8.1.1.5. skimpy.mechanisms

[———]

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.

8.1.1.5.1. Submodules

8.1.1.5.2. Package Contents

8.1.1.5.2.1. 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

8.1.1.5.2.2. 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=None)

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=None)

Stoichiometry looks like [-2, -1, 3]

make_convenience_with_inhibition(stoichiometry, inihbitor_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=None)

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=None)

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=None)

Stoichiometry looks like [-2, -1, 3]

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

make_parameter_set(mechanism, param_declaration)

make_reactant_set(mechanism, reactant_declaration)

make_subclasses_dict(cls)

stringify_stoichiometry(stoichiometry, inihibitors=None)

Stoichiometry looks like [-2, -1, 3]

make_generalized_elementary_kinetics(stoichiometry, generalized_reactants)

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=None)

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=None)

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=None)

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=None)

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=None)

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=None)

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=None)

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=None)

Stoichiometry looks like [-2, -1, 3]

8.1.1.5.2.3. 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

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.

__reduce__(self)

helper for pickle

property parameters(self)
property Reactants(self)

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

property Parameters(self)

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

abstract get_qssa_rate_expression(self)
abstract update_qssa_rate_expression(self)
abstract get_full_rate_expression(self)
abstract calculate_rate_constants(self)
get_parameters_from_expression(self, expr)
class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)

Bases: object

__str__(self)

Return str(self).

__repr__(self)

Return repr(self).

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

Bases: object

Global reaction class

property reactants(self)
property reactant_stoichiometry(self)
property parameters(self)
property rates(self)
__str__(self)

Return str(self).

parametrize(self, 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

class skimpy.TabDict

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__(self)

__dir__() -> list default dir() implementation

__getattr__(self, attr)
iloc(self, ix)
class skimpy.ReversibleMichaelisMenten(name, reactants, parameters=None, **kwargs)

Bases: skimpy.mechanisms.mechanism.KineticMechanism

A reversible uni uni reaction enzmye class

Reactants
Parameters
reactant_stoichiometry
ElementaryReactions
get_qssa_rate_expression(self)
update_qssa_rate_expression(self)
get_full_rate_expression(self)
calculate_rate_constants(self)
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
__reduce__(self)

helper for pickle

link_parameters_and_reactants(self)
property parameters(self)
property Reactants(self)

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

property Parameters(self)

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

abstract get_qssa_rate_expression(self)
abstract update_qssa_rate_expression(self)
abstract get_full_rate_expression(self)
abstract calculate_rate_constants(self)
get_parameters_from_expression(self, expr)
class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)

Bases: object

__str__(self)

Return str(self).

__repr__(self)

Return repr(self).

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

Bases: object

Global reaction class

property reactants(self)
property reactant_stoichiometry(self)
property parameters(self)
property rates(self)
__str__(self)

Return str(self).

parametrize(self, params)
class skimpy.TabDict

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__(self)

__dir__() -> list default dir() implementation

__getattr__(self, attr)
iloc(self, 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
Parameters
reactant_stoichiometry
ElementaryReactions
get_qssa_rate_expression(self)
update_qssa_rate_expression(self)
abstract get_full_rate_expression(self)
abstract calculate_rate_constants(self)
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
__reduce__(self)

helper for pickle

link_parameters_and_reactants(self)
property parameters(self)
property Reactants(self)

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

property Parameters(self)

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

abstract get_qssa_rate_expression(self)
abstract update_qssa_rate_expression(self)
abstract get_full_rate_expression(self)
abstract calculate_rate_constants(self)
get_parameters_from_expression(self, expr)
class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)

Bases: object

__str__(self)

Return str(self).

__repr__(self)

Return repr(self).

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

Bases: object

Global reaction class

property reactants(self)
property reactant_stoichiometry(self)
property parameters(self)
property rates(self)
__str__(self)

Return str(self).

parametrize(self, params)
class skimpy.TabDict

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__(self)

__dir__() -> list default dir() implementation

__getattr__(self, attr)
iloc(self, 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
__reduce__(self)

helper for pickle

link_parameters_and_reactants(self)
property parameters(self)
property Reactants(self)

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

property Parameters(self)

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

abstract get_qssa_rate_expression(self)
abstract update_qssa_rate_expression(self)
abstract get_full_rate_expression(self)
abstract calculate_rate_constants(self)
get_parameters_from_expression(self, expr)
class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)

Bases: object

__str__(self)

Return str(self).

__repr__(self)

Return repr(self).

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

Bases: object

Global reaction class

property reactants(self)
property reactant_stoichiometry(self)
property parameters(self)
property rates(self)
__str__(self)

Return str(self).

parametrize(self, params)
class skimpy.TabDict

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__(self)

__dir__() -> list default dir() implementation

__getattr__(self, attr)
iloc(self, 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
__reduce__(self)

helper for pickle

link_parameters_and_reactants(self)
property parameters(self)
property Reactants(self)

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

property Parameters(self)

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

abstract get_qssa_rate_expression(self)
abstract update_qssa_rate_expression(self)
abstract get_full_rate_expression(self)
abstract calculate_rate_constants(self)
get_parameters_from_expression(self, expr)
class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)

Bases: object

__str__(self)

Return str(self).

__repr__(self)

Return repr(self).

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

Bases: object

Global reaction class

property reactants(self)
property reactant_stoichiometry(self)
property parameters(self)
property rates(self)
__str__(self)

Return str(self).

parametrize(self, params)
class skimpy.TabDict

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__(self)

__dir__() -> list default dir() implementation

__getattr__(self, attr)
iloc(self, 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
__reduce__(self)

helper for pickle

link_parameters_and_reactants(self)
property parameters(self)
property Reactants(self)

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

property Parameters(self)

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

abstract get_qssa_rate_expression(self)
abstract update_qssa_rate_expression(self)
abstract get_full_rate_expression(self)
abstract calculate_rate_constants(self)
get_parameters_from_expression(self, expr)
class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)

Bases: object

__str__(self)

Return str(self).

__repr__(self)

Return repr(self).

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

Bases: object

Global reaction class

property reactants(self)
property reactant_stoichiometry(self)
property parameters(self)
property rates(self)
__str__(self)

Return str(self).

parametrize(self, params)
class skimpy.TabDict

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__(self)

__dir__() -> list default dir() implementation

__getattr__(self, attr)
iloc(self, 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
__reduce__(self)

helper for pickle

link_parameters_and_reactants(self)
property parameters(self)
property Reactants(self)

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

property Parameters(self)

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

abstract get_qssa_rate_expression(self)
abstract update_qssa_rate_expression(self)
abstract get_full_rate_expression(self)
abstract calculate_rate_constants(self)
get_parameters_from_expression(self, expr)
class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)

Bases: object

__str__(self)

Return str(self).

__repr__(self)

Return repr(self).

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

Bases: object

Global reaction class

property reactants(self)
property reactant_stoichiometry(self)
property parameters(self)
property rates(self)
__str__(self)

Return str(self).

parametrize(self, params)
class skimpy.TabDict

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__(self)

__dir__() -> list default dir() implementation

__getattr__(self, attr)
iloc(self, 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
__reduce__(self)

helper for pickle

link_parameters_and_reactants(self)
property parameters(self)
property Reactants(self)

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

property Parameters(self)

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

abstract get_qssa_rate_expression(self)
abstract update_qssa_rate_expression(self)
abstract get_full_rate_expression(self)
abstract calculate_rate_constants(self)
get_parameters_from_expression(self, expr)
class skimpy.TabDict

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__(self)

__dir__() -> list default dir() implementation

__getattr__(self, attr)
iloc(self, 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
__reduce__(self)

helper for pickle

link_parameters_and_reactants(self)
property parameters(self)
property Reactants(self)

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

property Parameters(self)

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

abstract get_qssa_rate_expression(self)
abstract update_qssa_rate_expression(self)
abstract get_full_rate_expression(self)
abstract calculate_rate_constants(self)
get_parameters_from_expression(self, expr)
class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)

Bases: object

__str__(self)

Return str(self).

__repr__(self)

Return repr(self).

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

Bases: object

Global reaction class

property reactants(self)
property reactant_stoichiometry(self)
property parameters(self)
property rates(self)
__str__(self)

Return str(self).

parametrize(self, params)
class skimpy.TabDict

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__(self)

__dir__() -> list default dir() implementation

__getattr__(self, attr)
iloc(self, 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
__reduce__(self)

helper for pickle

link_parameters_and_reactants(self)
property parameters(self)
property Reactants(self)

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

property Parameters(self)

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

abstract get_qssa_rate_expression(self)
abstract update_qssa_rate_expression(self)
abstract get_full_rate_expression(self)
abstract calculate_rate_constants(self)
get_parameters_from_expression(self, expr)
class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)

Bases: object

__str__(self)

Return str(self).

__repr__(self)

Return repr(self).

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

Bases: object

Global reaction class

property reactants(self)
property reactant_stoichiometry(self)
property parameters(self)
property rates(self)
__str__(self)

Return str(self).

parametrize(self, params)
class skimpy.TabDict

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__(self)

__dir__() -> list default dir() implementation

__getattr__(self, attr)
iloc(self, 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
__reduce__(self)

helper for pickle

link_parameters_and_reactants(self)
property parameters(self)
property Reactants(self)

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

property Parameters(self)

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

abstract get_qssa_rate_expression(self)
abstract update_qssa_rate_expression(self)
abstract get_full_rate_expression(self)
abstract calculate_rate_constants(self)
get_parameters_from_expression(self, expr)
class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)

Bases: object

__str__(self)

Return str(self).

__repr__(self)

Return repr(self).

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

Bases: object

Global reaction class

property reactants(self)
property reactant_stoichiometry(self)
property parameters(self)
property rates(self)
__str__(self)

Return str(self).

parametrize(self, params)
class skimpy.TabDict

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__(self)

__dir__() -> list default dir() implementation

__getattr__(self, attr)
iloc(self, 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
Parameters
reactant_stoichiometry
ElementaryReactions
get_qssa_rate_expression(self)
update_qssa_rate_expression(self)
abstract get_full_rate_expression(self)
abstract calculate_rate_constants(self)
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
__reduce__(self)

helper for pickle

link_parameters_and_reactants(self)
property parameters(self)
property Reactants(self)

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

property Parameters(self)

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

abstract get_qssa_rate_expression(self)
abstract update_qssa_rate_expression(self)
abstract get_full_rate_expression(self)
abstract calculate_rate_constants(self)
get_parameters_from_expression(self, expr)
class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)

Bases: object

__str__(self)

Return str(self).

__repr__(self)

Return repr(self).

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

Bases: object

Global reaction class

property reactants(self)
property reactant_stoichiometry(self)
property parameters(self)
property rates(self)
__str__(self)

Return str(self).

parametrize(self, params)
class skimpy.TabDict

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__(self)

__dir__() -> list default dir() implementation

__getattr__(self, attr)
iloc(self, 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
__reduce__(self)

helper for pickle

link_parameters_and_reactants(self)
property parameters(self)
property Reactants(self)

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

property Parameters(self)

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

abstract get_qssa_rate_expression(self)
abstract update_qssa_rate_expression(self)
abstract get_full_rate_expression(self)
abstract calculate_rate_constants(self)
get_parameters_from_expression(self, expr)
class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)

Bases: object

__str__(self)

Return str(self).

__repr__(self)

Return repr(self).

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

Bases: object

Global reaction class

property reactants(self)
property reactant_stoichiometry(self)
property parameters(self)
property rates(self)
__str__(self)

Return str(self).

parametrize(self, params)
class skimpy.TabDict

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__(self)

__dir__() -> list default dir() implementation

__getattr__(self, attr)
iloc(self, 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
__reduce__(self)

helper for pickle

link_parameters_and_reactants(self)
property parameters(self)
property Reactants(self)

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

property Parameters(self)

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

abstract get_qssa_rate_expression(self)
abstract update_qssa_rate_expression(self)
abstract get_full_rate_expression(self)
abstract calculate_rate_constants(self)
get_parameters_from_expression(self, expr)
class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)

Bases: object

__str__(self)

Return str(self).

__repr__(self)

Return repr(self).

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

Bases: object

Global reaction class

property reactants(self)
property reactant_stoichiometry(self)
property parameters(self)
property rates(self)
__str__(self)

Return str(self).

parametrize(self, params)
class skimpy.TabDict

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__(self)

__dir__() -> list default dir() implementation

__getattr__(self, attr)
iloc(self, 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
Parameters
reactant_stoichiometry
ElementaryReactions
get_qssa_rate_expression(self)
update_qssa_rate_expression(self)
abstract get_full_rate_expression(self)
abstract calculate_rate_constants(self)
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
__reduce__(self)

helper for pickle

link_parameters_and_reactants(self)
property parameters(self)
property Reactants(self)

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

property Parameters(self)

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

abstract get_qssa_rate_expression(self)
abstract update_qssa_rate_expression(self)
abstract get_full_rate_expression(self)
abstract calculate_rate_constants(self)
get_parameters_from_expression(self, expr)
class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)

Bases: object

__str__(self)

Return str(self).

__repr__(self)

Return repr(self).

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

Bases: object

Global reaction class

property reactants(self)
property reactant_stoichiometry(self)
property parameters(self)
property rates(self)
__str__(self)

Return str(self).

parametrize(self, params)
class skimpy.TabDict

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__(self)

__dir__() -> list default dir() implementation

__getattr__(self, attr)
iloc(self, 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
Parameters
reactant_stoichiometry
ElementaryReactions
get_qssa_rate_expression(self)
update_qssa_rate_expression(self)
abstract get_full_rate_expression(self)
abstract calculate_rate_constants(self)
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
__reduce__(self)

helper for pickle

link_parameters_and_reactants(self)
property parameters(self)
property Reactants(self)

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

property Parameters(self)

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

abstract get_qssa_rate_expression(self)
abstract update_qssa_rate_expression(self)
abstract get_full_rate_expression(self)
abstract calculate_rate_constants(self)
get_parameters_from_expression(self, expr)
class skimpy.ElementrayReactionStep(educts, products, rate_constant_name)

Bases: object

__str__(self)

Return str(self).

__repr__(self)

Return repr(self).

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

Bases: object

Global reaction class

property reactants(self)
property reactant_stoichiometry(self)
property parameters(self)
property rates(self)
__str__(self)

Return str(self).

parametrize(self, params)
class skimpy.TabDict

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__(self)

__dir__() -> list default dir() implementation

__getattr__(self, attr)
iloc(self, 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
regulator_list = ['factor_1']
SingleRegulator
regulator_list = ['factor_1', 'factor_2']
Regulators
Parameters
reactant_stoichiometry
ElementaryReactions
get_qssa_rate_expression(self)
update_qssa_rate_expression(self)
abstract get_full_rate_expression(self)
abstract calculate_rate_constants(self)
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
__reduce__(self)

helper for pickle

link_parameters_and_reactants(self)
property parameters(self)
property Reactants(self)

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

property Parameters(self)

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

abstract get_qssa_rate_expression(self)
abstract update_qssa_rate_expression(self)
abstract get_full_rate_expression(self)
abstract calculate_rate_constants(self)
get_parameters_from_expression(self, expr)