8.1.1.2. skimpy.core¶

[———]

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. Submodules¶

8.1.1.2.2. 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`

8.1.1.2.3. Classes¶

`KineticModel`	This class contains the kinetic model as described by reaction and
`KineticMechanism`	Helper class that provides a standard way to create an ABC using
`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
`Reaction`	Global reaction class
`TabDict`	Really just an ordered dict with tab completion in interactive terminals
`Item`
`ItemSet`	Helper class that provides a standard way to create an ABC using
`Parameter`
`ParameterSet`	Helper class that provides a standard way to create an ABC using
`Reactant`
`ReactantSet`	Helper class that provides a standard way to create an ABC using
`TabDict`	Really just an ordered dict with tab completion in interactive terminals
`ParameterValues`	Parameters set for kinetic models wich can be indexed with symbols or
`ParameterValuePopulation`

8.1.1.2.4. Functions¶

`check_is_symbol`(s_in)
`make_parameter_set`(mechanism, param_declaration)
`make_reactant_set`(mechanism, reactant_declaration)
`make_parameter_set`(mechanism, param_declaration)
`make_reactant_set`(mechanism, reactant_declaration)
`load_parameter_population`(filename[, lower_index, ...])
`concat_populations`(values[, kmodel, index])

8.1.1.2.5. Package Contents¶

class skimpy.KineticModel(reactions=None, boundary_conditions=None, constraints=None, name='Unnamed')¶

Bases: object

This class contains the kinetic model as described by reaction and boundary conditions and constratins.

:param : :return:

name = 'Unnamed'¶

reactions¶

boundary_conditions¶

constraints¶

initial_conditions¶

logger¶

_simtype = None¶

_modified = True¶

_recompiled = False¶

compartments¶

property reactants¶

property parameters¶

property moieties¶

add_reaction(reaction)¶

Adds a SKiMPy reaction to the model

Parameters:: reaction (skimpy.core.Reaction) – The reaction to add
Returns:

add_compartment(compartment)¶

Parameters:: compartment
Returns:

add_constraint(constraint)¶

add_boundary_condition(boundary_condition)¶

Enforces a boundary condition (e.g. a constant concentration) on the kinetic model

Parameters:: boundary_condition (skimpy.core.BoundaryCondition) – the boundary condition to enforce
Returns:

add_to_tabdict(element, kind)¶

parametrize_by_reaction(param_dict)¶

If has input: apply as dict to reactions in the model by: reaction.parametrize(args)

Returns:

parametrize(param_dict)¶

repair()¶: Link inhibitors and activators to reactants FIXME: Any idea to avoid this is dearly welcome :return:

property sim_type¶

prepare(mca=True, ode=True, **kwargs)¶

Model preparation for different analysis types. The preparation is done before the compiling step to be able to curate the model in between

Parameters:

mca
ode

Returns:

compile_jacobian(type=NUMERICAL, sim_type=QSSA, ncpu=1)¶

compile_ode(sim_type=QSSA, ncpu=1)¶

solve_ode(time_out, solver_type='cvode', **kwargs)¶

The solver types are from ::scikits.odes::, and can be found at <https://scikits-odes.readthedocs.io/en/latest/solvers.html>`_.

Parameters:

time_out (list(float) or similar) – The times at which the solution is evaluated
solver_type – must be among [‘cvode’,’ida’,’dopri5’,’dop853’]
kwargs

Returns:

compile_mca(parameter_list=[], mca_type=NET, sim_type=QSSA, ncpu=1)¶: Compile MCA expressions: elasticities, jacobian and control coeffcients

skimpy.check_is_symbol(s_in)¶

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)¶

skimpy.make_parameter_set(mechanism, param_declaration)¶

skimpy.make_reactant_set(mechanism, reactant_declaration)¶

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()¶

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.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)¶

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

Bases: object

name¶

model = None¶

value = None¶

_suffix = ''¶

_symbol = None¶

hook = None¶

type = None¶

_lower_bound = None¶

_upper_bound = None¶

_generate_symbol()¶

property symbol¶

property suffix¶

property bounds¶

__str__()¶

__repr__()¶

class skimpy.ItemSet(mechanism)¶

Bases: abc.ABC, skimpy.utils.tabdict.TabDict

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

mechanism¶

__reduce__()¶: Helper for pickle.

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

Bases: Item

type = 'parameter'¶

class skimpy.ParameterSet(mechanism, param_declaration, param_values, suffix='')¶

Bases: ItemSet

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

property required_for¶

skimpy.make_parameter_set(mechanism, param_declaration)¶

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

Bases: Item

type = 'variable'¶

compartment = None¶

class skimpy.ReactantSet(mechanism, reactant_declaration, reactant_values)¶

Bases: ItemSet

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

skimpy.make_reactant_set(mechanism, reactant_declaration)¶

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.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.ParameterValues(parameter_values, kmodel=None)¶

Bases: object

Parameters set for kinetic models wich can be indexed with symbols or

_parameter_values¶

_sym_to_str¶

__getitem__(item)¶

__setitem__(item, value)¶

items()¶

keys()¶

values()¶

class skimpy.ParameterValuePopulation(data, kmodel=None, index=None)¶

Bases: object

kmodel = None¶

__getitem__(index)¶

__len__()¶

__iter__()¶

__next__()¶

_dataframe(dropna=True)¶

mean()¶

Return Computes the mean parameter values for the population:

var()¶

Return Computes the variance parameter values for the population:

cov()¶

Return Computes the covaraince parameter values for the population:

log_mean()¶

Return Computes the logarithmic mean parameter values for the population:

log_var()¶

Return Computes the logarithmic variance parameter values for the population:

log_cov()¶

Return Computes the logarithmic covaraince parameter values for the population:

save(filename)¶: Saves the parameter population as hdf5 file :param filename: string XXX.h5 / XXX.hdf5 :return:

skimpy.load_parameter_population(filename, lower_index=None, upper_index=None)¶

skimpy.concat_populations(values, kmodel=None, index=None)¶