Index (cdk-group 2.9 API)

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

addCell(int...) - Method in class org.openscience.cdk.group.Partition: Adds a new cell to the end of the partition containing these elements.
addCell(Collection<Integer>) - Method in class org.openscience.cdk.group.Partition: Adds a new cell to the end of the partition.
addSingletonCell(int) - Method in class org.openscience.cdk.group.Partition: Add a new singleton cell to the end of the partition containing only this element.
addToCell(int, int) - Method in class org.openscience.cdk.group.Partition: Add an element to a particular cell.
all() - Method in class org.openscience.cdk.group.PermutationGroup: Generate the whole group from the compact list of permutations.
apply(PermutationGroup.Backtracker) - Method in class org.openscience.cdk.group.PermutationGroup: Apply the backtracker to all permutations in the larger group.
applyTo(Permutation) - Method in interface org.openscience.cdk.group.PermutationGroup.Backtracker: Do something to the permutation
AtomContainerDiscretePartitionRefiner - Interface in org.openscience.cdk.group: A tool for determining the automorphism group of the atoms in a molecule, or for checking for a canonical form of a molecule.
AtomRefinerBuilder() - Constructor for class org.openscience.cdk.group.PartitionRefinement.AtomRefinerBuilder

B

BondRefinerBuilder() - Constructor for class org.openscience.cdk.group.PartitionRefinement.BondRefinerBuilder

C

changeBase(Permutation) - Method in class org.openscience.cdk.group.PermutationGroup: Change the base of the group to the new base newBase.
copyBlock(int) - Method in class org.openscience.cdk.group.Partition: Creates and returns a copy of the cell at cell index.
create() - Method in class org.openscience.cdk.group.PartitionRefinement.AtomRefinerBuilder
create() - Method in class org.openscience.cdk.group.PartitionRefinement.BondRefinerBuilder

D

DiscretePartitionRefiner - Interface in org.openscience.cdk.group: A mechanism for refining partitions of graph-like objects.

E

enter(Permutation) - Method in class org.openscience.cdk.group.PermutationGroup: Enter the permutation g into this group.
equals(Object) - Method in class org.openscience.cdk.group.Partition
equals(Object) - Method in class org.openscience.cdk.group.Permutation

F

firstIndexOfDifference(Permutation) - Method in class org.openscience.cdk.group.Permutation: Find an r such that this[r] != other[r].
firstIsIdentity() - Method in interface org.openscience.cdk.group.DiscretePartitionRefiner: Check that the first refined partition is the identity.
forAtoms() - Static method in class org.openscience.cdk.group.PartitionRefinement
forBonds() - Method in class org.openscience.cdk.group.PartitionRefinement
fromString(String) - Static method in class org.openscience.cdk.group.Partition: Parse a string like "[0,2|1,3]" to form the partition; cells are separated by '|' characters and elements within the cell by commas.

G

get(int) - Method in class org.openscience.cdk.group.Permutation: Get the value at this index.
get(int, int) - Method in class org.openscience.cdk.group.PermutationGroup: Get one of the permutations that make up the compact representation.
getAutomorphismGroup() - Method in interface org.openscience.cdk.group.DiscretePartitionRefiner: Get the automorphism group used to prune the search.
getAutomorphismGroup(IAtomContainer) - Method in interface org.openscience.cdk.group.AtomContainerDiscretePartitionRefiner: Gets the automorphism group of the atom container.
getAutomorphismGroup(IAtomContainer, Partition) - Method in interface org.openscience.cdk.group.AtomContainerDiscretePartitionRefiner: Get the automorphism group of the molecule given an initial partition.
getAutomorphismGroup(IAtomContainer, PermutationGroup) - Method in interface org.openscience.cdk.group.AtomContainerDiscretePartitionRefiner: Speed up the search for the automorphism group using the automorphisms in the supplied group.
getAutomorphismPartition() - Method in interface org.openscience.cdk.group.DiscretePartitionRefiner: The automorphism partition is a partition of the elements of the group.
getAutomorphismPartition(IAtomContainer) - Method in interface org.openscience.cdk.group.AtomContainerDiscretePartitionRefiner: Get the automorphism partition (equivalence classes) of the atoms.
getBest() - Method in interface org.openscience.cdk.group.DiscretePartitionRefiner: Get the best permutation found.
getCell(int) - Method in class org.openscience.cdk.group.Partition: Gets the cell at this index.
getConnectivity(int, int) - Method in interface org.openscience.cdk.group.Refinable: Get the connectivity between two vertices as an integer, to allow for multigraphs : so a single edge is 1, a double edge 2, etc.
getFirst() - Method in interface org.openscience.cdk.group.DiscretePartitionRefiner: Get the first permutation reached by the search.
getFirstInCell(int) - Method in class org.openscience.cdk.group.Partition: Gets the first element in the specified cell.
getIndexOfFirstNonDiscreteCell() - Method in class org.openscience.cdk.group.Partition: Gets the index of the first cell in the partition that is discrete.
getInitialPartition() - Method in interface org.openscience.cdk.group.Refinable: Get an initial partition of the vertices of the refinable - for example, by color.
getLeftTransversal(int) - Method in class org.openscience.cdk.group.PermutationGroup: Get the traversal U_i from the list of transversals.
getOrbit(int) - Method in class org.openscience.cdk.group.Permutation: Get all the elements in the same orbit in the permutation (unsorted).
getSize() - Method in class org.openscience.cdk.group.PermutationGroup: Get the number of elements in each permutation in the group.
getValues() - Method in class org.openscience.cdk.group.Permutation: Get all the values as an array.
getVertexCount() - Method in interface org.openscience.cdk.group.Refinable: Get the number of vertices in the graph to be refined.

H

hashCode() - Method in class org.openscience.cdk.group.Partition
hashCode() - Method in class org.openscience.cdk.group.Permutation

I

ignoringAtomTypes() - Method in class org.openscience.cdk.group.PartitionRefinement.AtomRefinerBuilder
ignoringBondOrders() - Method in class org.openscience.cdk.group.PartitionRefinement.AtomRefinerBuilder
ignoringBondOrders() - Method in class org.openscience.cdk.group.PartitionRefinement.BondRefinerBuilder
inOrder() - Method in class org.openscience.cdk.group.Partition: Check whether the cells are ordered such that for cells i and j, first(j) > first(i) and last(j) > last(i).
inSameCell(int, int) - Method in class org.openscience.cdk.group.Partition: Check that two elements are in the same cell of the partition.
insertCell(int, SortedSet<Integer>) - Method in class org.openscience.cdk.group.Partition: Insert a cell into the partition at the specified index.
Invariant - Interface in org.openscience.cdk.group: Marker interface for invariants.
invert() - Method in class org.openscience.cdk.group.Permutation: Invert the permutation, so that for all i : inv[p[i]] = i.
isCanonical(IAtomContainer) - Method in interface org.openscience.cdk.group.AtomContainerDiscretePartitionRefiner: Checks if the atom container is canonical.
isDiscrete() - Method in class org.openscience.cdk.group.Partition: Checks that all the cells are singletons - that is, they only have one element.
isDiscreteCell(int) - Method in class org.openscience.cdk.group.Partition: Check to see if the cell at cellIndex is discrete - that is, it only has one element.
isFinished() - Method in interface org.openscience.cdk.group.PermutationGroup.Backtracker: Check to see if the backtracker is finished.
isIdentity() - Method in class org.openscience.cdk.group.Permutation: Check to see if this permutation is the identity permutation.

M

makeSymN(int) - Static method in class org.openscience.cdk.group.PermutationGroup: Make the symmetric group Sym(N) for N.
multiply(Permutation) - Method in class org.openscience.cdk.group.Permutation: Multiply this permutation by another such that for all i, this[i] = this[other[i]].

N

neighboursInBlock(Set<Integer>, int) - Method in interface org.openscience.cdk.group.Refinable: Given a block (or cell) of a partition, determine the invariant that represents the intersection between the block and the neighbours of vertexIndex supplied.
numberOfElements() - Method in class org.openscience.cdk.group.Partition: Calculate the size of the partition as the sum of the sizes of the cells.

O

order() - Method in class org.openscience.cdk.group.Partition: Sort the cells in increasing order.
order() - Method in class org.openscience.cdk.group.PermutationGroup: Calculates the size of the group.
org.openscience.cdk.group - package org.openscience.cdk.group

P

Partition - Class in org.openscience.cdk.group: A partition of a set of integers, such as the discrete partition {{1}, {2}, {3}, {4}} or the unit partition {{1, 2, 3, 4}} or an intermediate like {{1, 2}, {3, 4}}.
Partition() - Constructor for class org.openscience.cdk.group.Partition: Creates a new, empty partition with no cells.
Partition(int[][]) - Constructor for class org.openscience.cdk.group.Partition: Constructor to make a partition from an array of int arrays.
Partition(Partition) - Constructor for class org.openscience.cdk.group.Partition: Copy constructor to make one partition from another.
PartitionRefinement - Class in org.openscience.cdk.group: Factory for partition refiners.
PartitionRefinement() - Constructor for class org.openscience.cdk.group.PartitionRefinement
PartitionRefinement.AtomRefinerBuilder - Class in org.openscience.cdk.group
PartitionRefinement.BondRefinerBuilder - Class in org.openscience.cdk.group
Permutation - Class in org.openscience.cdk.group: A permutation with some associated methods to multiply, invert, and convert to cycle strings.
Permutation(int) - Constructor for class org.openscience.cdk.group.Permutation: Constructs an identity permutation with size elements.
Permutation(int...) - Constructor for class org.openscience.cdk.group.Permutation: Make a permutation from a set of values such that p[i] = x for the value x at position i.
Permutation(Permutation) - Constructor for class org.openscience.cdk.group.Permutation: Construct a permutation from another one by cloning the values.
PermutationGroup - Class in org.openscience.cdk.group: A permutation group with a Schreier-Sims representation.
PermutationGroup(int) - Constructor for class org.openscience.cdk.group.PermutationGroup: Make a group with just a single identity permutation of size n.
PermutationGroup(int, List<Permutation>) - Constructor for class org.openscience.cdk.group.PermutationGroup: Creates a group from a set of generators.
PermutationGroup(Permutation) - Constructor for class org.openscience.cdk.group.PermutationGroup: Creates the initial group, with the base base.
PermutationGroup.Backtracker - Interface in org.openscience.cdk.group: An interface for use with the apply method, which runs through all the permutations in this group.

R

Refinable - Interface in org.openscience.cdk.group: Implementors are graph-like objects that are refinable by the equitable and discrete partition refiners.
refine(IAtomContainer) - Method in interface org.openscience.cdk.group.AtomContainerDiscretePartitionRefiner: Refine an atom container, which has the side effect of calculating the automorphism group.
refine(IAtomContainer, Partition) - Method in interface org.openscience.cdk.group.AtomContainerDiscretePartitionRefiner: Refine an atom partition based on the connectivity in the atom container.
removeCell(int) - Method in class org.openscience.cdk.group.Partition: Removes the cell at the specified index.

S

set(int, int) - Method in class org.openscience.cdk.group.Permutation: Set the value at the specified index.
setAsPermutation(int) - Method in class org.openscience.cdk.group.Partition: Fill the elements of a permutation from the first element of each cell, up to the point upTo.
setTo(Permutation) - Method in class org.openscience.cdk.group.Permutation: Alter a permutation by setting it to the values in the other permutation.
size() - Method in class org.openscience.cdk.group.Partition: Gets the size of the partition, in terms of the number of cells.
size() - Method in class org.openscience.cdk.group.Permutation: Get the number of elements in the permutation.
splitAfter(int, int) - Method in class org.openscience.cdk.group.Partition: Splits this partition by taking the cell at cellIndex and making two new cells - the first with the the rest of the elements from that cell and the second with the singleton splitElement.
splitBefore(int, int) - Method in class org.openscience.cdk.group.Partition: Splits this partition by taking the cell at cellIndex and making two new cells - the first with the singleton splitElement and the second with the rest of the elements from that cell.

T

test(Permutation) - Method in class org.openscience.cdk.group.PermutationGroup: Test a permutation to see if it is in the group.
toCycleString() - Method in class org.openscience.cdk.group.Permutation: An easily-readable version of the permutation as a product of cycles.
toPermutation() - Method in class org.openscience.cdk.group.Partition: Converts the whole partition into a permutation.
toString() - Method in class org.openscience.cdk.group.Partition
toString() - Method in class org.openscience.cdk.group.Permutation
toString() - Method in class org.openscience.cdk.group.PermutationGroup
transversal(PermutationGroup) - Method in class org.openscience.cdk.group.PermutationGroup: Generate a transversal of a subgroup in this group.

U

unit(int) - Static method in class org.openscience.cdk.group.Partition: Create a unit partition - in other words, the coarsest possible partition where all the elements are in one cell.

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