Index (cdk-structgen 2.9 API)

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

A

acceptStructure() - Method in class org.openscience.cdk.structgen.RandomGenerator: Tell the RandomGenerator to accept the last structure that had been proposed.
actArray(int[], Permutation) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Performing the permutation action on an int array.
addHydrogens(int[][], int, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: After generating matrices, adding the hydrogen with respect to the pre-hydrogen distribution.
addOnes(int[], int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Add number of 1s into an ArrayList
addPartition(int, int[], int[][], int[][]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Updating canonical partition list.
allIs0(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Checks whether all the entries are equal to 0 or not.
atomOccurrence(String[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Getting the number of atoms' occurrences.

B

backward(int[][], int[], int[], int[], boolean[], int[], int[][][], int[][][], int[][][], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Backward step in the algorithm.
backwardCriteria(int, int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: The criteria to decide which function is needed: forward or backward.
biggerCheck(int, int[], int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Checks two arrays in descending order.
buildArray(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Building the copy of the partition array
buildAtomContainerFromMatrix(int[][], IAtomContainer) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Building an atom container for an adjacency matrix.
buildContainer4SDF(int[][]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Building an atom container for an adjacency matrix.
buildContainer4SDF(String[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Building an atom container for SDF output from its symbols
buildContainer4SDF(IAtomContainer, int[][]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Building an atom container for an adjacency matrix.
buildSymbolArray() - Method in class org.openscience.cdk.structgen.maygen.Maygen

C

canBuildIsomer(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Checking whether a molecular formula can represent a graph or not.
canBuildIsomerSingle(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Checking whether a molecular formula can represent a graph or not.
candidatePermutations(int, List<Permutation>, List<ArrayList<Permutation>>) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Calculating all candidate permutations for row canonical test.
canonicalPartition(int, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: To get the canonical partition.
canonicalTest(int[][], int[], int[][], int[], List<ArrayList<Permutation>>, int[], int[], int[], int[], int[][], int[][], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
check(int, int, int[][], int[], List<ArrayList<Permutation>>) - Method in class org.openscience.cdk.structgen.maygen.Maygen
checkJustH(int[][][], int, int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen
checkLengthTwoFormula(String[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: checking whether a molecular formula is length 2 or not.
checkOxygenSulfur(String[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
ChemGraph - Class in org.openscience.cdk.structgen.stochastic.operator
ChemGraph(IAtomContainer) - Constructor for class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
cInverse(int, int, int[][], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Calculating the sum of the entries in the jth column until the ith row.
clearFormers(boolean, int, int[][], List<ArrayList<Permutation>>) - Method in class org.openscience.cdk.structgen.maygen.Maygen: When an adjacency matrix is non-canonical, cleaning the formerPermutations and partitionList from the first row of the tested block.
clearGlobals() - Method in class org.openscience.cdk.structgen.maygen.Maygen: For several calls of the run function, setting the global variables.
cloneArray(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Cloning int array
close() - Method in interface org.openscience.cdk.structgen.maygen.Maygen.Consumer
closeFilesAndDisplayStatistic(long) - Method in class org.openscience.cdk.structgen.maygen.Maygen
compare(int[], int[], int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Comparing two arrays for specific range of entries, whether the first array is bigger than the second one or not.
compareIndexwise(int[], int[], int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Comparing two int arrays are equal or not for given range of entries.
configure(String) - Method in interface org.openscience.cdk.structgen.maygen.Maygen.Consumer
connectivityTest(int[][], int[], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Test whether an adjacency matrix is connected or disconnected.
consume(IAtomContainer) - Method in interface org.openscience.cdk.structgen.maygen.Maygen.Consumer
contab - Variable in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
CrossoverMachine - Class in org.openscience.cdk.structgen.stochastic.operator: Modified molecular structures by applying crossover operator on a pair of parent structures and generate a pair of offspring structures.
CrossoverMachine() - Constructor for class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine: Constructs a new CrossoverMachine operator.
csum(int, int, int[][][]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Summing ith column entries starting from the jth row.
cycleTranspositions(int, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Getting the list of cycle transpositions for a given atom partition and the row index

D

degree2graph() - Method in class org.openscience.cdk.structgen.maygen.Maygen: Building a degree 2 graph for a single element type.
descendingOrderCheck(int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Checks a int array is in descending order or not with respect to a given atom partition.
descendingOrderCheck(int[], int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Checks subarray of specified range of entries, the array is descending order or not.
descendingOrderUpperMatrixCheck(int, int[], int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Checks the first row is bigger than the second row just in the upper matrix.
descendingSort(int[], int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Sorting entries of a subarray specified by indices.
descendingSortWithPartition(int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Sorting entries of a int array for a given atom partition.
dim - Variable in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
displayStatistic(long, String) - Method in class org.openscience.cdk.structgen.maygen.Maygen
distributeHydrogens() - Method in class org.openscience.cdk.structgen.maygen.Maygen: If there are hydrogens in the formula, calling the hydrogenDistributor.
distributeSulfurOxygen(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen
distributeSymbols(int, int, int, int, int, int, int, boolean) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Main function for the distribution of atom symbols: O and S for OnSm form formulae.
distributeSymbolsNextSizeAboveGraphSize(int, boolean) - Method in class org.openscience.cdk.structgen.maygen.Maygen
doCrossover(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine: Performs the n point crossover of two IAtomContainer.
doRun(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen

E

emit(IAtomContainer) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Emits a molecule to whomever is listening.
equalRowsCheck(int, int[][], Permutation, Permutation) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Comparing two arrays are equal.
equalSetCheck(int[], int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Checks two int[] arrays are equal with respect to an atom partition.
equalSetCheck2(int[], int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Checks two int[] arrays are equal with respect to an atom partition.
extendFormula(String, int, String) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Adding new entry to the new molecular formula

F

fillDegreeListHindexIsTwo(List<int[]>, List<int[]>) - Method in class org.openscience.cdk.structgen.maygen.Maygen
findIndex(int, Permutation) - Method in class org.openscience.cdk.structgen.maygen.Maygen: With the cycle permutation, mapping the row index to another row in the block.
findMatch(int[], int[], int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Find the matching entries index in compared two rows.
findMatchingAtomType(IAtomContainer, IAtom) - Method in class org.openscience.cdk.atomtype.StructGenMatcher: Finds the AtomType matching the Atom's element symbol, formal charge and hybridization state.
findMatchingAtomTypes(IAtomContainer) - Method in class org.openscience.cdk.atomtype.StructGenMatcher
findMaximalIndexInComponent(int[], int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Finding the maximal index in a component to compare with other components.
findR(int[], int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Finding the R index of a block
findY(int, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: For a block index r, calculating its first row index.
findZ(int, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: For a block index r, calculating its last row index.
findZeros(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
forward(IAtomContainer, String[], int[][], int[], int[], int[], int[][], boolean[], int[], boolean[], int[], List<ArrayList<Permutation>>, int[], int[], int[], int[], int[], int[][][], int[][][], int[][][], int[][], int[][], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Setting successor indices entry if there is a possible filling.
forward(IAtomContainer, String[], int, int, int, int, int, int[][], int[], int[], int[][], boolean[], int[], boolean[], int[], List<ArrayList<Permutation>>, int[], int[], int[], int[], int[], int[][][], int[][][], int[][][], int[][], int[][], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen

G

generate() - Method in class org.openscience.cdk.structgen.SingleStructureRandomGenerator: Generates a random structure based on the atoms in the given IAtomContainer.
generate(IAtomContainer, String[], int[], int[], int[][], int[], boolean[], int[], List<ArrayList<Permutation>>, int[], int[], int[], int[], int[], int[][], int[][], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Initialization of global variables for the generate of structures for given degree list.
generate(IAtomContainerSet) - Method in class org.openscience.cdk.structgen.stochastic.PartialFilledStructureMerger: Randomly generates a single, connected, correctly bonded structure from a number of fragments.
generateFormulae(List<String>, List<String>, Map<String, Integer[]>, String, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Formulae generator for each element ranges
generateOnSmMat() - Method in class org.openscience.cdk.structgen.maygen.Maygen: Building an OnSm molecule for a given total number of atoms.
getBlocks(int[], int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Getting a part of a int array specified by two entry indices
getBuilder() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getCanonicalCycle(int, int, int[][], int[], Permutation) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Getting the canonical cycle of a row.
getCanonicalPermutation(int[], int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Calculating the canonical permutation of a row.
getCanonicalPermutation2(int[], int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Calculating the canonical permutation of a row.
getConsumer() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getCount() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getCyclesList(int[], int[], int, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: For maximal and tested rows, getting the cycle lists
getEqualPerm(Permutation, int, int[][], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Getting the permutation making two rows identical.
getFormula() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getFormulaList(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Generating list of formulae for the input fuzzy formula
getFuzzyCount() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getFuzzyFormula() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getFuzzyFormulaRanges(String, List<String>) - Method in class org.openscience.cdk.structgen.maygen.Maygen: To get the fuzzy formula ranges for each element type in the molecular formula
getFuzzyFormulaRangesWithNewElements(String, List<String>) - Method in class org.openscience.cdk.structgen.maygen.Maygen
getHigherValences(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Reading the molecular formula and setting the higher valences.
getHydrogensInfoLengthIsOne(List<String>, String[], int) - Method in class org.openscience.cdk.structgen.maygen.Maygen
getLernenIndices(int, int[][], List<Permutation>, int[], int[], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Get indices from "learning from canonical test" method.
getMaximumPair(int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Between two index pairs, getting the bigger indices.
getMolecule() - Method in class org.openscience.cdk.structgen.RandomGenerator: Returns the molecule which reflects the current state of this stochastic structure generator.
getNonCanonicalMakerPermutation(int[], Permutation, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Calculating the permutation, permuting the second row and making first row non maximal.
getNumAtoms() - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
getOccurrences() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getOxygenSulfur() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getPartition(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Based on the new degrees and the former partition, getting the new atom partition.
getPartition(List<String>) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Getting the partition of symbols
getPermutedIndex(Permutation, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: By a given permutation, checking which entry is mapped to the index.
getSingleAtomVariables(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen
getSize() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getSubgraph() - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
getSubPartition(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Calculating the sub partitions for a given group of degrees.
getSymbol(String[], Integer[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
getSymbolArray() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getSymbolOccurrences(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Getting the symbol occurrences from the input local formula.
getSymbols() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getTotal() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getTotalHydrogen() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getTranspose(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: For an index pair, getting its transpose.
getVerbose() - Method in class org.openscience.cdk.structgen.maygen.Maygen

I

idPermutation(int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Builds id permutation.
idValues(int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Values for an id permutation for a given localSize
indexYZ(int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Based on the molecules automorphisms, testing an adjacency matrix is canonical or not.
initAC(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Building an atom container from a string of atom-implicit hydrogen information.
initAC(IAtomContainer, String[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Building an atom container from a string of atom-implicit hydrogen information.
initialDegrees() - Method in class org.openscience.cdk.structgen.maygen.Maygen: Initial degree arrays are set based on the molecular formula.
initialKList(int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Initializing the first connectivity partition.
initialPartition(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Initial atom partition of the input molecular formula
initSingleAC() - Method in class org.openscience.cdk.structgen.maygen.Maygen: Setting the initial atom container of a molecular formula with a single heavy atom
intAC(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Setting the initial atom container of a molecular formula
isBoundary() - Method in class org.openscience.cdk.structgen.maygen.Maygen
isMultiThread() - Method in class org.openscience.cdk.structgen.maygen.Maygen
isOnSm() - Method in class org.openscience.cdk.structgen.maygen.Maygen
isReversalIsSmaller(int, int, boolean) - Method in class org.openscience.cdk.structgen.maygen.Maygen
isSetElement() - Method in class org.openscience.cdk.structgen.maygen.Maygen
IStructureGenerationListener - Interface in org.openscience.cdk.structgen
isTsvoutput() - Method in class org.openscience.cdk.structgen.maygen.Maygen

K

kValues(int, Set<Integer>, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Finding the connectivity partition, so the smallest index in the neighborhood.

L

limit(int, int, int[][], Permutation) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Looking for the upper limit where the original entry is smaller.
lInverse(int, int, int[][], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Calculating the sum of the entries in the ith row until the jth column.
lowerIndex(int, int, int[][], Permutation) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Looking for the maximum index where the entry is not zero.
lsum(int, int, int[][][]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Summing ith rows entries starting from the jth column.
lValue(int[], int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: To calculate the number of conjugacy classes, used in cycle transposition calculation.

M

maximalEntry(int, int, int, int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Calculating the maximal entry for the indices.
maximalIndexWithNonZeroEntry(int[][], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: In case if the index' entry is zero, updating the index with next index with non-zero entry.
maximalMatrix(int[], int[][][]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Possible maximal edge multiplicity for the atom pair (i,j).
Maygen - Class in org.openscience.cdk.structgen.maygen: The main class of the MAYGEN package.
Maygen(IChemObjectBuilder) - Constructor for class org.openscience.cdk.structgen.maygen.Maygen
Maygen.Consumer - Interface in org.openscience.cdk.structgen.maygen
minComponentIndex(Set<Integer>, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Getting the minimum component index.
mutate(IAtomContainer) - Method in class org.openscience.cdk.structgen.RandomGenerator: Randomly chooses four atoms and alters the bonding pattern between them according to rules described in "Faulon, JCICS 1996, 36, 731".

N

nextCount(int, int, int, int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Counting the occurrence of a value in a degree.
nextCount(int, int, int, List<String>, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
nextStep(IAtomContainer, String[], int[][], int[], int[], int[], int[][], boolean[], int[], boolean[], int[], List<ArrayList<Permutation>>, int[], int[], int[], int[], int[], int[][][], int[][][], int[][][], int[][], int[][], boolean[], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Calling foward or backward function in a nextstep function.
NOOP_CONSUMER - Static variable in class org.openscience.cdk.structgen.maygen.Maygen
normalizeFormula(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen
numAtoms - Variable in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
nValues(int, int, int[][]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Finding the neighbors of a given index.

O

orderDegreeSymbols(int[], String[], int, int, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Ordering degrees, hydrogens and symbols in ascending order
org.openscience.cdk.atomtype - package org.openscience.cdk.atomtype
org.openscience.cdk.structgen - package org.openscience.cdk.structgen
org.openscience.cdk.structgen.maygen - package org.openscience.cdk.structgen.maygen
org.openscience.cdk.structgen.stochastic - package org.openscience.cdk.structgen.stochastic
org.openscience.cdk.structgen.stochastic.operator - package org.openscience.cdk.structgen.stochastic.operator

P

PartialFilledStructureMerger - Class in org.openscience.cdk.structgen.stochastic: Randomly generates a single, connected, correctly bonded structure from a number of fragments.
PartialFilledStructureMerger() - Constructor for class org.openscience.cdk.structgen.stochastic.PartialFilledStructureMerger: Constructor for the PartialFilledStructureMerger object.
partitionCriteria(int[], int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Partitioning criteria
permuteArray(int[], int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Permuting two entries of an Integer array.
pickBFgraph() - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
pickDFgraph() - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
possibleAtomTypes(IAtomContainer, IAtom) - Method in class org.openscience.cdk.atomtype.StructGenAtomTypeGuesser: Finds the AtomType matching the Atom's element symbol, formal charge and hybridization state.
predecessor(int[], int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Calculation of the former index pair in a matrix.
processFormula(String, long) - Method in class org.openscience.cdk.structgen.maygen.Maygen
processRun(String, long) - Method in class org.openscience.cdk.structgen.maygen.Maygen
proposeStructure() - Method in class org.openscience.cdk.structgen.RandomGenerator: Proposes a structure which can be accepted or rejected by an external entity.

R

RandomGenerator - Class in org.openscience.cdk.structgen: RandomGenerator is a generator of constitutional isomers.
RandomGenerator(IAtomContainer) - Constructor for class org.openscience.cdk.structgen.RandomGenerator: Constructs a RandomGenerator with a given starting structure.
refinedPartitioning(int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Refining the input partition based on the row entries.
reOrder(int[], int[], String[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Re-order all the global variables based on the refined new partitioning.
reverseComparison(int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: The function to compare a node labelling array when the number of left consecutive entries is equal to the right consecutive entries.
row2compare(int, int[][], Permutation) - Method in class org.openscience.cdk.structgen.maygen.Maygen: For a row given by index, detecting the other row to compare in the block.
rowCanonicalTest(int, int[], int[][], int[], int[], int[], int[][], int[], List<ArrayList<Permutation>>, int[], int[][], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Canonical test for a row in the tested block.
rowDescendingTest(int, int[][], int[], int[], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: The row descending test is the part of canonical test function.
run() - Method in class org.openscience.cdk.structgen.maygen.Maygen: Main function to initialize the global variables and calling the generate function.
runDistributeSymbols(int, int, int, int, int, boolean, int, int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen
runDistributeSymbolsCheckNodeLabels(int, int, int, int, int, int, boolean) - Method in class org.openscience.cdk.structgen.maygen.Maygen

S

sample(IAtomContainer) - Static method in class org.openscience.cdk.structgen.VicinitySampler: Choose any possible quadruple of the set of atoms in ac and establish all of the possible bonding schemes according to Faulon's equations.
setAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.structgen.SingleStructureRandomGenerator: Sets the AtomContainer attribute of the SingleStructureRandomGenerator object.
setBiggest(int, int[][], Permutation, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Checks whether there is a permutation making the row bigger in descending order.
setBoundary(boolean) - Method in class org.openscience.cdk.structgen.maygen.Maygen
setConsumer(Maygen.Consumer) - Method in class org.openscience.cdk.structgen.maygen.Maygen
setFormula(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen
setFuzzyFormula(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen
setHydrogens(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Calling the generate function for each degree values after the hydrogen distribution.
setLearningFromConnectivity(Set<Integer>, int[], int[], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: If matrix is not connected, setting learninfFromConnectivity global variables.
setLernenIndices(int, Permutation, int[][], int[], int[], int[], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Setting the nonCanonicalIndices global variable.
setMolecule(IAtomContainer) - Method in class org.openscience.cdk.structgen.RandomGenerator: Assigns a starting structure to this generator.
setMultiThread(boolean) - Method in class org.openscience.cdk.structgen.maygen.Maygen
setNumAtoms(int) - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
setSetElement(boolean) - Method in class org.openscience.cdk.structgen.maygen.Maygen
setSubgraph(List<Integer>) - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
setSymbols(List<String>) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Setting the firstSymbols and symbols global variables for the initial sorted list of symbols.
setTsvoutput(boolean) - Method in class org.openscience.cdk.structgen.maygen.Maygen
setVerbose(boolean) - Method in class org.openscience.cdk.structgen.maygen.Maygen
setYZValues(int[], int[][], int[][]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Setting the y and z values for each block.
singleAtomCheck(String[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
singleAtomCheckLengthIsBiggerThanOne(String[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
SingleStructureRandomGenerator - Class in org.openscience.cdk.structgen: Randomly generates a single, connected, correctly bonded structure for a given molecular formula.
SingleStructureRandomGenerator() - Constructor for class org.openscience.cdk.structgen.SingleStructureRandomGenerator: Constructor for the SingleStructureRandomGenerator object.
SingleStructureRandomGenerator(long) - Constructor for class org.openscience.cdk.structgen.SingleStructureRandomGenerator: Constructor for the SingleStructureRandomGenerator object.
sort(List<String>, Set<Map.Entry<String, Integer>>) - Method in class org.openscience.cdk.structgen.maygen.Maygen
sortAscending(List<String>) - Method in class org.openscience.cdk.structgen.maygen.Maygen: The initializer function, reading the formula to set the degrees, partition and file directory variables.
sortWithPartition(int[], int[], String[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Sort arrays with partitions.
SPLIT_MODE_BREADTH_FIRST - Static variable in class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine: Indicates that crossover is using SPLIT_MODE_BREADTH_FIRST mode.
SPLIT_MODE_DEPTH_FIRST - Static variable in class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine: Indicates that crossover is using SPLIT_MODE_DEPTH_FIRST mode.
SPLIT_MODE_RADNDOM - Static variable in class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine: Indicates that crossover is using SPLIT_MODE_RADNDOM mode.
stateChanged(List) - Method in interface org.openscience.cdk.structgen.IStructureGenerationListener
StructGenAtomTypeGuesser - Class in org.openscience.cdk.atomtype: AtomTypeMatcher that finds an AtomType by matching the Atom's element symbol.
StructGenAtomTypeGuesser() - Constructor for class org.openscience.cdk.atomtype.StructGenAtomTypeGuesser: Constructor for the StructGenMatcher object.
StructGenMatcher - Class in org.openscience.cdk.atomtype: AtomTypeMatcher that finds an AtomType by matching the Atom's element symbol.
StructGenMatcher() - Constructor for class org.openscience.cdk.atomtype.StructGenMatcher: Constructor for the StructGenMatcher object.
structureGenerator(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen: After the hydrogen distribution, calling the structure generator functions.
subGraph - Variable in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
successor(int[], int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Calculation of the next index pair in a matrix.
sum(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Summing entries of an array.
sum(int[], int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Summing entries of a list until a given index.
swap(int[], int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen
swap(String[], int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen

T

travIndex - Variable in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph

U

upperIndex(int, int, int[][], Permutation) - Method in class org.openscience.cdk.structgen.maygen.Maygen: We need to calculate upperIndex.
upperTriangularC(int[], int[][][], int[][][]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: c; upper triangular matrix like given in 3.2.1.
upperTriangularL(int[], int[][][], int[][][]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: l; upper triangular matrix like given in 3.2.1.

V

validateFormula(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen
validateFuzzyFormula(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen
VicinitySampler - Class in org.openscience.cdk.structgen: The VicinitySampler is a generator of constitutional isomers.
VicinitySampler() - Constructor for class org.openscience.cdk.structgen.VicinitySampler
visited - Variable in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph

W

writeSingleAtom(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Writing the single atom molecule in a output file.
wValues(Set<Integer>, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Finding the W values of neighbors in the former connectivity partition.

Z

zero(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: For a row given by index, checking whether it is in maximal form or not.

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