4.1.1.4. wc_lang.transform package¶

4.1.1.4.1. Submodules¶

4.1.1.4.2. wc_lang.transform.change_value module¶

Change a value of an attribute of a model

Author: Jonathan Karr <karr@mssm.edu>
Date: 2018-06-19
Copyright: 2018, Karr Lab
License: MIT

class wc_lang.transform.change_value.ChangeValueTransform(attr_path=None, value=None)[source]¶

Bases: wc_lang.transform.core.Transform

Change a value of an attribute of a model

attr_path[source]¶

list that represents the path to an attribute or nested attribute of a model

Examples:

model.name --> 'name'

model.reactions.get_one(id='rxn_1').reversible --> (('reactions', {'id': 'rxn_1'}), 'reversible')

model.parameters.get_one(id='param_1').value --> (('parameters', {'id': 'param_1'}), 'value')

model                     .reactions.get_one(id='rxn_1')                     .rate_laws.get_one(direction=RateLawDirection.forward)                     .expression                     .parameters.get_one(id='param_1')                     .value
  --> (
        ('reactions', {'id': 'rxn_1'},
        ('rate_laws', {'direction': RateLawDirection.forward}),
        'expression',
        ('parameters', {'id': 'param_1'}),
        'value',
      )

Type: list of list of str

value[source]¶

new value

Type: object

class Meta[source]¶

Bases: object

id = 'ChangeValue'[source]¶

label = 'Change a value of an attribute of a model'[source]¶

__eq__(other, tol=0.0)[source]¶

Compare two ChangeValueTransform objects

Parameters

other (Object) – other object
tol (float, optional) – equality tolerance

Returns

true if ChangeValueTransform objects are semantically equal

Return type

bool

static attr_path_from_str(str)[source]¶

Generate attr_path from its string representation

Parameters: str (str) – string representation of attr_path
Returns: attr_path
Return type: Object

attr_path_to_str()[source]¶

Generate a string representation of attr_path

Returns: string representation of attr_path
Return type: str

run(model)[source]¶

Change a value of an attribute of a model

Parameters: model (Model) – model
Returns: same model, but with a different value of an attribute
Return type: Model

4.1.1.4.3. wc_lang.transform.core module¶

Transform models.

Author: Jonathan Karr <karr@mssm.edu>
Date: 2016-11-10
Copyright: 2016, Karr Lab
License: MIT

class wc_lang.transform.core.CompositeTransform[source]¶

Bases: wc_lang.transform.core.Transform

Transform which is composed of multiple transforms

COMPONENT_TRANSFORMS[source]¶

default transforms

Type: tuple of Transform

COMPONENT_TRANSFORMS = ()[source]

run(model)[source]¶

Transform model

Parameters: model (Model) – model
Returns: same model, but transformed
Return type: Model

class wc_lang.transform.core.Transform[source]¶

Bases: abc.ABC

abstract run(model)[source]¶

Transform a model

Parameters: model (Model) – model
Returns: transformed model
Return type: Model

wc_lang.transform.core.get_transforms()[source]¶

Get dictionary of available transform classes

Returns: class: dictionary of available transform classes
Return type: dict of str

4.1.1.4.4. wc_lang.transform.create_implicit_dfba_ex_rxns module¶

Create implicit exchange reactions for dFBA submodels.

Author: Arthur Goldberg <Arthur.Goldberg@mssm.edu>
Author: Jonathan Karr <jonrkarr@gmail.com>
Date: 2018-11-28
Copyright: 2017-2018, Karr Lab
License: MIT

class wc_lang.transform.create_implicit_dfba_ex_rxns.CreateImplicitDfbaExchangeReactionsTransform[source]¶

Bases: wc_lang.transform.core.Transform

Create implicit exchange reactions for dFBA submodels.

To enable FBA to represent a closed system, create implicit forward exchange reactions

Metabolites transported from the extracellular environment (generate a “-> species_type[e]” reaction for each extracellular species involved in each dFBA submodel)
TODO: Metabolites recycled from the byproducts of other submodels and products produced for other submodels

class Meta[source]¶

Bases: object

id = 'CreateImplicitDfbaExchangeReactions'[source]¶

label = 'Create implicit exchange reactions for dFBA submodels'[source]¶

run(model)[source]¶

Create implicit exchange reactions for dFBA submodels

Parameters: model (Model) – model
Returns: same model, but transformed
Return type: Model

4.1.1.4.5. wc_lang.transform.create_implicit_dist_zero_init_concs module¶

Create the implicit zero concentrations in a model

Author: Arthur Goldberg <Arthur.Goldberg@mssm.edu>
Author: Jonathan Karr <jonrkarr@gmail.com>
Date: 2018-11-28
Copyright: 2017-2018, Karr Lab
License: MIT

class wc_lang.transform.create_implicit_dist_zero_init_concs.CreateImplicitDistributionZeroInitConcentrationsTransform[source]¶

Bases: wc_lang.transform.core.Transform

Create the implicit zero concentrations in a model

class Meta[source]¶

Bases: object

id = 'CreateImplicitDistributionZeroInitConcentrations'[source]¶

label = 'Create the implicit zero concentrations in a model'[source]¶

run(model)[source]¶

Create the implicit zero concentrations in a model

Parameters: model (Model) – model
Returns: same model, but transformed
Return type: Model

4.1.1.4.6. wc_lang.transform.merge_submodels module¶

Merge groups of algorithmically-like submodels into individual submodels.

Author: Jonathan Karr <karr@mssm.edu>
Date: 2018-06-19
Copyright: 2018, Karr Lab
License: MIT

class wc_lang.transform.merge_submodels.MergeAlgorithmicallyLikeSubmodelsTransform[source]¶

Bases: wc_lang.transform.core.Transform

Merge groups of algorithmically-like submodels into individual submodels

class Meta[source]¶

Bases: object

id = 'MergeAlgorithmicallyLikeSubmodels'[source]¶

label = 'Merge groups of algorithmically-like submodels into individual submodels'[source]¶

run(model)[source]¶

Merge groups of algorithmically-like submodels into individual submodels

dFBA objectives are merged by summing

Parameters: model (Model) – model definition
Returns: same model definition, but with submodels of the same simulation framework merged
Return type: Model

4.1.1.4.7. wc_lang.transform.nullify_attrs module¶

Generate a reduced model by nullifying specific attributes

Author: Jonathan Karr <karr@mssm.edu>
Date: 2019-03-20
Copyright: 2019, Karr Lab
License: MIT

class wc_lang.transform.nullify_attrs.NullifyAttrsTransform(attrs_to_keep)[source]¶

Bases: wc_lang.transform.core.Transform

Generate a reduced model by nullifying specific attributes

attrs_to_keep[source]¶

name of meta attribute which encodes lists of the attributes to keep (not nullify)

Type: str

class Meta[source]¶

Bases: object

id = 'NullifyAttrs'[source]¶

label = 'Generate a reduced model by nullifying specific attributes'[source]¶

run(model)[source]¶

Generate a reduced model by nullifying specific attributes

Parameters: model (Model) – model
Returns: same model, but transformed
Return type: Model

4.1.1.4.8. wc_lang.transform.prep_for_sbml module¶

Transform model into SBML-compatible representation and discard information that cannot be exported to SBML.

Author: Jonathan Karr <karr@mssm.edu>
Author: Arthur Goldberg <Arthur.Goldberg@mssm.edu>
Date: 2019-03-20
License: MIT

class wc_lang.transform.prep_for_sbml.PrepForSbmlTransform[source]¶

Bases: wc_lang.transform.core.CompositeTransform

Transform model into SBML-compatible representation and discard information that cannot be exported to SBML

COMPONENT_TRANSFORMS = (<wc_lang.transform.create_implicit_dist_zero_init_concs.CreateImplicitDistributionZeroInitConcentrationsTransform object>, <wc_lang.transform.create_implicit_dfba_ex_rxns.CreateImplicitDfbaExchangeReactionsTransform object>, <wc_lang.transform.split_reversible_reactions.SplitReversibleReactionsTransform object>, <wc_lang.transform.nullify_attrs.NullifyAttrsTransform object>)[source]¶

class Meta[source]¶

Bases: object

id = 'PrepForSbml'[source]¶

label = 'Transform model into SBML-compatible representation and discard information that cannot be exported to SBML'[source]¶

dfba_framework = [Term('WC:dynamic_flux_balance_analysis', name='dynamic flux balance analysis')][source]¶

4.1.1.4.9. wc_lang.transform.prep_for_wc_sim module¶

Prepare a model for simulation by wc_sim.

Author: Arthur Goldberg <Arthur.Goldberg@mssm.edu>
Author: Jonathan Karr <jonrkarr@gmail.com>
Date: 2018-11-28
License: MIT

class wc_lang.transform.prep_for_wc_sim.PrepForWcSimTransform[source]¶

Bases: wc_lang.transform.core.CompositeTransform

Prepare a model for simulation by making implicit information in the model explicit.

Create explicit distributions of initial zero concentrations for species that don’t have explicit distributions of initial concentrations (i.e. implicit distributions of initial zero concentrations)
Create implicit exchange reactions for dFBA submodels
Clip the flux bounds for the reactions in dFBA submodels to the default flux range
Split reversible reactions into separate forward and reverse reactions

COMPONENT_TRANSFORMS = (<wc_lang.transform.create_implicit_dist_zero_init_concs.CreateImplicitDistributionZeroInitConcentrationsTransform object>, <wc_lang.transform.create_implicit_dfba_ex_rxns.CreateImplicitDfbaExchangeReactionsTransform object>, <wc_lang.transform.set_finite_dfba_flux_bounds.SetFiniteDfbaFluxBoundsTransform object>, <wc_lang.transform.split_reversible_reactions.SplitReversibleReactionsTransform object>, <wc_lang.transform.nullify_attrs.NullifyAttrsTransform object>)[source]¶

class Meta[source]¶

Bases: object

id = 'PrepForWCSim'[source]¶

label = 'Prepare model for simulation by making implicit information in the model explicit'[source]¶

4.1.1.4.10. wc_lang.transform.set_finite_dfba_flux_bounds module¶

Clip the flux bounds for the reactions in dFBA submodels

Author: Arthur Goldberg <Arthur.Goldberg@mssm.edu>
Author: Jonathan Karr <jonrkarr@gmail.com>
Date: 2018-11-28
License: MIT

class wc_lang.transform.set_finite_dfba_flux_bounds.SetFiniteDfbaFluxBoundsTransform[source]¶

Bases: wc_lang.transform.core.Transform

Clip the flux bounds for the reactions in dFBA submodels to the default flux range

Bounds need to be clipped because some linear programming solvers require finite minimum and maximum flux bounds. The default bounds are provided in the wc_lang configuration.

Specifically, the default minimum and maximum flux bounds are applied as follows:

reversible reactions:

flux_min = max(flux_min, flux_min_bound_reversible)

flux_max = min(flux_max, flux_max_bound)

irreversible reactions:

flux_min = max(flux_min, flux_min_bound_irreversible)

flux_max = min(flux_max, flux_max_bound)

class Meta[source]¶

Bases: object

id = 'SetFiniteDfbaFluxBoundsTransform'[source]¶

label = 'Clip the flux bounds for the reactions in dFBA submodels to the default flux range'[source]¶

run(model)[source]¶

Transform model

Parameters: model (Model) – model
Returns: same model, but transformed
Return type: Model

4.1.1.4.11. wc_lang.transform.split_reversible_reactions module¶

Transform models.

Author: Jonathan Karr <karr@mssm.edu>
Author: Arthur Goldberg <Arthur.Goldberg@mssm.edu>
Date: 2018-06-19
License: MIT

class wc_lang.transform.split_reversible_reactions.SplitReversibleReactionsTransform(excluded_frameworks=None)[source]¶

Bases: wc_lang.transform.core.Transform

Split reversible reactions in submodels into separate forward and backward reactions

class Meta[source]¶

Bases: object

id = 'SplitReversibleReactions'[source]¶

label = 'Split reversible reactions into separate forward and backward reactions'[source]¶

run(model)[source]¶

Split reversible reactions in submodels into separate forward and backward reactions

Parameters: model (Model) – model definition
Returns: same model definition, but with reversible reactions split into separate forward and backward reactions, their flux bounds adjusted accordingly, and the dFBA objective expression adjusted accordingly
Return type: Model

4.1.1.4. wc_lang.transform package¶

4.1.1.4.1. Submodules¶

4.1.1.4.2. wc_lang.transform.change_value module¶

4.1.1.4.3. wc_lang.transform.core module¶

4.1.1.4.4. wc_lang.transform.create_implicit_dfba_ex_rxns module¶

4.1.1.4.5. wc_lang.transform.create_implicit_dist_zero_init_concs module¶

4.1.1.4.6. wc_lang.transform.merge_submodels module¶

4.1.1.4.7. wc_lang.transform.nullify_attrs module¶

4.1.1.4.8. wc_lang.transform.prep_for_sbml module¶

4.1.1.4.9. wc_lang.transform.prep_for_wc_sim module¶

4.1.1.4.10. wc_lang.transform.set_finite_dfba_flux_bounds module¶

4.1.1.4.11. wc_lang.transform.split_reversible_reactions module¶

4.1.1.4.12. Module contents¶