comparison mayachemtools/docs/modules/txt/GraphMatrix.txt @ 0:73ae111cf86f draft

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NAME
    GraphMatrix

SYNOPSIS
    use Graph::GraphMatrix;

    use Graph::GraphMatrix qw(:all);

DESCRIPTION
    GraphMatrix class provides the following methods:

    new, GenerateAdjacencyMatrix, GenerateAdmittanceMatrix,
    GenerateDegreeMatrix, GenerateDistanceMatrix, GenerateIncidenceMatrix,
    GenerateKirchhoffMatrix, GenerateLaplacianMatrix,
    GenerateNormalizedLaplacianMatrix, GenerateSiedelAdjacencyMatrix,
    GetColumnIDs, GetMatrix, GetMatrixType, GetRowIDs, StringifyGraphMatrix

  METHODS
    new
            $NewGraphMatrix = new Graph::GraphMatrix($Graph);

        Using specified *Graph*, new method creates a new GraphMatrix and
        returns newly created GraphMatrix.

    GenerateAdjacencyMatrix
            $AdjacencyGraphMatrix = $GraphMatrix->GenerateAdjacencyMatrix();

        Generates a new *AdjacencyGraphMatrix* for specified Graph and
        returns *AdjacencyGraphMatrix*.

        For a simple graph G with n vertices, the adjacency matrix for G is
        a n x n square matrix and its elements Mij are:

            . 0    if i == j
            . 1    if i != j and vertex Vi is adjacent to vertex Vj
            . 0    if i != j and vertex Vi is not adjacent to vertex Vj

    GenerateAdmittanceMatrix
            $AdmittanceGraphMatrix = $GraphMatrix->GenerateAdmittanceMatrix();

        Generates a new *AdmittanceGraphMatrix* for specified Graph and
        returns *AdmittanceGraphMatrix*.

        AdmittanceMatrix is another name for LaplacianMatrix.

    GenerateDegreeMatrix
            $DegreeGraphMatrix = $GraphMatrix->GenerateDegreeMatrix();

        Generates a new *DegreeGraphMatrix* for specified Graph and returns
        *DegreeGraphMatrix*.

        For a simple graph G with n vertices, the degree matrix for G is a n
        x n square matrix and its elements Mij are:

            . deg(Vi)   if i == j and deg(Vi) is the degree of vertex Vi
            . 0         otherwise

    GenerateDistanceMatrix
            $DistanceGraphMatrix = $GraphMatrix->GenerateDistanceMatrix();

        Generates a new *DistanceGraphMatrix* for specified Graph using
        Floyd-Marshall algorithm [Ref 67] and returns *DistanceGraphMatrix*.

        For a simple graph G with n vertices, the distance matrix for G is a
        n x n square matrix and its elements Mij are:

            . 0    if i == j
            . d    if i != j and d is the shortest distance between vertex Vi and vertex Vj

        In the final matrix, value of constant BigNumber defined in
        Constants.pm module corresponds to vertices with no edges.

    GenerateIncidenceMatrix
            $IncidenceGraphMatrix = $GraphMatrix->GenerateIncidenceMatrix();

        Generates a new *IncidenceGraphMatrix* for specified Graph and
        returns *IncidenceGraphMatrix*.

        For a simple graph G with n vertices and e edges, the incidence
        matrix for G is a n x e matrix its elements Mij are:

            . 1    if vertex Vi and the edge Ej are incident; in other words, Vi and Ej are related
            . 0    otherwise

    GenerateKirchhoffMatrix
            $KirchhoffGraphMatrix = $GraphMatrix->GenerateKirchhoffMatrix();

        Generates a new *KirchhoffGraphMatrix* for specified Graph and
        returns *KirchhoffGraphMatrix*.

        KirchhoffMatrix is another name for LaplacianMatrix.

    GenerateLaplacianMatrix
            $LaplacianGraphMatrix = $GraphMatrix->GenerateLaplacianMatrix();

        Generates a new *LaplacianGraphMatrix* for specified Graph and
        returns *LaplacianGraphMatrix*.

        For a simple graph G with n vertices, the Laplacian matrix for G is
        a n x n square matrix and its elements Mij are:

            . deg(Vi)   if i == j and deg(Vi) is the degree of vertex Vi
            . -1        if i != j and vertex Vi is adjacent to vertex Vj
            . 0         otherwise

        The Laplacian matrix is the difference between the degree matrix and
        adjacency matrix.

    GenerateNormalizedLaplacianMatrix
            $NormalizedLaplacianGraphMatrix = $GraphMatrix->GenerateNormalizedLaplacianMatrix();

        Generates a new *NormalizedLaplacianGraphMatrix* for specified Graph
        and returns *NormalizedLaplacianGraphMatrix*.

        For a simple graph G with n vertices, the normalized Laplacian
        matrix L for G is a n x n square matrix and its elements Lij are:

            .  1                           if i == j and deg(Vi) != 0
            .  -1/SQRT(deg(Vi) * deg(Vj))  if i != j and vertex Vi is adjacent to vertex Vj
            .  0                           otherwise

    GenerateSiedelAdjacencyMatrix
            $SiedelAdjacencyGraphMatrix = $GraphMatrix->GenerateSiedelAdjacencyMatrix();

        Generates a new *SiedelAdjacencyGraphMatrix* for specified Graph and
        returns *SiedelAdjacencyGraphMatrix*.

        For a simple graph G with n vertices, the Siedal adjacency matrix
        for G is a n x n square matrix and its elements Mij are:

            . 0    if i == j
            . -1   if i != j and vertex Vi is adjacent to vertex Vj
            . 1    if i != j and vertex Vi is not adjacent to vertex Vj

    GetColumnIDs
            @ColumnIDs = $GraphMatrix->GetColumnIDs();

        Returns an array containing any specified column IDs for
        *GraphMatrix*.

    GetMatrix
            $Matrix = $GraphMatrix->GetMatrix();

        Returns *Matrix* object corresponding to *GraphMatrix* object.

    GetMatrixType
            $MatrixType = $GraphMatrix->GetMatrixType();

        Returns MatrixType of *GraphMatrix*.

    GetRowIDs
            @RowIDs = $GraphMatrix->GetRowIDs();

        Returns an array containing any specified rowIDs IDs for
        *GraphMatrix*.

    StringifyGraphMatrix
            $String = $GraphMatrix->StringifyGraphMatrix();

        Returns a string containing information about *GraphMatrix* object.

AUTHOR
    Manish Sud <[e-mail]>

SEE ALSO
    Constants.pm, Graph.pm, Matrix.pm

COPYRIGHT
    Copyright (C) 2015 Manish Sud. All rights reserved.

    This file is part of MayaChemTools.

    MayaChemTools is free software; you can redistribute it and/or modify it
    under the terms of the GNU Lesser General Public License as published by
    the Free Software Foundation; either version 3 of the License, or (at
    your option) any later version.