8.1.1.2.1.4. skimpy.core.modifiers

[———]

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.

8.1.1.2.1.4.1. Classes

ExpressionModifier	This class describes a modifier to an expression, like a boundary condition
BoundaryCondition	We differentiate boundary conditions as modifiers that define the boundaries
ConstantConcentration
AdditiveConcentrationRate	Add a concentration rate term to your rate expression
BoundaryFlux	We differentiate boundary conditions as modifiers that define the boundaries
FirstOrderSmallMoleculeModifier	Helper class that provides a standard way to create an ABC using
DisplacementSmallMoleculeModifier	Helper class that provides a standard way to create an ABC using
ActivationModifier	Helper class that provides a standard way to create an ABC using
InhibitionModifier	Helper class that provides a standard way to create an ABC using
HillActivationModifier	Helper class that provides a standard way to create an ABC using
SimpleHillActivationModifier	Helper class that provides a standard way to create an ABC using
HillInhibitionModifier	Helper class that provides a standard way to create an ABC using

8.1.1.2.1.4.2. Module Contents

class skimpy.ExpressionModifier(name, reaction=None, modifier=None)

Bases: object

This class describes a modifier to an expression, like a boundary condition or constraint. For example, changing a rate to a constant (boundary condition), or linking it to another variable of the model (constraint). It accepts as an argument a modifier.

A modifier is a function which will look at all your expressions, and apply its transformation to them. As a result, its arguments have to be a TabDict of expressions, such as KinModel.ODEFun.expressions

prefix = 'MOD'

_name

_reaction = None

__call__(expressions)

property modifier

link(model)

Link the modifier to a model, to gain awareness of the inner/outer variables :param model: :return:

property name

class skimpy.BoundaryCondition(name, modifier=None, reaction=None)

Bases: ExpressionModifier

We differentiate boundary conditions as modifiers that define the boundaries of the observed system.

prefix = 'BC'

class skimpy.ConstantConcentration(reactant, name=None, reaction=None)

Bases: BoundaryCondition

prefix = 'CC'

reactant

modifier(expressions)

Set the rate to 0 :param expressions: :return:

__del__()

class skimpy.AdditiveConcentrationRate(reactant, flux_value, name=None, reaction=None)

Bases: ExpressionModifier

Add a concentration rate term to your rate expression

prefix = 'ADDCR'

reactant

flux_value

modifier(expressions)

Add to the rate expression :param expressions: :return:

class skimpy.BoundaryFlux(reactant, flux_value, reaction=None)

Bases: BoundaryCondition, AdditiveConcentrationRate

We differentiate boundary conditions as modifiers that define the boundaries of the observed system.

prefix = 'BF'

check_dependency(expression)

class skimpy.FirstOrderSmallMoleculeModifier(small_molecule, mechanism_stoichiometry, name=None, reaction=None)

Bases: skimpy.mechanisms.mechanism.KineticMechanism, ExpressionModifier

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

prefix = 'HSM'

Reactants

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

Parameters

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

parameter_reactant_links

modifier(expressions)

change the flux reaction rate expressions :param expression: {vnet, vfwd, vbwd} :return:

get_qssa_rate_expression()

update_qssa_rate_expression()

abstract get_full_rate_expression()

abstract calculate_rate_constants()

class skimpy.DisplacementSmallMoleculeModifier(small_molecule, mechanism_stoichiometry, name=None, reaction=None)

Bases: skimpy.mechanisms.mechanism.KineticMechanism, ExpressionModifier

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

prefix = 'DSM'

Reactants

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

Parameters

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

parameter_reactant_links

modifier(expressions)

change the flux reaction rate expressions :param expression: {vnet, vfwd, vbwd} :return:

get_qssa_rate_expression()

update_qssa_rate_expression()

abstract get_full_rate_expression()

abstract calculate_rate_constants()

class skimpy.ActivationModifier(activator, name=None, k_activation=None, reaction=None)

Bases: skimpy.mechanisms.mechanism.KineticMechanism, ExpressionModifier

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

prefix = 'AM'

Reactants

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

Parameters

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

parameter_reactant_links

reactant_stoichiometry

modifier(expressions)

change the flux reaction rate expressions :param expression: {vnet, vfwd, vbwd} :return:

get_qssa_rate_expression()

update_qssa_rate_expression()

abstract get_full_rate_expression()

abstract calculate_rate_constants()

class skimpy.InhibitionModifier(inhibitor, name=None, k_inhibition=None, reaction=None)

Bases: skimpy.mechanisms.mechanism.KineticMechanism, ExpressionModifier

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

prefix = 'IM'

Reactants

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

Parameters

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

parameter_reactant_links

reactant_stoichiometry

modifier(expressions)

change the flux reaction rate expressions :param expression: {vnet, vfwd, vbwd} :return:

get_qssa_rate_expression()

update_qssa_rate_expression()

abstract get_full_rate_expression()

abstract calculate_rate_constants()

class skimpy.HillActivationModifier(activator, name=None, k_activation=None, a_max=None, hill_coefficient=None, reaction=None)

Bases: skimpy.mechanisms.mechanism.KineticMechanism, ExpressionModifier

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

prefix = 'HAM'

Reactants

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

Parameters

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

parameter_reactant_links

reactant_stoichiometry

modifier(expressions)

change the flux reaction rate expressions :param expression: {vnet, vfwd, vbwd} :return:

get_qssa_rate_expression()

update_qssa_rate_expression()

abstract get_full_rate_expression()

abstract calculate_rate_constants()

class skimpy.SimpleHillActivationModifier(activator, name=None, k_activation=None, a_max=None, hill_coefficient=None, reaction=None)

Bases: skimpy.mechanisms.mechanism.KineticMechanism, ExpressionModifier

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

prefix = 'SHAM'

Reactants

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

Parameters

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

parameter_reactant_links

reactant_stoichiometry

modifier(expressions)

change the flux reaction rate expressions :param expression: {vnet, vfwd, vbwd} :return:

get_qssa_rate_expression()

update_qssa_rate_expression()

abstract get_full_rate_expression()

abstract calculate_rate_constants()

class skimpy.HillInhibitionModifier(inhibitor, name=None, k_inhibition=None, hill_coefficient=None, reaction=None)

Bases: skimpy.mechanisms.mechanism.KineticMechanism, ExpressionModifier

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

prefix = 'HIM'

Reactants

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

Parameters

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

parameter_reactant_links

reactant_stoichiometry

modifier(expressions)

change the flux reaction rate expressions :param expression: {vnet, vfwd, vbwd} :return:

get_qssa_rate_expression()

update_qssa_rate_expression()

abstract get_full_rate_expression()

abstract calculate_rate_constants()