Uses of Class
org.openscience.cdk.group.Permutation

Packages that use Permutation

Package	Description
org.openscience.cdk.group
org.openscience.cdk.structgen.maygen

Uses of Permutation in org.openscience.cdk.group

Methods in org.openscience.cdk.group that return Permutation

Modifier and Type	Method	Description
Permutation	PermutationGroup.get(int uIndex, int uSubIndex)	Get one of the permutations that make up the compact representation.
Permutation	DiscretePartitionRefiner.getBest()	Get the best permutation found.
Permutation	DiscretePartitionRefiner.getFirst()	Get the first permutation reached by the search.
Permutation	Permutation.invert()	Invert the permutation, so that for all i : inv[p[i]] = i.
Permutation	Permutation.multiply(Permutation other)	Multiply this permutation by another such that for all i, this[i] = this[other[i]].
Permutation	Partition.setAsPermutation(int upTo)	Fill the elements of a permutation from the first element of each cell, up to the point upTo.
Permutation	Partition.toPermutation()	Converts the whole partition into a permutation.

Methods in org.openscience.cdk.group that return types with arguments of type Permutation

Modifier and Type	Method	Description
List<Permutation>	PermutationGroup.all()	Generate the whole group from the compact list of permutations.
List<Permutation>	PermutationGroup.getLeftTransversal(int index)	Get the traversal Ui from the list of transversals.
List<Permutation>	PermutationGroup.transversal(PermutationGroup subgroup)	Generate a transversal of a subgroup in this group.

Methods in org.openscience.cdk.group with parameters of type Permutation

Modifier and Type	Method	Description
void	PermutationGroup.Backtracker.applyTo(Permutation p)	Do something to the permutation
void	PermutationGroup.changeBase(Permutation newBase)	Change the base of the group to the new base newBase.
void	PermutationGroup.enter(Permutation g)	Enter the permutation g into this group.
int	Permutation.firstIndexOfDifference(Permutation other)	Find an r such that this[r] != other[r].
Permutation	Permutation.multiply(Permutation other)	Multiply this permutation by another such that for all i, this[i] = this[other[i]].
void	Permutation.setTo(Permutation other)	Alter a permutation by setting it to the values in the other permutation.
int	PermutationGroup.test(Permutation permutation)	Test a permutation to see if it is in the group.

Constructors in org.openscience.cdk.group with parameters of type Permutation

Modifier	Constructor	Description
	Permutation(Permutation other)	Construct a permutation from another one by cloning the values.
	PermutationGroup(Permutation base)	Creates the initial group, with the base base.

Constructor parameters in org.openscience.cdk.group with type arguments of type Permutation

Modifier	Constructor	Description
	PermutationGroup(int size, List<Permutation> generators)	Creates a group from a set of generators.

Uses of Permutation in org.openscience.cdk.structgen.maygen

Methods in org.openscience.cdk.structgen.maygen that return Permutation

Modifier and Type	Method	Description
Permutation	Maygen.getCanonicalCycle(int index, int total, int[][] a, int[] newPartition, Permutation cycleTransposition)	Getting the canonical cycle of a row.
Permutation	Maygen.getCanonicalPermutation(int[] originalRow, int[] rowToCheck, int[] partition)	Calculating the canonical permutation of a row.
Permutation	Maygen.getEqualPerm(Permutation cycleTransposition, int index, int[][] a, int[] newPartition)	Getting the permutation making two rows identical.
Permutation	Maygen.getNonCanonicalMakerPermutation(int[] array, Permutation cycle, int[] partition)	Calculating the permutation, permuting the second row and making first row non maximal.
Permutation	Maygen.idPermutation(int localSize)	Builds id permutation.

Methods in org.openscience.cdk.structgen.maygen that return types with arguments of type Permutation

Modifier and Type	Method	Description
List<Permutation>	Maygen.cycleTranspositions(int index, int[] partition)	Getting the list of cycle transpositions for a given atom partition and the row index

Methods in org.openscience.cdk.structgen.maygen with parameters of type Permutation

Modifier and Type	Method	Description
int[]	Maygen.actArray(int[] array, Permutation permutation)	Performing the permutation action on an int array.
boolean	Maygen.equalRowsCheck(int index, int[][] a, Permutation cycleTransposition, Permutation permutation)	Comparing two arrays are equal.
int	Maygen.findIndex(int index, Permutation cycle)	With the cycle permutation, mapping the row index to another row in the block.
Permutation	Maygen.getCanonicalCycle(int index, int total, int[][] a, int[] newPartition, Permutation cycleTransposition)	Getting the canonical cycle of a row.
Permutation	Maygen.getEqualPerm(Permutation cycleTransposition, int index, int[][] a, int[] newPartition)	Getting the permutation making two rows identical.
Permutation	Maygen.getNonCanonicalMakerPermutation(int[] array, Permutation cycle, int[] partition)	Calculating the permutation, permuting the second row and making first row non maximal.
int	Maygen.getPermutedIndex(Permutation permutation, int index)	By a given permutation, checking which entry is mapped to the index.
int[]	Maygen.limit(int index, int nextRowIndex, int[][] a, Permutation permutation)	Looking for the upper limit where the original entry is smaller.
int[]	Maygen.lowerIndex(int index, int nextRowIndex, int[][] a, Permutation permutation)	Looking for the maximum index where the entry is not zero.
int[]	Maygen.row2compare(int index, int[][] a, Permutation cycleTransposition)	For a row given by index, detecting the other row to compare in the block.
boolean	Maygen.setBiggest(int index, int[][] a, Permutation permutation, int[] partition)	Checks whether there is a permutation making the row bigger in descending order.
void	Maygen.setLernenIndices(int rowIndex1, Permutation cycle, int[][] a, int[] secondRow, int[] partition, int[] nonCanonicalIndices, boolean[] learningFromCanonicalTest)	Setting the nonCanonicalIndices global variable.
int[]	Maygen.upperIndex(int index, int nextRowIndex, int[][] a, Permutation permutation)	We need to calculate upperIndex.

Method parameters in org.openscience.cdk.structgen.maygen with type arguments of type Permutation

Modifier and Type	Method	Description
void	Maygen.candidatePermutations(int index, List<Permutation> cycles, List<ArrayList<Permutation>> formerPermutations)	Calculating all candidate permutations for row canonical test.
boolean	Maygen.canonicalTest(int[][] a, int[] initialPartition, int[][] partitionList, int[] nonCanonicalIndices, List<ArrayList<Permutation>> formerPermutations, int[] partSize, int[] r, int[] y, int[] z, int[][] ys, int[][] zs, boolean[] learningFromCanonicalTest)
boolean	Maygen.check(int index, int total, int[][] a, int[] newPartition, List<ArrayList<Permutation>> formerPermutations)
void	Maygen.clearFormers(boolean check, int y, int[][] partitionList, List<ArrayList<Permutation>> formerPermutations)	When an adjacency matrix is non-canonical, cleaning the formerPermutations and partitionList from the first row of the tested block.
int[][]	Maygen.forward(IAtomContainer ac, String[] symbolArrayCopy, int[][] a, int[] indices, int[] degrees, int[] initialPartition, int[][] partitionList, boolean[] callForward, int[] connectivityIndices, boolean[] learningFromConnectivity, int[] nonCanonicalIndices, List<ArrayList<Permutation>> formerPermutations, int[] hydrogens, int[] partSize, int[] r, int[] y, int[] z, int[][][] max, int[][][] l, int[][][] c, int[][] ys, int[][] zs, boolean[] learningFromCanonicalTest)	Setting successor indices entry if there is a possible filling.
int[][]	Maygen.forward(IAtomContainer ac, String[] symbolArrayCopy, int lInverse, int cInverse, int maximalX, int i, int j, int[][] a, int[] indices, int[] initialPartition, int[][] partitionList, boolean[] callForward, int[] connectivityIndices, boolean[] learningFromConnectivity, int[] nonCanonicalIndices, List<ArrayList<Permutation>> formerPermutations, int[] hydrogens, int[] partSize, int[] r, int[] y, int[] z, int[][][] max, int[][][] l, int[][][] c, int[][] ys, int[][] zs, boolean[] learningFromCanonicalTest)
void	Maygen.generate(IAtomContainer ac, String[] symbolArrayCopy, int[] degreeList, int[] initialPartition, int[][] partitionList, int[] connectivityIndices, boolean[] learningFromConnectivity, int[] nonCanonicalIndices, List<ArrayList<Permutation>> formerPermutations, int[] hydrogens, int[] partSize, int[] r, int[] y, int[] z, int[][] ys, int[][] zs, boolean[] learningFromCanonicalTest)	Initialization of global variables for the generate of structures for given degree list.
void	Maygen.getLernenIndices(int index, int[][] a, List<Permutation> cycles, int[] partition, int[] nonCanonicalIndices, boolean[] learningFromCanonicalTest)	Get indices from "learning from canonical test" method.
void	Maygen.nextStep(IAtomContainer ac, String[] symbolArrayCopy, int[][] a, int[] indices, int[] degrees, int[] initialPartition, int[][] partitionList, boolean[] callForward, int[] connectivityIndices, boolean[] learningFromConnectivity, int[] nonCanonicalIndices, List<ArrayList<Permutation>> formerPermutations, int[] hydrogens, int[] partSize, int[] r, int[] y, int[] z, int[][][] max, int[][][] l, int[][][] c, int[][] ys, int[][] zs, boolean[] learningFromCanonicalTest, boolean[] flag)	Calling foward or backward function in a nextstep function.
boolean	Maygen.rowCanonicalTest(int index, int[] r, int[][] a, int[] partition, int[] newPartition, int[] initialPartition, int[][] partitionList, int[] nonCanonicalIndices, List<ArrayList<Permutation>> formerPermutations, int[] y, int[][] ys, boolean[] learningFromCanonicalTest)	Canonical test for a row in the tested block.