorphismTester: Checks whether a given molecule is isomorphic with the one that has been assigned to this IsomorphismTester at construction time.
isLeft(IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools: Says if an atom is on the left side of a another atom seen from a certain atom or not.
isOctahedral(IAtom, IAtom, IAtom, IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool: Checks these 7 atoms to see if they are at the points of an octahedron.
IsomorphismTester - Class in org.openscience.cdk.isomorphism: A too simplistic implementation of an isomorphism test for chemical graphs.
IsomorphismTester() - Constructor for class org.openscience.cdk.isomorphism.IsomorphismTester: Constructor for the IsomorphismTester object
IsomorphismTester(IAtomContainer) - Constructor for class org.openscience.cdk.isomorphism.IsomorphismTester: Constructor for the IsomorphismTester object
isSameRing(IRingSet, IAtom, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator: Checks if atom1 and atom2 share membership in the same ring or ring system.
isSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.LonePairElectronChecker: Determines of all atoms on the AtomContainer have the right number the lone pair electrons.
isSaturated(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.LonePairElectronChecker: Checks if an Atom is saturated their lone pair electrons by comparing it with known AtomTypes.
isSquarePlanar(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools: Says if an atom as a center of a square planar chirality.
isSquarePlanar(IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool: Checks these four atoms for square planarity.
isStereo(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools: Says if an atom as a center of any valid stereo configuration or not.
isStereocenter(int) - Method in class org.openscience.cdk.stereo.Stereocenters: Is the atom be a stereocenter (i.e.
isSubgraph(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Tests if g2 a subgraph of g1.
isSubset(BitSet, BitSet) - Static method in class org.openscience.cdk.fingerprint.FingerprinterTool: Checks whether all the positive bits in BitSet bs2 occur in BitSet bs1.
isTetrahedral(IAtomContainer, IAtom, boolean) - Static method in class org.openscience.cdk.geometry.BondTools: Says if an atom as a center of a tetrahedral chirality.
isTrigonalBipyramidal(IAtom, IAtom, IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool: Checks these 6 atoms to see if they form a trigonal-bipyramidal shape.
isTrigonalBipyramidalOrOctahedral(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools: Says if an atom as a center of a trigonal-bipyramidal or actahedral chirality.
isValidDoubleBondConfiguration(IAtomContainer, IBond) - Static method in class org.openscience.cdk.geometry.BondTools: Tells if a certain bond is center of a valid double bond configuration.

K

Kekulization - Class in org.openscience.cdk.aromaticity: Assign a Kekulé representation to the aromatic systems of a compound.
Kekulization() - Constructor for class org.openscience.cdk.aromaticity.Kekulization
kekulize(IAtomContainer) - Static method in class org.openscience.cdk.aromaticity.Kekulization: Assign a Kekulé representation to the aromatic systems of a compound.

L

label(IAtomContainer, int[][]) - Static method in class org.openscience.cdk.graph.invariant.Canon: Compute the canonical labels for the provided structure.
label(IAtomContainer, int[][], long[]) - Static method in class org.openscience.cdk.graph.invariant.Canon: Compute the canonical labels for the provided structure.
LARGE_FIRST - Static variable in class org.openscience.cdk.tools.manipulator.RingSizeComparator: Flag to denote that the set is order with the largest ring first
length() - Method in class org.openscience.cdk.qsar.result.BooleanResultType
length() - Method in class org.openscience.cdk.qsar.result.DoubleArrayResult
length() - Method in class org.openscience.cdk.qsar.result.DoubleArrayResultType
length() - Method in class org.openscience.cdk.qsar.result.DoubleResult
length() - Method in class org.openscience.cdk.qsar.result.DoubleResultType
length() - Method in interface org.openscience.cdk.qsar.result.IDescriptorResult: Returns the length of this descriptor.
length() - Method in class org.openscience.cdk.qsar.result.IntegerArrayResult
length() - Method in class org.openscience.cdk.qsar.result.IntegerArrayResultType
length() - Method in class org.openscience.cdk.qsar.result.IntegerResult
length() - Method in class org.openscience.cdk.qsar.result.IntegerResultType
listDifferences(BitSet, BitSet) - Static method in class org.openscience.cdk.fingerprint.FingerprinterTool: This lists all bits set in bs2 and not in bs2 (other way round not considered) in a list and to logger.
LonePairElectronChecker - Class in org.openscience.cdk.tools: Provides methods for checking whether an atoms lone pair electrons are saturated with respect to a particular atom type.
LonePairElectronChecker() - Constructor for class org.openscience.cdk.tools.LonePairElectronChecker

M

makeAtomsMapOfBondsMap(List<RMap>, IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: This makes a map of matching atoms out of a map of matching bonds as produced by the get(Subgraph|Ismorphism)Map methods.
makeAtomsMapsOfBondsMaps(List<List<RMap>>, IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: This makes maps of matching atoms out of a maps of matching bonds as produced by the get(Subgraph|Ismorphism)Maps methods.
makeBitFingerprint(Map<String, Integer>) - Static method in class org.openscience.cdk.fingerprint.FingerprinterTool: Convert a mapping of features and their counts to a 1024-bit binary fingerprint.
makeBitFingerprint(Map<String, Integer>, int) - Static method in class org.openscience.cdk.fingerprint.FingerprinterTool: Convert a mapping of features and their counts to a binary fingerprint.
makeBitFingerprint(Map<String, Integer>, int, int) - Static method in class org.openscience.cdk.fingerprint.FingerprinterTool: Convert a mapping of features and their counts to a binary fingerprint.
makeBremserCompliant(String) - Method in class org.openscience.cdk.tools.HOSECodeGenerator
makeCountFingerprint(Map<String, Integer>) - Static method in class org.openscience.cdk.fingerprint.FingerprinterTool: Wrap a mapping of features and their counts to a continuous (count based) fingerprint.
makeUnion(int, int) - Method in class org.openscience.cdk.group.DisjointSetForest: Union these two elements - in other words, put them in the same set.
makeUpDownBonds(IAtomContainer) - Static method in class org.openscience.cdk.geometry.BondTools
mapAtomsOfAlignedStructures(IAtomContainer, IAtomContainer, double, Map<Integer, Integer>) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns a Map with the AtomNumbers, the first number corresponds to the first (or the largest AtomContainer) atomcontainer.
mapAtomsOfAlignedStructures(IAtomContainer, IAtomContainer, Map<Integer, Integer>) - Static method in class org.openscience.cdk.isomorphism.AtomMappingTools: Returns a Map with the AtomNumbers, the first number corresponds to the first (or the largest AtomContainer) atomContainer.
markAromaticRings(IRing) - Static method in class org.openscience.cdk.tools.manipulator.RingManipulator: Marks the ring aromatic if all atoms and all bonds are aromatic.
markAromaticRings(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator: Iterates over the rings in the ring set, and marks the ring aromatic if all atoms and all bonds are aromatic.
markWithError(IChemObject) - Static method in class org.openscience.cdk.validate.ProblemMarker
markWithWarning(IChemObject) - Static method in class org.openscience.cdk.validate.ProblemMarker
match(int, int) - Method in class org.openscience.cdk.graph.Matching: Add the edge '{u,v}' to the matched edge set.
matched(int) - Method in class org.openscience.cdk.graph.Matching: Determine if a vertex has a match.
Matching - Class in org.openscience.cdk.graph: A matching is an independent edge set of a graph.
MAX_AXIS_ANGLE - Static variable in class org.openscience.cdk.stereo.StereoTool: The maximum angle in radians for two lines to be 'diaxial'.
maxSphere - Variable in class org.openscience.cdk.tools.HOSECodeGenerator: How many spheres are we supposed inspect.
merge(ICountFingerprint) - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
MIN_COLINEAR_NORMAL - Static variable in class org.openscience.cdk.stereo.StereoTool: The maximum tolerance for the normal calculated during colinearity.
MoleculeSetManipulator - Class in org.openscience.cdk.tools.manipulator
MoleculeSetManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
MorganNumbersTools - Class in org.openscience.cdk.graph.invariant: Compute the extended connectivity values (Morgan Numbers) [Morgan, H.L., The Generation of a Unique Machine Description for Chemical Structures - A Technique Developed at Chemical Abstracts Service., J.Chem.Doc., 1965, 5:107-113].
MorganNumbersTools() - Constructor for class org.openscience.cdk.graph.invariant.MorganNumbersTools

N

newChemModel(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator: Create a new ChemModel containing an IAtomContainer.
next() - Method in class org.openscience.cdk.graph.AtomContainerPermutor
nextSphereNodes - Variable in class org.openscience.cdk.tools.HOSECodeGenerator: Container for the node in the next sphere Assembled in a recursive method and then passed to the next recursion to become "sphereNodes".
normalize(Point3d) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Normalizes a point.
notionalToCartesian(double, double, double, double, double, double) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools: Calculates Cartesian vectors for unit cell axes from axes lengths and angles between axes.
numOfPopulatedbins() - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint

O

OBJECT_UNIQUE_POLICY - Static variable in class org.openscience.cdk.tools.IDCreator: New ID generation policy - to generate IDs unique only in a molecule
of(IAtomContainer) - Static method in class org.openscience.cdk.stereo.Stereocenters: Determine the stereocenter atoms in the provided container based on connectivity.
or(IBitFingerprint) - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
or(IBitFingerprint) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
or(IntArrayFingerprint) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
org.openscience.cdk - package org.openscience.cdk
org.openscience.cdk.aromaticity - package org.openscience.cdk.aromaticity
org.openscience.cdk.event - package org.openscience.cdk.event
org.openscience.cdk.fingerprint - package org.openscience.cdk.fingerprint
org.openscience.cdk.geometry - package org.openscience.cdk.geometry
org.openscience.cdk.geometry.volume - package org.openscience.cdk.geometry.volume
org.openscience.cdk.graph - package org.openscience.cdk.graph
org.openscience.cdk.graph.invariant - package org.openscience.cdk.graph.invariant
org.openscience.cdk.graph.matrix - package org.openscience.cdk.graph.matrix
org.openscience.cdk.graph.rebond - package org.openscience.cdk.graph.rebond
org.openscience.cdk.group - package org.openscience.cdk.group
org.openscience.cdk.isomorphism - package org.openscience.cdk.isomorphism
org.openscience.cdk.isomorphism.mcss - package org.openscience.cdk.isomorphism.mcss
org.openscience.cdk.math - package org.openscience.cdk.math
org.openscience.cdk.qsar - package org.openscience.cdk.qsar
org.openscience.cdk.qsar.result - package org.openscience.cdk.qsar.result
org.openscience.cdk.ringsearch - package org.openscience.cdk.ringsearch
org.openscience.cdk.smiles - package org.openscience.cdk.smiles
org.openscience.cdk.stereo - package org.openscience.cdk.stereo
org.openscience.cdk.tools - package org.openscience.cdk.tools
org.openscience.cdk.tools.manipulator - package org.openscience.cdk.tools.manipulator
org.openscience.cdk.validate - package org.openscience.cdk.validate
other(int) - Method in class org.openscience.cdk.graph.Matching: Access the vertex matched with 'v'.

P

parse(BitSet, BitSet, boolean, boolean) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Parsing of the RGraph.
partitionIntoMolecules(IAtomContainer) - Static method in class org.openscience.cdk.graph.ConnectivityChecker: Partitions the atoms in an AtomContainer into covalently connected components.
partitionIntoMolecules(IAtomContainer, int[]) - Static method in class org.openscience.cdk.graph.ConnectivityChecker
partitionRings(IRingSet) - Static method in class org.openscience.cdk.ringsearch.RingPartitioner: Partitions a RingSet into RingSets of connected rings.
percieveAtomTypesAndConfigureAtoms(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Convenience method to perceive atom types for all IAtoms in the IAtomContainer, using the CDKAtomTypeMatcher.
percieveAtomTypesAndConfigureUnsetProperties(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Convenience method to perceive atom types for all IAtoms in the IAtomContainer, using the CDKAtomTypeMatcher.
perfect(int[][], BitSet) - Method in class org.openscience.cdk.graph.Matching: Attempt to augment the matching such that it is perfect over the subset of vertices in the provided graph.
Permutor - Class in org.openscience.cdk.graph: General permutation generator, that uses orderly generation by ranking and unranking.
Permutor(int) - Constructor for class org.openscience.cdk.graph.Permutor: Create a permutor that will generate permutations of numbers up to size.
piBonds() - Static method in class org.openscience.cdk.aromaticity.ElectronDonation: A very simple aromaticity model which only allows atoms adjacent to cyclic pi bonds.
PLANE_TOLERANCE - Static variable in class org.openscience.cdk.stereo.StereoTool
Point - Class in org.openscience.cdk.graph.rebond
Point(double, double, double) - Constructor for class org.openscience.cdk.graph.rebond.Point
Primes - Class in org.openscience.cdk.math: Deprecated.
Primes() - Constructor for class org.openscience.cdk.math.Primes: Deprecated.
ProblemMarker - Class in org.openscience.cdk.validate: Tool to mark IChemObject's as having a problem.
ProblemMarker() - Constructor for class org.openscience.cdk.validate.ProblemMarker
project(List<RMap>, IAtomContainer, int) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Projects a list of RMap on a molecule.
projectG1(BitSet) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Projects a RGraph bitset on the source graph G1.
projectG2(BitSet) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Projects a RGraph bitset on the source graph G2.
Projection - Enum in org.openscience.cdk.stereo: Stereochemistry projection types.
projections - Variable in class org.openscience.cdk.stereo.StereoElementFactory
projectList(List<List<RMap>>, IAtomContainer, int) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Projects a list of RMapsList on a molecule.

R

randomBit() - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random bit: either 0 or 1.
randomBoolean() - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random boolean.
randomDouble() - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random double between 0 and 1.
randomDouble(double, double) - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random double between the specified values.
randomFloat() - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random float between 0 and 1.
randomFloat(float, float) - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random float between the specified values.
randomInt() - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random integer between 0 and 1.
randomInt(int, int) - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random integer between the specified values.
randomLong() - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random long between 0 and 1.
randomLong(long, long) - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random long between the specified values.
randomNext() - Method in class org.openscience.cdk.graph.AtomContainerPermutor: Get a new container, but randomly skip forwards in the list of possible permutations to generate it.
RandomNumbersTool - Class in org.openscience.cdk.math: Class supplying useful methods to generate random numbers.
RandomNumbersTool() - Constructor for class org.openscience.cdk.math.RandomNumbersTool
ReactionManipulator - Class in org.openscience.cdk.tools.manipulator
ReactionManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ReactionManipulator
ReactionSchemeManipulator - Class in org.openscience.cdk.tools.manipulator
ReactionSchemeManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator
ReactionSetManipulator - Class in org.openscience.cdk.tools.manipulator
ReactionSetManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
rebond(IAtomContainer) - Method in class org.openscience.cdk.graph.rebond.RebondTool: Rebonding using a Binary Space Partition Tree.
RebondTool - Class in org.openscience.cdk.graph.rebond: Provides tools to rebond a molecule from 3D coordinates only.
RebondTool(double, double, double) - Constructor for class org.openscience.cdk.graph.rebond.RebondTool
remove() - Method in class org.openscience.cdk.graph.AtomContainerPermutor
removeAcidicOxygen(IAminoAcid) - Static method in class org.openscience.cdk.tools.manipulator.AminoAcidManipulator: Removes the singly bonded oxygen from the acid group of the AminoAcid.
removeAtomAndConnectedElectronContainers(IAtomContainerSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
removeAtomAndConnectedElectronContainers(IChemModel, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator: Remove an Atom and the connected ElectronContainers from all AtomContainers inside an IChemModel.
removeAtomAndConnectedElectronContainers(IAtomContainerSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
removeAtomAndConnectedElectronContainers(IReaction, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
removeAtomAndConnectedElectronContainers(IReactionSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
removeElectronContainer(IAtomContainerSet, IElectronContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
removeElectronContainer(IChemModel, IElectronContainer) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator: Remove an ElectronContainer from all AtomContainers inside an IChemModel.
removeElectronContainer(IAtomContainerSet, IElectronContainer) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
removeElectronContainer(IReaction, IElectronContainer) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
removeElectronContainer(IReactionSet, IElectronContainer) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
removeHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Create an copy of the org structure with explicit hydrogens removed.
removeHydrogensPreserveMultiplyBonded(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Deprecated.
AtomContainerManipulator.suppressHydrogens(org.openscience.cdk.interfaces.IAtomContainer) will now not removed bridging hydrogens by default
removeNonChiralHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Produces an AtomContainer without explicit non stereo-relevant Hs but with H count from one with Hs.
replaceAtomByAtom(IAtomContainer, IAtom, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Substitute one atom in a container for another adjusting bonds, single electrons, lone pairs, and stereochemistry as required.
reset(String) - Method in class org.openscience.cdk.tools.FormatStringBuffer: Reset this FormatStringBuffer.
reset() - Method in class org.openscience.cdk.tools.FormatStringBuffer: Reset this FormatStringBuffer with the format string given in the constructor or last call to reset(String).
reverse(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: Returns a new Reaction object which is the reverse of the given Reaction.
RGraph - Class in org.openscience.cdk.isomorphism.mcss: This class implements the Resolution Graph (RGraph).
RGraph() - Constructor for class org.openscience.cdk.isomorphism.mcss.RGraph: Constructor for the RGraph object and creates an empty RGraph.
ringAlreadyInSet(IRing, IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator: Checks - and returns 'true' - if a certain ring is already stored in the ringset.
RingManipulator - Class in org.openscience.cdk.tools.manipulator
RingManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.RingManipulator
RingPartitioner - Class in org.openscience.cdk.ringsearch: Partitions a RingSet into RingSets of connected rings.
RingPartitioner() - Constructor for class org.openscience.cdk.ringsearch.RingPartitioner
RingSetManipulator - Class in org.openscience.cdk.tools.manipulator
RingSetManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.RingSetManipulator
RingSizeComparator - Class in org.openscience.cdk.tools.manipulator
RingSizeComparator(int) - Constructor for class org.openscience.cdk.tools.manipulator.RingSizeComparator: Constructs a new comparator to sort rings by size.
RMap - Class in org.openscience.cdk.isomorphism.mcss: An RMap implements the association between an edge (bond) in G1 and an edge (bond) in G2, G1 and G2 being the compared graphs in a RGraph context.
RMap(int, int) - Constructor for class org.openscience.cdk.isomorphism.mcss.RMap: Constructor for the RMap.
RNode - Class in org.openscience.cdk.isomorphism.mcss: Node of the resolution graph (RGraph) An RNode represents an association between two edges of the source graphs G1 and G2 that are compared.
RNode(int, int) - Constructor for class org.openscience.cdk.isomorphism.mcss.RNode: Constructor for the RNode object.
rootNode - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
rotate(IAtomContainer, Point2d, double) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Rotates a molecule around a given center by a given angle.
rotate(IAtom, Point3d, Point3d, double) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Rotates a 3D point about a specified line segment by a specified angle.

S

saturate(IAtomContainer) - Method in class org.openscience.cdk.tools.LonePairElectronChecker: Saturates a molecule by setting appropriate number lone pair electrons.
saturate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.LonePairElectronChecker: Saturates an IAtom by adding the appropriate number lone pairs.
scaleMolecule(IAtomContainer, double[], double) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Scales a molecule such that it fills a given percentage of a given dimension.
scaleMolecule(IAtomContainer, double) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Multiplies all the coordinates of the atoms of the given molecule with the scalefactor.
search(IAtomContainer, IAtomContainer, BitSet, BitSet, boolean, boolean) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: General RGraph parsing method (usually not used directly) This method is the entry point for the recursive search adapted to the atom container input.
set(int, boolean) - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
set(int) - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
set(int, boolean) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
set(int) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
SET_UNIQUE_POLICY - Static variable in class org.openscience.cdk.tools.IDCreator: Old ID generation policy - to generate IDs unique over the entire set
setAllMap(boolean) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Sets the 'finAllMap' option.
setAllStructure(boolean) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Sets the 'AllStructres' option.
setAtom(IAtom) - Method in class org.openscience.cdk.smiles.InvPair
setAtomProperties(IAtomContainer, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Sets a property on all Atoms in the given container.
setAtomProperties(IAtomContainerSet, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
setAtomProperties(IChemModel, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator: Sets the AtomProperties of all Atoms inside an IChemModel.
setAtomProperties(IAtomContainerSet, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
setAtomProperties(IReaction, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
setAtomProperties(IReactionSet, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
setBehaveAsBitFingerprint(boolean) - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
setCurr(long) - Method in class org.openscience.cdk.smiles.InvPair: Set the value of the seed.
setExtension(BitSet) - Method in class org.openscience.cdk.isomorphism.mcss.RNode: Sets the extension attribute of the RNode object.
setFirstGraphSize(int) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Sets the size of the first of the two compared graphs.
setForbidden(BitSet) - Method in class org.openscience.cdk.isomorphism.mcss.RNode: Sets the forbidden attribute of the RNode object.
setHashPseudoAtoms(boolean) - Method in class org.openscience.cdk.fingerprint.Fingerprinter
setId1(int) - Method in class org.openscience.cdk.isomorphism.mcss.RMap: Sets the id1 attribute of the RMap object.
setId2(int) - Method in class org.openscience.cdk.isomorphism.mcss.RMap: Sets the id2 attribute of the RMap object.
setIDPolicy(int) - Static method in class org.openscience.cdk.tools.IDCreator: Alters the policy of ID generation.
setLast(long) - Method in class org.openscience.cdk.smiles.InvPair
setMaxIteration(int) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Sets the maxIteration for the RGraph parsing.
setPathLimit(int) - Method in class org.openscience.cdk.fingerprint.Fingerprinter
setPermutation(int[]) - Method in class org.openscience.cdk.graph.Permutor: Set the currently used permutation.
setPrime() - Method in class org.openscience.cdk.smiles.InvPair: Sets the prime number based on the current seed.
setRandom(Random) - Static method in class org.openscience.cdk.math.RandomNumbersTool: Sets the base generator to be used by this class.
setRandomSeed(long) - Static method in class org.openscience.cdk.math.RandomNumbersTool: Sets the seed of this random number generator using a single long seed.
setRank(int) - Method in class org.openscience.cdk.graph.Permutor: Set the permutation to use, given its rank.
setRMap(RMap) - Method in class org.openscience.cdk.isomorphism.mcss.RNode: Sets the rMap attribute of the RNode object.
setSecondGraphSize(int) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Returns the size of the second of the two compared graphs.
setSingleOrDoubleFlags(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Assigns CDKConstants.SINGLE_OR_DOUBLE flags to the bonds of a container.
setStart(long) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
setTimeout(long) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Sets the time in milliseconds until the substructure search will be breaked.
setTimeout(long) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Sets the time in milliseconds until the substructure search will be breaked.
setTimeout(long) - Method in class org.openscience.cdk.ringsearch.AllRingsFinder: Deprecated.
use the new threshold (during construction)
shiftContainer(IAtomContainer, double[], double[], double) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Shift the container horizontally to the right to make its bounds not overlap with the other bounds.
shiftReactionVertical(IReaction, double[], double[], double) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Shift the containers in a reaction vertically upwards to not overlap with the reference rectangle.
signedDistanceToPlane(Vector3d, Point3d, Point3d) - Static method in class org.openscience.cdk.stereo.StereoTool: Given a normalized normal for a plane, any point in that plane, and a point, will return the distance between the plane and that point.
size() - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
size() - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
size() - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
skeleton(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Create a skeleton copy of the provided structure.
SMALL_FIRST - Static variable in class org.openscience.cdk.tools.manipulator.RingSizeComparator: Flag to denote that the set is order with the smallest ring first
sort(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator: Sorts the IAtomContainers in the given IAtomContainerSet by the following criteria with decreasing priority:
sort(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator: Sorts the rings in the set by size.
sortBy2DDistance(IAtom[], Point2d) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Sorts a Vector of atoms such that the 2D distances of the atom locations from a given point are smallest for the first atoms in the vector.
sphere - Variable in class org.openscience.cdk.tools.HOSECodeGenerator: Counter for the sphere in which we currently work.
sphereDelimiters - Variable in class org.openscience.cdk.tools.HOSECodeGenerator: Delimiters used to separate spheres in the output string.
sphereNodes - Variable in class org.openscience.cdk.tools.HOSECodeGenerator: Container for the nodes in a sphere.
sphereNodesWithAtoms - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
spheres - Variable in class org.openscience.cdk.tools.HOSECodeGenerator: Here we store the spheres that we assemble, in order to parse them into a code later.
spheresWithAtoms - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
stateChanged(EventObject) - Method in interface org.openscience.cdk.event.ICDKSelectionChangeListener: Invoked when the target of the listener has changed its state.
Stereocenters - Class in org.openscience.cdk.stereo: Find atoms which can support stereo chemistry based on the connectivity.
Stereocenters.Stereocenter - Enum in org.openscience.cdk.stereo: Defines the type of a stereocenter.
Stereocenters.Type - Enum in org.openscience.cdk.stereo
stereocenterType(int) - Method in class org.openscience.cdk.stereo.Stereocenters: Determine the type of stereocenter is the atom at index v.
StereoElementFactory - Class in org.openscience.cdk.stereo: Create stereo elements for a structure with 2D and 3D coordinates.
StereoElementFactory(IAtomContainer, int[][], GraphUtil.EdgeToBondMap) - Constructor for class org.openscience.cdk.stereo.StereoElementFactory: Internal constructor.
stereosAreOpposite(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools: Says if of four atoms connected two one atom the up and down bonds are opposite or not, i.
StereoTool - Class in org.openscience.cdk.stereo: Methods to determine or check the stereo class of a set of atoms.
StereoTool() - Constructor for class org.openscience.cdk.stereo.StereoTool
StereoTool.SquarePlanarShape - Enum in org.openscience.cdk.stereo: The shape that four atoms take in a plane.
StereoTool.StereoClass - Enum in org.openscience.cdk.stereo: Currently unused, but intended for the StereoTool to indicate what it 'means' by an assignment of some atoms to a class.
StereoTool.TetrahedralSign - Enum in org.openscience.cdk.stereo: The handedness of a tetrahedron, in terms of the point-plane distance of three of the corners, compared to the fourth.
suppressHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Suppress any explicit hydrogens in the provided container.
symmetry(IAtomContainer, int[][]) - Static method in class org.openscience.cdk.graph.invariant.Canon: Compute the symmetry classes for the provided structure.

T

toMolecule(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: Converts a reaction to an 'inlined' reaction stored as a molecule.
toReaction(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: Converts an 'inlined' reaction stored in a molecule back to a reaction.
toString() - Method in class org.openscience.cdk.graph.Matching
toString() - Method in class org.openscience.cdk.graph.rebond.Bspt
toString() - Method in class org.openscience.cdk.graph.rebond.Point
toString() - Method in class org.openscience.cdk.group.DisjointSetForest
toString() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Returns a string representation of the RGraph.
toString() - Method in class org.openscience.cdk.isomorphism.mcss.RNode: Returns a string representation of the RNode.
toString() - Method in class org.openscience.cdk.qsar.result.BooleanResult
toString() - Method in class org.openscience.cdk.qsar.result.BooleanResultType
toString() - Method in class org.openscience.cdk.qsar.result.DoubleArrayResult
toString() - Method in class org.openscience.cdk.qsar.result.DoubleArrayResultType
toString() - Method in class org.openscience.cdk.qsar.result.DoubleResult
toString() - Method in class org.openscience.cdk.qsar.result.DoubleResultType
toString() - Method in interface org.openscience.cdk.qsar.result.IDescriptorResult: String representation of the result.
toString() - Method in class org.openscience.cdk.qsar.result.IntegerArrayResult
toString() - Method in class org.openscience.cdk.qsar.result.IntegerArrayResultType
toString() - Method in class org.openscience.cdk.qsar.result.IntegerResult
toString() - Method in class org.openscience.cdk.qsar.result.IntegerResultType
toString() - Method in class org.openscience.cdk.smiles.InvPair: String representation.
toString() - Method in class org.openscience.cdk.tools.FormatStringBuffer: Get the result of the formatting.
translate2D(IAtomContainer, double, double) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Translates the given molecule by the given Vector.
translate2D(IAtomContainer, Vector2d) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Translates a molecule from the origin to a new point denoted by a vector.
translate2DCenterTo(IAtomContainer, Point2d) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Translates the geometric 2DCenter of the given AtomContainer container to the specified Point2d p.
translate2DCentreOfMassTo(IAtomContainer, Point2d) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Translates a molecule from the origin to a new point denoted by a vector.
translateAllPositive(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Adds an automatically calculated offset to the coordinates of all atoms such that all coordinates are positive and the smallest x or y coordinate is exactly zero.

U

UniversalIsomorphismTester - Class in org.openscience.cdk.isomorphism: This class implements a multipurpose structure comparison tool.
UniversalIsomorphismTester() - Constructor for class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
unmark(IChemObject) - Static method in class org.openscience.cdk.validate.ProblemMarker
unmarkWithError(IChemObject) - Static method in class org.openscience.cdk.validate.ProblemMarker
unmarkWithWarning(IChemObject) - Static method in class org.openscience.cdk.validate.ProblemMarker
unmatch(int) - Method in class org.openscience.cdk.graph.Matching: Remove a matching for the specified vertex.
unmatched(int) - Method in class org.openscience.cdk.graph.Matching: Determine if a vertex is not matched.
unregisterAtomListeners(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: A method to remove AtomListeners.
unregisterElectronContainerListeners(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: A method to remove ElectronContainerListeners.
using2DCoordinates(IAtomContainer) - Static method in class org.openscience.cdk.stereo.StereoElementFactory: Create a stereo element factory for creating stereo elements using 2D coordinates and depiction labels (up/down, wedge/hatch).
using3DCoordinates(IAtomContainer) - Static method in class org.openscience.cdk.stereo.StereoElementFactory: Create a stereo element factory for creating stereo elements using 3D coordinates and depiction labels (up/down, wedge/hatch).
usingThreshold(AllRingsFinder.Threshold) - Static method in class org.openscience.cdk.ringsearch.AllRingsFinder: Create an AllRingsFinder instance using the given threshold.

V

VABCVolume - Class in org.openscience.cdk.geometry.volume: Calculates the Van der Waals volume using the method proposed in [Zhao, Yuan H. and Abraham, Michael H. and Zissimos, Andreas M., Fast Calculation of van der Waals Volume as a Sum of Atomic and Bond Contributions and Its Application to Drug Compounds, The Journal of Organic Chemistry, 2003, 68:7368-7373, doi:10.1021/jo034808o].
VABCVolume() - Constructor for class org.openscience.cdk.geometry.volume.VABCVolume
valueOf(String) - Static method in enum org.openscience.cdk.geometry.GeometryUtil.CoordinateCoverage: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.ringsearch.AllRingsFinder.Threshold: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.stereo.Projection: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.stereo.Stereocenters.Stereocenter: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.stereo.Stereocenters.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.stereo.StereoTool.SquarePlanarShape: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.stereo.StereoTool.StereoClass: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.stereo.StereoTool.TetrahedralSign: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.openscience.cdk.geometry.GeometryUtil.CoordinateCoverage: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.ringsearch.AllRingsFinder.Threshold: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.stereo.Projection: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.stereo.Stereocenters.Stereocenter: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.stereo.Stereocenters.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.stereo.StereoTool.SquarePlanarShape: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.stereo.StereoTool.StereoClass: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.stereo.StereoTool.TetrahedralSign: Returns an array containing the constants of this enum type, in the order they are declared.

W

WARNING_MARKER - Static variable in class org.openscience.cdk.validate.ProblemMarker
withCapacity(int) - Static method in class org.openscience.cdk.graph.Matching: Create an empty matching with the specified capacity.

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