8.1.1.5. skimpy.mechanisms¶

[———]

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.

8.1.1.5.1. Submodules¶

8.1.1.5.2. Attributes¶

`QSSA`
`TQSSA`
`MCA`
`ODE`
`ELEMENTARY`	Jacobian Types
`NUMERICAL`
`SYMBOLIC`	MCA Types
`NET`
`SPLIT`	Item types
`PARAMETER`
`VARIABLE`	Units
`KCAL`
`KJ`
`JOULE`	OTHER
`WATER_FORMULA`
`QSSA`
`TQSSA`
`MCA`
`ODE`
`ELEMENTARY`	Jacobian Types
`NUMERICAL`
`SYMBOLIC`	MCA Types
`NET`
`SPLIT`	Item types
`PARAMETER`
`VARIABLE`	Units
`KCAL`
`KJ`
`JOULE`	OTHER
`WATER_FORMULA`
`QSSA`
`TQSSA`
`MCA`
`ODE`
`ELEMENTARY`	Jacobian Types
`NUMERICAL`
`SYMBOLIC`	MCA Types
`NET`
`SPLIT`	Item types
`PARAMETER`
`VARIABLE`	Units
`KCAL`
`KJ`
`JOULE`	OTHER
`WATER_FORMULA`
`QSSA`
`TQSSA`
`MCA`
`ODE`
`ELEMENTARY`	Jacobian Types
`NUMERICAL`
`SYMBOLIC`	MCA Types
`NET`
`SPLIT`	Item types
`PARAMETER`
`VARIABLE`	Units
`KCAL`
`KJ`
`JOULE`	OTHER
`WATER_FORMULA`
`QSSA`
`TQSSA`
`MCA`
`ODE`
`ELEMENTARY`	Jacobian Types
`NUMERICAL`
`SYMBOLIC`	MCA Types
`NET`
`SPLIT`	Item types
`PARAMETER`
`VARIABLE`	Units
`KCAL`
`KJ`
`JOULE`	OTHER
`WATER_FORMULA`
`QSSA`
`TQSSA`
`MCA`
`ODE`
`ELEMENTARY`	Jacobian Types
`NUMERICAL`
`SYMBOLIC`	MCA Types
`NET`
`SPLIT`	Item types
`PARAMETER`
`VARIABLE`	Units
`KCAL`
`KJ`
`JOULE`	OTHER
`WATER_FORMULA`
`QSSA`
`TQSSA`
`MCA`
`ODE`
`ELEMENTARY`	Jacobian Types
`NUMERICAL`
`SYMBOLIC`	MCA Types
`NET`
`SPLIT`	Item types
`PARAMETER`
`VARIABLE`	Units
`KCAL`
`KJ`
`JOULE`	OTHER
`WATER_FORMULA`
`QSSA`
`TQSSA`
`MCA`
`ODE`
`ELEMENTARY`	Jacobian Types
`NUMERICAL`
`SYMBOLIC`	MCA Types
`NET`
`SPLIT`	Item types
`PARAMETER`
`VARIABLE`	Units
`KCAL`
`KJ`
`JOULE`	OTHER
`WATER_FORMULA`
`QSSA`
`TQSSA`
`MCA`
`ODE`
`ELEMENTARY`	Jacobian Types
`NUMERICAL`
`SYMBOLIC`	MCA Types
`NET`
`SPLIT`	Item types
`PARAMETER`
`VARIABLE`	Units
`KCAL`
`KJ`
`JOULE`	OTHER
`WATER_FORMULA`
`QSSA`
`TQSSA`
`MCA`
`ODE`
`ELEMENTARY`	Jacobian Types
`NUMERICAL`
`SYMBOLIC`	MCA Types
`NET`
`SPLIT`	Item types
`PARAMETER`
`VARIABLE`	Units
`KCAL`
`KJ`
`JOULE`	OTHER
`WATER_FORMULA`
`QSSA`
`TQSSA`
`MCA`
`ODE`
`ELEMENTARY`	Jacobian Types
`NUMERICAL`
`SYMBOLIC`	MCA Types
`NET`
`SPLIT`	Item types
`PARAMETER`
`VARIABLE`	Units
`KCAL`
`KJ`
`JOULE`	OTHER
`WATER_FORMULA`
`QSSA`
`TQSSA`
`MCA`
`ODE`
`ELEMENTARY`	Jacobian Types
`NUMERICAL`
`SYMBOLIC`	MCA Types
`NET`
`SPLIT`	Item types
`PARAMETER`
`VARIABLE`	Units
`KCAL`
`KJ`
`JOULE`	OTHER
`WATER_FORMULA`
`QSSA`
`TQSSA`
`MCA`
`ODE`
`ELEMENTARY`	Jacobian Types
`NUMERICAL`
`SYMBOLIC`	MCA Types
`NET`
`SPLIT`	Item types
`PARAMETER`
`VARIABLE`	Units
`KCAL`
`KJ`
`JOULE`	OTHER
`WATER_FORMULA`
`QSSA`
`TQSSA`
`MCA`
`ODE`
`ELEMENTARY`	Jacobian Types
`NUMERICAL`
`SYMBOLIC`	MCA Types
`NET`
`SPLIT`	Item types
`PARAMETER`
`VARIABLE`	Units
`KCAL`
`KJ`
`JOULE`	OTHER
`WATER_FORMULA`
`QSSA`
`TQSSA`
`MCA`
`ODE`
`ELEMENTARY`	Jacobian Types
`NUMERICAL`
`SYMBOLIC`	MCA Types
`NET`
`SPLIT`	Item types
`PARAMETER`
`VARIABLE`	Units
`KCAL`
`KJ`
`JOULE`	OTHER
`WATER_FORMULA`
`QSSA`
`TQSSA`
`MCA`
`ODE`
`ELEMENTARY`	Jacobian Types
`NUMERICAL`
`SYMBOLIC`	MCA Types
`NET`
`SPLIT`	Item types
`PARAMETER`
`VARIABLE`	Units
`KCAL`
`KJ`
`JOULE`	OTHER
`WATER_FORMULA`

8.1.1.5.3. Classes¶

`KineticMechanism`	Helper class that provides a standard way to create an ABC using
`ElementrayReactionStep`
`Reaction`	Global reaction class
`Reactant`
`TabDict`	Really just an ordered dict with tab completion in interactive terminals
`ReversibleMichaelisMenten`	A reversible uni uni reaction enzmye class
`KineticMechanism`	Helper class that provides a standard way to create an ABC using
`ElementrayReactionStep`
`Reaction`	Global reaction class
`TabDict`	Really just an ordered dict with tab completion in interactive terminals
`RandBiBiReversibleMichaelisMenten`	A reversible random ordered bi bi reaction enzmye class
`KineticMechanism`	Helper class that provides a standard way to create an ABC using
`ElementrayReactionStep`
`Reaction`	Global reaction class
`TabDict`	Really just an ordered dict with tab completion in interactive terminals
`KineticMechanism`	Helper class that provides a standard way to create an ABC using
`ElementrayReactionStep`
`Reaction`	Global reaction class
`TabDict`	Really just an ordered dict with tab completion in interactive terminals
`KineticMechanism`	Helper class that provides a standard way to create an ABC using
`ElementrayReactionStep`
`Reaction`	Global reaction class
`TabDict`	Really just an ordered dict with tab completion in interactive terminals
`KineticMechanism`	Helper class that provides a standard way to create an ABC using
`ElementrayReactionStep`
`Reaction`	Global reaction class
`TabDict`	Really just an ordered dict with tab completion in interactive terminals
`KineticMechanism`	Helper class that provides a standard way to create an ABC using
`ElementrayReactionStep`
`Reaction`	Global reaction class
`TabDict`	Really just an ordered dict with tab completion in interactive terminals
`KineticMechanism`	Helper class that provides a standard way to create an ABC using
`TabDict`	Really just an ordered dict with tab completion in interactive terminals
`KineticMechanism`	Helper class that provides a standard way to create an ABC using
`ElementrayReactionStep`
`Reaction`	Global reaction class
`TabDict`	Really just an ordered dict with tab completion in interactive terminals
`KineticMechanism`	Helper class that provides a standard way to create an ABC using
`ElementrayReactionStep`
`Reaction`	Global reaction class
`TabDict`	Really just an ordered dict with tab completion in interactive terminals
`KineticMechanism`	Helper class that provides a standard way to create an ABC using
`ElementrayReactionStep`
`Reaction`	Global reaction class
`TabDict`	Really just an ordered dict with tab completion in interactive terminals
`IrreversibleHill`	Irreversible hill Uni-Uni enzyme class
`KineticMechanism`	Helper class that provides a standard way to create an ABC using
`ElementrayReactionStep`
`Reaction`	Global reaction class
`TabDict`	Really just an ordered dict with tab completion in interactive terminals
`KineticMechanism`	Helper class that provides a standard way to create an ABC using
`ElementrayReactionStep`
`Reaction`	Global reaction class
`TabDict`	Really just an ordered dict with tab completion in interactive terminals
`KineticMechanism`	Helper class that provides a standard way to create an ABC using
`ElementrayReactionStep`
`Reaction`	Global reaction class
`TabDict`	Really just an ordered dict with tab completion in interactive terminals
`BiUniReversibleHill`	A reversible hill Bi-Uni enzyme class
`KineticMechanism`	Helper class that provides a standard way to create an ABC using
`ElementrayReactionStep`
`Reaction`	Global reaction class
`TabDict`	Really just an ordered dict with tab completion in interactive terminals
`UniBiReversibleHill`	A reversible hill Uni-Bi enzyme class
`KineticMechanism`	Helper class that provides a standard way to create an ABC using
`ElementrayReactionStep`
`Reaction`	Global reaction class
`TabDict`	Really just an ordered dict with tab completion in interactive terminals
`SimpleRegulatedGeneExpression`	Apprxoimate gene regulation according to XX et al
`KineticMechanism`	Helper class that provides a standard way to create an ABC using

8.1.1.5.4. Functions¶

`make_parameter_set`(mechanism, param_declaration)
`make_reactant_set`(mechanism, reactant_declaration)
`make_parameter_set`(mechanism, param_declaration)
`make_reactant_set`(mechanism, reactant_declaration)
`make_parameter_set`(mechanism, param_declaration)
`make_reactant_set`(mechanism, reactant_declaration)
`make_subclasses_dict`(cls)
`stringify_stoichiometry`(stoichiometry[, inihibitors])	Stoichiometry looks like [-2, -1, 3]
`make_convenience`(stoichiometry)	:param stoichiometry is a list of the reaction stoichioemtry
`make_parameter_set`(mechanism, param_declaration)
`make_reactant_set`(mechanism, reactant_declaration)
`make_subclasses_dict`(cls)
`stringify_stoichiometry`(stoichiometry[, inihibitors])	Stoichiometry looks like [-2, -1, 3]
`make_convenience_with_inhibition`(stoichiometry, ...)	:param stoichiometry is a list of the reaction stoichioemtry
`make_parameter_set`(mechanism, param_declaration)
`make_reactant_set`(mechanism, reactant_declaration)
`make_subclasses_dict`(cls)
`stringify_stoichiometry`(stoichiometry[, inihibitors])	Stoichiometry looks like [-2, -1, 3]
`make_generalized_reversible_hill_n_n`(stoichiometry)	:param stoichiometry is a list of the reaction stoichioemtry
`make_parameter_set`(mechanism, param_declaration)
`make_reactant_set`(mechanism, reactant_declaration)
`make_subclasses_dict`(cls)
`stringify_stoichiometry`(stoichiometry[, inihibitors])	Stoichiometry looks like [-2, -1, 3]
`make_generalized_reversible_hill_n_n_h1`(stoichiometry)	This function generxied
`make_parameter_set`(mechanism, param_declaration)
`make_reactant_set`(mechanism, reactant_declaration)
`make_subclasses_dict`(cls)
`stringify_stoichiometry`(stoichiometry[, inihibitors])	Stoichiometry looks like [-2, -1, 3]
`make_generalized_reversible_hill_n_n_h1_with_inhibition`(...)	This function creates the Generalized Rev. Hill with h = 1 and adds competitive inhibition
`make_parameter_set`(mechanism, param_declaration)
`make_reactant_set`(mechanism, reactant_declaration)
`make_subclasses_dict`(cls)
`stringify_stoichiometry`(stoichiometry[, inihibitors])	Stoichiometry looks like [-2, -1, 3]
`make_generalized_elementary_kinetics`(stoichiometry, ...)	Creates a reversible N-M GeneralizedElementaryKinetics class
`make_parameter_set`(mechanism, param_declaration)
`make_reactant_set`(mechanism, reactant_declaration)
`make_subclasses_dict`(cls)
`stringify_stoichiometry`(stoichiometry[, inihibitors])	Stoichiometry looks like [-2, -1, 3]
`make_irrev_m_n_michaelis_menten`(stoichiometry)	:param stoichiometry is a list of the reaction stoichioemtry
`make_parameter_set`(mechanism, param_declaration)
`make_reactant_set`(mechanism, reactant_declaration)
`make_subclasses_dict`(cls)
`stringify_stoichiometry`(stoichiometry[, inihibitors])	Stoichiometry looks like [-2, -1, 3]
`make_irrev_massaction`(stoichiometry)	:param stoichiometry is a list of the reaction stoichioemtry
`make_parameter_set`(mechanism, param_declaration)
`make_reactant_set`(mechanism, reactant_declaration)
`make_subclasses_dict`(cls)
`stringify_stoichiometry`(stoichiometry[, inihibitors])	Stoichiometry looks like [-2, -1, 3]
`make_parameter_set`(mechanism, param_declaration)
`make_reactant_set`(mechanism, reactant_declaration)
`make_subclasses_dict`(cls)
`stringify_stoichiometry`(stoichiometry[, inihibitors])	Stoichiometry looks like [-2, -1, 3]
`make_irrev_m_n_hill`(stoichiometry)	:param stoichiometry is a list of the reaction stoichioemtry
`make_parameter_set`(mechanism, param_declaration)
`make_reactant_set`(mechanism, reactant_declaration)
`make_subclasses_dict`(cls)
`stringify_stoichiometry`(stoichiometry[, inihibitors])	Stoichiometry looks like [-2, -1, 3]
`make_rev_massaction`(stoichiometry)	:param stoichiometry is a list of the reaction stoichioemtry
`make_parameter_set`(mechanism, param_declaration)
`make_reactant_set`(mechanism, reactant_declaration)
`make_subclasses_dict`(cls)
`stringify_stoichiometry`(stoichiometry[, inihibitors])	Stoichiometry looks like [-2, -1, 3]
`make_parameter_set`(mechanism, param_declaration)
`make_reactant_set`(mechanism, reactant_declaration)
`make_subclasses_dict`(cls)
`stringify_stoichiometry`(stoichiometry[, inihibitors])	Stoichiometry looks like [-2, -1, 3]
`make_parameter_set`(mechanism, param_declaration)
`make_reactant_set`(mechanism, reactant_declaration)
`make_subclasses_dict`(cls)
`stringify_stoichiometry`(stoichiometry[, inihibitors])	Stoichiometry looks like [-2, -1, 3]

8.1.1.5.5. Package Contents¶

class skimpy.KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None)¶

Bases: abc.ABC

Helper class that provides a standard way to create an ABC using inheritance.

parameter_reactant_links¶

name¶

reactants¶

inhibitors = None¶

_parameters = None¶

enzyme = None¶

__reduce__()¶

link_parameters_and_reactants()¶

property parameters¶

abstract property Reactants¶: Class to define metabolites and their roles in the reaction :return:

abstract property Parameters¶: Class to define parameters and their roles in the reaction :return:

abstract get_qssa_rate_expression()¶

abstract update_qssa_rate_expression()¶

abstract get_full_rate_expression()¶

abstract calculate_rate_constants()¶

get_parameters_from_expression(expr)¶

class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)¶

Bases: object

educts¶

products¶

rate_constant_name¶

__str__()¶

__repr__()¶

class skimpy.Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None)¶

Bases: object

Global reaction class

name¶

enzyme = None¶

modifiers¶

property reactants¶

property reactant_stoichiometry¶

property parameters¶

property rates¶

__str__()¶

parametrize(params)¶

skimpy.make_parameter_set(mechanism, param_declaration)¶

skimpy.make_reactant_set(mechanism, reactant_declaration)¶

class skimpy.Reactant(name, value=None, model=None, suffix='')¶

Bases: Item

type = 'variable'¶

compartment = None¶

class skimpy.TabDict¶

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__()¶: Default dir() implementation.

__getattr__(attr)¶

iloc(ix)¶

class skimpy.ReversibleMichaelisMenten(name, reactants, parameters=None, **kwargs)¶

Bases: skimpy.mechanisms.mechanism.KineticMechanism

A reversible uni uni reaction enzmye class

Reactants¶: Class to define metabolites and their roles in the reaction :return:

Parameters¶: Class to define parameters and their roles in the reaction :return:

reactant_stoichiometry¶

parameter_reactant_links¶

class ElementaryReactions¶

Bases: tuple

r1f¶

r1b¶

r2f¶

r2b¶

get_qssa_rate_expression()¶

update_qssa_rate_expression()¶

get_full_rate_expression()¶

calculate_rate_constants()¶

skimpy.QSSA = 'qssa'¶

skimpy.TQSSA = 'tqssa'¶

skimpy.MCA = 'mca'¶

skimpy.ODE = 'ode'¶

skimpy.ELEMENTARY = 'elementary'¶: Jacobian Types

skimpy.NUMERICAL = 'numerical'¶

skimpy.SYMBOLIC = 'symbolic'¶: MCA Types

skimpy.NET = 'net'¶

skimpy.SPLIT = 'split'¶: Item types

skimpy.PARAMETER = 'parameter'¶

skimpy.VARIABLE = 'variable'¶: Units

skimpy.KCAL = 'kcal'¶

skimpy.KJ = 'kJ'¶

skimpy.JOULE = 'JOULE'¶: OTHER

skimpy.WATER_FORMULA = 'H2O'¶

class skimpy.KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None)¶

Bases: abc.ABC

Helper class that provides a standard way to create an ABC using inheritance.

parameter_reactant_links¶

name¶

reactants¶

inhibitors = None¶

_parameters = None¶

enzyme = None¶

__reduce__()¶

link_parameters_and_reactants()¶

property parameters¶

abstract property Reactants¶: Class to define metabolites and their roles in the reaction :return:

abstract property Parameters¶: Class to define parameters and their roles in the reaction :return:

abstract get_qssa_rate_expression()¶

abstract update_qssa_rate_expression()¶

abstract get_full_rate_expression()¶

abstract calculate_rate_constants()¶

get_parameters_from_expression(expr)¶

class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)¶

Bases: object

educts¶

products¶

rate_constant_name¶

__str__()¶

__repr__()¶

class skimpy.Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None)¶

Bases: object

Global reaction class

name¶

enzyme = None¶

modifiers¶

property reactants¶

property reactant_stoichiometry¶

property parameters¶

property rates¶

__str__()¶

parametrize(params)¶

class skimpy.TabDict¶

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__()¶: Default dir() implementation.

__getattr__(attr)¶

iloc(ix)¶

skimpy.make_parameter_set(mechanism, param_declaration)¶

skimpy.make_reactant_set(mechanism, reactant_declaration)¶

class skimpy.RandBiBiReversibleMichaelisMenten(name, reactants, parameters=None, **kwargs)¶

Bases: skimpy.mechanisms.mechanism.KineticMechanism

A reversible random ordered bi bi reaction enzmye class

Reactants¶: Class to define metabolites and their roles in the reaction :return:

Parameters¶: Class to define parameters and their roles in the reaction :return:

reactant_stoichiometry¶

parameter_reactant_links¶

class ElementaryReactions¶: Bases: tuple

get_qssa_rate_expression()¶

update_qssa_rate_expression()¶

abstract get_full_rate_expression()¶

abstract calculate_rate_constants()¶

skimpy.QSSA = 'qssa'¶

skimpy.TQSSA = 'tqssa'¶

skimpy.MCA = 'mca'¶

skimpy.ODE = 'ode'¶

skimpy.ELEMENTARY = 'elementary'¶: Jacobian Types

skimpy.NUMERICAL = 'numerical'¶

skimpy.SYMBOLIC = 'symbolic'¶: MCA Types

skimpy.NET = 'net'¶

skimpy.SPLIT = 'split'¶: Item types

skimpy.PARAMETER = 'parameter'¶

skimpy.VARIABLE = 'variable'¶: Units

skimpy.KCAL = 'kcal'¶

skimpy.KJ = 'kJ'¶

skimpy.JOULE = 'JOULE'¶: OTHER

skimpy.WATER_FORMULA = 'H2O'¶

class skimpy.KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None)¶

Bases: abc.ABC

Helper class that provides a standard way to create an ABC using inheritance.

parameter_reactant_links¶

name¶

reactants¶

inhibitors = None¶

_parameters = None¶

enzyme = None¶

__reduce__()¶

link_parameters_and_reactants()¶

property parameters¶

abstract property Reactants¶: Class to define metabolites and their roles in the reaction :return:

abstract property Parameters¶: Class to define parameters and their roles in the reaction :return:

abstract get_qssa_rate_expression()¶

abstract update_qssa_rate_expression()¶

abstract get_full_rate_expression()¶

abstract calculate_rate_constants()¶

get_parameters_from_expression(expr)¶

class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)¶

Bases: object

educts¶

products¶

rate_constant_name¶

__str__()¶

__repr__()¶

class skimpy.Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None)¶

Bases: object

Global reaction class

name¶

enzyme = None¶

modifiers¶

property reactants¶

property reactant_stoichiometry¶

property parameters¶

property rates¶

__str__()¶

parametrize(params)¶

class skimpy.TabDict¶

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__()¶: Default dir() implementation.

__getattr__(attr)¶

iloc(ix)¶

skimpy.make_parameter_set(mechanism, param_declaration)¶

skimpy.make_reactant_set(mechanism, reactant_declaration)¶

skimpy.make_subclasses_dict(cls)¶

skimpy.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

skimpy.make_convenience(stoichiometry)¶: :param stoichiometry is a list of the reaction stoichioemtry

skimpy.QSSA = 'qssa'¶

skimpy.TQSSA = 'tqssa'¶

skimpy.MCA = 'mca'¶

skimpy.ODE = 'ode'¶

skimpy.ELEMENTARY = 'elementary'¶: Jacobian Types

skimpy.NUMERICAL = 'numerical'¶

skimpy.SYMBOLIC = 'symbolic'¶: MCA Types

skimpy.NET = 'net'¶

skimpy.SPLIT = 'split'¶: Item types

skimpy.PARAMETER = 'parameter'¶

skimpy.VARIABLE = 'variable'¶: Units

skimpy.KCAL = 'kcal'¶

skimpy.KJ = 'kJ'¶

skimpy.JOULE = 'JOULE'¶: OTHER

skimpy.WATER_FORMULA = 'H2O'¶

class skimpy.KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None)¶

Bases: abc.ABC

Helper class that provides a standard way to create an ABC using inheritance.

parameter_reactant_links¶

name¶

reactants¶

inhibitors = None¶

_parameters = None¶

enzyme = None¶

__reduce__()¶

link_parameters_and_reactants()¶

property parameters¶

abstract property Reactants¶: Class to define metabolites and their roles in the reaction :return:

abstract property Parameters¶: Class to define parameters and their roles in the reaction :return:

abstract get_qssa_rate_expression()¶

abstract update_qssa_rate_expression()¶

abstract get_full_rate_expression()¶

abstract calculate_rate_constants()¶

get_parameters_from_expression(expr)¶

class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)¶

Bases: object

educts¶

products¶

rate_constant_name¶

__str__()¶

__repr__()¶

class skimpy.Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None)¶

Bases: object

Global reaction class

name¶

enzyme = None¶

modifiers¶

property reactants¶

property reactant_stoichiometry¶

property parameters¶

property rates¶

__str__()¶

parametrize(params)¶

class skimpy.TabDict¶

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__()¶: Default dir() implementation.

__getattr__(attr)¶

iloc(ix)¶

skimpy.make_parameter_set(mechanism, param_declaration)¶

skimpy.make_reactant_set(mechanism, reactant_declaration)¶

skimpy.make_subclasses_dict(cls)¶

skimpy.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

skimpy.make_convenience_with_inhibition(stoichiometry, inihbitor_stoichiometry)¶: :param stoichiometry is a list of the reaction stoichioemtry

skimpy.QSSA = 'qssa'¶

skimpy.TQSSA = 'tqssa'¶

skimpy.MCA = 'mca'¶

skimpy.ODE = 'ode'¶

skimpy.ELEMENTARY = 'elementary'¶: Jacobian Types

skimpy.NUMERICAL = 'numerical'¶

skimpy.SYMBOLIC = 'symbolic'¶: MCA Types

skimpy.NET = 'net'¶

skimpy.SPLIT = 'split'¶: Item types

skimpy.PARAMETER = 'parameter'¶

skimpy.VARIABLE = 'variable'¶: Units

skimpy.KCAL = 'kcal'¶

skimpy.KJ = 'kJ'¶

skimpy.JOULE = 'JOULE'¶: OTHER

skimpy.WATER_FORMULA = 'H2O'¶

class skimpy.KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None)¶

Bases: abc.ABC

Helper class that provides a standard way to create an ABC using inheritance.

parameter_reactant_links¶

name¶

reactants¶

inhibitors = None¶

_parameters = None¶

enzyme = None¶

__reduce__()¶

link_parameters_and_reactants()¶

property parameters¶

abstract property Reactants¶: Class to define metabolites and their roles in the reaction :return:

abstract property Parameters¶: Class to define parameters and their roles in the reaction :return:

abstract get_qssa_rate_expression()¶

abstract update_qssa_rate_expression()¶

abstract get_full_rate_expression()¶

abstract calculate_rate_constants()¶

get_parameters_from_expression(expr)¶

class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)¶

Bases: object

educts¶

products¶

rate_constant_name¶

__str__()¶

__repr__()¶

class skimpy.Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None)¶

Bases: object

Global reaction class

name¶

enzyme = None¶

modifiers¶

property reactants¶

property reactant_stoichiometry¶

property parameters¶

property rates¶

__str__()¶

parametrize(params)¶

class skimpy.TabDict¶

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__()¶: Default dir() implementation.

__getattr__(attr)¶

iloc(ix)¶

skimpy.make_parameter_set(mechanism, param_declaration)¶

skimpy.make_reactant_set(mechanism, reactant_declaration)¶

skimpy.make_subclasses_dict(cls)¶

skimpy.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

skimpy.make_generalized_reversible_hill_n_n(stoichiometry)¶: :param stoichiometry is a list of the reaction stoichioemtry

skimpy.QSSA = 'qssa'¶

skimpy.TQSSA = 'tqssa'¶

skimpy.MCA = 'mca'¶

skimpy.ODE = 'ode'¶

skimpy.ELEMENTARY = 'elementary'¶: Jacobian Types

skimpy.NUMERICAL = 'numerical'¶

skimpy.SYMBOLIC = 'symbolic'¶: MCA Types

skimpy.NET = 'net'¶

skimpy.SPLIT = 'split'¶: Item types

skimpy.PARAMETER = 'parameter'¶

skimpy.VARIABLE = 'variable'¶: Units

skimpy.KCAL = 'kcal'¶

skimpy.KJ = 'kJ'¶

skimpy.JOULE = 'JOULE'¶: OTHER

skimpy.WATER_FORMULA = 'H2O'¶

class skimpy.KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None)¶

Bases: abc.ABC

Helper class that provides a standard way to create an ABC using inheritance.

parameter_reactant_links¶

name¶

reactants¶

inhibitors = None¶

_parameters = None¶

enzyme = None¶

__reduce__()¶

link_parameters_and_reactants()¶

property parameters¶

abstract property Reactants¶: Class to define metabolites and their roles in the reaction :return:

abstract property Parameters¶: Class to define parameters and their roles in the reaction :return:

abstract get_qssa_rate_expression()¶

abstract update_qssa_rate_expression()¶

abstract get_full_rate_expression()¶

abstract calculate_rate_constants()¶

get_parameters_from_expression(expr)¶

class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)¶

Bases: object

educts¶

products¶

rate_constant_name¶

__str__()¶

__repr__()¶

class skimpy.Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None)¶

Bases: object

Global reaction class

name¶

enzyme = None¶

modifiers¶

property reactants¶

property reactant_stoichiometry¶

property parameters¶

property rates¶

__str__()¶

parametrize(params)¶

class skimpy.TabDict¶

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__()¶: Default dir() implementation.

__getattr__(attr)¶

iloc(ix)¶

skimpy.make_parameter_set(mechanism, param_declaration)¶

skimpy.make_reactant_set(mechanism, reactant_declaration)¶

skimpy.make_subclasses_dict(cls)¶

skimpy.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

skimpy.make_generalized_reversible_hill_n_n_h1(stoichiometry)¶: This function generxied :param stoichiometry is a list of the reaction stoichioemtry

skimpy.QSSA = 'qssa'¶

skimpy.TQSSA = 'tqssa'¶

skimpy.MCA = 'mca'¶

skimpy.ODE = 'ode'¶

skimpy.ELEMENTARY = 'elementary'¶: Jacobian Types

skimpy.NUMERICAL = 'numerical'¶

skimpy.SYMBOLIC = 'symbolic'¶: MCA Types

skimpy.NET = 'net'¶

skimpy.SPLIT = 'split'¶: Item types

skimpy.PARAMETER = 'parameter'¶

skimpy.VARIABLE = 'variable'¶: Units

skimpy.KCAL = 'kcal'¶

skimpy.KJ = 'kJ'¶

skimpy.JOULE = 'JOULE'¶: OTHER

skimpy.WATER_FORMULA = 'H2O'¶

class skimpy.KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None)¶

Bases: abc.ABC

Helper class that provides a standard way to create an ABC using inheritance.

parameter_reactant_links¶

name¶

reactants¶

inhibitors = None¶

_parameters = None¶

enzyme = None¶

__reduce__()¶

link_parameters_and_reactants()¶

property parameters¶

abstract property Reactants¶: Class to define metabolites and their roles in the reaction :return:

abstract property Parameters¶: Class to define parameters and their roles in the reaction :return:

abstract get_qssa_rate_expression()¶

abstract update_qssa_rate_expression()¶

abstract get_full_rate_expression()¶

abstract calculate_rate_constants()¶

get_parameters_from_expression(expr)¶

class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)¶

Bases: object

educts¶

products¶

rate_constant_name¶

__str__()¶

__repr__()¶

class skimpy.Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None)¶

Bases: object

Global reaction class

name¶

enzyme = None¶

modifiers¶

property reactants¶

property reactant_stoichiometry¶

property parameters¶

property rates¶

__str__()¶

parametrize(params)¶

class skimpy.TabDict¶

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__()¶: Default dir() implementation.

__getattr__(attr)¶

iloc(ix)¶

skimpy.make_parameter_set(mechanism, param_declaration)¶

skimpy.make_reactant_set(mechanism, reactant_declaration)¶

skimpy.make_subclasses_dict(cls)¶

skimpy.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

skimpy.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

skimpy.QSSA = 'qssa'¶

skimpy.TQSSA = 'tqssa'¶

skimpy.MCA = 'mca'¶

skimpy.ODE = 'ode'¶

skimpy.ELEMENTARY = 'elementary'¶: Jacobian Types

skimpy.NUMERICAL = 'numerical'¶

skimpy.SYMBOLIC = 'symbolic'¶: MCA Types

skimpy.NET = 'net'¶

skimpy.SPLIT = 'split'¶: Item types

skimpy.PARAMETER = 'parameter'¶

skimpy.VARIABLE = 'variable'¶: Units

skimpy.KCAL = 'kcal'¶

skimpy.KJ = 'kJ'¶

skimpy.JOULE = 'JOULE'¶: OTHER

skimpy.WATER_FORMULA = 'H2O'¶

class skimpy.KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None)¶

Bases: abc.ABC

Helper class that provides a standard way to create an ABC using inheritance.

parameter_reactant_links¶

name¶

reactants¶

inhibitors = None¶

_parameters = None¶

enzyme = None¶

__reduce__()¶

link_parameters_and_reactants()¶

property parameters¶

abstract property Reactants¶: Class to define metabolites and their roles in the reaction :return:

abstract property Parameters¶: Class to define parameters and their roles in the reaction :return:

abstract get_qssa_rate_expression()¶

abstract update_qssa_rate_expression()¶

abstract get_full_rate_expression()¶

abstract calculate_rate_constants()¶

get_parameters_from_expression(expr)¶

class skimpy.TabDict¶

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__()¶: Default dir() implementation.

__getattr__(attr)¶

iloc(ix)¶

skimpy.make_parameter_set(mechanism, param_declaration)¶

skimpy.make_reactant_set(mechanism, reactant_declaration)¶

skimpy.make_subclasses_dict(cls)¶

skimpy.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

skimpy.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

skimpy.QSSA = 'qssa'¶

skimpy.TQSSA = 'tqssa'¶

skimpy.MCA = 'mca'¶

skimpy.ODE = 'ode'¶

skimpy.ELEMENTARY = 'elementary'¶: Jacobian Types

skimpy.NUMERICAL = 'numerical'¶

skimpy.SYMBOLIC = 'symbolic'¶: MCA Types

skimpy.NET = 'net'¶

skimpy.SPLIT = 'split'¶: Item types

skimpy.PARAMETER = 'parameter'¶

skimpy.VARIABLE = 'variable'¶: Units

skimpy.KCAL = 'kcal'¶

skimpy.KJ = 'kJ'¶

skimpy.JOULE = 'JOULE'¶: OTHER

skimpy.WATER_FORMULA = 'H2O'¶

class skimpy.KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None)¶

Bases: abc.ABC

Helper class that provides a standard way to create an ABC using inheritance.

parameter_reactant_links¶

name¶

reactants¶

inhibitors = None¶

_parameters = None¶

enzyme = None¶

__reduce__()¶

link_parameters_and_reactants()¶

property parameters¶

abstract property Reactants¶: Class to define metabolites and their roles in the reaction :return:

abstract property Parameters¶: Class to define parameters and their roles in the reaction :return:

abstract get_qssa_rate_expression()¶

abstract update_qssa_rate_expression()¶

abstract get_full_rate_expression()¶

abstract calculate_rate_constants()¶

get_parameters_from_expression(expr)¶

class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)¶

Bases: object

educts¶

products¶

rate_constant_name¶

__str__()¶

__repr__()¶

class skimpy.Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None)¶

Bases: object

Global reaction class

name¶

enzyme = None¶

modifiers¶

property reactants¶

property reactant_stoichiometry¶

property parameters¶

property rates¶

__str__()¶

parametrize(params)¶

class skimpy.TabDict¶

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__()¶: Default dir() implementation.

__getattr__(attr)¶

iloc(ix)¶

skimpy.make_parameter_set(mechanism, param_declaration)¶

skimpy.make_reactant_set(mechanism, reactant_declaration)¶

skimpy.make_subclasses_dict(cls)¶

skimpy.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

skimpy.make_irrev_m_n_michaelis_menten(stoichiometry)¶: :param stoichiometry is a list of the reaction stoichioemtry

skimpy.QSSA = 'qssa'¶

skimpy.TQSSA = 'tqssa'¶

skimpy.MCA = 'mca'¶

skimpy.ODE = 'ode'¶

skimpy.ELEMENTARY = 'elementary'¶: Jacobian Types

skimpy.NUMERICAL = 'numerical'¶

skimpy.SYMBOLIC = 'symbolic'¶: MCA Types

skimpy.NET = 'net'¶

skimpy.SPLIT = 'split'¶: Item types

skimpy.PARAMETER = 'parameter'¶

skimpy.VARIABLE = 'variable'¶: Units

skimpy.KCAL = 'kcal'¶

skimpy.KJ = 'kJ'¶

skimpy.JOULE = 'JOULE'¶: OTHER

skimpy.WATER_FORMULA = 'H2O'¶

class skimpy.KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None)¶

Bases: abc.ABC

Helper class that provides a standard way to create an ABC using inheritance.

parameter_reactant_links¶

name¶

reactants¶

inhibitors = None¶

_parameters = None¶

enzyme = None¶

__reduce__()¶

link_parameters_and_reactants()¶

property parameters¶

abstract property Reactants¶: Class to define metabolites and their roles in the reaction :return:

abstract property Parameters¶: Class to define parameters and their roles in the reaction :return:

abstract get_qssa_rate_expression()¶

abstract update_qssa_rate_expression()¶

abstract get_full_rate_expression()¶

abstract calculate_rate_constants()¶

get_parameters_from_expression(expr)¶

class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)¶

Bases: object

educts¶

products¶

rate_constant_name¶

__str__()¶

__repr__()¶

class skimpy.Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None)¶

Bases: object

Global reaction class

name¶

enzyme = None¶

modifiers¶

property reactants¶

property reactant_stoichiometry¶

property parameters¶

property rates¶

__str__()¶

parametrize(params)¶

class skimpy.TabDict¶

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__()¶: Default dir() implementation.

__getattr__(attr)¶

iloc(ix)¶

skimpy.make_parameter_set(mechanism, param_declaration)¶

skimpy.make_reactant_set(mechanism, reactant_declaration)¶

skimpy.make_subclasses_dict(cls)¶

skimpy.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

skimpy.make_irrev_massaction(stoichiometry)¶: :param stoichiometry is a list of the reaction stoichioemtry

skimpy.QSSA = 'qssa'¶

skimpy.TQSSA = 'tqssa'¶

skimpy.MCA = 'mca'¶

skimpy.ODE = 'ode'¶

skimpy.ELEMENTARY = 'elementary'¶: Jacobian Types

skimpy.NUMERICAL = 'numerical'¶

skimpy.SYMBOLIC = 'symbolic'¶: MCA Types

skimpy.NET = 'net'¶

skimpy.SPLIT = 'split'¶: Item types

skimpy.PARAMETER = 'parameter'¶

skimpy.VARIABLE = 'variable'¶: Units

skimpy.KCAL = 'kcal'¶

skimpy.KJ = 'kJ'¶

skimpy.JOULE = 'JOULE'¶: OTHER

skimpy.WATER_FORMULA = 'H2O'¶

class skimpy.KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None)¶

Bases: abc.ABC

Helper class that provides a standard way to create an ABC using inheritance.

parameter_reactant_links¶

name¶

reactants¶

inhibitors = None¶

_parameters = None¶

enzyme = None¶

__reduce__()¶

link_parameters_and_reactants()¶

property parameters¶

abstract property Reactants¶: Class to define metabolites and their roles in the reaction :return:

abstract property Parameters¶: Class to define parameters and their roles in the reaction :return:

abstract get_qssa_rate_expression()¶

abstract update_qssa_rate_expression()¶

abstract get_full_rate_expression()¶

abstract calculate_rate_constants()¶

get_parameters_from_expression(expr)¶

class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)¶

Bases: object

educts¶

products¶

rate_constant_name¶

__str__()¶

__repr__()¶

class skimpy.Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None)¶

Bases: object

Global reaction class

name¶

enzyme = None¶

modifiers¶

property reactants¶

property reactant_stoichiometry¶

property parameters¶

property rates¶

__str__()¶

parametrize(params)¶

class skimpy.TabDict¶

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__()¶: Default dir() implementation.

__getattr__(attr)¶

iloc(ix)¶

skimpy.make_parameter_set(mechanism, param_declaration)¶

skimpy.make_reactant_set(mechanism, reactant_declaration)¶

skimpy.make_subclasses_dict(cls)¶

skimpy.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

class skimpy.IrreversibleHill(name, reactants, parameters=None, **kwargs)¶

Bases: skimpy.mechanisms.mechanism.KineticMechanism

Irreversible hill Uni-Uni enzyme class e.g.: A -> B

reactant_list = ['substrate', 'product']¶

Reactants¶: Class to define metabolites and their roles in the reaction :return:

Parameters¶: Class to define parameters and their roles in the reaction :return:

reactant_stoichiometry¶

parameter_reactant_links¶

class ElementaryReactions¶: Bases: tuple

get_qssa_rate_expression()¶

update_qssa_rate_expression()¶

abstract get_full_rate_expression()¶

abstract calculate_rate_constants()¶

skimpy.QSSA = 'qssa'¶

skimpy.TQSSA = 'tqssa'¶

skimpy.MCA = 'mca'¶

skimpy.ODE = 'ode'¶

skimpy.ELEMENTARY = 'elementary'¶: Jacobian Types

skimpy.NUMERICAL = 'numerical'¶

skimpy.SYMBOLIC = 'symbolic'¶: MCA Types

skimpy.NET = 'net'¶

skimpy.SPLIT = 'split'¶: Item types

skimpy.PARAMETER = 'parameter'¶

skimpy.VARIABLE = 'variable'¶: Units

skimpy.KCAL = 'kcal'¶

skimpy.KJ = 'kJ'¶

skimpy.JOULE = 'JOULE'¶: OTHER

skimpy.WATER_FORMULA = 'H2O'¶

class skimpy.KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None)¶

Bases: abc.ABC

Helper class that provides a standard way to create an ABC using inheritance.

parameter_reactant_links¶

name¶

reactants¶

inhibitors = None¶

_parameters = None¶

enzyme = None¶

__reduce__()¶

link_parameters_and_reactants()¶

property parameters¶

abstract property Reactants¶: Class to define metabolites and their roles in the reaction :return:

abstract property Parameters¶: Class to define parameters and their roles in the reaction :return:

abstract get_qssa_rate_expression()¶

abstract update_qssa_rate_expression()¶

abstract get_full_rate_expression()¶

abstract calculate_rate_constants()¶

get_parameters_from_expression(expr)¶

class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)¶

Bases: object

educts¶

products¶

rate_constant_name¶

__str__()¶

__repr__()¶

class skimpy.Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None)¶

Bases: object

Global reaction class

name¶

enzyme = None¶

modifiers¶

property reactants¶

property reactant_stoichiometry¶

property parameters¶

property rates¶

__str__()¶

parametrize(params)¶

class skimpy.TabDict¶

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__()¶: Default dir() implementation.

__getattr__(attr)¶

iloc(ix)¶

skimpy.make_parameter_set(mechanism, param_declaration)¶

skimpy.make_reactant_set(mechanism, reactant_declaration)¶

skimpy.make_subclasses_dict(cls)¶

skimpy.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

skimpy.make_irrev_m_n_hill(stoichiometry)¶: :param stoichiometry is a list of the reaction stoichioemtry

skimpy.QSSA = 'qssa'¶

skimpy.TQSSA = 'tqssa'¶

skimpy.MCA = 'mca'¶

skimpy.ODE = 'ode'¶

skimpy.ELEMENTARY = 'elementary'¶: Jacobian Types

skimpy.NUMERICAL = 'numerical'¶

skimpy.SYMBOLIC = 'symbolic'¶: MCA Types

skimpy.NET = 'net'¶

skimpy.SPLIT = 'split'¶: Item types

skimpy.PARAMETER = 'parameter'¶

skimpy.VARIABLE = 'variable'¶: Units

skimpy.KCAL = 'kcal'¶

skimpy.KJ = 'kJ'¶

skimpy.JOULE = 'JOULE'¶: OTHER

skimpy.WATER_FORMULA = 'H2O'¶

class skimpy.KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None)¶

Bases: abc.ABC

Helper class that provides a standard way to create an ABC using inheritance.

parameter_reactant_links¶

name¶

reactants¶

inhibitors = None¶

_parameters = None¶

enzyme = None¶

__reduce__()¶

link_parameters_and_reactants()¶

property parameters¶

abstract property Reactants¶: Class to define metabolites and their roles in the reaction :return:

abstract property Parameters¶: Class to define parameters and their roles in the reaction :return:

abstract get_qssa_rate_expression()¶

abstract update_qssa_rate_expression()¶

abstract get_full_rate_expression()¶

abstract calculate_rate_constants()¶

get_parameters_from_expression(expr)¶

class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)¶

Bases: object

educts¶

products¶

rate_constant_name¶

__str__()¶

__repr__()¶

class skimpy.Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None)¶

Bases: object

Global reaction class

name¶

enzyme = None¶

modifiers¶

property reactants¶

property reactant_stoichiometry¶

property parameters¶

property rates¶

__str__()¶

parametrize(params)¶

class skimpy.TabDict¶

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__()¶: Default dir() implementation.

__getattr__(attr)¶

iloc(ix)¶

skimpy.make_parameter_set(mechanism, param_declaration)¶

skimpy.make_reactant_set(mechanism, reactant_declaration)¶

skimpy.make_subclasses_dict(cls)¶

skimpy.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

skimpy.make_rev_massaction(stoichiometry)¶: :param stoichiometry is a list of the reaction stoichioemtry

skimpy.QSSA = 'qssa'¶

skimpy.TQSSA = 'tqssa'¶

skimpy.MCA = 'mca'¶

skimpy.ODE = 'ode'¶

skimpy.ELEMENTARY = 'elementary'¶: Jacobian Types

skimpy.NUMERICAL = 'numerical'¶

skimpy.SYMBOLIC = 'symbolic'¶: MCA Types

skimpy.NET = 'net'¶

skimpy.SPLIT = 'split'¶: Item types

skimpy.PARAMETER = 'parameter'¶

skimpy.VARIABLE = 'variable'¶: Units

skimpy.KCAL = 'kcal'¶

skimpy.KJ = 'kJ'¶

skimpy.JOULE = 'JOULE'¶: OTHER

skimpy.WATER_FORMULA = 'H2O'¶

class skimpy.KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None)¶

Bases: abc.ABC

Helper class that provides a standard way to create an ABC using inheritance.

parameter_reactant_links¶

name¶

reactants¶

inhibitors = None¶

_parameters = None¶

enzyme = None¶

__reduce__()¶

link_parameters_and_reactants()¶

property parameters¶

abstract property Reactants¶: Class to define metabolites and their roles in the reaction :return:

abstract property Parameters¶: Class to define parameters and their roles in the reaction :return:

abstract get_qssa_rate_expression()¶

abstract update_qssa_rate_expression()¶

abstract get_full_rate_expression()¶

abstract calculate_rate_constants()¶

get_parameters_from_expression(expr)¶

class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)¶

Bases: object

educts¶

products¶

rate_constant_name¶

__str__()¶

__repr__()¶

class skimpy.Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None)¶

Bases: object

Global reaction class

name¶

enzyme = None¶

modifiers¶

property reactants¶

property reactant_stoichiometry¶

property parameters¶

property rates¶

__str__()¶

parametrize(params)¶

class skimpy.TabDict¶

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__()¶: Default dir() implementation.

__getattr__(attr)¶

iloc(ix)¶

skimpy.make_parameter_set(mechanism, param_declaration)¶

skimpy.make_reactant_set(mechanism, reactant_declaration)¶

skimpy.make_subclasses_dict(cls)¶

skimpy.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

class skimpy.BiUniReversibleHill(name, reactants, parameters=None, **kwargs)¶

Bases: skimpy.mechanisms.mechanism.KineticMechanism

A reversible hill Bi-Uni enzyme class e.g.: A + B -> C

reactant_list = ['substrate1', 'substrate2', 'product']¶

Reactants¶: Class to define metabolites and their roles in the reaction :return:

Parameters¶: Class to define parameters and their roles in the reaction :return:

reactant_stoichiometry¶

parameter_reactant_links¶

class ElementaryReactions¶: Bases: tuple

get_qssa_rate_expression()¶

update_qssa_rate_expression()¶

abstract get_full_rate_expression()¶

abstract calculate_rate_constants()¶

skimpy.QSSA = 'qssa'¶

skimpy.TQSSA = 'tqssa'¶

skimpy.MCA = 'mca'¶

skimpy.ODE = 'ode'¶

skimpy.ELEMENTARY = 'elementary'¶: Jacobian Types

skimpy.NUMERICAL = 'numerical'¶

skimpy.SYMBOLIC = 'symbolic'¶: MCA Types

skimpy.NET = 'net'¶

skimpy.SPLIT = 'split'¶: Item types

skimpy.PARAMETER = 'parameter'¶

skimpy.VARIABLE = 'variable'¶: Units

skimpy.KCAL = 'kcal'¶

skimpy.KJ = 'kJ'¶

skimpy.JOULE = 'JOULE'¶: OTHER

skimpy.WATER_FORMULA = 'H2O'¶

class skimpy.KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None)¶

Bases: abc.ABC

Helper class that provides a standard way to create an ABC using inheritance.

parameter_reactant_links¶

name¶

reactants¶

inhibitors = None¶

_parameters = None¶

enzyme = None¶

__reduce__()¶

link_parameters_and_reactants()¶

property parameters¶

abstract property Reactants¶: Class to define metabolites and their roles in the reaction :return:

abstract property Parameters¶: Class to define parameters and their roles in the reaction :return:

abstract get_qssa_rate_expression()¶

abstract update_qssa_rate_expression()¶

abstract get_full_rate_expression()¶

abstract calculate_rate_constants()¶

get_parameters_from_expression(expr)¶

class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)¶

Bases: object

educts¶

products¶

rate_constant_name¶

__str__()¶

__repr__()¶

class skimpy.Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None)¶

Bases: object

Global reaction class

name¶

enzyme = None¶

modifiers¶

property reactants¶

property reactant_stoichiometry¶

property parameters¶

property rates¶

__str__()¶

parametrize(params)¶

class skimpy.TabDict¶

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__()¶: Default dir() implementation.

__getattr__(attr)¶

iloc(ix)¶

skimpy.make_parameter_set(mechanism, param_declaration)¶

skimpy.make_reactant_set(mechanism, reactant_declaration)¶

skimpy.make_subclasses_dict(cls)¶

skimpy.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

class skimpy.UniBiReversibleHill(name, reactants, parameters=None, **kwargs)¶

Bases: skimpy.mechanisms.mechanism.KineticMechanism

A reversible hill Uni-Bi enzyme class e.g.: A -> B + C

reactant_list = ['substrate', 'product1', 'product2']¶

Reactants¶: Class to define metabolites and their roles in the reaction :return:

Parameters¶: Class to define parameters and their roles in the reaction :return:

reactant_stoichiometry¶

parameter_reactant_links¶

class ElementaryReactions¶: Bases: tuple

get_qssa_rate_expression()¶

update_qssa_rate_expression()¶

abstract get_full_rate_expression()¶

abstract calculate_rate_constants()¶

skimpy.QSSA = 'qssa'¶

skimpy.TQSSA = 'tqssa'¶

skimpy.MCA = 'mca'¶

skimpy.ODE = 'ode'¶

skimpy.ELEMENTARY = 'elementary'¶: Jacobian Types

skimpy.NUMERICAL = 'numerical'¶

skimpy.SYMBOLIC = 'symbolic'¶: MCA Types

skimpy.NET = 'net'¶

skimpy.SPLIT = 'split'¶: Item types

skimpy.PARAMETER = 'parameter'¶

skimpy.VARIABLE = 'variable'¶: Units

skimpy.KCAL = 'kcal'¶

skimpy.KJ = 'kJ'¶

skimpy.JOULE = 'JOULE'¶: OTHER

skimpy.WATER_FORMULA = 'H2O'¶

class skimpy.KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None)¶

Bases: abc.ABC

Helper class that provides a standard way to create an ABC using inheritance.

parameter_reactant_links¶

name¶

reactants¶

inhibitors = None¶

_parameters = None¶

enzyme = None¶

__reduce__()¶

link_parameters_and_reactants()¶

property parameters¶

abstract property Reactants¶: Class to define metabolites and their roles in the reaction :return:

abstract property Parameters¶: Class to define parameters and their roles in the reaction :return:

abstract get_qssa_rate_expression()¶

abstract update_qssa_rate_expression()¶

abstract get_full_rate_expression()¶

abstract calculate_rate_constants()¶

get_parameters_from_expression(expr)¶

class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)¶

Bases: object

educts¶

products¶

rate_constant_name¶

__str__()¶

__repr__()¶

class skimpy.Reaction(name, reactants, mechanism, parameters=None, inhibitors=None, enzyme=None)¶

Bases: object

Global reaction class

name¶

enzyme = None¶

modifiers¶

property reactants¶

property reactant_stoichiometry¶

property parameters¶

property rates¶

__str__()¶

parametrize(params)¶

class skimpy.TabDict¶

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__()¶: Default dir() implementation.

__getattr__(attr)¶

iloc(ix)¶

skimpy.make_parameter_set(mechanism, param_declaration)¶

skimpy.make_reactant_set(mechanism, reactant_declaration)¶

skimpy.make_subclasses_dict(cls)¶

skimpy.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

class skimpy.SimpleRegulatedGeneExpression(name, reactants, inhibitors, parameters=None, **kwargs)¶

Bases: skimpy.mechanisms.mechanism.KineticMechanism

Apprxoimate gene regulation according to XX et al e.g.: A + B -> C

reactant_list = ['product']¶

Reactants¶: Class to define metabolites and their roles in the reaction :return:

regulator_list = ['factor_1']¶

SingleRegulator¶

Regulators¶

Parameters¶: Class to define parameters and their roles in the reaction :return:

reactant_stoichiometry¶

parameter_reactant_links¶

class ElementaryReactions¶: Bases: tuple

get_qssa_rate_expression()¶

update_qssa_rate_expression()¶

abstract get_full_rate_expression()¶

abstract calculate_rate_constants()¶

skimpy.QSSA = 'qssa'¶

skimpy.TQSSA = 'tqssa'¶

skimpy.MCA = 'mca'¶

skimpy.ODE = 'ode'¶

skimpy.ELEMENTARY = 'elementary'¶: Jacobian Types

skimpy.NUMERICAL = 'numerical'¶

skimpy.SYMBOLIC = 'symbolic'¶: MCA Types

skimpy.NET = 'net'¶

skimpy.SPLIT = 'split'¶: Item types

skimpy.PARAMETER = 'parameter'¶

skimpy.VARIABLE = 'variable'¶: Units

skimpy.KCAL = 'kcal'¶

skimpy.KJ = 'kJ'¶

skimpy.JOULE = 'JOULE'¶: OTHER

skimpy.WATER_FORMULA = 'H2O'¶

class skimpy.KineticMechanism(name, reactants, parameters=None, inhibitors=None, enzyme=None)¶

Bases: abc.ABC

Helper class that provides a standard way to create an ABC using inheritance.

parameter_reactant_links¶

name¶

reactants¶

inhibitors = None¶

_parameters = None¶

enzyme = None¶

__reduce__()¶

link_parameters_and_reactants()¶

property parameters¶

abstract property Reactants¶: Class to define metabolites and their roles in the reaction :return:

abstract property Parameters¶: Class to define parameters and their roles in the reaction :return:

abstract get_qssa_rate_expression()¶

abstract update_qssa_rate_expression()¶

abstract get_full_rate_expression()¶

abstract calculate_rate_constants()¶

get_parameters_from_expression(expr)¶