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How to use the pysces.PyscesStoich.StructMatrix function in pysces

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github PySCeS / pysces / pysces / PyscesMiniModel.py View on Github external
self.Nmatrix.setRow(self.species)
        self.Nmatrix.setCol(self.reactions)

        self.Nrmatrix = PyscesStoich.StructMatrix(self.__structural__.nrmatrix, self.__structural__.nrmatrix_row, self.__structural__.nrmatrix_col)
        self.Nrmatrix.setRow(self.species)
        self.Nrmatrix.setCol(self.reactions)

        self.Kmatrix = PyscesStoich.StructMatrix(self.__structural__.kmatrix, self.__structural__.kmatrix_row, self.__structural__.kmatrix_col)
        self.Kmatrix.setRow(self.reactions)
        self.Kmatrix.setCol(self.reactions)

        self.K0matrix = PyscesStoich.StructMatrix(self.__structural__.kzeromatrix, self.__structural__.kzeromatrix_row, self.__structural__.kzeromatrix_col)
        self.K0matrix.setRow(self.reactions)
        self.K0matrix.setCol(self.reactions)

        self.Lmatrix = PyscesStoich.StructMatrix(self.__structural__.lmatrix, self.__structural__.lmatrix_row, self.__structural__.lmatrix_col)
        self.Lmatrix.setRow(self.species)
        self.Lmatrix.setCol(self.species)

        self.L0matrix = PyscesStoich.StructMatrix(self.__structural__.lzeromatrix, self.__structural__.lzeromatrix_row, self.__structural__.lzeromatrix_col)
        self.L0matrix.setRow(self.species)
        self.L0matrix.setCol(self.species)

        if self.__structural__.info_moiety_conserve:
            self.Consmatrix = PyscesStoich.StructMatrix(self.__structural__.conservation_matrix, self.__structural__.conservation_matrix_row, self.__structural__.conservation_matrix_col)
            self.Consmatrix.setRow(self.species)
            self.Consmatrix.setCol(self.species)
        else:
            self.Consmatrix = None
        self.__StoichOK = 1
        print(' ')
github PySCeS / pysces / pysces / PyscesMiniModel.py View on Github external
self.Nrmatrix.setRow(self.species)
        self.Nrmatrix.setCol(self.reactions)

        self.Kmatrix = PyscesStoich.StructMatrix(self.__structural__.kmatrix, self.__structural__.kmatrix_row, self.__structural__.kmatrix_col)
        self.Kmatrix.setRow(self.reactions)
        self.Kmatrix.setCol(self.reactions)

        self.K0matrix = PyscesStoich.StructMatrix(self.__structural__.kzeromatrix, self.__structural__.kzeromatrix_row, self.__structural__.kzeromatrix_col)
        self.K0matrix.setRow(self.reactions)
        self.K0matrix.setCol(self.reactions)

        self.Lmatrix = PyscesStoich.StructMatrix(self.__structural__.lmatrix, self.__structural__.lmatrix_row, self.__structural__.lmatrix_col)
        self.Lmatrix.setRow(self.species)
        self.Lmatrix.setCol(self.species)

        self.L0matrix = PyscesStoich.StructMatrix(self.__structural__.lzeromatrix, self.__structural__.lzeromatrix_row, self.__structural__.lzeromatrix_col)
        self.L0matrix.setRow(self.species)
        self.L0matrix.setCol(self.species)

        if self.__structural__.info_moiety_conserve:
            self.Consmatrix = PyscesStoich.StructMatrix(self.__structural__.conservation_matrix, self.__structural__.conservation_matrix_row, self.__structural__.conservation_matrix_col)
            self.Consmatrix.setRow(self.species)
            self.Consmatrix.setCol(self.species)
        else:
            self.Consmatrix = None
        self.__StoichOK = 1
        print(' ')
github PySCeS / pysces / pysces / PyscesMiniModel.py View on Github external
self.__lmatrix__ = copy.copy(self.lmatrix)
            self.__lzeromatrix__ = copy.copy(self.lzeromatrix)
            self.__nrmatrix__ = copy.copy(self.nrmatrix)
        # switch that is set if the stoichiometric analysis is up to date

        self.__structural__.species = self.species
        self.__structural__.reactions = self.reactions
        self.Nmatrix = PyscesStoich.StructMatrix(self.__structural__.nmatrix, self.__structural__.nmatrix_row, self.__structural__.nmatrix_col)
        self.Nmatrix.setRow(self.species)
        self.Nmatrix.setCol(self.reactions)

        self.Nrmatrix = PyscesStoich.StructMatrix(self.__structural__.nrmatrix, self.__structural__.nrmatrix_row, self.__structural__.nrmatrix_col)
        self.Nrmatrix.setRow(self.species)
        self.Nrmatrix.setCol(self.reactions)

        self.Kmatrix = PyscesStoich.StructMatrix(self.__structural__.kmatrix, self.__structural__.kmatrix_row, self.__structural__.kmatrix_col)
        self.Kmatrix.setRow(self.reactions)
        self.Kmatrix.setCol(self.reactions)

        self.K0matrix = PyscesStoich.StructMatrix(self.__structural__.kzeromatrix, self.__structural__.kzeromatrix_row, self.__structural__.kzeromatrix_col)
        self.K0matrix.setRow(self.reactions)
        self.K0matrix.setCol(self.reactions)

        self.Lmatrix = PyscesStoich.StructMatrix(self.__structural__.lmatrix, self.__structural__.lmatrix_row, self.__structural__.lmatrix_col)
        self.Lmatrix.setRow(self.species)
        self.Lmatrix.setCol(self.species)

        self.L0matrix = PyscesStoich.StructMatrix(self.__structural__.lzeromatrix, self.__structural__.lzeromatrix_row, self.__structural__.lzeromatrix_col)
        self.L0matrix.setRow(self.species)
        self.L0matrix.setCol(self.species)

        if self.__structural__.info_moiety_conserve:
github PySCeS / pysces / pysces / PyscesMiniModel.py View on Github external
self.conservation_matrix_row = self.__structural__.conservation_matrix_row
            self.conservation_matrix_col = self.__structural__.conservation_matrix_col
            self.nrmatrix = self.__structural__.nrmatrix
            self.nrmatrix_row = self.__structural__.nrmatrix_row
            self.nrmatrix_col = self.__structural__.nrmatrix_col

            self.__kmatrix__ = copy.copy(self.kmatrix)
            self.__kzeromatrix__ = copy.copy(self.kzeromatrix)
            self.__lmatrix__ = copy.copy(self.lmatrix)
            self.__lzeromatrix__ = copy.copy(self.lzeromatrix)
            self.__nrmatrix__ = copy.copy(self.nrmatrix)
        # switch that is set if the stoichiometric analysis is up to date

        self.__structural__.species = self.species
        self.__structural__.reactions = self.reactions
        self.Nmatrix = PyscesStoich.StructMatrix(self.__structural__.nmatrix, self.__structural__.nmatrix_row, self.__structural__.nmatrix_col)
        self.Nmatrix.setRow(self.species)
        self.Nmatrix.setCol(self.reactions)

        self.Nrmatrix = PyscesStoich.StructMatrix(self.__structural__.nrmatrix, self.__structural__.nrmatrix_row, self.__structural__.nrmatrix_col)
        self.Nrmatrix.setRow(self.species)
        self.Nrmatrix.setCol(self.reactions)

        self.Kmatrix = PyscesStoich.StructMatrix(self.__structural__.kmatrix, self.__structural__.kmatrix_row, self.__structural__.kmatrix_col)
        self.Kmatrix.setRow(self.reactions)
        self.Kmatrix.setCol(self.reactions)

        self.K0matrix = PyscesStoich.StructMatrix(self.__structural__.kzeromatrix, self.__structural__.kzeromatrix_row, self.__structural__.kzeromatrix_col)
        self.K0matrix.setRow(self.reactions)
        self.K0matrix.setCol(self.reactions)

        self.Lmatrix = PyscesStoich.StructMatrix(self.__structural__.lmatrix, self.__structural__.lmatrix_row, self.__structural__.lmatrix_col)
github PySCeS / pysces / pysces / PyscesMiniModel.py View on Github external
self.nrmatrix_col = self.__structural__.nrmatrix_col

            self.__kmatrix__ = copy.copy(self.kmatrix)
            self.__kzeromatrix__ = copy.copy(self.kzeromatrix)
            self.__lmatrix__ = copy.copy(self.lmatrix)
            self.__lzeromatrix__ = copy.copy(self.lzeromatrix)
            self.__nrmatrix__ = copy.copy(self.nrmatrix)
        # switch that is set if the stoichiometric analysis is up to date

        self.__structural__.species = self.species
        self.__structural__.reactions = self.reactions
        self.Nmatrix = PyscesStoich.StructMatrix(self.__structural__.nmatrix, self.__structural__.nmatrix_row, self.__structural__.nmatrix_col)
        self.Nmatrix.setRow(self.species)
        self.Nmatrix.setCol(self.reactions)

        self.Nrmatrix = PyscesStoich.StructMatrix(self.__structural__.nrmatrix, self.__structural__.nrmatrix_row, self.__structural__.nrmatrix_col)
        self.Nrmatrix.setRow(self.species)
        self.Nrmatrix.setCol(self.reactions)

        self.Kmatrix = PyscesStoich.StructMatrix(self.__structural__.kmatrix, self.__structural__.kmatrix_row, self.__structural__.kmatrix_col)
        self.Kmatrix.setRow(self.reactions)
        self.Kmatrix.setCol(self.reactions)

        self.K0matrix = PyscesStoich.StructMatrix(self.__structural__.kzeromatrix, self.__structural__.kzeromatrix_row, self.__structural__.kzeromatrix_col)
        self.K0matrix.setRow(self.reactions)
        self.K0matrix.setCol(self.reactions)

        self.Lmatrix = PyscesStoich.StructMatrix(self.__structural__.lmatrix, self.__structural__.lmatrix_row, self.__structural__.lmatrix_col)
        self.Lmatrix.setRow(self.species)
        self.Lmatrix.setCol(self.species)

        self.L0matrix = PyscesStoich.StructMatrix(self.__structural__.lzeromatrix, self.__structural__.lzeromatrix_row, self.__structural__.lzeromatrix_col)
github PySCeS / pysces / pysces / PyscesMiniModel.py View on Github external
self.__structural__.species = self.species
        self.__structural__.reactions = self.reactions
        self.Nmatrix = PyscesStoich.StructMatrix(self.__structural__.nmatrix, self.__structural__.nmatrix_row, self.__structural__.nmatrix_col)
        self.Nmatrix.setRow(self.species)
        self.Nmatrix.setCol(self.reactions)

        self.Nrmatrix = PyscesStoich.StructMatrix(self.__structural__.nrmatrix, self.__structural__.nrmatrix_row, self.__structural__.nrmatrix_col)
        self.Nrmatrix.setRow(self.species)
        self.Nrmatrix.setCol(self.reactions)

        self.Kmatrix = PyscesStoich.StructMatrix(self.__structural__.kmatrix, self.__structural__.kmatrix_row, self.__structural__.kmatrix_col)
        self.Kmatrix.setRow(self.reactions)
        self.Kmatrix.setCol(self.reactions)

        self.K0matrix = PyscesStoich.StructMatrix(self.__structural__.kzeromatrix, self.__structural__.kzeromatrix_row, self.__structural__.kzeromatrix_col)
        self.K0matrix.setRow(self.reactions)
        self.K0matrix.setCol(self.reactions)

        self.Lmatrix = PyscesStoich.StructMatrix(self.__structural__.lmatrix, self.__structural__.lmatrix_row, self.__structural__.lmatrix_col)
        self.Lmatrix.setRow(self.species)
        self.Lmatrix.setCol(self.species)

        self.L0matrix = PyscesStoich.StructMatrix(self.__structural__.lzeromatrix, self.__structural__.lzeromatrix_row, self.__structural__.lzeromatrix_col)
        self.L0matrix.setRow(self.species)
        self.L0matrix.setCol(self.species)

        if self.__structural__.info_moiety_conserve:
            self.Consmatrix = PyscesStoich.StructMatrix(self.__structural__.conservation_matrix, self.__structural__.conservation_matrix_row, self.__structural__.conservation_matrix_col)
            self.Consmatrix.setRow(self.species)
            self.Consmatrix.setCol(self.species)
        else:
github PySCeS / pysces / pysces / PyscesMiniModel.py View on Github external
self.Kmatrix.setCol(self.reactions)

        self.K0matrix = PyscesStoich.StructMatrix(self.__structural__.kzeromatrix, self.__structural__.kzeromatrix_row, self.__structural__.kzeromatrix_col)
        self.K0matrix.setRow(self.reactions)
        self.K0matrix.setCol(self.reactions)

        self.Lmatrix = PyscesStoich.StructMatrix(self.__structural__.lmatrix, self.__structural__.lmatrix_row, self.__structural__.lmatrix_col)
        self.Lmatrix.setRow(self.species)
        self.Lmatrix.setCol(self.species)

        self.L0matrix = PyscesStoich.StructMatrix(self.__structural__.lzeromatrix, self.__structural__.lzeromatrix_row, self.__structural__.lzeromatrix_col)
        self.L0matrix.setRow(self.species)
        self.L0matrix.setCol(self.species)

        if self.__structural__.info_moiety_conserve:
            self.Consmatrix = PyscesStoich.StructMatrix(self.__structural__.conservation_matrix, self.__structural__.conservation_matrix_row, self.__structural__.conservation_matrix_col)
            self.Consmatrix.setRow(self.species)
            self.Consmatrix.setCol(self.species)
        else:
            self.Consmatrix = None
        self.__StoichOK = 1
        print(' ')

pysces

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

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Latest version published 3 months ago

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