def setStructMatrices(self):
self.N = StructMatrix(self.nmatrix, self.nmatrix_row, self.nmatrix_col)
self.N.setRow(self.species)
self.N.setCol(self.reactions)
self.Nr = StructMatrix(self.nrmatrix, self.nrmatrix_row, self.nrmatrix_col)
self.Nr.setRow(self.species)
self.Nr.setCol(self.reactions)
self.K = StructMatrix(self.kmatrix, self.kmatrix_row, self.kmatrix_col)
self.K.setRow(self.reactions)
self.K.setCol(self.reactions)
self.K0 = StructMatrix(self.kzeromatrix, self.kzeromatrix_row, self.kzeromatrix_col)
self.K0.setRow(self.reactions)
self.K0.setCol(self.reactions)
self.L = StructMatrix(self.lmatrix, self.lmatrix_row, self.lmatrix_col)
self.L.setRow(self.species)
self.L.setCol(self.species)
self.L0 = StructMatrix(self.lzeromatrix, self.lzeromatrix_row, self.lzeromatrix_col)
self.L0.setRow(self.species)
self.L0.setCol(self.species)
if self.info_moiety_conserve:
self.Gamma = StructMatrix(self.conservation_matrix, self.conservation_matrix_row, self.conservation_matrix_col)
self.Gamma.setRow(self.species)
self.Gamma.setCol(self.species)
def setStructMatrices(self):
self.N = StructMatrix(self.nmatrix, self.nmatrix_row, self.nmatrix_col)
self.N.setRow(self.species)
self.N.setCol(self.reactions)
self.Nr = StructMatrix(self.nrmatrix, self.nrmatrix_row,
self.nrmatrix_col)
self.Nr.setRow(self.species)
self.Nr.setCol(self.reactions)
self.K = StructMatrix(self.kmatrix, self.kmatrix_row, self.kmatrix_col)
self.K.setRow(self.reactions)
self.K.setCol(self.reactions)
self.K0 = StructMatrix(self.kzeromatrix, self.kzeromatrix_row,
self.kzeromatrix_col)
self.K0.setRow(self.reactions)
self.K0.setCol(self.reactions)
self.L = StructMatrix(self.lmatrix, self.lmatrix_row, self.lmatrix_col)
self.L.setRow(self.species)
self.L.setCol(self.species)
self.L0 = StructMatrix(self.lzeromatrix, self.lzeromatrix_row,
self.lzeromatrix_col)
self.L0.setRow(self.species)
self.L0.setCol(self.species)
if self.info_moiety_conserve:
self.Gamma = StructMatrix(self.conservation_matrix,
self.conservation_matrix_row,
self.conservation_matrix_col)
self.Gamma.setRow(self.species)
self.Gamma.setCol(self.species)
class PyscesEnhancedStoich(Stoich):
"""PySCeS stoichiometry class for use with core2"""
N = None
Nr = None
K = None
K0 = None
L = None
L0 = None
Gamma = None
def __init__(self, core):
Stoich.__init__(self, core.stoichiometric_matrix.array)
self.species = core.stoichiometric_matrix.row
self.reactions = core.stoichiometric_matrix.col
def getNullSpaces(self):
self.AnalyseK()
self.AnalyseL()
def testNullSpaces(self):
#TODO: build in nullspace validity checks from PyscesModel
pass
def setStructMatrices(self):
self.N = StructMatrix(self.nmatrix, self.nmatrix_row, self.nmatrix_col)
self.N.setRow(self.species)
self.N.setCol(self.reactions)
self.Nr = StructMatrix(self.nrmatrix, self.nrmatrix_row, self.nrmatrix_col)
self.Nr.setRow(self.species)
self.Nr.setCol(self.reactions)
self.K = StructMatrix(self.kmatrix, self.kmatrix_row, self.kmatrix_col)
self.K.setRow(self.reactions)
self.K.setCol(self.reactions)
self.K0 = StructMatrix(self.kzeromatrix, self.kzeromatrix_row, self.kzeromatrix_col)
self.K0.setRow(self.reactions)
self.K0.setCol(self.reactions)
self.L = StructMatrix(self.lmatrix, self.lmatrix_row, self.lmatrix_col)
self.L.setRow(self.species)
self.L.setCol(self.species)
self.L0 = StructMatrix(self.lzeromatrix, self.lzeromatrix_row, self.lzeromatrix_col)
self.L0.setRow(self.species)
self.L0.setCol(self.species)
if self.info_moiety_conserve:
self.Gamma = StructMatrix(self.conservation_matrix, self.conservation_matrix_row, self.conservation_matrix_col)
self.Gamma.setRow(self.species)
self.Gamma.setCol(self.species)
class PyscesEnhancedStoich(Stoich):
"""PySCeS stoichiometry class for use with core2"""
N = None
Nr = None
K = None
K0 = None
L = None
L0 = None
Gamma = None
def __init__(self, core):
Stoich.__init__(self, core.stoichiometric_matrix.array)
self.species = core.stoichiometric_matrix.row
self.reactions = core.stoichiometric_matrix.col
def getNullSpaces(self):
self.AnalyseK()
self.AnalyseL()
def testNullSpaces(self):
#TODO: build in nullspace validity checks from PyscesModel
pass
def setStructMatrices(self):
self.N = StructMatrix(self.nmatrix, self.nmatrix_row, self.nmatrix_col)
self.N.setRow(self.species)
self.N.setCol(self.reactions)
self.Nr = StructMatrix(self.nrmatrix, self.nrmatrix_row,
self.nrmatrix_col)
self.Nr.setRow(self.species)
self.Nr.setCol(self.reactions)
self.K = StructMatrix(self.kmatrix, self.kmatrix_row, self.kmatrix_col)
self.K.setRow(self.reactions)
self.K.setCol(self.reactions)
self.K0 = StructMatrix(self.kzeromatrix, self.kzeromatrix_row,
self.kzeromatrix_col)
self.K0.setRow(self.reactions)
self.K0.setCol(self.reactions)
self.L = StructMatrix(self.lmatrix, self.lmatrix_row, self.lmatrix_col)
self.L.setRow(self.species)
self.L.setCol(self.species)
self.L0 = StructMatrix(self.lzeromatrix, self.lzeromatrix_row,
self.lzeromatrix_col)
self.L0.setRow(self.species)
self.L0.setCol(self.species)
if self.info_moiety_conserve:
self.Gamma = StructMatrix(self.conservation_matrix,
self.conservation_matrix_row,
self.conservation_matrix_col)
self.Gamma.setRow(self.species)
self.Gamma.setCol(self.species)