Uses of Class
com.actelion.research.calc.Matrix
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Uses of Matrix in com.actelion.research.calc
Methods in com.actelion.research.calc that return Matrix Modifier and Type Method Description Matrix
Matrix. add(double v)
Matrix
Matrix. add2CompleteCol(Matrix maRow)
The value in the col from the input matrix is added to all values in the corresponding col in the matrix.Matrix
Matrix. correlation()
Generate a correlation matrix, each column contains values of a pulling.Matrix
Matrix. covariance()
Generate a covariance matrix, each column contains values of a pulling.Matrix
Matrix. devide(double dDivisor)
Matrix
Matrix. devide(Matrix maDivisor)
Matrix
Matrix. devideCols(Matrix maDivisor)
Matrix
Matrix. devideDivisorBigger(Matrix maDivisor)
Matrix
Matrix. diagonalize()
Matrix
Matrix. getAbs()
Matrix
Matrix. getCenteredMatrix()
Matrix
Matrix. getCenteredMatrix(Matrix maMean)
Matrix
Matrix. getCol(int col)
Matrix
Matrix. getColumns(java.util.List<java.lang.Integer> liIndex)
Matrix
Matrix. getColumns(java.util.Vector<java.lang.Integer> vecIndices)
Deprecated.use getColumns(ListvecIndices) instead Matrix
Matrix. getDeleteColsZeroVar(java.util.List<java.lang.Integer> vecIndices)
Deletes columns with zero variance.Matrix
Matrix. getDiagonal()
Matrix diagonal extraction.Matrix
Matrix. getFlipped()
Opposite direction to transpose.Matrix
LUDecomposition. getL()
Return lower triangular factorMatrix
Matrix. getLinedCol()
Matrix
Matrix. getMatrix(int[] r, int[] c)
Get a submatrix.Matrix
Matrix. getMatrix(int[] r, int j0, int j1)
Get a submatrix.Matrix
Matrix. getMatrix(int i0, int i1, int[] c)
Get a submatrix.Matrix
Matrix. getMatrix(int i0, int i1, int j0, int j1)
Matrix
Matrix. getMaxMin()
max and min vals for all colsMatrix
Matrix. getMeanCols()
Matrix
Matrix. getMeanCols(int[] rowIndex)
Matrix
Matrix. getMeanRows()
Matrix
Matrix. getMedianCols()
Matrix
Matrix. getMergeRows(Matrix ma)
Matrix
Matrix. getMinRows()
Matrix
Matrix. getMinRowsPosCol()
Matrix
Matrix. getNormalizedMatrix()
Matrix
Matrix. getNormalizedMatrix(Matrix maStandardDeviation)
static Matrix
Matrix. getParsed(java.util.Vector<java.lang.String> vecStringMatrix)
Parses an vector with Strings and converts it to a Matrix.static Matrix
Matrix. getRND(int rows, int cols)
Matrix
Matrix. getSorted()
Sorts the row of the matrix according the compareTo(...) function in DoubleVecMatrix
Matrix. getSQRT()
Matrix
Matrix. getStandardDeviationCols()
Matrix
Matrix. getStandardized()
Get the standard scores, also known as z-scores.Matrix
Matrix. getSubMatrix(int indexRowStart, int indexRowEnd, int indexColStart, int indexColEnd)
Matrix
Matrix. getSubMatrix(java.util.List<java.lang.Integer> liIndexRow)
Matrix
Matrix. getSumCols()
Matrix
Matrix. getSumRows()
Matrix
Matrix. getTranspose()
Matrix
LUDecomposition. getU()
Return upper triangular factorMatrix
Matrix. getVarianceCols()
Matrix
Matrix. log()
Log function from the class Math .Matrix
Matrix. multCols(Matrix maMuiltiplicant)
Matrix
Matrix. multiply(boolean transA, boolean transB, Matrix ma)
Multiplication of two matrices.Matrix
Matrix. multiply(double dScalar)
Matrix
Matrix. multiply(Matrix ma)
Matrix
Matrix. multiplyValByVal(Matrix ma)
Value by value multiplication Matrices must have the same dimensions.Matrix
Matrix. plus(Matrix ma)
Matrix
Matrix. pow(double exp)
static Matrix
Matrix. readSerialized(java.io.File fiIn)
Matrix
Matrix. removeCol(int col2Remove)
Matrix
Matrix. row2Matrix(int row, int len)
Matrix
LUDecomposition. solve(Matrix B)
Solve A*X = BMatrix
Matrix. subtract(double val)
Matrix
Matrix. subtract(Matrix ma)
Matrix
Matrix. subtractFromCols(Matrix maDivisor)
Matrix
Matrix. toRow()
Methods in com.actelion.research.calc with parameters of type Matrix Modifier and Type Method Description Matrix
Matrix. add2CompleteCol(Matrix maRow)
The value in the col from the input matrix is added to all values in the corresponding col in the matrix.void
Matrix. add2Row(int row, Matrix ma2, int row2)
void
Matrix. assignCol(int iCol, Matrix ma)
void
Matrix. assignCol(int iCol, Matrix ma, int iColMa)
void
Matrix. copy(Matrix maSource)
Copies a matrix ma into this, the pointer to ma1 is not changed.void
Matrix. copyColumn(Matrix maSource, int colSource, int colDestination)
Matrix
Matrix. devide(Matrix maDivisor)
Matrix
Matrix. devideCols(Matrix maDivisor)
Matrix
Matrix. devideDivisorBigger(Matrix maDivisor)
boolean
Matrix. equal(Matrix ma)
boolean
Matrix. equal(Matrix ma, double dLimit)
boolean
Matrix. equalDimension(Matrix ma)
Checks two matrices for equal dimensions.Matrix
Matrix. getCenteredMatrix(Matrix maMean)
static double
ArrayUtilsCalc. getCorrPearson(Matrix A, Matrix B)
static void
Matrix. getEigenvector(Matrix A, int n, Matrix D, Matrix E)
Householder reduction according num rec 11.2.double
Matrix. getEuclideanDistanceFastRows(int iRow, Matrix A, int iRowA)
Skipping the sqrt.Matrix
Matrix. getMergeRows(Matrix ma)
Matrix
Matrix. getNormalizedMatrix(Matrix maStandardDeviation)
Matrix
Matrix. multCols(Matrix maMuiltiplicant)
Matrix
Matrix. multiply(boolean transA, boolean transB, Matrix ma)
Multiplication of two matrices.double
Matrix. multiply(int row1, Matrix ma2, int row2)
Matrix
Matrix. multiply(Matrix ma)
Matrix
Matrix. multiplyValByVal(Matrix ma)
Value by value multiplication Matrices must have the same dimensions.Matrix
Matrix. plus(Matrix ma)
void
Matrix. set(Matrix ma)
Matrix
LUDecomposition. solve(Matrix B)
Solve A*X = BMatrix
Matrix. subtract(Matrix ma)
Matrix
Matrix. subtractFromCols(Matrix maDivisor)
Constructors in com.actelion.research.calc with parameters of type Matrix Constructor Description LUDecomposition(Matrix A)
LU Decomposition Structure to access L, U and piv.Matrix(Matrix ma)
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Uses of Matrix in com.actelion.research.calc.graph
Methods in com.actelion.research.calc.graph that return Matrix Modifier and Type Method Description Matrix
MinimumSpanningTree. getMST()
Constructors in com.actelion.research.calc.graph with parameters of type Matrix Constructor Description MinimumSpanningTree(Matrix maAdjacency)
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Uses of Matrix in com.actelion.research.calc.histogram
Methods in com.actelion.research.calc.histogram that return Matrix Modifier and Type Method Description Matrix
Histogram. getHistogram()
static Matrix
MatrixBasedHistogram. getHistogram(double[] arrValues, Matrix maHistogramBins)
static Matrix
MatrixBasedHistogram. getHistogram(float[][] ma, int col, Matrix maHistogramBins)
static Matrix
MatrixBasedHistogram. getHistogram(float[] ma, Matrix maHistogramBins)
static Matrix
MatrixBasedHistogram. getHistogram(Matrix maHistogramBins)
static Matrix
MatrixBasedHistogram. getHistogram(Matrix ma, int numBins)
static Matrix
MatrixBasedHistogram. getHistogram(Matrix ma, Matrix maHistogramBins)
static Matrix
MatrixBasedHistogram. getHistogramBins(double dMin, double dMax, int iNumBins)
Methods in com.actelion.research.calc.histogram with parameters of type Matrix Modifier and Type Method Description static double[]
MatrixBasedHistogram. getBordersMostFreqOccBin(Matrix maHistogram, int radius)
Gets the upper and lower limit of the most occupied bin.static Histogram
MatrixBasedHistogram. getFromQuadraticMatrix(Matrix ma, double min, double max, int bins)
static Matrix
MatrixBasedHistogram. getHistogram(double[] arrValues, Matrix maHistogramBins)
static Matrix
MatrixBasedHistogram. getHistogram(float[][] ma, int col, Matrix maHistogramBins)
static Matrix
MatrixBasedHistogram. getHistogram(float[] ma, Matrix maHistogramBins)
static Matrix
MatrixBasedHistogram. getHistogram(Matrix maHistogramBins)
static Matrix
MatrixBasedHistogram. getHistogram(Matrix ma, int numBins)
static Matrix
MatrixBasedHistogram. getHistogram(Matrix ma, Matrix maHistogramBins)
static double
MatrixBasedHistogram. getMaxOccBin(Matrix maHist)
static double
MatrixBasedHistogram. getMinOccBin(Matrix maHist)
static java.lang.String
MatrixBasedHistogram. histogram2String(Matrix hist, int digits, int totalWidth)
static void
MatrixBasedHistogram. writeHistogram(java.lang.String sFile, Matrix hist, boolean bApppend, int digits, int totalWidth)
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Uses of Matrix in com.actelion.research.chem.alignment3d
Methods in com.actelion.research.chem.alignment3d with parameters of type Matrix Modifier and Type Method Description void
KabschAlignment. align(Coordinates trans1, Matrix rot, Coordinates trans2)
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Uses of Matrix in com.actelion.research.chem.docking
Methods in com.actelion.research.chem.docking that return Matrix Modifier and Type Method Description static Matrix
DockingUtils. calculateMassCovarianceMatrix(Conformer conf)
static Matrix
DockingUtils. createInitialOrientation(Conformer conf)
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Uses of Matrix in com.actelion.research.chem.phesa
Methods in com.actelion.research.chem.phesa that return Matrix Modifier and Type Method Description static Matrix
PheSAAlignment. createCanonicalOrientation(Conformer conf, MolecularVolume molGauss)
Matrix
Quaternion. getRotMatrix()
static Matrix
PheSAAlignment. preProcess(Conformer conf, MolecularVolume molVol)
Move COM of the molecular volume to the origin of the lab-frame and orient molecules so that their principal moments of inertia coincide with the 3 axis of the coordinate systemMethods in com.actelion.research.chem.phesa with parameters of type Matrix Modifier and Type Method Description static void
PheSAAlignment. rotateMol(Conformer conf, Matrix rotMat)
static void
PheSAAlignment. rotateMol(StereoMolecule mol, Matrix rotMat)
void
VolumeGaussian. rotateShift(Matrix rotMat)
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Uses of Matrix in com.actelion.research.util.datamodel.table
Methods in com.actelion.research.util.datamodel.table with parameters of type Matrix Modifier and Type Method Description void
TableModelString. set(Matrix m, int digits)
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