A B C D E F G H I M N P R S V

A

abbrev() - Method in enum info.mrupp.isoak1.Element
The two-character abbreviation of the element.
argName() - Method in enum info.mrupp.isoak1.VertexEdgeKernel
Short name of vertex/edge kernel.
Array2Float - Class in info.mrupp.isoak1
Two-dimensional array of single precision floating point numbers.
Array2Float() - Constructor for class info.mrupp.isoak1.Array2Float
Creates an empty array.
Array2Float(int, int) - Constructor for class info.mrupp.isoak1.Array2Float
Creates an array of given size.
Array2Float(float[][]) - Constructor for class info.mrupp.isoak1.Array2Float
Creates a copy from a rectangular built-in array.
Array2Float(float[][], boolean) - Constructor for class info.mrupp.isoak1.Array2Float
Creates a copy from a rectangular built-in array.
Array2Float(Array2Float) - Constructor for class info.mrupp.isoak1.Array2Float
Creates a copy of another Array2Float.
Array2Float(Array2Float, boolean) - Constructor for class info.mrupp.isoak1.Array2Float
Creates a copy of another Array2Float.
atomDescriptor(int, int) - Method in class info.mrupp.isoak1.MolecularGraph
Returns the value of the given descriptor for the given atom.
atomicNumber() - Method in enum info.mrupp.isoak1.Element
Atomic number ("Ordnungszahl"), the number of protons.

B

bondDescriptor(int, int) - Method in class info.mrupp.isoak1.MolecularGraph
Returns the value of the given descriptor for the given bond.
bondIndex(int, int) - Method in class info.mrupp.isoak1.MolecularGraph
Returns the index of the bond between two atoms.

C

cols() - Method in class info.mrupp.isoak1.Array2Float
The number of columns.
create(float[]) - Method in enum info.mrupp.isoak1.VertexEdgeKernel
Creates a new vertex/edge kernel with given parameters.

D

description() - Method in enum info.mrupp.isoak1.VertexEdgeKernel
Human readable description of vertex/edge kernel.

E

Element - Enum in info.mrupp.isoak1
Periodic table of the elements.
elems() - Method in class info.mrupp.isoak1.Array2Float
The total number of elements in the array.
eval(MolecularGraph, int, MolecularGraph, int) - Method in interface info.mrupp.isoak1.IVertexEdgeKernel
Evaluates the vertex/edge subkernel on two vertices/edges.
evalNorm(MolecularGraph, MolecularGraph, float, float, int[], Array2Float) - Method in class info.mrupp.isoak1.IsoaKernel1
Evalutes the iterative optimal assignment kernel with normalization.
evalRaw(MolecularGraph, MolecularGraph, float, float, int[], Array2Float) - Method in class info.mrupp.isoak1.IsoaKernel1
Evaluates the iterative optimal assignment kernel without normalization.

F

Factorial - Class in info.mrupp.isoak1
Precomputed factorial function.
Factorial() - Constructor for class info.mrupp.isoak1.Factorial
Provides precomputed results for the factorial function.
factorial(int) - Static method in class info.mrupp.isoak1.Factorial
Returns the factorial for arguments 0,1,...,12.
factorial(long) - Static method in class info.mrupp.isoak1.Factorial
Returns the factorial for arguments 0,1,...,20.
fromString(String) - Static method in enum info.mrupp.isoak1.Element
Returns the element constant for a one or two letter abbreviation.
fromString(String) - Static method in enum info.mrupp.isoak1.VertexEdgeKernel
Retrieve vertex/edge kernel by short name.
fullName() - Method in enum info.mrupp.isoak1.Element
The unabbreviated english name of the element.

G

get(int) - Method in class info.mrupp.isoak1.Array2Float
Reads an element using a single index.
get(int, int) - Method in class info.mrupp.isoak1.Array2Float
Reads an element using row and column indices.

H

HungarianAlgorithm - Class in info.mrupp.isoak1
The Hungarian algorithm (Kuhn-Munkres assignment algorithm).
HungarianAlgorithm() - Constructor for class info.mrupp.isoak1.HungarianAlgorithm
Initializes the optimizer.
hungarianAlgorithm(Array2Float, HungarianAlgorithm.OptimizationType, int[]) - Method in class info.mrupp.isoak1.HungarianAlgorithm
The Hungarian algorithm.
HungarianAlgorithm.OptimizationType - Enum in info.mrupp.isoak1
Optimization type (either minimization or maximization of the assignment value).

I

info.mrupp.isoak1 - package info.mrupp.isoak1
Iterative similarity optimal assignment kernel, Java implementation

Written by Matthias Rupp 2006-2007.
Copyright (c) 2006-2007, Matthias Rupp, Ewgenij Proschak, Gisbert Schneider.

All rights reserved. See description for license terms.

Please cite

Matthias Rupp, Ewgenij Proschak, Gisbert Schneider: A Kernel Approach to Molecular Similarity Based on Iterative Graph Similarity, Journal of Chemical Information and Molecular Modeling, 47(6): 2280-2286, 2007, DOI http://dx.doi.org/10.1021/ci700274r.

if you use this software.
Isoak1Example - Class in info.mrupp.isoak1
Sample program demonstrating the usage of the IsoaKernel1 class.
Isoak1Example() - Constructor for class info.mrupp.isoak1.Isoak1Example
Just run the #main method of this class.
IsoaKernel1 - Class in info.mrupp.isoak1
The iterative similarity optimal assignment kernel.
IsoaKernel1() - Constructor for class info.mrupp.isoak1.IsoaKernel1
Initializes internal data structures to an empty state.
IVertexEdgeKernel - Interface in info.mrupp.isoak1
Interface for vertex and edge subkernels.

M

main(String[]) - Static method in class info.mrupp.isoak1.Isoak1Example
Run this class with the file 'example.sdf' in the current directory.
MAX_DEGREE - Static variable in class info.mrupp.isoak1.MolecularGraph
Maximum degree of any vertex.
MolecularGraph - Class in info.mrupp.isoak1
Query-only data structure for molecular graphs.
MolecularGraph(LineNumberReader, MolecularGraph.FileFormat) - Constructor for class info.mrupp.isoak1.MolecularGraph
Creates a new molecular graph from a given source.
MolecularGraph.FileFormat - Enum in info.mrupp.isoak1
The supported chemical file formats (currently only SDF).

N

name() - Method in interface info.mrupp.isoak1.IVertexEdgeKernel
Returns the name of the vertex/edge kernel.
name() - Method in class info.mrupp.isoak1.MolecularGraph
Returns an identifier for the molecular graph.
neighbour(int, int) - Method in class info.mrupp.isoak1.MolecularGraph
Returns the n-th neighbour (index) of given atom.
numArgs() - Method in enum info.mrupp.isoak1.VertexEdgeKernel
Number of arguments needed for construction of vertex/edge kernel.
numAtoms() - Method in class info.mrupp.isoak1.MolecularGraph
Returns the total number of atoms in the molecular graph.
numBonds() - Method in class info.mrupp.isoak1.MolecularGraph
Returns the total number of bonds in the molecular graph.
numNeighbours(int) - Method in class info.mrupp.isoak1.MolecularGraph
Returns the degree of given atom.

P

Permutations - Class in info.mrupp.isoak1
Permutation related functions.
Permutations() - Constructor for class info.mrupp.isoak1.Permutations
All functionality is provided via static methods, so there is no need to construct objects of this type.
permutations(int) - Static method in class info.mrupp.isoak1.Permutations
All permutations of {0,1,...,n-1}.
prefixes(int, int) - Static method in class info.mrupp.isoak1.Permutations
All prefixes of given length of all permutations of given length.
prefixesPrecomputed(int, int) - Static method in class info.mrupp.isoak1.Permutations
Precomputed prefixes of given length of permutations of given length.

R

redim(int, int) - Method in class info.mrupp.isoak1.Array2Float
Changes the dimensions of the array.
rows() - Method in class info.mrupp.isoak1.Array2Float
The number of rows.

S

set(int, float) - Method in class info.mrupp.isoak1.Array2Float
Writes an element using a single index.
set(int, int, float) - Method in class info.mrupp.isoak1.Array2Float
Writes an element using row and column indices.
setEdgeKernel(IVertexEdgeKernel) - Method in class info.mrupp.isoak1.IsoaKernel1
Sets the edge kernel to be used.
setVertexKernel(IVertexEdgeKernel) - Method in class info.mrupp.isoak1.IsoaKernel1
Sets the vertex kernel to be used.

V

valueOf(String) - Static method in enum info.mrupp.isoak1.Element
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum info.mrupp.isoak1.HungarianAlgorithm.OptimizationType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum info.mrupp.isoak1.MolecularGraph.FileFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum info.mrupp.isoak1.VertexEdgeKernel
Returns the enum constant of this type with the specified name.
values() - Static method in enum info.mrupp.isoak1.Element
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum info.mrupp.isoak1.HungarianAlgorithm.OptimizationType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum info.mrupp.isoak1.MolecularGraph.FileFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum info.mrupp.isoak1.VertexEdgeKernel
Returns an array containing the constants of this enum type, in the order they are declared.
VertexEdgeKernel - Enum in info.mrupp.isoak1
Available vertex and edge subkernels.

A B C D E F G H I M N P R S V