Modifier and Type | Method and Description |
---|---|
EBIMatrix |
Holder.getCliqueMatrix() |
EBIMatrix |
Holder.getEnergyMatrix() |
EBIMatrix |
Holder.getFPSimilarityMatrix() |
EBIMatrix |
Holder.getFragmentMatrix() |
EBIMatrix |
Holder.getGraphSimilarityMatrix() |
EBIMatrix |
Holder.getStereoMatrix() |
Modifier and Type | Method and Description |
---|---|
EBIMatrix |
ChooseWinner.getEnergyMatrix() |
EBIMatrix |
ChooseWinner.getStereoMatrix() |
Modifier and Type | Method and Description |
---|---|
protected boolean |
Selector.isMajorSubgraphColumn(EBIMatrix similarityMatrix,
int IndexI,
int IndexJ) |
protected boolean |
Selector.isMajorSubgraphRow(EBIMatrix similarityMatrix,
int IndexI,
int IndexJ) |
protected boolean |
Selector.isMinorSubgraphColumn(EBIMatrix similarityMatrix,
int IndexI,
int IndexJ) |
protected boolean |
Selector.isMinorSubgraphRow(EBIMatrix similarityMatrix,
int IndexI,
int IndexJ) |
void |
ChooseWinner.setEnergyMatrix(EBIMatrix energyMatrix) |
void |
ChooseWinner.setStereoMatrix(EBIMatrix stereoMatrix) |
Modifier and Type | Class and Description |
---|---|
class |
BEMatrix
This class create the BEMatrix of a set of molecule according to the
DU-Theory.
|
class |
RMatrix
This class create the RMatrix of a reaction according to the DU-Theory.
|
Modifier and Type | Method and Description |
---|---|
EBIMatrix |
EBIMatrix.arrayLeftDivide(EBIMatrix B)
Element-by-element left division, data = matrix.\B
|
EBIMatrix |
EBIMatrix.arrayLeftDivideEquals(EBIMatrix B)
Element-by-element left division in place, matrix = matrix.\B
|
EBIMatrix |
EBIMatrix.arrayRightDivide(EBIMatrix B)
Element-by-element right division, data = matrix./B
|
EBIMatrix |
EBIMatrix.arrayRightDivideEquals(EBIMatrix B)
Element-by-element right division in place, matrix = matrix./B
|
EBIMatrix |
EBIMatrix.arrayTimes(EBIMatrix B)
Element-by-element multiplication, data = matrix.*B
|
EBIMatrix |
EBIMatrix.arrayTimesEquals(EBIMatrix B)
Element-by-element multiplication in place, matrix = matrix.*B
|
static EBIMatrix |
EBIMatrix.constructWithCopy(double[][] A) |
EBIMatrix |
EBIMatrix.diagonalize(int nrot)
Diagonalize this matrix with the Jacobi algorithm.
|
EBIMatrix |
EBIMatrix.duplicate()
Make a deep duplicate of a matrix
|
EBIMatrix |
EBIMatrix.getMatrix(int[] r,
int[] c)
Get a submatrix.
|
EBIMatrix |
EBIMatrix.getMatrix(int[] r,
int colStart,
int colEnd)
Get a submatrix.
|
EBIMatrix |
EBIMatrix.getMatrix(int rowStart,
int rowEnd,
int[] c)
Get a submatrix.
|
EBIMatrix |
EBIMatrix.getMatrix(int rowStart,
int rowEnd,
int colStart,
int colEnd)
Get a sub-matrix.
|
static EBIMatrix |
EBIMatrix.identity(int m,
int n)
Generate identity matrix
|
EBIMatrix |
EBIMatrix.inverse()
EBIMatrix inverse or pseudoinverse
|
EBIMatrix |
EBIMatrix.minus(EBIMatrix B)
data = matrix - B
|
EBIMatrix |
EBIMatrix.minusEquals(EBIMatrix B)
matrix = matrix - B
|
EBIMatrix |
EBIMatrix.mul(double a)
Multiplies a scalar with this EBIMatrix.
|
EBIMatrix |
EBIMatrix.mul(EBIMatrix b)
Multiplies this EBIMatrix with another one.
|
EBIMatrix |
EBIMatrix.normalize(EBIMatrix S)
Normalizes the vectors of this matrix.
|
EBIMatrix |
EBIMatrix.orthonormalize(EBIMatrix S)
Orthonormalize the vectors of this matrix by Gram-Schmidt.
|
EBIMatrix |
EBIMatrix.plus(EBIMatrix B)
data = matrix + B
|
EBIMatrix |
EBIMatrix.plusEquals(EBIMatrix B)
matrix = matrix + B
|
static EBIMatrix |
EBIMatrix.random(int m,
int n)
Generate matrix with random elements
|
static EBIMatrix |
EBIMatrix.read(java.io.BufferedReader input)
Read a matrix from a stream.
|
EBIMatrix |
EBIMatrix.similar(EBIMatrix U)
Similar transformation Ut * M * U
|
EBIMatrix |
EBIMatrix.solve(EBIMatrix B)
Solve matrix*result = B
|
EBIMatrix |
EBIMatrix.solveTranspose(EBIMatrix B)
Solve result*matrix = B, which is also matrix'*result' = B'
|
EBIMatrix |
EBIMatrix.times(double s)
Multiply a matrix by a scalar, data = s*matrix
|
EBIMatrix |
EBIMatrix.times(EBIMatrix B)
Linear algebraic matrix multiplication, matrix * B
|
EBIMatrix |
EBIMatrix.timesEquals(double s)
Multiply a matrix by a scalar in place, matrix = s*matrix
|
EBIMatrix |
EBIMatrix.transpose()
EBIMatrix transpose.
|
EBIMatrix |
EBIMatrix.uminus()
Unary minus
|
Modifier and Type | Method and Description |
---|---|
EBIMatrix |
EBIMatrix.arrayLeftDivide(EBIMatrix B)
Element-by-element left division, data = matrix.\B
|
EBIMatrix |
EBIMatrix.arrayLeftDivideEquals(EBIMatrix B)
Element-by-element left division in place, matrix = matrix.\B
|
EBIMatrix |
EBIMatrix.arrayRightDivide(EBIMatrix B)
Element-by-element right division, data = matrix./B
|
EBIMatrix |
EBIMatrix.arrayRightDivideEquals(EBIMatrix B)
Element-by-element right division in place, matrix = matrix./B
|
EBIMatrix |
EBIMatrix.arrayTimes(EBIMatrix B)
Element-by-element multiplication, data = matrix.*B
|
EBIMatrix |
EBIMatrix.arrayTimesEquals(EBIMatrix B)
Element-by-element multiplication in place, matrix = matrix.*B
|
static java.util.List<java.lang.Double> |
EBIMatrix.elimination(EBIMatrix matrix,
java.util.List<java.lang.Double> vector)
Solves a linear equation system with Gauss elimination.
|
EBIMatrix |
EBIMatrix.minus(EBIMatrix B)
data = matrix - B
|
EBIMatrix |
EBIMatrix.minusEquals(EBIMatrix B)
matrix = matrix - B
|
EBIMatrix |
EBIMatrix.mul(EBIMatrix b)
Multiplies this EBIMatrix with another one.
|
EBIMatrix |
EBIMatrix.normalize(EBIMatrix S)
Normalizes the vectors of this matrix.
|
EBIMatrix |
EBIMatrix.orthonormalize(EBIMatrix S)
Orthonormalize the vectors of this matrix by Gram-Schmidt.
|
EBIMatrix |
EBIMatrix.plus(EBIMatrix B)
data = matrix + B
|
EBIMatrix |
EBIMatrix.plusEquals(EBIMatrix B)
matrix = matrix + B
|
void |
EBIMatrix.setMatrix(int[] r,
int[] c,
EBIMatrix X)
Set a submatrix.
|
void |
EBIMatrix.setMatrix(int[] r,
int colStart,
int colEnd,
EBIMatrix X)
Set a submatrix.
|
void |
EBIMatrix.setMatrix(int rowStart,
int rowEnd,
int[] c,
EBIMatrix X)
Set a submatrix.
|
void |
EBIMatrix.setMatrix(int rowStart,
int rowEnd,
int colStart,
int colEnd,
EBIMatrix X)
Set a submatrix.
|
EBIMatrix |
EBIMatrix.similar(EBIMatrix U)
Similar transformation Ut * M * U
|
EBIMatrix |
EBIMatrix.solve(EBIMatrix B)
Solve matrix*result = B
|
EBIMatrix |
EBIMatrix.solveTranspose(EBIMatrix B)
Solve result*matrix = B, which is also matrix'*result' = B'
|
EBIMatrix |
EBIMatrix.times(EBIMatrix B)
Linear algebraic matrix multiplication, matrix * B
|
Modifier and Type | Method and Description |
---|---|
EBIMatrix |
EigenvalueDecomposition.getD()
Return the block diagonal eigenvalue matrix
|
EBIMatrix |
QRDecomposition.getH()
Return the Householder vectors
|
EBIMatrix |
CholeskyDecomposition.getL()
Return triangular factor.
|
EBIMatrix |
LUDecomposition.getL()
Return lower triangular factor
|
EBIMatrix |
QRDecomposition.getQ()
Generate and return the (economy-sized) orthogonal factor
|
EBIMatrix |
QRDecomposition.getR()
Return the upper triangular factor
|
EBIMatrix |
SingularValueDecomposition.getS()
Return the diagonal matrix of singular values
|
EBIMatrix |
LUDecomposition.getU()
Return upper triangular factor
|
EBIMatrix |
SingularValueDecomposition.getU()
Return the left singular vectors
|
EBIMatrix |
EigenvalueDecomposition.getV()
Return the eigenvector matrix
|
EBIMatrix |
SingularValueDecomposition.getV()
Return the right singular vectors
|
EBIMatrix |
CholeskyDecomposition.solve(EBIMatrix B)
Solve A*X = B
|
EBIMatrix |
LUDecomposition.solve(EBIMatrix B)
Solve A*X = B
|
EBIMatrix |
QRDecomposition.solve(EBIMatrix B)
Least squares solution of A*X = B
|
Modifier and Type | Method and Description |
---|---|
EBIMatrix |
CholeskyDecomposition.solve(EBIMatrix B)
Solve A*X = B
|
EBIMatrix |
LUDecomposition.solve(EBIMatrix B)
Solve A*X = B
|
EBIMatrix |
QRDecomposition.solve(EBIMatrix B)
Least squares solution of A*X = B
|
Constructor and Description |
---|
CholeskyDecomposition(EBIMatrix Arg)
Cholesky algorithm for symmetric and positive definite matrix.
|
EigenvalueDecomposition(EBIMatrix Arg)
Check for symmetry, then construct the eigenvalue decomposition
|
LUDecomposition(EBIMatrix A)
LU Decomposition
|
QRDecomposition(EBIMatrix A)
QR Decomposition, computed by Householder reflections.
|
SingularValueDecomposition(EBIMatrix Arg)
Construct the singular value decomposition
|