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...
RRDoubleMatrixPtr	getLinkMatrix (RRHandle handle)
	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.