skimpy.mechanisms ================= .. py:module:: skimpy.mechanisms .. autoapi-nested-parse:: .. module:: skimpy :platform: Unix, Windows :synopsis: Simple Kinetic Models in Python .. moduleauthor:: SKiMPy team [---------] Copyright 2017 Laboratory of Computational Systems Biotechnology (LCSB), Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. Submodules ---------- .. toctree:: :maxdepth: 1 /autoapi/skimpy/mechanisms/bi_uni_reversible_hill/index /autoapi/skimpy/mechanisms/convenience/index /autoapi/skimpy/mechanisms/convenience_with_inihibition/index /autoapi/skimpy/mechanisms/direct_expression/index /autoapi/skimpy/mechanisms/gene_expression/index /autoapi/skimpy/mechanisms/generalized_elementary_kinetics/index /autoapi/skimpy/mechanisms/generalized_reversible_hill_n_n/index /autoapi/skimpy/mechanisms/generalized_reversible_hill_n_n_h1/index /autoapi/skimpy/mechanisms/generalized_reversible_hill_n_n_h1_with_inhibition/index /autoapi/skimpy/mechanisms/irrev_hill/index /autoapi/skimpy/mechanisms/irrev_m_n_hill/index /autoapi/skimpy/mechanisms/irrev_m_n_michaelis_menten/index /autoapi/skimpy/mechanisms/irrev_massaction/index /autoapi/skimpy/mechanisms/mechanism/index /autoapi/skimpy/mechanisms/michaelis_menten/index /autoapi/skimpy/mechanisms/rand_bi_bi_michaelis_menten/index /autoapi/skimpy/mechanisms/rev_massaction/index /autoapi/skimpy/mechanisms/uni_bi_reversible_hill/index /autoapi/skimpy/mechanisms/utils/index Attributes ---------- .. autoapisummary:: skimpy.mechanisms.QSSA skimpy.mechanisms.TQSSA skimpy.mechanisms.MCA skimpy.mechanisms.ODE skimpy.mechanisms.ELEMENTARY skimpy.mechanisms.NUMERICAL skimpy.mechanisms.SYMBOLIC skimpy.mechanisms.NET skimpy.mechanisms.SPLIT skimpy.mechanisms.PARAMETER skimpy.mechanisms.VARIABLE skimpy.mechanisms.KCAL skimpy.mechanisms.KJ skimpy.mechanisms.JOULE skimpy.mechanisms.WATER_FORMULA skimpy.mechanisms.QSSA skimpy.mechanisms.TQSSA skimpy.mechanisms.MCA skimpy.mechanisms.ODE skimpy.mechanisms.ELEMENTARY skimpy.mechanisms.NUMERICAL skimpy.mechanisms.SYMBOLIC skimpy.mechanisms.NET skimpy.mechanisms.SPLIT skimpy.mechanisms.PARAMETER skimpy.mechanisms.VARIABLE skimpy.mechanisms.KCAL skimpy.mechanisms.KJ skimpy.mechanisms.JOULE skimpy.mechanisms.WATER_FORMULA skimpy.mechanisms.QSSA skimpy.mechanisms.TQSSA skimpy.mechanisms.MCA skimpy.mechanisms.ODE skimpy.mechanisms.ELEMENTARY skimpy.mechanisms.NUMERICAL skimpy.mechanisms.SYMBOLIC skimpy.mechanisms.NET skimpy.mechanisms.SPLIT skimpy.mechanisms.PARAMETER skimpy.mechanisms.VARIABLE skimpy.mechanisms.KCAL skimpy.mechanisms.KJ skimpy.mechanisms.JOULE skimpy.mechanisms.WATER_FORMULA skimpy.mechanisms.QSSA skimpy.mechanisms.TQSSA skimpy.mechanisms.MCA skimpy.mechanisms.ODE skimpy.mechanisms.ELEMENTARY skimpy.mechanisms.NUMERICAL skimpy.mechanisms.SYMBOLIC skimpy.mechanisms.NET skimpy.mechanisms.SPLIT skimpy.mechanisms.PARAMETER skimpy.mechanisms.VARIABLE skimpy.mechanisms.KCAL skimpy.mechanisms.KJ skimpy.mechanisms.JOULE skimpy.mechanisms.WATER_FORMULA skimpy.mechanisms.QSSA skimpy.mechanisms.TQSSA skimpy.mechanisms.MCA skimpy.mechanisms.ODE skimpy.mechanisms.ELEMENTARY skimpy.mechanisms.NUMERICAL skimpy.mechanisms.SYMBOLIC skimpy.mechanisms.NET skimpy.mechanisms.SPLIT skimpy.mechanisms.PARAMETER skimpy.mechanisms.VARIABLE skimpy.mechanisms.KCAL skimpy.mechanisms.KJ skimpy.mechanisms.JOULE skimpy.mechanisms.WATER_FORMULA skimpy.mechanisms.QSSA skimpy.mechanisms.TQSSA skimpy.mechanisms.MCA skimpy.mechanisms.ODE skimpy.mechanisms.ELEMENTARY skimpy.mechanisms.NUMERICAL skimpy.mechanisms.SYMBOLIC skimpy.mechanisms.NET skimpy.mechanisms.SPLIT skimpy.mechanisms.PARAMETER skimpy.mechanisms.VARIABLE skimpy.mechanisms.KCAL skimpy.mechanisms.KJ skimpy.mechanisms.JOULE skimpy.mechanisms.WATER_FORMULA skimpy.mechanisms.QSSA skimpy.mechanisms.TQSSA skimpy.mechanisms.MCA skimpy.mechanisms.ODE skimpy.mechanisms.ELEMENTARY skimpy.mechanisms.NUMERICAL skimpy.mechanisms.SYMBOLIC skimpy.mechanisms.NET skimpy.mechanisms.SPLIT skimpy.mechanisms.PARAMETER skimpy.mechanisms.VARIABLE skimpy.mechanisms.KCAL skimpy.mechanisms.KJ skimpy.mechanisms.JOULE skimpy.mechanisms.WATER_FORMULA skimpy.mechanisms.QSSA skimpy.mechanisms.TQSSA skimpy.mechanisms.MCA skimpy.mechanisms.ODE skimpy.mechanisms.ELEMENTARY skimpy.mechanisms.NUMERICAL skimpy.mechanisms.SYMBOLIC skimpy.mechanisms.NET skimpy.mechanisms.SPLIT skimpy.mechanisms.PARAMETER skimpy.mechanisms.VARIABLE skimpy.mechanisms.KCAL skimpy.mechanisms.KJ skimpy.mechanisms.JOULE skimpy.mechanisms.WATER_FORMULA skimpy.mechanisms.QSSA skimpy.mechanisms.TQSSA skimpy.mechanisms.MCA skimpy.mechanisms.ODE skimpy.mechanisms.ELEMENTARY skimpy.mechanisms.NUMERICAL skimpy.mechanisms.SYMBOLIC skimpy.mechanisms.NET skimpy.mechanisms.SPLIT skimpy.mechanisms.PARAMETER skimpy.mechanisms.VARIABLE skimpy.mechanisms.KCAL skimpy.mechanisms.KJ skimpy.mechanisms.JOULE skimpy.mechanisms.WATER_FORMULA skimpy.mechanisms.QSSA skimpy.mechanisms.TQSSA skimpy.mechanisms.MCA skimpy.mechanisms.ODE skimpy.mechanisms.ELEMENTARY skimpy.mechanisms.NUMERICAL skimpy.mechanisms.SYMBOLIC skimpy.mechanisms.NET skimpy.mechanisms.SPLIT skimpy.mechanisms.PARAMETER skimpy.mechanisms.VARIABLE skimpy.mechanisms.KCAL skimpy.mechanisms.KJ skimpy.mechanisms.JOULE skimpy.mechanisms.WATER_FORMULA skimpy.mechanisms.QSSA skimpy.mechanisms.TQSSA skimpy.mechanisms.MCA skimpy.mechanisms.ODE skimpy.mechanisms.ELEMENTARY skimpy.mechanisms.NUMERICAL skimpy.mechanisms.SYMBOLIC skimpy.mechanisms.NET skimpy.mechanisms.SPLIT skimpy.mechanisms.PARAMETER skimpy.mechanisms.VARIABLE skimpy.mechanisms.KCAL skimpy.mechanisms.KJ skimpy.mechanisms.JOULE skimpy.mechanisms.WATER_FORMULA skimpy.mechanisms.QSSA skimpy.mechanisms.TQSSA skimpy.mechanisms.MCA skimpy.mechanisms.ODE skimpy.mechanisms.ELEMENTARY skimpy.mechanisms.NUMERICAL skimpy.mechanisms.SYMBOLIC skimpy.mechanisms.NET skimpy.mechanisms.SPLIT skimpy.mechanisms.PARAMETER skimpy.mechanisms.VARIABLE skimpy.mechanisms.KCAL skimpy.mechanisms.KJ skimpy.mechanisms.JOULE skimpy.mechanisms.WATER_FORMULA skimpy.mechanisms.QSSA skimpy.mechanisms.TQSSA skimpy.mechanisms.MCA skimpy.mechanisms.ODE skimpy.mechanisms.ELEMENTARY skimpy.mechanisms.NUMERICAL skimpy.mechanisms.SYMBOLIC skimpy.mechanisms.NET skimpy.mechanisms.SPLIT skimpy.mechanisms.PARAMETER skimpy.mechanisms.VARIABLE skimpy.mechanisms.KCAL skimpy.mechanisms.KJ skimpy.mechanisms.JOULE skimpy.mechanisms.WATER_FORMULA skimpy.mechanisms.QSSA skimpy.mechanisms.TQSSA skimpy.mechanisms.MCA skimpy.mechanisms.ODE skimpy.mechanisms.ELEMENTARY skimpy.mechanisms.NUMERICAL skimpy.mechanisms.SYMBOLIC skimpy.mechanisms.NET skimpy.mechanisms.SPLIT skimpy.mechanisms.PARAMETER skimpy.mechanisms.VARIABLE skimpy.mechanisms.KCAL skimpy.mechanisms.KJ skimpy.mechanisms.JOULE skimpy.mechanisms.WATER_FORMULA skimpy.mechanisms.QSSA skimpy.mechanisms.TQSSA skimpy.mechanisms.MCA skimpy.mechanisms.ODE skimpy.mechanisms.ELEMENTARY skimpy.mechanisms.NUMERICAL skimpy.mechanisms.SYMBOLIC skimpy.mechanisms.NET skimpy.mechanisms.SPLIT skimpy.mechanisms.PARAMETER skimpy.mechanisms.VARIABLE skimpy.mechanisms.KCAL skimpy.mechanisms.KJ skimpy.mechanisms.JOULE skimpy.mechanisms.WATER_FORMULA skimpy.mechanisms.QSSA skimpy.mechanisms.TQSSA skimpy.mechanisms.MCA skimpy.mechanisms.ODE skimpy.mechanisms.ELEMENTARY skimpy.mechanisms.NUMERICAL skimpy.mechanisms.SYMBOLIC skimpy.mechanisms.NET skimpy.mechanisms.SPLIT skimpy.mechanisms.PARAMETER skimpy.mechanisms.VARIABLE skimpy.mechanisms.KCAL skimpy.mechanisms.KJ skimpy.mechanisms.JOULE skimpy.mechanisms.WATER_FORMULA Classes ------- .. autoapisummary:: skimpy.mechanisms.KineticMechanism skimpy.mechanisms.ElementrayReactionStep skimpy.mechanisms.Reaction skimpy.mechanisms.Reactant skimpy.mechanisms.TabDict skimpy.mechanisms.ReversibleMichaelisMenten skimpy.mechanisms.KineticMechanism skimpy.mechanisms.ElementrayReactionStep skimpy.mechanisms.Reaction skimpy.mechanisms.TabDict skimpy.mechanisms.RandBiBiReversibleMichaelisMenten skimpy.mechanisms.KineticMechanism skimpy.mechanisms.ElementrayReactionStep skimpy.mechanisms.Reaction skimpy.mechanisms.TabDict skimpy.mechanisms.KineticMechanism skimpy.mechanisms.ElementrayReactionStep skimpy.mechanisms.Reaction skimpy.mechanisms.TabDict skimpy.mechanisms.KineticMechanism skimpy.mechanisms.ElementrayReactionStep skimpy.mechanisms.Reaction skimpy.mechanisms.TabDict skimpy.mechanisms.KineticMechanism skimpy.mechanisms.ElementrayReactionStep skimpy.mechanisms.Reaction skimpy.mechanisms.TabDict skimpy.mechanisms.KineticMechanism skimpy.mechanisms.ElementrayReactionStep skimpy.mechanisms.Reaction skimpy.mechanisms.TabDict skimpy.mechanisms.KineticMechanism skimpy.mechanisms.TabDict skimpy.mechanisms.KineticMechanism skimpy.mechanisms.ElementrayReactionStep skimpy.mechanisms.Reaction skimpy.mechanisms.TabDict skimpy.mechanisms.KineticMechanism skimpy.mechanisms.ElementrayReactionStep skimpy.mechanisms.Reaction skimpy.mechanisms.TabDict skimpy.mechanisms.KineticMechanism skimpy.mechanisms.ElementrayReactionStep skimpy.mechanisms.Reaction skimpy.mechanisms.TabDict skimpy.mechanisms.IrreversibleHill skimpy.mechanisms.KineticMechanism skimpy.mechanisms.ElementrayReactionStep skimpy.mechanisms.Reaction skimpy.mechanisms.TabDict skimpy.mechanisms.KineticMechanism skimpy.mechanisms.ElementrayReactionStep skimpy.mechanisms.Reaction skimpy.mechanisms.TabDict skimpy.mechanisms.KineticMechanism skimpy.mechanisms.ElementrayReactionStep skimpy.mechanisms.Reaction skimpy.mechanisms.TabDict skimpy.mechanisms.BiUniReversibleHill skimpy.mechanisms.KineticMechanism skimpy.mechanisms.ElementrayReactionStep skimpy.mechanisms.Reaction skimpy.mechanisms.TabDict skimpy.mechanisms.UniBiReversibleHill skimpy.mechanisms.KineticMechanism skimpy.mechanisms.ElementrayReactionStep skimpy.mechanisms.Reaction skimpy.mechanisms.TabDict skimpy.mechanisms.SimpleRegulatedGeneExpression skimpy.mechanisms.KineticMechanism Functions --------- .. autoapisummary:: skimpy.mechanisms.make_parameter_set skimpy.mechanisms.make_reactant_set skimpy.mechanisms.make_parameter_set skimpy.mechanisms.make_reactant_set skimpy.mechanisms.make_parameter_set skimpy.mechanisms.make_reactant_set skimpy.mechanisms.make_subclasses_dict skimpy.mechanisms.stringify_stoichiometry skimpy.mechanisms.make_convenience skimpy.mechanisms.make_parameter_set skimpy.mechanisms.make_reactant_set skimpy.mechanisms.make_subclasses_dict skimpy.mechanisms.stringify_stoichiometry skimpy.mechanisms.make_convenience_with_inhibition skimpy.mechanisms.make_parameter_set skimpy.mechanisms.make_reactant_set skimpy.mechanisms.make_subclasses_dict skimpy.mechanisms.stringify_stoichiometry skimpy.mechanisms.make_generalized_reversible_hill_n_n skimpy.mechanisms.make_parameter_set skimpy.mechanisms.make_reactant_set skimpy.mechanisms.make_subclasses_dict skimpy.mechanisms.stringify_stoichiometry skimpy.mechanisms.make_generalized_reversible_hill_n_n_h1 skimpy.mechanisms.make_parameter_set skimpy.mechanisms.make_reactant_set skimpy.mechanisms.make_subclasses_dict skimpy.mechanisms.stringify_stoichiometry skimpy.mechanisms.make_generalized_reversible_hill_n_n_h1_with_inhibition skimpy.mechanisms.make_parameter_set skimpy.mechanisms.make_reactant_set skimpy.mechanisms.make_subclasses_dict skimpy.mechanisms.stringify_stoichiometry skimpy.mechanisms.make_generalized_elementary_kinetics skimpy.mechanisms.make_parameter_set skimpy.mechanisms.make_reactant_set skimpy.mechanisms.make_subclasses_dict skimpy.mechanisms.stringify_stoichiometry skimpy.mechanisms.make_irrev_m_n_michaelis_menten skimpy.mechanisms.make_parameter_set skimpy.mechanisms.make_reactant_set skimpy.mechanisms.make_subclasses_dict skimpy.mechanisms.stringify_stoichiometry skimpy.mechanisms.make_irrev_massaction skimpy.mechanisms.make_parameter_set skimpy.mechanisms.make_reactant_set skimpy.mechanisms.make_subclasses_dict skimpy.mechanisms.stringify_stoichiometry skimpy.mechanisms.make_parameter_set skimpy.mechanisms.make_reactant_set skimpy.mechanisms.make_subclasses_dict skimpy.mechanisms.stringify_stoichiometry skimpy.mechanisms.make_irrev_m_n_hill skimpy.mechanisms.make_parameter_set skimpy.mechanisms.make_reactant_set skimpy.mechanisms.make_subclasses_dict skimpy.mechanisms.stringify_stoichiometry skimpy.mechanisms.make_rev_massaction skimpy.mechanisms.make_parameter_set skimpy.mechanisms.make_reactant_set skimpy.mechanisms.make_subclasses_dict skimpy.mechanisms.stringify_stoichiometry skimpy.mechanisms.make_parameter_set skimpy.mechanisms.make_reactant_set skimpy.mechanisms.make_subclasses_dict skimpy.mechanisms.stringify_stoichiometry skimpy.mechanisms.make_parameter_set skimpy.mechanisms.make_reactant_set skimpy.mechanisms.make_subclasses_dict skimpy.mechanisms.stringify_stoichiometry Package Contents ---------------- .. py:class:: KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`abc.ABC` Helper class that provides a standard way to create an ABC using inheritance. .. py:attribute:: parameter_reactant_links .. py:attribute:: name .. py:attribute:: reactants .. py:attribute:: inhibitors :value: None .. py:attribute:: _parameters :value: None .. py:attribute:: enzyme :value: None .. py:method:: __reduce__() .. py:method:: link_parameters_and_reactants() .. py:property:: parameters .. py:property:: Reactants :abstractmethod: Class to define metabolites and their roles in the reaction :return: .. py:property:: Parameters :abstractmethod: Class to define parameters and their roles in the reaction :return: .. py:method:: get_qssa_rate_expression() :abstractmethod: .. py:method:: update_qssa_rate_expression() :abstractmethod: .. py:method:: get_full_rate_expression() :abstractmethod: .. py:method:: calculate_rate_constants() :abstractmethod: .. py:method:: get_parameters_from_expression(expr) .. py:class:: ElementrayReactionStep(educts, products, rate_constant_name) Bases: :py:obj:`object` .. py:attribute:: educts .. py:attribute:: products .. py:attribute:: rate_constant_name .. py:method:: __str__() .. py:method:: __repr__() .. py:class:: Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`object` Global reaction class .. py:attribute:: name .. py:attribute:: enzyme :value: None .. py:attribute:: modifiers .. py:property:: reactants .. py:property:: reactant_stoichiometry .. py:property:: parameters .. py:property:: rates .. py:method:: __str__() .. py:method:: parametrize(params) .. py:function:: make_parameter_set(mechanism, param_declaration) .. py:function:: make_reactant_set(mechanism, reactant_declaration) .. py:class:: Reactant(name, value=None, model=None, suffix='') Bases: :py:obj:`Item` .. py:attribute:: type :value: 'variable' .. py:attribute:: compartment :value: None .. py:class:: TabDict Bases: :py:obj:`collections.OrderedDict` Really just an ordered dict with tab completion in interactive terminals .. py:method:: __dir__() Default dir() implementation. .. py:method:: __getattr__(attr) .. py:method:: iloc(ix) .. py:class:: ReversibleMichaelisMenten(name, reactants, parameters=None, **kwargs) Bases: :py:obj:`skimpy.mechanisms.mechanism.KineticMechanism` A reversible uni uni reaction enzmye class .. py:attribute:: Reactants Class to define metabolites and their roles in the reaction :return: .. py:attribute:: Parameters Class to define parameters and their roles in the reaction :return: .. py:attribute:: reactant_stoichiometry .. py:attribute:: parameter_reactant_links .. py:class:: ElementaryReactions Bases: :py:obj:`tuple` .. py:attribute:: r1f .. py:attribute:: r1b .. py:attribute:: r2f .. py:attribute:: r2b .. py:method:: get_qssa_rate_expression() .. py:method:: update_qssa_rate_expression() .. py:method:: get_full_rate_expression() .. py:method:: calculate_rate_constants() .. py:data:: QSSA :value: 'qssa' .. py:data:: TQSSA :value: 'tqssa' .. py:data:: MCA :value: 'mca' .. py:data:: ODE :value: 'ode' .. py:data:: ELEMENTARY :value: 'elementary' Jacobian Types .. py:data:: NUMERICAL :value: 'numerical' .. py:data:: SYMBOLIC :value: 'symbolic' MCA Types .. py:data:: NET :value: 'net' .. py:data:: SPLIT :value: 'split' Item types .. py:data:: PARAMETER :value: 'parameter' .. py:data:: VARIABLE :value: 'variable' Units .. py:data:: KCAL :value: 'kcal' .. py:data:: KJ :value: 'kJ' .. py:data:: JOULE :value: 'JOULE' OTHER .. py:data:: WATER_FORMULA :value: 'H2O' .. py:class:: KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`abc.ABC` Helper class that provides a standard way to create an ABC using inheritance. .. py:attribute:: parameter_reactant_links .. py:attribute:: name .. py:attribute:: reactants .. py:attribute:: inhibitors :value: None .. py:attribute:: _parameters :value: None .. py:attribute:: enzyme :value: None .. py:method:: __reduce__() .. py:method:: link_parameters_and_reactants() .. py:property:: parameters .. py:property:: Reactants :abstractmethod: Class to define metabolites and their roles in the reaction :return: .. py:property:: Parameters :abstractmethod: Class to define parameters and their roles in the reaction :return: .. py:method:: get_qssa_rate_expression() :abstractmethod: .. py:method:: update_qssa_rate_expression() :abstractmethod: .. py:method:: get_full_rate_expression() :abstractmethod: .. py:method:: calculate_rate_constants() :abstractmethod: .. py:method:: get_parameters_from_expression(expr) .. py:class:: ElementrayReactionStep(educts, products, rate_constant_name) Bases: :py:obj:`object` .. py:attribute:: educts .. py:attribute:: products .. py:attribute:: rate_constant_name .. py:method:: __str__() .. py:method:: __repr__() .. py:class:: Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`object` Global reaction class .. py:attribute:: name .. py:attribute:: enzyme :value: None .. py:attribute:: modifiers .. py:property:: reactants .. py:property:: reactant_stoichiometry .. py:property:: parameters .. py:property:: rates .. py:method:: __str__() .. py:method:: parametrize(params) .. py:class:: TabDict Bases: :py:obj:`collections.OrderedDict` Really just an ordered dict with tab completion in interactive terminals .. py:method:: __dir__() Default dir() implementation. .. py:method:: __getattr__(attr) .. py:method:: iloc(ix) .. py:function:: make_parameter_set(mechanism, param_declaration) .. py:function:: make_reactant_set(mechanism, reactant_declaration) .. py:class:: RandBiBiReversibleMichaelisMenten(name, reactants, parameters=None, **kwargs) Bases: :py:obj:`skimpy.mechanisms.mechanism.KineticMechanism` A reversible random ordered bi bi reaction enzmye class .. py:attribute:: Reactants Class to define metabolites and their roles in the reaction :return: .. py:attribute:: Parameters Class to define parameters and their roles in the reaction :return: .. py:attribute:: reactant_stoichiometry .. py:attribute:: parameter_reactant_links .. py:class:: ElementaryReactions Bases: :py:obj:`tuple` .. py:method:: get_qssa_rate_expression() .. py:method:: update_qssa_rate_expression() .. py:method:: get_full_rate_expression() :abstractmethod: .. py:method:: calculate_rate_constants() :abstractmethod: .. py:data:: QSSA :value: 'qssa' .. py:data:: TQSSA :value: 'tqssa' .. py:data:: MCA :value: 'mca' .. py:data:: ODE :value: 'ode' .. py:data:: ELEMENTARY :value: 'elementary' Jacobian Types .. py:data:: NUMERICAL :value: 'numerical' .. py:data:: SYMBOLIC :value: 'symbolic' MCA Types .. py:data:: NET :value: 'net' .. py:data:: SPLIT :value: 'split' Item types .. py:data:: PARAMETER :value: 'parameter' .. py:data:: VARIABLE :value: 'variable' Units .. py:data:: KCAL :value: 'kcal' .. py:data:: KJ :value: 'kJ' .. py:data:: JOULE :value: 'JOULE' OTHER .. py:data:: WATER_FORMULA :value: 'H2O' .. py:class:: KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`abc.ABC` Helper class that provides a standard way to create an ABC using inheritance. .. py:attribute:: parameter_reactant_links .. py:attribute:: name .. py:attribute:: reactants .. py:attribute:: inhibitors :value: None .. py:attribute:: _parameters :value: None .. py:attribute:: enzyme :value: None .. py:method:: __reduce__() .. py:method:: link_parameters_and_reactants() .. py:property:: parameters .. py:property:: Reactants :abstractmethod: Class to define metabolites and their roles in the reaction :return: .. py:property:: Parameters :abstractmethod: Class to define parameters and their roles in the reaction :return: .. py:method:: get_qssa_rate_expression() :abstractmethod: .. py:method:: update_qssa_rate_expression() :abstractmethod: .. py:method:: get_full_rate_expression() :abstractmethod: .. py:method:: calculate_rate_constants() :abstractmethod: .. py:method:: get_parameters_from_expression(expr) .. py:class:: ElementrayReactionStep(educts, products, rate_constant_name) Bases: :py:obj:`object` .. py:attribute:: educts .. py:attribute:: products .. py:attribute:: rate_constant_name .. py:method:: __str__() .. py:method:: __repr__() .. py:class:: Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`object` Global reaction class .. py:attribute:: name .. py:attribute:: enzyme :value: None .. py:attribute:: modifiers .. py:property:: reactants .. py:property:: reactant_stoichiometry .. py:property:: parameters .. py:property:: rates .. py:method:: __str__() .. py:method:: parametrize(params) .. py:class:: TabDict Bases: :py:obj:`collections.OrderedDict` Really just an ordered dict with tab completion in interactive terminals .. py:method:: __dir__() Default dir() implementation. .. py:method:: __getattr__(attr) .. py:method:: iloc(ix) .. py:function:: make_parameter_set(mechanism, param_declaration) .. py:function:: make_reactant_set(mechanism, reactant_declaration) .. py:function:: make_subclasses_dict(cls) .. py:function:: stringify_stoichiometry(stoichiometry, inihibitors=None) Stoichiometry looks like [-2, -1, 3] This is not nice as a suffix for a class name We transform it to _m2_m1_3 :param stoichiometry: :type stoichiometry: list(float) :return: suffix .. py:function:: make_convenience(stoichiometry) :param stoichiometry is a list of the reaction stoichioemtry .. py:data:: QSSA :value: 'qssa' .. py:data:: TQSSA :value: 'tqssa' .. py:data:: MCA :value: 'mca' .. py:data:: ODE :value: 'ode' .. py:data:: ELEMENTARY :value: 'elementary' Jacobian Types .. py:data:: NUMERICAL :value: 'numerical' .. py:data:: SYMBOLIC :value: 'symbolic' MCA Types .. py:data:: NET :value: 'net' .. py:data:: SPLIT :value: 'split' Item types .. py:data:: PARAMETER :value: 'parameter' .. py:data:: VARIABLE :value: 'variable' Units .. py:data:: KCAL :value: 'kcal' .. py:data:: KJ :value: 'kJ' .. py:data:: JOULE :value: 'JOULE' OTHER .. py:data:: WATER_FORMULA :value: 'H2O' .. py:class:: KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`abc.ABC` Helper class that provides a standard way to create an ABC using inheritance. .. py:attribute:: parameter_reactant_links .. py:attribute:: name .. py:attribute:: reactants .. py:attribute:: inhibitors :value: None .. py:attribute:: _parameters :value: None .. py:attribute:: enzyme :value: None .. py:method:: __reduce__() .. py:method:: link_parameters_and_reactants() .. py:property:: parameters .. py:property:: Reactants :abstractmethod: Class to define metabolites and their roles in the reaction :return: .. py:property:: Parameters :abstractmethod: Class to define parameters and their roles in the reaction :return: .. py:method:: get_qssa_rate_expression() :abstractmethod: .. py:method:: update_qssa_rate_expression() :abstractmethod: .. py:method:: get_full_rate_expression() :abstractmethod: .. py:method:: calculate_rate_constants() :abstractmethod: .. py:method:: get_parameters_from_expression(expr) .. py:class:: ElementrayReactionStep(educts, products, rate_constant_name) Bases: :py:obj:`object` .. py:attribute:: educts .. py:attribute:: products .. py:attribute:: rate_constant_name .. py:method:: __str__() .. py:method:: __repr__() .. py:class:: Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`object` Global reaction class .. py:attribute:: name .. py:attribute:: enzyme :value: None .. py:attribute:: modifiers .. py:property:: reactants .. py:property:: reactant_stoichiometry .. py:property:: parameters .. py:property:: rates .. py:method:: __str__() .. py:method:: parametrize(params) .. py:class:: TabDict Bases: :py:obj:`collections.OrderedDict` Really just an ordered dict with tab completion in interactive terminals .. py:method:: __dir__() Default dir() implementation. .. py:method:: __getattr__(attr) .. py:method:: iloc(ix) .. py:function:: make_parameter_set(mechanism, param_declaration) .. py:function:: make_reactant_set(mechanism, reactant_declaration) .. py:function:: make_subclasses_dict(cls) .. py:function:: stringify_stoichiometry(stoichiometry, inihibitors=None) Stoichiometry looks like [-2, -1, 3] This is not nice as a suffix for a class name We transform it to _m2_m1_3 :param stoichiometry: :type stoichiometry: list(float) :return: suffix .. py:function:: make_convenience_with_inhibition(stoichiometry, inihbitor_stoichiometry) :param stoichiometry is a list of the reaction stoichioemtry .. py:data:: QSSA :value: 'qssa' .. py:data:: TQSSA :value: 'tqssa' .. py:data:: MCA :value: 'mca' .. py:data:: ODE :value: 'ode' .. py:data:: ELEMENTARY :value: 'elementary' Jacobian Types .. py:data:: NUMERICAL :value: 'numerical' .. py:data:: SYMBOLIC :value: 'symbolic' MCA Types .. py:data:: NET :value: 'net' .. py:data:: SPLIT :value: 'split' Item types .. py:data:: PARAMETER :value: 'parameter' .. py:data:: VARIABLE :value: 'variable' Units .. py:data:: KCAL :value: 'kcal' .. py:data:: KJ :value: 'kJ' .. py:data:: JOULE :value: 'JOULE' OTHER .. py:data:: WATER_FORMULA :value: 'H2O' .. py:class:: KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`abc.ABC` Helper class that provides a standard way to create an ABC using inheritance. .. py:attribute:: parameter_reactant_links .. py:attribute:: name .. py:attribute:: reactants .. py:attribute:: inhibitors :value: None .. py:attribute:: _parameters :value: None .. py:attribute:: enzyme :value: None .. py:method:: __reduce__() .. py:method:: link_parameters_and_reactants() .. py:property:: parameters .. py:property:: Reactants :abstractmethod: Class to define metabolites and their roles in the reaction :return: .. py:property:: Parameters :abstractmethod: Class to define parameters and their roles in the reaction :return: .. py:method:: get_qssa_rate_expression() :abstractmethod: .. py:method:: update_qssa_rate_expression() :abstractmethod: .. py:method:: get_full_rate_expression() :abstractmethod: .. py:method:: calculate_rate_constants() :abstractmethod: .. py:method:: get_parameters_from_expression(expr) .. py:class:: ElementrayReactionStep(educts, products, rate_constant_name) Bases: :py:obj:`object` .. py:attribute:: educts .. py:attribute:: products .. py:attribute:: rate_constant_name .. py:method:: __str__() .. py:method:: __repr__() .. py:class:: Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`object` Global reaction class .. py:attribute:: name .. py:attribute:: enzyme :value: None .. py:attribute:: modifiers .. py:property:: reactants .. py:property:: reactant_stoichiometry .. py:property:: parameters .. py:property:: rates .. py:method:: __str__() .. py:method:: parametrize(params) .. py:class:: TabDict Bases: :py:obj:`collections.OrderedDict` Really just an ordered dict with tab completion in interactive terminals .. py:method:: __dir__() Default dir() implementation. .. py:method:: __getattr__(attr) .. py:method:: iloc(ix) .. py:function:: make_parameter_set(mechanism, param_declaration) .. py:function:: make_reactant_set(mechanism, reactant_declaration) .. py:function:: make_subclasses_dict(cls) .. py:function:: stringify_stoichiometry(stoichiometry, inihibitors=None) Stoichiometry looks like [-2, -1, 3] This is not nice as a suffix for a class name We transform it to _m2_m1_3 :param stoichiometry: :type stoichiometry: list(float) :return: suffix .. py:function:: make_generalized_reversible_hill_n_n(stoichiometry) :param stoichiometry is a list of the reaction stoichioemtry .. py:data:: QSSA :value: 'qssa' .. py:data:: TQSSA :value: 'tqssa' .. py:data:: MCA :value: 'mca' .. py:data:: ODE :value: 'ode' .. py:data:: ELEMENTARY :value: 'elementary' Jacobian Types .. py:data:: NUMERICAL :value: 'numerical' .. py:data:: SYMBOLIC :value: 'symbolic' MCA Types .. py:data:: NET :value: 'net' .. py:data:: SPLIT :value: 'split' Item types .. py:data:: PARAMETER :value: 'parameter' .. py:data:: VARIABLE :value: 'variable' Units .. py:data:: KCAL :value: 'kcal' .. py:data:: KJ :value: 'kJ' .. py:data:: JOULE :value: 'JOULE' OTHER .. py:data:: WATER_FORMULA :value: 'H2O' .. py:class:: KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`abc.ABC` Helper class that provides a standard way to create an ABC using inheritance. .. py:attribute:: parameter_reactant_links .. py:attribute:: name .. py:attribute:: reactants .. py:attribute:: inhibitors :value: None .. py:attribute:: _parameters :value: None .. py:attribute:: enzyme :value: None .. py:method:: __reduce__() .. py:method:: link_parameters_and_reactants() .. py:property:: parameters .. py:property:: Reactants :abstractmethod: Class to define metabolites and their roles in the reaction :return: .. py:property:: Parameters :abstractmethod: Class to define parameters and their roles in the reaction :return: .. py:method:: get_qssa_rate_expression() :abstractmethod: .. py:method:: update_qssa_rate_expression() :abstractmethod: .. py:method:: get_full_rate_expression() :abstractmethod: .. py:method:: calculate_rate_constants() :abstractmethod: .. py:method:: get_parameters_from_expression(expr) .. py:class:: ElementrayReactionStep(educts, products, rate_constant_name) Bases: :py:obj:`object` .. py:attribute:: educts .. py:attribute:: products .. py:attribute:: rate_constant_name .. py:method:: __str__() .. py:method:: __repr__() .. py:class:: Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`object` Global reaction class .. py:attribute:: name .. py:attribute:: enzyme :value: None .. py:attribute:: modifiers .. py:property:: reactants .. py:property:: reactant_stoichiometry .. py:property:: parameters .. py:property:: rates .. py:method:: __str__() .. py:method:: parametrize(params) .. py:class:: TabDict Bases: :py:obj:`collections.OrderedDict` Really just an ordered dict with tab completion in interactive terminals .. py:method:: __dir__() Default dir() implementation. .. py:method:: __getattr__(attr) .. py:method:: iloc(ix) .. py:function:: make_parameter_set(mechanism, param_declaration) .. py:function:: make_reactant_set(mechanism, reactant_declaration) .. py:function:: make_subclasses_dict(cls) .. py:function:: stringify_stoichiometry(stoichiometry, inihibitors=None) Stoichiometry looks like [-2, -1, 3] This is not nice as a suffix for a class name We transform it to _m2_m1_3 :param stoichiometry: :type stoichiometry: list(float) :return: suffix .. py:function:: make_generalized_reversible_hill_n_n_h1(stoichiometry) This function generxied :param stoichiometry is a list of the reaction stoichioemtry .. py:data:: QSSA :value: 'qssa' .. py:data:: TQSSA :value: 'tqssa' .. py:data:: MCA :value: 'mca' .. py:data:: ODE :value: 'ode' .. py:data:: ELEMENTARY :value: 'elementary' Jacobian Types .. py:data:: NUMERICAL :value: 'numerical' .. py:data:: SYMBOLIC :value: 'symbolic' MCA Types .. py:data:: NET :value: 'net' .. py:data:: SPLIT :value: 'split' Item types .. py:data:: PARAMETER :value: 'parameter' .. py:data:: VARIABLE :value: 'variable' Units .. py:data:: KCAL :value: 'kcal' .. py:data:: KJ :value: 'kJ' .. py:data:: JOULE :value: 'JOULE' OTHER .. py:data:: WATER_FORMULA :value: 'H2O' .. py:class:: KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`abc.ABC` Helper class that provides a standard way to create an ABC using inheritance. .. py:attribute:: parameter_reactant_links .. py:attribute:: name .. py:attribute:: reactants .. py:attribute:: inhibitors :value: None .. py:attribute:: _parameters :value: None .. py:attribute:: enzyme :value: None .. py:method:: __reduce__() .. py:method:: link_parameters_and_reactants() .. py:property:: parameters .. py:property:: Reactants :abstractmethod: Class to define metabolites and their roles in the reaction :return: .. py:property:: Parameters :abstractmethod: Class to define parameters and their roles in the reaction :return: .. py:method:: get_qssa_rate_expression() :abstractmethod: .. py:method:: update_qssa_rate_expression() :abstractmethod: .. py:method:: get_full_rate_expression() :abstractmethod: .. py:method:: calculate_rate_constants() :abstractmethod: .. py:method:: get_parameters_from_expression(expr) .. py:class:: ElementrayReactionStep(educts, products, rate_constant_name) Bases: :py:obj:`object` .. py:attribute:: educts .. py:attribute:: products .. py:attribute:: rate_constant_name .. py:method:: __str__() .. py:method:: __repr__() .. py:class:: Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`object` Global reaction class .. py:attribute:: name .. py:attribute:: enzyme :value: None .. py:attribute:: modifiers .. py:property:: reactants .. py:property:: reactant_stoichiometry .. py:property:: parameters .. py:property:: rates .. py:method:: __str__() .. py:method:: parametrize(params) .. py:class:: TabDict Bases: :py:obj:`collections.OrderedDict` Really just an ordered dict with tab completion in interactive terminals .. py:method:: __dir__() Default dir() implementation. .. py:method:: __getattr__(attr) .. py:method:: iloc(ix) .. py:function:: make_parameter_set(mechanism, param_declaration) .. py:function:: make_reactant_set(mechanism, reactant_declaration) .. py:function:: make_subclasses_dict(cls) .. py:function:: stringify_stoichiometry(stoichiometry, inihibitors=None) Stoichiometry looks like [-2, -1, 3] This is not nice as a suffix for a class name We transform it to _m2_m1_3 :param stoichiometry: :type stoichiometry: list(float) :return: suffix .. py:function:: make_generalized_reversible_hill_n_n_h1_with_inhibition(stoichiometry, inihbitor_stoichiometry) This function creates the Generalized Rev. Hill with h = 1 and adds competitive inhibition :param inihbitor_stoichiometry: :param stoichiometry is a list of the reaction stoichioemtry .. py:data:: QSSA :value: 'qssa' .. py:data:: TQSSA :value: 'tqssa' .. py:data:: MCA :value: 'mca' .. py:data:: ODE :value: 'ode' .. py:data:: ELEMENTARY :value: 'elementary' Jacobian Types .. py:data:: NUMERICAL :value: 'numerical' .. py:data:: SYMBOLIC :value: 'symbolic' MCA Types .. py:data:: NET :value: 'net' .. py:data:: SPLIT :value: 'split' Item types .. py:data:: PARAMETER :value: 'parameter' .. py:data:: VARIABLE :value: 'variable' Units .. py:data:: KCAL :value: 'kcal' .. py:data:: KJ :value: 'kJ' .. py:data:: JOULE :value: 'JOULE' OTHER .. py:data:: WATER_FORMULA :value: 'H2O' .. py:class:: KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`abc.ABC` Helper class that provides a standard way to create an ABC using inheritance. .. py:attribute:: parameter_reactant_links .. py:attribute:: name .. py:attribute:: reactants .. py:attribute:: inhibitors :value: None .. py:attribute:: _parameters :value: None .. py:attribute:: enzyme :value: None .. py:method:: __reduce__() .. py:method:: link_parameters_and_reactants() .. py:property:: parameters .. py:property:: Reactants :abstractmethod: Class to define metabolites and their roles in the reaction :return: .. py:property:: Parameters :abstractmethod: Class to define parameters and their roles in the reaction :return: .. py:method:: get_qssa_rate_expression() :abstractmethod: .. py:method:: update_qssa_rate_expression() :abstractmethod: .. py:method:: get_full_rate_expression() :abstractmethod: .. py:method:: calculate_rate_constants() :abstractmethod: .. py:method:: get_parameters_from_expression(expr) .. py:class:: TabDict Bases: :py:obj:`collections.OrderedDict` Really just an ordered dict with tab completion in interactive terminals .. py:method:: __dir__() Default dir() implementation. .. py:method:: __getattr__(attr) .. py:method:: iloc(ix) .. py:function:: make_parameter_set(mechanism, param_declaration) .. py:function:: make_reactant_set(mechanism, reactant_declaration) .. py:function:: make_subclasses_dict(cls) .. py:function:: stringify_stoichiometry(stoichiometry, inihibitors=None) Stoichiometry looks like [-2, -1, 3] This is not nice as a suffix for a class name We transform it to _m2_m1_3 :param stoichiometry: :type stoichiometry: list(float) :return: suffix .. py:function:: make_generalized_elementary_kinetics(stoichiometry, generalized_reactants) Creates a reversible N-M GeneralizedElementaryKinetics class GeneralizedElementaryKinetics iplementing the kinetic scheme to account for non ideal effects in large scale kinetic model: Weilandt, Daniel R., and Vassily Hatzimanikatis. "Particle-based simulation reveals macromolecular crowding effects on the Michaelis-Menten mechanism." Biophysical Journal (2019). :param stoichiometry is a list of the reaction stoichioemtry :param generalized_reactants is a list of reactants that contribute in a powerlaw form: v = v_0 * exp(beta_forward) ... * (x_1/x_1_0)^(alpha_f_x_1 ) ... * (x_n/x_n_0)^(alpha_f_x_n ) with v_0 beeing the reversible Massaction flux .. py:data:: QSSA :value: 'qssa' .. py:data:: TQSSA :value: 'tqssa' .. py:data:: MCA :value: 'mca' .. py:data:: ODE :value: 'ode' .. py:data:: ELEMENTARY :value: 'elementary' Jacobian Types .. py:data:: NUMERICAL :value: 'numerical' .. py:data:: SYMBOLIC :value: 'symbolic' MCA Types .. py:data:: NET :value: 'net' .. py:data:: SPLIT :value: 'split' Item types .. py:data:: PARAMETER :value: 'parameter' .. py:data:: VARIABLE :value: 'variable' Units .. py:data:: KCAL :value: 'kcal' .. py:data:: KJ :value: 'kJ' .. py:data:: JOULE :value: 'JOULE' OTHER .. py:data:: WATER_FORMULA :value: 'H2O' .. py:class:: KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`abc.ABC` Helper class that provides a standard way to create an ABC using inheritance. .. py:attribute:: parameter_reactant_links .. py:attribute:: name .. py:attribute:: reactants .. py:attribute:: inhibitors :value: None .. py:attribute:: _parameters :value: None .. py:attribute:: enzyme :value: None .. py:method:: __reduce__() .. py:method:: link_parameters_and_reactants() .. py:property:: parameters .. py:property:: Reactants :abstractmethod: Class to define metabolites and their roles in the reaction :return: .. py:property:: Parameters :abstractmethod: Class to define parameters and their roles in the reaction :return: .. py:method:: get_qssa_rate_expression() :abstractmethod: .. py:method:: update_qssa_rate_expression() :abstractmethod: .. py:method:: get_full_rate_expression() :abstractmethod: .. py:method:: calculate_rate_constants() :abstractmethod: .. py:method:: get_parameters_from_expression(expr) .. py:class:: ElementrayReactionStep(educts, products, rate_constant_name) Bases: :py:obj:`object` .. py:attribute:: educts .. py:attribute:: products .. py:attribute:: rate_constant_name .. py:method:: __str__() .. py:method:: __repr__() .. py:class:: Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`object` Global reaction class .. py:attribute:: name .. py:attribute:: enzyme :value: None .. py:attribute:: modifiers .. py:property:: reactants .. py:property:: reactant_stoichiometry .. py:property:: parameters .. py:property:: rates .. py:method:: __str__() .. py:method:: parametrize(params) .. py:class:: TabDict Bases: :py:obj:`collections.OrderedDict` Really just an ordered dict with tab completion in interactive terminals .. py:method:: __dir__() Default dir() implementation. .. py:method:: __getattr__(attr) .. py:method:: iloc(ix) .. py:function:: make_parameter_set(mechanism, param_declaration) .. py:function:: make_reactant_set(mechanism, reactant_declaration) .. py:function:: make_subclasses_dict(cls) .. py:function:: stringify_stoichiometry(stoichiometry, inihibitors=None) Stoichiometry looks like [-2, -1, 3] This is not nice as a suffix for a class name We transform it to _m2_m1_3 :param stoichiometry: :type stoichiometry: list(float) :return: suffix .. py:function:: make_irrev_m_n_michaelis_menten(stoichiometry) :param stoichiometry is a list of the reaction stoichioemtry .. py:data:: QSSA :value: 'qssa' .. py:data:: TQSSA :value: 'tqssa' .. py:data:: MCA :value: 'mca' .. py:data:: ODE :value: 'ode' .. py:data:: ELEMENTARY :value: 'elementary' Jacobian Types .. py:data:: NUMERICAL :value: 'numerical' .. py:data:: SYMBOLIC :value: 'symbolic' MCA Types .. py:data:: NET :value: 'net' .. py:data:: SPLIT :value: 'split' Item types .. py:data:: PARAMETER :value: 'parameter' .. py:data:: VARIABLE :value: 'variable' Units .. py:data:: KCAL :value: 'kcal' .. py:data:: KJ :value: 'kJ' .. py:data:: JOULE :value: 'JOULE' OTHER .. py:data:: WATER_FORMULA :value: 'H2O' .. py:class:: KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`abc.ABC` Helper class that provides a standard way to create an ABC using inheritance. .. py:attribute:: parameter_reactant_links .. py:attribute:: name .. py:attribute:: reactants .. py:attribute:: inhibitors :value: None .. py:attribute:: _parameters :value: None .. py:attribute:: enzyme :value: None .. py:method:: __reduce__() .. py:method:: link_parameters_and_reactants() .. py:property:: parameters .. py:property:: Reactants :abstractmethod: Class to define metabolites and their roles in the reaction :return: .. py:property:: Parameters :abstractmethod: Class to define parameters and their roles in the reaction :return: .. py:method:: get_qssa_rate_expression() :abstractmethod: .. py:method:: update_qssa_rate_expression() :abstractmethod: .. py:method:: get_full_rate_expression() :abstractmethod: .. py:method:: calculate_rate_constants() :abstractmethod: .. py:method:: get_parameters_from_expression(expr) .. py:class:: ElementrayReactionStep(educts, products, rate_constant_name) Bases: :py:obj:`object` .. py:attribute:: educts .. py:attribute:: products .. py:attribute:: rate_constant_name .. py:method:: __str__() .. py:method:: __repr__() .. py:class:: Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`object` Global reaction class .. py:attribute:: name .. py:attribute:: enzyme :value: None .. py:attribute:: modifiers .. py:property:: reactants .. py:property:: reactant_stoichiometry .. py:property:: parameters .. py:property:: rates .. py:method:: __str__() .. py:method:: parametrize(params) .. py:class:: TabDict Bases: :py:obj:`collections.OrderedDict` Really just an ordered dict with tab completion in interactive terminals .. py:method:: __dir__() Default dir() implementation. .. py:method:: __getattr__(attr) .. py:method:: iloc(ix) .. py:function:: make_parameter_set(mechanism, param_declaration) .. py:function:: make_reactant_set(mechanism, reactant_declaration) .. py:function:: make_subclasses_dict(cls) .. py:function:: stringify_stoichiometry(stoichiometry, inihibitors=None) Stoichiometry looks like [-2, -1, 3] This is not nice as a suffix for a class name We transform it to _m2_m1_3 :param stoichiometry: :type stoichiometry: list(float) :return: suffix .. py:function:: make_irrev_massaction(stoichiometry) :param stoichiometry is a list of the reaction stoichioemtry .. py:data:: QSSA :value: 'qssa' .. py:data:: TQSSA :value: 'tqssa' .. py:data:: MCA :value: 'mca' .. py:data:: ODE :value: 'ode' .. py:data:: ELEMENTARY :value: 'elementary' Jacobian Types .. py:data:: NUMERICAL :value: 'numerical' .. py:data:: SYMBOLIC :value: 'symbolic' MCA Types .. py:data:: NET :value: 'net' .. py:data:: SPLIT :value: 'split' Item types .. py:data:: PARAMETER :value: 'parameter' .. py:data:: VARIABLE :value: 'variable' Units .. py:data:: KCAL :value: 'kcal' .. py:data:: KJ :value: 'kJ' .. py:data:: JOULE :value: 'JOULE' OTHER .. py:data:: WATER_FORMULA :value: 'H2O' .. py:class:: KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`abc.ABC` Helper class that provides a standard way to create an ABC using inheritance. .. py:attribute:: parameter_reactant_links .. py:attribute:: name .. py:attribute:: reactants .. py:attribute:: inhibitors :value: None .. py:attribute:: _parameters :value: None .. py:attribute:: enzyme :value: None .. py:method:: __reduce__() .. py:method:: link_parameters_and_reactants() .. py:property:: parameters .. py:property:: Reactants :abstractmethod: Class to define metabolites and their roles in the reaction :return: .. py:property:: Parameters :abstractmethod: Class to define parameters and their roles in the reaction :return: .. py:method:: get_qssa_rate_expression() :abstractmethod: .. py:method:: update_qssa_rate_expression() :abstractmethod: .. py:method:: get_full_rate_expression() :abstractmethod: .. py:method:: calculate_rate_constants() :abstractmethod: .. py:method:: get_parameters_from_expression(expr) .. py:class:: ElementrayReactionStep(educts, products, rate_constant_name) Bases: :py:obj:`object` .. py:attribute:: educts .. py:attribute:: products .. py:attribute:: rate_constant_name .. py:method:: __str__() .. py:method:: __repr__() .. py:class:: Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`object` Global reaction class .. py:attribute:: name .. py:attribute:: enzyme :value: None .. py:attribute:: modifiers .. py:property:: reactants .. py:property:: reactant_stoichiometry .. py:property:: parameters .. py:property:: rates .. py:method:: __str__() .. py:method:: parametrize(params) .. py:class:: TabDict Bases: :py:obj:`collections.OrderedDict` Really just an ordered dict with tab completion in interactive terminals .. py:method:: __dir__() Default dir() implementation. .. py:method:: __getattr__(attr) .. py:method:: iloc(ix) .. py:function:: make_parameter_set(mechanism, param_declaration) .. py:function:: make_reactant_set(mechanism, reactant_declaration) .. py:function:: make_subclasses_dict(cls) .. py:function:: stringify_stoichiometry(stoichiometry, inihibitors=None) Stoichiometry looks like [-2, -1, 3] This is not nice as a suffix for a class name We transform it to _m2_m1_3 :param stoichiometry: :type stoichiometry: list(float) :return: suffix .. py:class:: IrreversibleHill(name, reactants, parameters=None, **kwargs) Bases: :py:obj:`skimpy.mechanisms.mechanism.KineticMechanism` Irreversible hill Uni-Uni enzyme class e.g.: A -> B .. py:attribute:: reactant_list :value: ['substrate', 'product'] .. py:attribute:: Reactants Class to define metabolites and their roles in the reaction :return: .. py:attribute:: Parameters Class to define parameters and their roles in the reaction :return: .. py:attribute:: reactant_stoichiometry .. py:attribute:: parameter_reactant_links .. py:class:: ElementaryReactions Bases: :py:obj:`tuple` .. py:method:: get_qssa_rate_expression() .. py:method:: update_qssa_rate_expression() .. py:method:: get_full_rate_expression() :abstractmethod: .. py:method:: calculate_rate_constants() :abstractmethod: .. py:data:: QSSA :value: 'qssa' .. py:data:: TQSSA :value: 'tqssa' .. py:data:: MCA :value: 'mca' .. py:data:: ODE :value: 'ode' .. py:data:: ELEMENTARY :value: 'elementary' Jacobian Types .. py:data:: NUMERICAL :value: 'numerical' .. py:data:: SYMBOLIC :value: 'symbolic' MCA Types .. py:data:: NET :value: 'net' .. py:data:: SPLIT :value: 'split' Item types .. py:data:: PARAMETER :value: 'parameter' .. py:data:: VARIABLE :value: 'variable' Units .. py:data:: KCAL :value: 'kcal' .. py:data:: KJ :value: 'kJ' .. py:data:: JOULE :value: 'JOULE' OTHER .. py:data:: WATER_FORMULA :value: 'H2O' .. py:class:: KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`abc.ABC` Helper class that provides a standard way to create an ABC using inheritance. .. py:attribute:: parameter_reactant_links .. py:attribute:: name .. py:attribute:: reactants .. py:attribute:: inhibitors :value: None .. py:attribute:: _parameters :value: None .. py:attribute:: enzyme :value: None .. py:method:: __reduce__() .. py:method:: link_parameters_and_reactants() .. py:property:: parameters .. py:property:: Reactants :abstractmethod: Class to define metabolites and their roles in the reaction :return: .. py:property:: Parameters :abstractmethod: Class to define parameters and their roles in the reaction :return: .. py:method:: get_qssa_rate_expression() :abstractmethod: .. py:method:: update_qssa_rate_expression() :abstractmethod: .. py:method:: get_full_rate_expression() :abstractmethod: .. py:method:: calculate_rate_constants() :abstractmethod: .. py:method:: get_parameters_from_expression(expr) .. py:class:: ElementrayReactionStep(educts, products, rate_constant_name) Bases: :py:obj:`object` .. py:attribute:: educts .. py:attribute:: products .. py:attribute:: rate_constant_name .. py:method:: __str__() .. py:method:: __repr__() .. py:class:: Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`object` Global reaction class .. py:attribute:: name .. py:attribute:: enzyme :value: None .. py:attribute:: modifiers .. py:property:: reactants .. py:property:: reactant_stoichiometry .. py:property:: parameters .. py:property:: rates .. py:method:: __str__() .. py:method:: parametrize(params) .. py:class:: TabDict Bases: :py:obj:`collections.OrderedDict` Really just an ordered dict with tab completion in interactive terminals .. py:method:: __dir__() Default dir() implementation. .. py:method:: __getattr__(attr) .. py:method:: iloc(ix) .. py:function:: make_parameter_set(mechanism, param_declaration) .. py:function:: make_reactant_set(mechanism, reactant_declaration) .. py:function:: make_subclasses_dict(cls) .. py:function:: stringify_stoichiometry(stoichiometry, inihibitors=None) Stoichiometry looks like [-2, -1, 3] This is not nice as a suffix for a class name We transform it to _m2_m1_3 :param stoichiometry: :type stoichiometry: list(float) :return: suffix .. py:function:: make_irrev_m_n_hill(stoichiometry) :param stoichiometry is a list of the reaction stoichioemtry .. py:data:: QSSA :value: 'qssa' .. py:data:: TQSSA :value: 'tqssa' .. py:data:: MCA :value: 'mca' .. py:data:: ODE :value: 'ode' .. py:data:: ELEMENTARY :value: 'elementary' Jacobian Types .. py:data:: NUMERICAL :value: 'numerical' .. py:data:: SYMBOLIC :value: 'symbolic' MCA Types .. py:data:: NET :value: 'net' .. py:data:: SPLIT :value: 'split' Item types .. py:data:: PARAMETER :value: 'parameter' .. py:data:: VARIABLE :value: 'variable' Units .. py:data:: KCAL :value: 'kcal' .. py:data:: KJ :value: 'kJ' .. py:data:: JOULE :value: 'JOULE' OTHER .. py:data:: WATER_FORMULA :value: 'H2O' .. py:class:: KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`abc.ABC` Helper class that provides a standard way to create an ABC using inheritance. .. py:attribute:: parameter_reactant_links .. py:attribute:: name .. py:attribute:: reactants .. py:attribute:: inhibitors :value: None .. py:attribute:: _parameters :value: None .. py:attribute:: enzyme :value: None .. py:method:: __reduce__() .. py:method:: link_parameters_and_reactants() .. py:property:: parameters .. py:property:: Reactants :abstractmethod: Class to define metabolites and their roles in the reaction :return: .. py:property:: Parameters :abstractmethod: Class to define parameters and their roles in the reaction :return: .. py:method:: get_qssa_rate_expression() :abstractmethod: .. py:method:: update_qssa_rate_expression() :abstractmethod: .. py:method:: get_full_rate_expression() :abstractmethod: .. py:method:: calculate_rate_constants() :abstractmethod: .. py:method:: get_parameters_from_expression(expr) .. py:class:: ElementrayReactionStep(educts, products, rate_constant_name) Bases: :py:obj:`object` .. py:attribute:: educts .. py:attribute:: products .. py:attribute:: rate_constant_name .. py:method:: __str__() .. py:method:: __repr__() .. py:class:: Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`object` Global reaction class .. py:attribute:: name .. py:attribute:: enzyme :value: None .. py:attribute:: modifiers .. py:property:: reactants .. py:property:: reactant_stoichiometry .. py:property:: parameters .. py:property:: rates .. py:method:: __str__() .. py:method:: parametrize(params) .. py:class:: TabDict Bases: :py:obj:`collections.OrderedDict` Really just an ordered dict with tab completion in interactive terminals .. py:method:: __dir__() Default dir() implementation. .. py:method:: __getattr__(attr) .. py:method:: iloc(ix) .. py:function:: make_parameter_set(mechanism, param_declaration) .. py:function:: make_reactant_set(mechanism, reactant_declaration) .. py:function:: make_subclasses_dict(cls) .. py:function:: stringify_stoichiometry(stoichiometry, inihibitors=None) Stoichiometry looks like [-2, -1, 3] This is not nice as a suffix for a class name We transform it to _m2_m1_3 :param stoichiometry: :type stoichiometry: list(float) :return: suffix .. py:function:: make_rev_massaction(stoichiometry) :param stoichiometry is a list of the reaction stoichioemtry .. py:data:: QSSA :value: 'qssa' .. py:data:: TQSSA :value: 'tqssa' .. py:data:: MCA :value: 'mca' .. py:data:: ODE :value: 'ode' .. py:data:: ELEMENTARY :value: 'elementary' Jacobian Types .. py:data:: NUMERICAL :value: 'numerical' .. py:data:: SYMBOLIC :value: 'symbolic' MCA Types .. py:data:: NET :value: 'net' .. py:data:: SPLIT :value: 'split' Item types .. py:data:: PARAMETER :value: 'parameter' .. py:data:: VARIABLE :value: 'variable' Units .. py:data:: KCAL :value: 'kcal' .. py:data:: KJ :value: 'kJ' .. py:data:: JOULE :value: 'JOULE' OTHER .. py:data:: WATER_FORMULA :value: 'H2O' .. py:class:: KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`abc.ABC` Helper class that provides a standard way to create an ABC using inheritance. .. py:attribute:: parameter_reactant_links .. py:attribute:: name .. py:attribute:: reactants .. py:attribute:: inhibitors :value: None .. py:attribute:: _parameters :value: None .. py:attribute:: enzyme :value: None .. py:method:: __reduce__() .. py:method:: link_parameters_and_reactants() .. py:property:: parameters .. py:property:: Reactants :abstractmethod: Class to define metabolites and their roles in the reaction :return: .. py:property:: Parameters :abstractmethod: Class to define parameters and their roles in the reaction :return: .. py:method:: get_qssa_rate_expression() :abstractmethod: .. py:method:: update_qssa_rate_expression() :abstractmethod: .. py:method:: get_full_rate_expression() :abstractmethod: .. py:method:: calculate_rate_constants() :abstractmethod: .. py:method:: get_parameters_from_expression(expr) .. py:class:: ElementrayReactionStep(educts, products, rate_constant_name) Bases: :py:obj:`object` .. py:attribute:: educts .. py:attribute:: products .. py:attribute:: rate_constant_name .. py:method:: __str__() .. py:method:: __repr__() .. py:class:: Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`object` Global reaction class .. py:attribute:: name .. py:attribute:: enzyme :value: None .. py:attribute:: modifiers .. py:property:: reactants .. py:property:: reactant_stoichiometry .. py:property:: parameters .. py:property:: rates .. py:method:: __str__() .. py:method:: parametrize(params) .. py:class:: TabDict Bases: :py:obj:`collections.OrderedDict` Really just an ordered dict with tab completion in interactive terminals .. py:method:: __dir__() Default dir() implementation. .. py:method:: __getattr__(attr) .. py:method:: iloc(ix) .. py:function:: make_parameter_set(mechanism, param_declaration) .. py:function:: make_reactant_set(mechanism, reactant_declaration) .. py:function:: make_subclasses_dict(cls) .. py:function:: stringify_stoichiometry(stoichiometry, inihibitors=None) Stoichiometry looks like [-2, -1, 3] This is not nice as a suffix for a class name We transform it to _m2_m1_3 :param stoichiometry: :type stoichiometry: list(float) :return: suffix .. py:class:: BiUniReversibleHill(name, reactants, parameters=None, **kwargs) Bases: :py:obj:`skimpy.mechanisms.mechanism.KineticMechanism` A reversible hill Bi-Uni enzyme class e.g.: A + B -> C .. py:attribute:: reactant_list :value: ['substrate1', 'substrate2', 'product'] .. py:attribute:: Reactants Class to define metabolites and their roles in the reaction :return: .. py:attribute:: Parameters Class to define parameters and their roles in the reaction :return: .. py:attribute:: reactant_stoichiometry .. py:attribute:: parameter_reactant_links .. py:class:: ElementaryReactions Bases: :py:obj:`tuple` .. py:method:: get_qssa_rate_expression() .. py:method:: update_qssa_rate_expression() .. py:method:: get_full_rate_expression() :abstractmethod: .. py:method:: calculate_rate_constants() :abstractmethod: .. py:data:: QSSA :value: 'qssa' .. py:data:: TQSSA :value: 'tqssa' .. py:data:: MCA :value: 'mca' .. py:data:: ODE :value: 'ode' .. py:data:: ELEMENTARY :value: 'elementary' Jacobian Types .. py:data:: NUMERICAL :value: 'numerical' .. py:data:: SYMBOLIC :value: 'symbolic' MCA Types .. py:data:: NET :value: 'net' .. py:data:: SPLIT :value: 'split' Item types .. py:data:: PARAMETER :value: 'parameter' .. py:data:: VARIABLE :value: 'variable' Units .. py:data:: KCAL :value: 'kcal' .. py:data:: KJ :value: 'kJ' .. py:data:: JOULE :value: 'JOULE' OTHER .. py:data:: WATER_FORMULA :value: 'H2O' .. py:class:: KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`abc.ABC` Helper class that provides a standard way to create an ABC using inheritance. .. py:attribute:: parameter_reactant_links .. py:attribute:: name .. py:attribute:: reactants .. py:attribute:: inhibitors :value: None .. py:attribute:: _parameters :value: None .. py:attribute:: enzyme :value: None .. py:method:: __reduce__() .. py:method:: link_parameters_and_reactants() .. py:property:: parameters .. py:property:: Reactants :abstractmethod: Class to define metabolites and their roles in the reaction :return: .. py:property:: Parameters :abstractmethod: Class to define parameters and their roles in the reaction :return: .. py:method:: get_qssa_rate_expression() :abstractmethod: .. py:method:: update_qssa_rate_expression() :abstractmethod: .. py:method:: get_full_rate_expression() :abstractmethod: .. py:method:: calculate_rate_constants() :abstractmethod: .. py:method:: get_parameters_from_expression(expr) .. py:class:: ElementrayReactionStep(educts, products, rate_constant_name) Bases: :py:obj:`object` .. py:attribute:: educts .. py:attribute:: products .. py:attribute:: rate_constant_name .. py:method:: __str__() .. py:method:: __repr__() .. py:class:: Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`object` Global reaction class .. py:attribute:: name .. py:attribute:: enzyme :value: None .. py:attribute:: modifiers .. py:property:: reactants .. py:property:: reactant_stoichiometry .. py:property:: parameters .. py:property:: rates .. py:method:: __str__() .. py:method:: parametrize(params) .. py:class:: TabDict Bases: :py:obj:`collections.OrderedDict` Really just an ordered dict with tab completion in interactive terminals .. py:method:: __dir__() Default dir() implementation. .. py:method:: __getattr__(attr) .. py:method:: iloc(ix) .. py:function:: make_parameter_set(mechanism, param_declaration) .. py:function:: make_reactant_set(mechanism, reactant_declaration) .. py:function:: make_subclasses_dict(cls) .. py:function:: stringify_stoichiometry(stoichiometry, inihibitors=None) Stoichiometry looks like [-2, -1, 3] This is not nice as a suffix for a class name We transform it to _m2_m1_3 :param stoichiometry: :type stoichiometry: list(float) :return: suffix .. py:class:: UniBiReversibleHill(name, reactants, parameters=None, **kwargs) Bases: :py:obj:`skimpy.mechanisms.mechanism.KineticMechanism` A reversible hill Uni-Bi enzyme class e.g.: A -> B + C .. py:attribute:: reactant_list :value: ['substrate', 'product1', 'product2'] .. py:attribute:: Reactants Class to define metabolites and their roles in the reaction :return: .. py:attribute:: Parameters Class to define parameters and their roles in the reaction :return: .. py:attribute:: reactant_stoichiometry .. py:attribute:: parameter_reactant_links .. py:class:: ElementaryReactions Bases: :py:obj:`tuple` .. py:method:: get_qssa_rate_expression() .. py:method:: update_qssa_rate_expression() .. py:method:: get_full_rate_expression() :abstractmethod: .. py:method:: calculate_rate_constants() :abstractmethod: .. py:data:: QSSA :value: 'qssa' .. py:data:: TQSSA :value: 'tqssa' .. py:data:: MCA :value: 'mca' .. py:data:: ODE :value: 'ode' .. py:data:: ELEMENTARY :value: 'elementary' Jacobian Types .. py:data:: NUMERICAL :value: 'numerical' .. py:data:: SYMBOLIC :value: 'symbolic' MCA Types .. py:data:: NET :value: 'net' .. py:data:: SPLIT :value: 'split' Item types .. py:data:: PARAMETER :value: 'parameter' .. py:data:: VARIABLE :value: 'variable' Units .. py:data:: KCAL :value: 'kcal' .. py:data:: KJ :value: 'kJ' .. py:data:: JOULE :value: 'JOULE' OTHER .. py:data:: WATER_FORMULA :value: 'H2O' .. py:class:: KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`abc.ABC` Helper class that provides a standard way to create an ABC using inheritance. .. py:attribute:: parameter_reactant_links .. py:attribute:: name .. py:attribute:: reactants .. py:attribute:: inhibitors :value: None .. py:attribute:: _parameters :value: None .. py:attribute:: enzyme :value: None .. py:method:: __reduce__() .. py:method:: link_parameters_and_reactants() .. py:property:: parameters .. py:property:: Reactants :abstractmethod: Class to define metabolites and their roles in the reaction :return: .. py:property:: Parameters :abstractmethod: Class to define parameters and their roles in the reaction :return: .. py:method:: get_qssa_rate_expression() :abstractmethod: .. py:method:: update_qssa_rate_expression() :abstractmethod: .. py:method:: get_full_rate_expression() :abstractmethod: .. py:method:: calculate_rate_constants() :abstractmethod: .. py:method:: get_parameters_from_expression(expr) .. py:class:: ElementrayReactionStep(educts, products, rate_constant_name) Bases: :py:obj:`object` .. py:attribute:: educts .. py:attribute:: products .. py:attribute:: rate_constant_name .. py:method:: __str__() .. py:method:: __repr__() .. py:class:: Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`object` Global reaction class .. py:attribute:: name .. py:attribute:: enzyme :value: None .. py:attribute:: modifiers .. py:property:: reactants .. py:property:: reactant_stoichiometry .. py:property:: parameters .. py:property:: rates .. py:method:: __str__() .. py:method:: parametrize(params) .. py:class:: TabDict Bases: :py:obj:`collections.OrderedDict` Really just an ordered dict with tab completion in interactive terminals .. py:method:: __dir__() Default dir() implementation. .. py:method:: __getattr__(attr) .. py:method:: iloc(ix) .. py:function:: make_parameter_set(mechanism, param_declaration) .. py:function:: make_reactant_set(mechanism, reactant_declaration) .. py:function:: make_subclasses_dict(cls) .. py:function:: stringify_stoichiometry(stoichiometry, inihibitors=None) Stoichiometry looks like [-2, -1, 3] This is not nice as a suffix for a class name We transform it to _m2_m1_3 :param stoichiometry: :type stoichiometry: list(float) :return: suffix .. py:class:: SimpleRegulatedGeneExpression(name, reactants, inhibitors, parameters=None, **kwargs) Bases: :py:obj:`skimpy.mechanisms.mechanism.KineticMechanism` Apprxoimate gene regulation according to XX et al e.g.: A + B -> C .. py:attribute:: reactant_list :value: ['product'] .. py:attribute:: Reactants Class to define metabolites and their roles in the reaction :return: .. py:attribute:: regulator_list :value: ['factor_1'] .. py:attribute:: SingleRegulator .. py:attribute:: Regulators .. py:attribute:: Parameters Class to define parameters and their roles in the reaction :return: .. py:attribute:: reactant_stoichiometry .. py:attribute:: parameter_reactant_links .. py:class:: ElementaryReactions Bases: :py:obj:`tuple` .. py:method:: get_qssa_rate_expression() .. py:method:: update_qssa_rate_expression() .. py:method:: get_full_rate_expression() :abstractmethod: .. py:method:: calculate_rate_constants() :abstractmethod: .. py:data:: QSSA :value: 'qssa' .. py:data:: TQSSA :value: 'tqssa' .. py:data:: MCA :value: 'mca' .. py:data:: ODE :value: 'ode' .. py:data:: ELEMENTARY :value: 'elementary' Jacobian Types .. py:data:: NUMERICAL :value: 'numerical' .. py:data:: SYMBOLIC :value: 'symbolic' MCA Types .. py:data:: NET :value: 'net' .. py:data:: SPLIT :value: 'split' Item types .. py:data:: PARAMETER :value: 'parameter' .. py:data:: VARIABLE :value: 'variable' Units .. py:data:: KCAL :value: 'kcal' .. py:data:: KJ :value: 'kJ' .. py:data:: JOULE :value: 'JOULE' OTHER .. py:data:: WATER_FORMULA :value: 'H2O' .. py:class:: KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None) Bases: :py:obj:`abc.ABC` Helper class that provides a standard way to create an ABC using inheritance. .. py:attribute:: parameter_reactant_links .. py:attribute:: name .. py:attribute:: reactants .. py:attribute:: inhibitors :value: None .. py:attribute:: _parameters :value: None .. py:attribute:: enzyme :value: None .. py:method:: __reduce__() .. py:method:: link_parameters_and_reactants() .. py:property:: parameters .. py:property:: Reactants :abstractmethod: Class to define metabolites and their roles in the reaction :return: .. py:property:: Parameters :abstractmethod: Class to define parameters and their roles in the reaction :return: .. py:method:: get_qssa_rate_expression() :abstractmethod: .. py:method:: update_qssa_rate_expression() :abstractmethod: .. py:method:: get_full_rate_expression() :abstractmethod: .. py:method:: calculate_rate_constants() :abstractmethod: .. py:method:: get_parameters_from_expression(expr)