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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)
def setStoichiometricMatrix(self):
vspec = self.hasVariableSpecies()
react = self.hasReactions()
nm = numpy.zeros((len(vspec), len(react)),'d')
for sp in vspec:
for r in self.get(sp).isReagentOf():
nm[vspec.index(sp)][react.index(r)] = self.get(r).stoichiometry[sp]
# this is if absolute stoichiometry value is used
## for r in self.get(sp).isSubstrateOf():
## nm[vspec.index(sp)][react.index(r)] = abs(self.get(r).stoichiometry[sp])
## for r in self.get(sp).isProductOf():
## nm[vspec.index(sp)][react.index(r)] = -abs(self.get(r).stoichiometry[sp])
self.stoichiometric_matrix = StructMatrix(nm, list(range(len(vspec))), list(range(len(react))))
self.stoichiometric_matrix.setRow(vspec)
self.stoichiometric_matrix.setCol(react)
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:
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)
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)
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)
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)