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How to use the pysces.core2.PyscesCore2.StructMatrix function in pysces

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github PySCeS / pysces / pysces / core2 / PyscesCore2Modules.py View on Github external
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)
github PySCeS / pysces / pysces / core2 / PyscesCore2.py View on Github external
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)
github PySCeS / pysces / pysces / core2 / PyscesCore2Modules.py View on Github external
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:
github PySCeS / pysces / pysces / core2 / PyscesCore2Modules.py View on Github external
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)
github PySCeS / pysces / pysces / core2 / PyscesCore2Modules.py View on Github external
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)
github PySCeS / pysces / pysces / core2 / PyscesCore2Modules.py View on Github external
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)
github PySCeS / pysces / pysces / core2 / PyscesCore2Modules.py View on Github external
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)
github PySCeS / pysces / pysces / core2 / PyscesCore2Modules.py View on Github external
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)

pysces

The Python Simulator for Cellular Systems - simulation and analysis tools for modelling biological systems

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