Class abstract_fortran_solver

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Instance Methods

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make_formula_fortran_compatible(self, formula)

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parameter_part_of_fortran_file(self)

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parameter_declaration_part_of_fortran_file(self)

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get_compile_call_list(self)

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specific_init(self)

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get_fortran_solver_call(self)

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fortran_code(self)

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read_output(self, flat_timecourses)

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__init__(self, species, species_values, differential_equations, signalling, steady_state_norm=1e-11, parameters=[], timecourses_to_fit_to=None, additional_options={})
timecourses have to be in the format {timepoint1:{species_1:concentration1,species2:concentration2}} source code

rename_parameters(self)
Function to rename parameter because Fortran lacks differentiation between capitalized and non-capitalized variables.

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__rename_parameters(self, rename_to)

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compile(self)

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call(self, endtime, titration_factor=0.0, starting_species_concentrations=None)

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unsafesolve(self, endtime=None, titration_factor=0.0, starting_species_concentrations=None)

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solve(self, endtime=None, titration_factor=0.0, starting_species_concentrations=None)

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__safe_remove_file__(self, filename)

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__del__(self)

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