Stoichiometry analysis

Linear algebra based methods for analyzing a reaction network. More...

## Functions

RRDoubleMatrixPtr getFullJacobian (RRHandle handle)
Retrieve the full Jacobian for the current model. More...

RRDoubleMatrixPtr getReducedJacobian (RRHandle handle)
Retrieve the reduced Jacobian for the current model. More...

RRDoubleMatrixPtr getEigenvalues (RRHandle handle)
Retrieve the eigenvalue matrix for the current model. More...

RRDoubleMatrixPtr getStoichiometryMatrix (RRHandle handle)
Retrieve the stoichiometry matrix for the current model. More...

Retrieve the Link matrix for the current model. More...

RRDoubleMatrixPtr getNrMatrix (RRHandle handle)
Retrieve the reduced stoichiometry matrix for the current model. More...

RRDoubleMatrixPtr getConservationMatrix (RRHandle handle)
Retrieve the conservation matrix for the current model. More...

RRDoubleMatrixPtr getL0Matrix (RRHandle handle)
Returns the L0 Matrix. More...

RRComplexMatrixPtr getEigenVectors (RRDoubleMatrixPtr matrix)
Calculates the eigen-vectors of a square real matrix. This function calculates the complex (right)eigenvectors of the given real matrix. The complex matrix returned contains the eigenvectors in the columns, in the same order as LibLA_getEigenValues. More...

RRComplexMatrixPtr getZEigenVectors (RRComplexMatrixPtr matrix)
Calculates the eigen-vectors of a square nonsymmetrix complex matrix. This function calculates the complex (right)eigenvectors of the given real matrix. The complex matrix returned contains the eigenvectors in the columns, in the same order as getZEigenValues. The right eigenvector v(j) of A satisfies: More...

RRVectorPtr getConservedSums (RRHandle handle)
Returns values for conservation laws using the current initial conditions. More...

## Detailed Description

Linear algebra based methods for analyzing a reaction network.

## Function Documentation

 RRDoubleMatrixPtr getConservationMatrix ( RRHandle handle )

Retrieve the conservation matrix for the current model.

The conservation laws as describe by row where the columns indicate the species Id.

Parameters
 [in] handle Handle to a RoadRunner instance
Returns
Returns null if it fails, otherwise returns the conservation matrix.
 RRVectorPtr getConservedSums ( RRHandle handle )

Returns values for conservation laws using the current initial conditions.

Remarks
free vector using freeVector function
Returns
The return value will be zero (0) when successful, and negative (-1) in case no stoichiometry matrix was loaded beforehand or none of the analysis methods has been called yet.
Parameters
 [in] handle Handle to a RoadRunner instance
Returns
Returns null if it fails, otherwise returns a RRVectorHandle.
 RRDoubleMatrixPtr getEigenvalues ( RRHandle handle )

Retrieve the eigenvalue matrix for the current model.

Parameters
 [in] handle Handle to a RoadRunner instance
Returns
Returns null if it fails, otherwise returns a matrix of eigenvalues. The first column will contain the real values and the second column the imaginary values
 RRComplexMatrixPtr getEigenVectors ( RRDoubleMatrixPtr matrix )

Calculates the eigen-vectors of a square real matrix. This function calculates the complex (right)eigenvectors of the given real matrix. The complex matrix returned contains the eigenvectors in the columns, in the same order as LibLA_getEigenValues.

The right eigenvector v(j) of A satisfies:

A * v(j) = lambda(j) * v(j)
Parameters
 [in] matrix Handle to a RRMatrix
Returns
Returns null if it fails, otherwise returns a RRComplexMatrix.
 RRDoubleMatrixPtr getFullJacobian ( RRHandle handle )

Retrieve the full Jacobian for the current model.

Parameters
 [in] handle Handle to a RoadRunner instance
Returns
Returns null if it fails, otherwise returns the full Jacobian matrix
 RRDoubleMatrixPtr getL0Matrix ( RRHandle handle )

Returns the L0 Matrix.

L0 is defined such that L0 Nr = N0. L0 forms part of the link matrix, L. N0 is the set of linear dependent rows from the lower portion of the reordered stoichiometry matrix.

Parameters
 [in] handle Handle to a RoadRunner instance
Returns
Returns null if it fails, otherwise returns the L0 matrix.
Remarks
To free the returned matrix call freeMatrix with the matrix as parameter.
 RRDoubleMatrixPtr getLinkMatrix ( RRHandle handle )

Retrieve the Link matrix for the current model.

Parameters
 [in] handle Handle to a RoadRunner instance
Returns
Returns null if it fails, otherwise returns the Link matrix.
 RRDoubleMatrixPtr getNrMatrix ( RRHandle handle )

Retrieve the reduced stoichiometry matrix for the current model.

Parameters
 [in] handle Handle to a RoadRunner instance
Returns
Returns null if it fails, otherwise returns reduced stoichiometry matrix
 RRDoubleMatrixPtr getReducedJacobian ( RRHandle handle )

Retrieve the reduced Jacobian for the current model.

setComputeAndAssignConservationLaws (true) must be enabled.

Parameters
 [in] handle Handle to a RoadRunner instance
Returns
Returns null if it fails, otherwise returns the reduced Jacobian matrix
 RRDoubleMatrixPtr getStoichiometryMatrix ( RRHandle handle )

Retrieve the stoichiometry matrix for the current model.

Parameters
 [in] handle Handle to a RoadRunner instance
Returns
Returns null if it fails, otherwise returns the stoichiometry matrix.
 RRComplexMatrixPtr getZEigenVectors ( RRComplexMatrixPtr matrix )

Calculates the eigen-vectors of a square nonsymmetrix complex matrix. This function calculates the complex (right)eigenvectors of the given real matrix. The complex matrix returned contains the eigenvectors in the columns, in the same order as getZEigenValues. The right eigenvector v(j) of A satisfies:

A * v(j) = lambda(j) * v(j)
Parameters
 [in] matrix Handle to a RRComplexMatrix
Returns
Returns null if it fails, otherwise returns a RRComplexMatrix.