4.1. wc_lang package¶

4.1.1. Subpackages¶

4.1.2. Submodules¶

4.1.3. wc_lang.main module¶

Command line programs for manipulating model definitions

Author: Jonathan Karr <karr@mssm.edu>
Author: Arthur Goldberg <Arthur.Goldberg@mssm.edu>
Date: 2016-12-07
Copyright: 2016, Karr Lab
License: MIT

class wc_lang.__main__.App(label=None, **kw)[source]¶

Bases: cement.core.foundation.App

Command line application

class Meta[source]¶

Bases: object

base_controller = 'base'[source]¶

handlers = [<class 'wc_lang.__main__.BaseController'>, <class 'wc_lang.__main__.CutSubmodelsController'>, <class 'wc_lang.__main__.MergeModelsController'>, <class 'wc_lang.__main__.ValidateController'>, <class 'wc_lang.__main__.DifferenceController'>, <class 'wc_lang.__main__.TransformController'>, <class 'wc_lang.__main__.NormalizeController'>, <class 'wc_lang.__main__.ConvertController'>, <class 'wc_lang.__main__.CreateTemplateController'>, <class 'wc_lang.__main__.UpdateVersionMetadataController'>, <class 'wc_lang.__main__.ExportController'>, <class 'wc_lang.__main__.ImportController'>, <class 'obj_tables.migrate.CementControllers.SchemaChangesTemplateController'>][source]¶

label = 'wc-lang'[source]¶

class wc_lang.__main__.BaseController(*args, **kw)[source]¶

Bases: cement.ext.ext_argparse.ArgparseController

Base controller for command line application

class Meta[source]¶

Bases: object

arguments = [(['-v', '--version'], {'action': 'version', 'version': '0.0.1'})][source]¶

description = 'Command line utilities for managing whole-cell model definitions'[source]¶

help = 'Command line utilities for managing whole-cell model definitions'[source]¶

label = 'base'[source]¶

class wc_lang.__main__.ConvertController(*args, **kw)[source]¶

Bases: cement.ext.ext_argparse.ArgparseController

Convert model among Excel (.xlsx), comma separated (.csv), JavaScript Object Notation (.json), tab separated (.tsv), and Yet Another Markup Language (.yaml, .yml) formats

class Meta[source]¶

Bases: object

arguments = [(['source'], {'type': <class 'str'>, 'help': 'Path to model'}), (['dest'], {'type': <class 'str'>, 'help': 'Path to save model in converted format'}), (['--unprotected'], {'action': 'store_true', 'default': False, 'help': 'If set, do not protect the outputted workbook'})][source]¶

description = 'Convert model among .csv, .json, .tsv, .xlsx, .yaml, and .yml formats'[source]¶

help = 'Convert model among .csv, .json, .tsv, .xlsx, .yaml, and .yml formats'[source]¶

label = 'convert'[source]¶

stacked_on = 'base'[source]¶

stacked_type = 'nested'[source]¶

class wc_lang.__main__.CreateTemplateController(*args, **kw)[source]¶

Bases: cement.ext.ext_argparse.ArgparseController

Create file with model template (i.e. create file with row and column labels)

class Meta[source]¶

Bases: object

arguments = [(['path'], {'type': <class 'str'>, 'help': 'Path to save model template'}), (['--ignore-repo-metadata'], {'dest': 'data_repo_metadata', 'default': True, 'action': 'store_false', 'help': 'If set, do not set the Git repository metadata for the knowledge base from the parent directory of `path`'}), (['--unprotected'], {'action': 'store_true', 'default': False, 'help': 'If set, do not protect the outputted workbook'})][source]¶

description = 'Create file with model template: blank file(s) with row and column labels'[source]¶

help = 'Create file with model template: blank file(s) with row and column labels'[source]¶

label = 'create-template'[source]¶

stacked_on = 'base'[source]¶

stacked_type = 'nested'[source]¶

class wc_lang.__main__.CutSubmodelsController(*args, **kw)[source]¶

Bases: cement.ext.ext_argparse.ArgparseController

Cut submodels into separate models

class Meta[source]¶

Bases: object

arguments = [(['in_file'], {'type': <class 'str'>, 'help': 'Path to model to cut'}), (['out_dir'], {'type': <class 'str'>, 'help': 'Directory to save cut submodels'}), (['--unprotected'], {'action': 'store_true', 'default': False, 'help': 'If set, do not protect the outputted workbook'})][source]¶

description = 'Cut submodels into separate models'[source]¶

help = 'Cut submodels into separate models'[source]¶

label = 'cut-submodels'[source]¶

stacked_on = 'base'[source]¶

stacked_type = 'nested'[source]¶

class wc_lang.__main__.DifferenceController(*args, **kw)[source]¶

Bases: cement.ext.ext_argparse.ArgparseController

Display difference between two model definitions

class Meta[source]¶

Bases: object

arguments = [(['path_1'], {'type': <class 'str'>, 'help': 'Path to first model'}), (['path_2'], {'type': <class 'str'>, 'help': 'Path to second model'}), (['--compare-files'], {'dest': 'compare_files', 'default': False, 'action': 'store_true', 'help': 'If true, compare models; otherwise compare files directly'}), (['--compare-metadata-in-files'], {'dest': 'compare_metadata_in_files', 'default': False, 'action': 'store_true', 'help': 'If true, compare metadata (tables of contents, header rows)'})][source]¶

description = 'Get difference between two model definitions'[source]¶

help = 'Get difference between two model definitions'[source]¶

label = 'difference'[source]¶

stacked_on = 'base'[source]¶

stacked_type = 'nested'[source]¶

static remove_metadata(model)[source]¶

Remove metadata from model

Parameters: model (wc_utils.workbook.Workbook) – model

class wc_lang.__main__.ExportController(*args, **kw)[source]¶

Bases: cement.ext.ext_argparse.ArgparseController

Export a model to SBML

class Meta[source]¶

Bases: object

arguments = [(['in_path'], {'type': <class 'str'>, 'help': 'Path to model to export'}), (['out_dir'], {'type': <class 'str'>, 'help': 'Directory to save exported model'})][source]¶

description = 'Export a model to SBML'[source]¶

help = 'Export a model to SBML'[source]¶

label = 'export'[source]¶

stacked_on = 'base'[source]¶

stacked_type = 'nested'[source]¶

class wc_lang.__main__.ImportController(*args, **kw)[source]¶

Bases: cement.ext.ext_argparse.ArgparseController

Import a model from SBML

class Meta[source]¶

Bases: object

arguments = [(['in_dir'], {'type': <class 'str'>, 'help': 'Directory with model to import'}), (['out_path'], {'type': <class 'str'>, 'help': 'Path to save model'}), (['--unprotected'], {'action': 'store_true', 'default': False, 'help': 'If set, do not protect the outputted workbook'})][source]¶

description = 'Import a model from SBML'[source]¶

help = 'Import a model from SBML'[source]¶

label = 'import'[source]¶

stacked_on = 'base'[source]¶

stacked_type = 'nested'[source]¶

class wc_lang.__main__.MergeModelsController(*args, **kw)[source]¶

Bases: cement.ext.ext_argparse.ArgparseController

Merge models

class Meta[source]¶

Bases: object

arguments = [(['-p', '--primary'], {'dest': 'primary_path', 'type': <class 'str'>, 'help': 'Path to base for merged model'}), (['-s', '--secondary'], {'dest': 'secondary_paths', 'type': <class 'str'>, 'nargs': '*', 'help': 'Path to models to merge into primary model'}), (['-o', '--out'], {'dest': 'out_path', 'type': <class 'str'>, 'help': 'Path to save merged model'}), (['--unprotected'], {'action': 'store_true', 'default': False, 'help': 'If set, do not protect the outputted workbook'})][source]¶

description = 'Merge multiple models'[source]¶

help = 'Merge multiple models'[source]¶

label = 'merge-models'[source]¶

stacked_on = 'base'[source]¶

stacked_type = 'nested'[source]¶

class wc_lang.__main__.NormalizeController(*args, **kw)[source]¶

Bases: cement.ext.ext_argparse.ArgparseController

Normalize model

class Meta[source]¶

Bases: object

arguments = [(['source'], {'type': <class 'str'>, 'help': 'Path to model'}), (['--dest'], {'default': '', 'type': <class 'str'>, 'help': 'Path to save normalized model'}), (['--unprotected'], {'action': 'store_true', 'default': False, 'help': 'If set, do not protect the outputted workbook'})][source]¶

description = 'Normalize model'[source]¶

help = 'Normalize model'[source]¶

label = 'normalize'[source]¶

stacked_on = 'base'[source]¶

stacked_type = 'nested'[source]¶

class wc_lang.__main__.TransformController(*args, **kw)[source]¶

Bases: cement.ext.ext_argparse.ArgparseController

Apply one, or more, transforms to a model and save the result

class Meta[source]¶

Bases: object

arguments = [(['source'], {'type': <class 'str'>, 'help': 'Path to model'}), (['dest'], {'type': <class 'str'>, 'help': 'Path to save transformed model'}), (['--transform'], {'dest': 'transforms', 'action': 'append', 'help': 'Model transform:\n ChangeValue: Change a value of an attribute of a model\n CreateImplicitDfbaExchangeReactions: Create implicit exchange reactions for dFBA submodels\n CreateImplicitDistributionZeroInitConcentrations: Create the implicit zero concentrations in a model\n MergeAlgorithmicallyLikeSubmodels: Merge groups of algorithmically-like submodels into individual submodels\n NullifyAttrs: Generate a reduced model by nullifying specific attributes\n PrepForSbml: Transform model into SBML-compatible representation and discard information that cannot be exported to SBML\n PrepForWCSim: Prepare model for simulation by making implicit information in the model explicit\n SetFiniteDfbaFluxBoundsTransform: Clip the flux bounds for the reactions in dFBA submodels to the default flux range\n SplitReversibleReactions: Split reversible reactions into separate forward and backward reactions'}), (['--unprotected'], {'action': 'store_true', 'default': False, 'help': 'If set, do not protect the outputted workbook'})][source]¶

description = 'Apply one, or more, transforms to a model and save the result'[source]¶

help = 'Apply one, or more, transforms to a model and save the result'[source]¶

label = 'transform'[source]¶

stacked_on = 'base'[source]¶

stacked_type = 'nested'[source]¶

class wc_lang.__main__.UpdateVersionMetadataController(*args, **kw)[source]¶

Bases: cement.ext.ext_argparse.ArgparseController

Update the version metadata (repository URL, branch, revision; wc_lang version) of a model

class Meta[source]¶

Bases: object

arguments = [(['path'], {'type': <class 'str'>, 'help': 'Path to model'}), (['--ignore-repo-metadata'], {'dest': 'data_repo_metadata', 'default': True, 'action': 'store_false', 'help': 'If set, do not set the Git repository metadata for the knowledge base from the parent directory of `path-core`'}), (['--unprotected'], {'action': 'store_true', 'default': False, 'help': 'If set, do not protect the outputted workbook'})][source]¶

description = 'Update the version metadata (repository URL, branch, revision; wc_lang version) of a model'[source]¶

help = 'Update the version metadata (repository URL, branch, revision; wc_lang version) of a model'[source]¶

label = 'update-version-metadata'[source]¶

stacked_on = 'base'[source]¶

stacked_type = 'nested'[source]¶

class wc_lang.__main__.ValidateController(*args, **kw)[source]¶

Bases: cement.ext.ext_argparse.ArgparseController

Validate model and display errors

class Meta[source]¶

Bases: object

arguments = [(['path'], {'type': <class 'str'>, 'help': 'Path to model'})][source]¶

description = 'Validate model and display errors'[source]¶

help = 'Validate model and display errors'[source]¶

label = 'validate'[source]¶

stacked_on = 'base'[source]¶

stacked_type = 'nested'[source]¶

wc_lang.__main__.main()[source]¶

4.1.4. wc_lang._version module¶

4.1.5. wc_lang.core module¶

Data model to represent composite, multi-algorithmic biochemical models.

This module defines classes that represent the schema and provenance of a biochemical model:

These are all instances of obj_tables.Model. A biochemical model may contain a list of instances of each of these classes, interlinked by object references. For example, a Species references the compartment which contains it as a Compartment instance and the species category to which it belongs as a SpeciesType instance.

This module also defines numerous classes that serve as attributes of these classes.

Author: Jonathan Karr <karr@mssm.edu>
Author: Arthur Goldberg <Arthur.Goldberg@mssm.edu>
Date: 2016-11-10
Copyright: 2016-2017, Karr Lab
License: MIT

class wc_lang.core.Author(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

An author of a model

id[source]¶

unique identifier

Type: str

name[source]¶

full name

Type: str

model[source]¶

model

Type: Model

last_name[source]¶

last name(s)

Type: str

first_name[source]¶

first name(s)

Type: str

middle_name[source]¶

middle name(s)

Type: str

title[source]¶

title

Type: str

organization[source]¶

organization

Type: str

email[source]¶

email address

Type: str

website[source]¶

website

Type: str

address[source]¶

physical address

Type: str

identifiers[source]¶

identifiers

Type: list of Identifier

comments[source]¶

comments

Type: str

Related attributes:

conclusions (list of Conclusion): conclusions

changes (list of Change): changes

class Meta[source]¶

Bases: obj_tables.core.Meta

attribute_order = ('id', 'name', 'last_name', 'first_name', 'middle_name', 'title', 'organization', 'email', 'website', 'address', 'identifiers', 'comments')[source]¶

attributes = {'address': <obj_tables.core.LongStringAttribute object>, 'comments': <obj_tables.core.LongStringAttribute object>, 'email': <obj_tables.core.EmailAttribute object>, 'first_name': <obj_tables.core.StringAttribute object>, 'id': <obj_tables.core.SlugAttribute object>, 'identifiers': <wc_lang.core.IdentifierManyToManyAttribute object>, 'last_name': <obj_tables.core.StringAttribute object>, 'middle_name': <obj_tables.core.StringAttribute object>, 'model': <obj_tables.core.ManyToOneAttribute object>, 'name': <obj_tables.core.StringAttribute object>, 'organization': <obj_tables.core.LongStringAttribute object>, 'title': <obj_tables.core.LongStringAttribute object>, 'website': <obj_tables.core.UrlAttribute object>}[source]¶

child_attrs = {'sbml': ('id', 'name', 'model', 'last_name', 'first_name', 'middle_name', 'title', 'organization', 'email', 'website', 'address', 'identifiers', 'comments'), 'wc_sim': ()}[source]¶

children = {'core_model': ('identifiers',), 'submodel': ('identifiers',)}[source]¶

frozen_columns = 2[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.Author'>,)[source]¶

local_attributes = {'address': <obj_tables.core.LocalAttribute object>, 'changes': <obj_tables.core.LocalAttribute object>, 'comments': <obj_tables.core.LocalAttribute object>, 'conclusions': <obj_tables.core.LocalAttribute object>, 'email': <obj_tables.core.LocalAttribute object>, 'first_name': <obj_tables.core.LocalAttribute object>, 'id': <obj_tables.core.LocalAttribute object>, 'identifiers': <obj_tables.core.LocalAttribute object>, 'last_name': <obj_tables.core.LocalAttribute object>, 'middle_name': <obj_tables.core.LocalAttribute object>, 'model': <obj_tables.core.LocalAttribute object>, 'name': <obj_tables.core.LocalAttribute object>, 'organization': <obj_tables.core.LocalAttribute object>, 'title': <obj_tables.core.LocalAttribute object>, 'website': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ('id',)[source]¶

primary_attribute = <obj_tables.core.SlugAttribute object>[source]¶

related_attributes = {'changes': <obj_tables.core.ManyToManyAttribute object>, 'conclusions': <obj_tables.core.ManyToManyAttribute object>}[source]¶

unique_together = ()[source]¶

verbose_name = 'Author'[source]¶

verbose_name_plural = 'Authors'[source]¶

address = <obj_tables.core.LongStringAttribute object>[source]

comments = <obj_tables.core.LongStringAttribute object>[source]

email = <obj_tables.core.EmailAttribute object>[source]

first_name = <obj_tables.core.StringAttribute object>[source]

get_identifier(namespace)[source]¶

Get the author’s id in a namespace (e.g., github.user, orcid)

Parameters: namespace (str) – namespace of the identifier to retrieve
Returns: user’s id in namespace
Return type: str
Raises: ValueError – if the author has multiple ids in namespace

id = <obj_tables.core.SlugAttribute object>[source]

identifiers = <wc_lang.core.IdentifierManyToManyAttribute object>[source]

last_name = <obj_tables.core.StringAttribute object>[source]

middle_name = <obj_tables.core.StringAttribute object>[source]

model = <obj_tables.core.ManyToOneAttribute object>[source]

name = <obj_tables.core.StringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

organization = <obj_tables.core.LongStringAttribute object>[source]

title = <obj_tables.core.LongStringAttribute object>[source]

website = <obj_tables.core.UrlAttribute object>[source]

class wc_lang.core.Change(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

A change to a model

id[source]¶

unique identifier

Type: str

name[source]¶

full name

Type: str

model[source]¶

model

Type: Model

type[source]¶

type

Type: pronto.term.Term

target[source]¶

target

Type: str

target_submodel[source]¶

target submodel

Type: Submodel

target_type[source]¶

target type

Type: pronto.term.Term

reason[source]¶

reason

Type: str

reason_type[source]¶

type of reason

Type: pronto.term.Term

intention[source]¶

intention

Type: str

intention_type[source]¶

type of intention

Type: pronto.term.Term

identifiers[source]¶

identifiers

Type: list of Identifier

evidence[source]¶

observation that supports/disputes a conclusion

Type: list of Evidence

conclusions[source]¶

conclusions

Type: list of Conclusion

comments[source]¶

comments

Type: str

references[source]¶

references

Type: list of Reference

authors[source]¶

authors

Type: list of Author

date[source]¶

date

Type: datetime.datetime

class Meta[source]¶

Bases: obj_tables.core.Meta

attribute_order = ('id', 'name', 'type', 'target', 'target_submodel', 'target_type', 'reason', 'reason_type', 'intention', 'intention_type', 'identifiers', 'evidence', 'conclusions', 'comments', 'references', 'authors', 'date')[source]¶

attributes = {'authors': <obj_tables.core.ManyToManyAttribute object>, 'comments': <obj_tables.core.LongStringAttribute object>, 'conclusions': <obj_tables.core.ManyToManyAttribute object>, 'date': <obj_tables.core.DateTimeAttribute object>, 'evidence': <wc_lang.core.EvidenceManyToManyAttribute object>, 'id': <obj_tables.core.SlugAttribute object>, 'identifiers': <wc_lang.core.IdentifierManyToManyAttribute object>, 'intention': <obj_tables.core.LongStringAttribute object>, 'intention_type': <obj_tables.sci.onto.OntoTermAttribute object>, 'model': <obj_tables.core.ManyToOneAttribute object>, 'name': <obj_tables.core.StringAttribute object>, 'reason': <obj_tables.core.LongStringAttribute object>, 'reason_type': <obj_tables.sci.onto.OntoTermAttribute object>, 'references': <obj_tables.core.ManyToManyAttribute object>, 'target': <obj_tables.core.LongStringAttribute object>, 'target_submodel': <obj_tables.core.ManyToOneAttribute object>, 'target_type': <obj_tables.sci.onto.OntoTermAttribute object>, 'type': <obj_tables.sci.onto.OntoTermAttribute object>}[source]¶

child_attrs = {'sbml': (), 'wc_sim': ()}[source]¶

children = {'core_model': ('identifiers', 'evidence', 'conclusions', 'references', 'authors'), 'submodel': ('identifiers', 'evidence', 'conclusions', 'references', 'authors')}[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.Change'>,)[source]¶

local_attributes = {'authors': <obj_tables.core.LocalAttribute object>, 'comments': <obj_tables.core.LocalAttribute object>, 'conclusions': <obj_tables.core.LocalAttribute object>, 'date': <obj_tables.core.LocalAttribute object>, 'evidence': <obj_tables.core.LocalAttribute object>, 'id': <obj_tables.core.LocalAttribute object>, 'identifiers': <obj_tables.core.LocalAttribute object>, 'intention': <obj_tables.core.LocalAttribute object>, 'intention_type': <obj_tables.core.LocalAttribute object>, 'model': <obj_tables.core.LocalAttribute object>, 'name': <obj_tables.core.LocalAttribute object>, 'reason': <obj_tables.core.LocalAttribute object>, 'reason_type': <obj_tables.core.LocalAttribute object>, 'references': <obj_tables.core.LocalAttribute object>, 'target': <obj_tables.core.LocalAttribute object>, 'target_submodel': <obj_tables.core.LocalAttribute object>, 'target_type': <obj_tables.core.LocalAttribute object>, 'type': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ('id',)[source]¶

primary_attribute = <obj_tables.core.SlugAttribute object>[source]¶

related_attributes = {}[source]¶

unique_together = ()[source]¶

verbose_name = 'Change'[source]¶

verbose_name_plural = 'Changes'[source]¶

authors = <obj_tables.core.ManyToManyAttribute object>[source]

comments = <obj_tables.core.LongStringAttribute object>[source]

conclusions = <obj_tables.core.ManyToManyAttribute object>[source]

date = <obj_tables.core.DateTimeAttribute object>[source]

evidence = <wc_lang.core.EvidenceManyToManyAttribute object>[source]

id = <obj_tables.core.SlugAttribute object>[source]

identifiers = <wc_lang.core.IdentifierManyToManyAttribute object>[source]

intention = <obj_tables.core.LongStringAttribute object>[source]

intention_type = <obj_tables.sci.onto.OntoTermAttribute object>[source]

model = <obj_tables.core.ManyToOneAttribute object>[source]

name = <obj_tables.core.StringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

reason = <obj_tables.core.LongStringAttribute object>[source]

reason_type = <obj_tables.sci.onto.OntoTermAttribute object>[source]

references = <obj_tables.core.ManyToManyAttribute object>[source]

target = <obj_tables.core.LongStringAttribute object>[source]

target_submodel = <obj_tables.core.ManyToOneAttribute object>[source]

target_type = <obj_tables.sci.onto.OntoTermAttribute object>[source]

type = <obj_tables.sci.onto.OntoTermAttribute object>[source]

class wc_lang.core.ChemicalStructure(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

Structure of a chemical compound

value[source]¶

Type: str

format[source]¶

format of the structure

Type: ChemicalStructureFormat

alphabet[source]¶

alphabet of BpForms-encoded structure

Type: ChemicalStructureAlphabet

empirical_formula[source]¶

empirical formula

Type: EmpiricalFormula

molecular_weight[source]¶

molecular weight

Type: float

charge[source]¶

charge

Type: int

class Meta[source]¶

Bases: obj_tables.core.Meta

attribute_order = ('value', 'format', 'alphabet', 'empirical_formula', 'molecular_weight', 'charge')[source]¶

attributes = {'alphabet': <obj_tables.core.EnumAttribute object>, 'charge': <obj_tables.core.IntegerAttribute object>, 'empirical_formula': <obj_tables.chem.core.ChemicalFormulaAttribute object>, 'format': <obj_tables.core.EnumAttribute object>, 'molecular_weight': <obj_tables.core.FloatAttribute object>, 'value': <obj_tables.core.LongStringAttribute object>}[source]¶

child_attrs = {'sbml': ('value', 'format', 'alphabet', 'empirical_formula', 'molecular_weight', 'charge'), 'wc_sim': ('molecular_weight', 'charge')}[source]¶

children = {'core_model': (), 'submodel': ()}[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.ChemicalStructure'>,)[source]¶

local_attributes = {'alphabet': <obj_tables.core.LocalAttribute object>, 'charge': <obj_tables.core.LocalAttribute object>, 'empirical_formula': <obj_tables.core.LocalAttribute object>, 'format': <obj_tables.core.LocalAttribute object>, 'molecular_weight': <obj_tables.core.LocalAttribute object>, 'species_types': <obj_tables.core.LocalAttribute object>, 'value': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ()[source]¶

primary_attribute = None[source]¶

related_attributes = {'species_types': <obj_tables.core.ManyToOneAttribute object>}[source]¶

table_format = 4[source]¶

unique_together = ()[source]¶

verbose_name = 'Chemical structure'[source]¶

verbose_name_plural = 'Chemical structures'[source]¶

alphabet = <obj_tables.core.EnumAttribute object>[source]

charge = <obj_tables.core.IntegerAttribute object>[source]

empirical_formula = <obj_tables.chem.core.ChemicalFormulaAttribute object>[source]

format = <obj_tables.core.EnumAttribute object>[source]

get_structure()[source]¶

Get structure

Returns: structure
Return type: openbabel.OBMol, bpforms.BpForm, or bcforms.BcForm
Raises: ValueError – if the structure cannot be parsed

has_carbon()[source]¶

Returns True is species contains at least one carbon atom.

Returns: True is species contains at least one carbon atom.
Return type: bool

molecular_weight = <obj_tables.core.FloatAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

serialize()[source]¶

Generate string representation

Returns: string representation
Return type: str

validate()[source]¶

Check that the structure is valid

Format provided when structure is not None
Value provided when format is not None
Alphabet provided for BpForms-encoded structures
Empirical formula, molecular weight, charge match structure (when provided)

Returns

None if the object is valid,: otherwise return a list of errors as an instance of InvalidObject

Return type

InvalidObject or None

value = <obj_tables.core.LongStringAttribute object>[source]

class wc_lang.core.ChemicalStructureAlphabet[source]¶

Bases: int, wc_utils.util.enumerate.CaseInsensitiveEnum

An enumeration.

canonical_dna = 4[source]¶

canonical_protein = 6[source]¶

canonical_rna = 5[source]¶

dna = 1[source]¶

protein = 3[source]¶

rna = 2[source]¶

class wc_lang.core.ChemicalStructureFormat[source]¶

Bases: int, wc_utils.util.enumerate.CaseInsensitiveEnum

Format of a chemical structure

bcforms = 2[source]¶

bpforms = 1[source]¶

smiles = 0[source]¶

class wc_lang.core.CommentAttribute(min_length=0, max_length=4294967295, none=False, default='', default_cleaned_value='', none_value='', verbose_name='', description='', primary=False, unique=False, unique_case_insensitive=False)[source]¶

Bases: obj_tables.core.LongStringAttribute

Comment attribute

SEPARATOR = '\n\n'[source]¶

merge(left, right, right_objs_in_left, left_objs_in_right)[source]¶

Merge an attribute of elements of two models

Parameters

left (Model) – an element in a model to merge
right (Model) – an element in a second model to merge
right_objs_in_left (dict) – mapping from objects in right model to objects in left model
left_objs_in_right (dict) – mapping from objects in left model to objects in right model

class wc_lang.core.Compartment(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

id[source]¶

unique identifier

Type: str

name[source]¶

name

Type: str

model[source]¶

model

Type: Model

biological_type[source]¶

biological type

Type: pronto.term.Term

physical_type[source]¶

physical type

Type: pronto.term.Term

geometry[source]¶

geometry

Type: pronto.term.Term

parent_compartment[source]¶

parent compartment

Type: Compartment

mass_units[source]¶

the units of the compartment mass returned when an Expression uses the compartment as a term, identified by its id

Type: unit_registry.Unit

init_volume[source]¶

initial volume

Type: InitVolume

init_density[source]¶

parameter that provides the density during the initialization of each simulation

Type: Parameter

ph[source]¶

pH

Type: Ph

identifiers[source]¶

identifiers

Type: list of Identifier

evidence[source]¶

observation that supports/disputes a conclusion

Type: list of Evidence

conclusions[source]¶

conclusions

Type: list of Conclusion

comments[source]¶

comments

Type: str

references[source]¶

references

Type: list of Reference

Related attributes:

sub_compartments (list of Compartment): compartments contained in this compartment

species (list of Species): species in this compartment

function_expressions (list of FunctionExpression): function expressions

rate_law_expressions (list of RateLawExpression): rate law expressions

stop_condition_expressions (list of StopConditionExpression): stop condition expressions

class Meta[source]¶

Bases: obj_tables.core.Meta, obj_tables.math.expression.ExpressionDynamicTermMeta

attribute_order = ('id', 'name', 'biological_type', 'physical_type', 'geometry', 'parent_compartment', 'mass_units', 'init_volume', 'init_density', 'ph', 'identifiers', 'evidence', 'conclusions', 'comments', 'references')[source]¶

attributes = {'biological_type': <obj_tables.sci.onto.OntoTermAttribute object>, 'comments': <wc_lang.core.CommentAttribute object>, 'conclusions': <obj_tables.core.ManyToManyAttribute object>, 'evidence': <wc_lang.core.EvidenceManyToManyAttribute object>, 'geometry': <obj_tables.sci.onto.OntoTermAttribute object>, 'id': <obj_tables.core.SlugAttribute object>, 'identifiers': <wc_lang.core.IdentifierManyToManyAttribute object>, 'init_density': <obj_tables.core.OneToOneAttribute object>, 'init_volume': <obj_tables.core.ManyToOneAttribute object>, 'mass_units': <obj_tables.sci.units.UnitAttribute object>, 'model': <obj_tables.core.ManyToOneAttribute object>, 'name': <obj_tables.core.StringAttribute object>, 'parent_compartment': <obj_tables.core.ManyToOneAttribute object>, 'ph': <obj_tables.core.ManyToOneAttribute object>, 'physical_type': <obj_tables.sci.onto.OntoTermAttribute object>, 'references': <obj_tables.core.ManyToManyAttribute object>}[source]¶

child_attrs = {'sbml': ('id', 'name', 'model', 'biological_type', 'physical_type', 'geometry', 'parent_compartment', 'mass_units', 'init_volume', 'init_density', 'ph', 'identifiers', 'comments'), 'wc_sim': ('id', 'model', 'mass_units', 'biological_type', 'physical_type', 'geometry', 'parent_compartment', 'init_volume', 'init_density')}[source]¶

children = {'core_model': ('parent_compartment', 'sub_compartments', 'init_volume', 'init_density', 'ph', 'identifiers', 'evidence', 'conclusions', 'references'), 'submodel': ('init_volume', 'init_density', 'ph', 'identifiers', 'evidence', 'conclusions', 'references')}[source]¶

expression_term_units = 'mass_units'[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.Compartment'>,)[source]¶

local_attributes = {'biological_type': <obj_tables.core.LocalAttribute object>, 'comments': <obj_tables.core.LocalAttribute object>, 'conclusions': <obj_tables.core.LocalAttribute object>, 'evidence': <obj_tables.core.LocalAttribute object>, 'function_expressions': <obj_tables.core.LocalAttribute object>, 'geometry': <obj_tables.core.LocalAttribute object>, 'id': <obj_tables.core.LocalAttribute object>, 'identifiers': <obj_tables.core.LocalAttribute object>, 'init_density': <obj_tables.core.LocalAttribute object>, 'init_volume': <obj_tables.core.LocalAttribute object>, 'mass_units': <obj_tables.core.LocalAttribute object>, 'model': <obj_tables.core.LocalAttribute object>, 'name': <obj_tables.core.LocalAttribute object>, 'parent_compartment': <obj_tables.core.LocalAttribute object>, 'ph': <obj_tables.core.LocalAttribute object>, 'physical_type': <obj_tables.core.LocalAttribute object>, 'rate_law_expressions': <obj_tables.core.LocalAttribute object>, 'references': <obj_tables.core.LocalAttribute object>, 'species': <obj_tables.core.LocalAttribute object>, 'stop_condition_expressions': <obj_tables.core.LocalAttribute object>, 'sub_compartments': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ('id',)[source]¶

primary_attribute = <obj_tables.core.SlugAttribute object>[source]¶

related_attributes = {'function_expressions': <obj_tables.core.ManyToManyAttribute object>, 'rate_law_expressions': <obj_tables.core.ManyToManyAttribute object>, 'species': <obj_tables.core.ManyToOneAttribute object>, 'stop_condition_expressions': <obj_tables.core.ManyToManyAttribute object>, 'sub_compartments': <obj_tables.core.ManyToOneAttribute object>}[source]¶

unique_together = ()[source]¶

verbose_name = 'Compartment'[source]¶

verbose_name_plural = 'Compartments'[source]¶

biological_type = <obj_tables.sci.onto.OntoTermAttribute object>[source]

comments = <wc_lang.core.CommentAttribute object>[source]

conclusions = <obj_tables.core.ManyToManyAttribute object>[source]

evidence = <wc_lang.core.EvidenceManyToManyAttribute object>[source]

export_relations_to_sbml(sbml_model, sbml)[source]¶

Add relationships to/from object to SBML compartment.

Parameters

sbml_model (libsbml.Model) – SBML model
sbml (libsbml.Compartment) – SBML compartment

export_to_sbml(sbml_model)[source]¶

Add this compartment to a SBML model.

Parameters: sbml_model (libsbml.Model) – SBML model
Returns: SBML compartment
Return type: libsbml.Compartment
Raises: ValueError – if the geometry cannot be exported to SBML

geometry = <obj_tables.sci.onto.OntoTermAttribute object>[source]

get_sub_compartments(nested=False)[source]¶

Get sub-compartments, optionally including all nested sub-compartments

Returns: list of sub-compartments
Return type: list of Compartment

get_tot_mean_init_volume()[source]¶

Get total mean initial volume of a compartment and its nested sub-compartments

Returns: total mean initial volume of a compartment and its nested sub-compartments
Return type: float

id = <obj_tables.core.SlugAttribute object>[source]

identifiers = <wc_lang.core.IdentifierManyToManyAttribute object>[source]

import_from_sbml(sbml)[source]¶

Load from SBML compartment

Parameters: sbml (libsbml.Compartment) – SBML compartment
Raises: ValueError – if the geometry cannot be imported from SBML

import_relations_from_sbml(sbml, objs)[source]¶

Load relationships from SBML compartment

Parameters

sbml (libsbml.Compartment) – SBML compartment
objs (dict) – dictionary that maps WC-Lang types to dictionaries that map the ids of WC-Lang objects to WC-Lang objects

init_density = <obj_tables.core.OneToOneAttribute object>[source]

init_volume = <obj_tables.core.ManyToOneAttribute object>[source]

mass_units = <obj_tables.sci.units.UnitAttribute object>[source]

model = <obj_tables.core.ManyToOneAttribute object>[source]

name = <obj_tables.core.StringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

parent_compartment = <obj_tables.core.ManyToOneAttribute object>[source]

ph = <obj_tables.core.ManyToOneAttribute object>[source]

physical_type = <obj_tables.sci.onto.OntoTermAttribute object>[source]

references = <obj_tables.core.ManyToManyAttribute object>[source]

validate()[source]¶

Check that the compartment is valid

Check that the units of density are g l^-1

Returns

None if the object is valid,: otherwise return a list of errors as an instance of InvalidObject

Return type

InvalidObject or None

class wc_lang.core.Conclusion(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model

Conclusion of one or more observations

id[source]¶

unique identifier

Type: str

name[source]¶

name

Type: str

model[source]¶

model

Type: Model

value[source]¶

value

Type: str

std[source]¶

standard error of the value

Type: str

units[source]¶

units

Type: unit_registry.Unit

type[source]¶

type

Type: pronto.term.Term

process[source]¶

procedure which produced the conclusion

Type: Process

identifiers[source]¶

identifiers

Type: list of Identifier

evidence[source]¶

evidence that supports/refutes the conclusion (e.g. individual observations underlying an average)

Type: list of Evidence

comments[source]¶

comments

Type: str

references[source]¶

references

Type: list of Reference

authors[source]¶

authors

Type: list of Author

date[source]¶

date and time when the conclusion was made

Type: datetime.datetime

Related attributes:

submodels (list of Submodel): submodels

compartments (list of Compartment): compartments

species_types (list of SpeciesType): species types

species (list of Species): species

distribution_init_concentrations (list of DistributionInitConcentration): distributions of initial concentrations of species at the beginning of each cell cycle

observables (list of Observable): observables

functions (list of Function): functions

reactions (list of Reaction): reactions

rate_laws (list of RateLaw): rate laws

dfba_objs (list of DfbaObjective): dFBA objectives

dfba_obj_reactions (list of DfbaObjReaction): dFBA objective reactions

dfba_obj_species (list of DfbaObjSpecies): dFBA objective species

stop_conditions (list of StopCondition): stop conditions

parameters (list of Parameter): parameters

changes (list of Change): changes

class Meta[source]¶

Bases: obj_tables.core.Meta

attribute_order = ('id', 'name', 'value', 'std', 'units', 'type', 'process', 'identifiers', 'evidence', 'comments', 'references', 'authors', 'date')[source]¶

attributes = {'authors': <obj_tables.core.ManyToManyAttribute object>, 'comments': <wc_lang.core.CommentAttribute object>, 'date': <obj_tables.core.DateTimeAttribute object>, 'evidence': <wc_lang.core.EvidenceManyToManyAttribute object>, 'id': <obj_tables.core.SlugAttribute object>, 'identifiers': <wc_lang.core.IdentifierManyToManyAttribute object>, 'model': <obj_tables.core.ManyToOneAttribute object>, 'name': <obj_tables.core.StringAttribute object>, 'process': <obj_tables.core.ManyToOneAttribute object>, 'references': <obj_tables.core.ManyToManyAttribute object>, 'std': <obj_tables.core.StringAttribute object>, 'type': <obj_tables.sci.onto.OntoTermAttribute object>, 'units': <obj_tables.sci.units.UnitAttribute object>, 'value': <obj_tables.core.StringAttribute object>}[source]¶

child_attrs = {'sbml': (), 'wc_sim': ()}[source]¶

children = {'core_model': ('process', 'identifiers', 'evidence', 'references', 'authors'), 'submodel': ('process', 'identifiers', 'evidence', 'references', 'authors')}[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.Conclusion'>,)[source]¶

local_attributes = {'authors': <obj_tables.core.LocalAttribute object>, 'changes': <obj_tables.core.LocalAttribute object>, 'comments': <obj_tables.core.LocalAttribute object>, 'compartments': <obj_tables.core.LocalAttribute object>, 'date': <obj_tables.core.LocalAttribute object>, 'dfba_obj_reactions': <obj_tables.core.LocalAttribute object>, 'dfba_obj_species': <obj_tables.core.LocalAttribute object>, 'dfba_objs': <obj_tables.core.LocalAttribute object>, 'distribution_init_concentrations': <obj_tables.core.LocalAttribute object>, 'evidence': <obj_tables.core.LocalAttribute object>, 'functions': <obj_tables.core.LocalAttribute object>, 'id': <obj_tables.core.LocalAttribute object>, 'identifiers': <obj_tables.core.LocalAttribute object>, 'model': <obj_tables.core.LocalAttribute object>, 'name': <obj_tables.core.LocalAttribute object>, 'observables': <obj_tables.core.LocalAttribute object>, 'parameters': <obj_tables.core.LocalAttribute object>, 'process': <obj_tables.core.LocalAttribute object>, 'rate_laws': <obj_tables.core.LocalAttribute object>, 'reactions': <obj_tables.core.LocalAttribute object>, 'references': <obj_tables.core.LocalAttribute object>, 'species': <obj_tables.core.LocalAttribute object>, 'species_types': <obj_tables.core.LocalAttribute object>, 'std': <obj_tables.core.LocalAttribute object>, 'stop_conditions': <obj_tables.core.LocalAttribute object>, 'submodels': <obj_tables.core.LocalAttribute object>, 'type': <obj_tables.core.LocalAttribute object>, 'units': <obj_tables.core.LocalAttribute object>, 'value': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ('id',)[source]¶

primary_attribute = <obj_tables.core.SlugAttribute object>[source]¶

related_attributes = {'changes': <obj_tables.core.ManyToManyAttribute object>, 'compartments': <obj_tables.core.ManyToManyAttribute object>, 'dfba_obj_reactions': <obj_tables.core.ManyToManyAttribute object>, 'dfba_obj_species': <obj_tables.core.ManyToManyAttribute object>, 'dfba_objs': <obj_tables.core.ManyToManyAttribute object>, 'distribution_init_concentrations': <obj_tables.core.ManyToManyAttribute object>, 'functions': <obj_tables.core.ManyToManyAttribute object>, 'observables': <obj_tables.core.ManyToManyAttribute object>, 'parameters': <obj_tables.core.ManyToManyAttribute object>, 'rate_laws': <obj_tables.core.ManyToManyAttribute object>, 'reactions': <obj_tables.core.ManyToManyAttribute object>, 'species': <obj_tables.core.ManyToManyAttribute object>, 'species_types': <obj_tables.core.ManyToManyAttribute object>, 'stop_conditions': <obj_tables.core.ManyToManyAttribute object>, 'submodels': <obj_tables.core.ManyToManyAttribute object>}[source]¶

unique_together = ()[source]¶

verbose_name = 'Conclusion'[source]¶

verbose_name_plural = 'Conclusions'[source]¶

authors = <obj_tables.core.ManyToManyAttribute object>[source]

comments = <wc_lang.core.CommentAttribute object>[source]

date = <obj_tables.core.DateTimeAttribute object>[source]

evidence = <wc_lang.core.EvidenceManyToManyAttribute object>[source]

id = <obj_tables.core.SlugAttribute object>[source]

identifiers = <wc_lang.core.IdentifierManyToManyAttribute object>[source]

model = <obj_tables.core.ManyToOneAttribute object>[source]

name = <obj_tables.core.StringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

process = <obj_tables.core.ManyToOneAttribute object>[source]

references = <obj_tables.core.ManyToManyAttribute object>[source]

std = <obj_tables.core.StringAttribute object>[source]

type = <obj_tables.sci.onto.OntoTermAttribute object>[source]

units = <obj_tables.sci.units.UnitAttribute object>[source]

value = <obj_tables.core.StringAttribute object>[source]

class wc_lang.core.DfbaObjReaction(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

A pseudo-reaction used to represent the interface between metabolism and other cell processes.

id[source]¶

unique identifier

Type: str

name[source]¶

name

Type: str

model[source]¶

model

Type: Model

submodel[source]¶

submodel that uses this reaction

Type: Submodel

units[source]¶

rate units

Type: unit_registry.Unit

cell_size_units[source]¶

cell size units

Type: unit_registry.Unit

identifiers[source]¶

identifiers

Type: list of Identifier

evidence[source]¶

observation that supports/disputes a conclusion

Type: list of Evidence

conclusions[source]¶

conclusions

Type: list of Conclusion

comments[source]¶

comments

Type: str

references[source]¶

references

Type: list of Reference

Related attributes:

dfba_obj_expression (DfbaObjectiveExpression): dFBA objective expression

dfba_obj_species (list of DfbaObjSpecies): the components of this dFBA objective reaction

class Meta[source]¶

Bases: obj_tables.core.Meta, obj_tables.math.expression.ExpressionDynamicTermMeta

attribute_order = ('id', 'name', 'submodel', 'units', 'cell_size_units', 'identifiers', 'evidence', 'conclusions', 'comments', 'references')[source]¶

attributes = {'cell_size_units': <obj_tables.sci.units.UnitAttribute object>, 'comments': <wc_lang.core.CommentAttribute object>, 'conclusions': <obj_tables.core.ManyToManyAttribute object>, 'evidence': <wc_lang.core.EvidenceManyToManyAttribute object>, 'id': <obj_tables.core.SlugAttribute object>, 'identifiers': <wc_lang.core.IdentifierManyToManyAttribute object>, 'model': <obj_tables.core.ManyToOneAttribute object>, 'name': <obj_tables.core.StringAttribute object>, 'references': <obj_tables.core.ManyToManyAttribute object>, 'submodel': <obj_tables.core.ManyToOneAttribute object>, 'units': <obj_tables.sci.units.UnitAttribute object>}[source]¶

child_attrs = {'sbml': ('id', 'name', 'model', 'submodel', 'units', 'cell_size_units', 'identifiers', 'comments'), 'wc_sim': ('id', 'model', 'submodel', 'units', 'cell_size_units')}[source]¶

children = {'core_model': ('dfba_obj_species', 'identifiers', 'evidence', 'conclusions', 'references'), 'submodel': ('dfba_obj_species', 'identifiers', 'evidence', 'conclusions', 'references')}[source]¶

expression_term_units = 'units'[source]¶

indexed_attrs_tuples = (('id',),)[source]¶

inheritance = (<class 'wc_lang.core.DfbaObjReaction'>,)[source]¶

local_attributes = {'cell_size_units': <obj_tables.core.LocalAttribute object>, 'comments': <obj_tables.core.LocalAttribute object>, 'conclusions': <obj_tables.core.LocalAttribute object>, 'dfba_obj_expression': <obj_tables.core.LocalAttribute object>, 'dfba_obj_species': <obj_tables.core.LocalAttribute object>, 'evidence': <obj_tables.core.LocalAttribute object>, 'id': <obj_tables.core.LocalAttribute object>, 'identifiers': <obj_tables.core.LocalAttribute object>, 'model': <obj_tables.core.LocalAttribute object>, 'name': <obj_tables.core.LocalAttribute object>, 'references': <obj_tables.core.LocalAttribute object>, 'submodel': <obj_tables.core.LocalAttribute object>, 'units': <obj_tables.core.LocalAttribute object>}[source]¶

merge = 2[source]¶

ordering = ('id',)[source]¶

primary_attribute = <obj_tables.core.SlugAttribute object>[source]¶

related_attributes = {'dfba_obj_expression': <obj_tables.core.OneToManyAttribute object>, 'dfba_obj_species': <obj_tables.core.ManyToOneAttribute object>}[source]¶

unique_together = ()[source]¶

verbose_name = 'dFBA objective reaction'[source]¶

verbose_name_plural = 'dFBA objective reactions'[source]¶

cell_size_units = <obj_tables.sci.units.UnitAttribute object>[source]

comments = <wc_lang.core.CommentAttribute object>[source]

conclusions = <obj_tables.core.ManyToManyAttribute object>[source]

evidence = <wc_lang.core.EvidenceManyToManyAttribute object>[source]

export_relations_to_sbml(sbml_model, sbml_rxn)[source]¶

Add relationships to/from object to SBML reaction.

Parameters

sbml_model (libsbml.Model) – SBML model
sbml_rxn (libsbml.Reaction) – SBML reaction

export_to_sbml(sbml_model)[source]¶

Add a dFBA objective reaction to a SBML model.

DfbaObjReactions are added to the SBML model because they can be used in a dFBA submodel’s objective function. In fact the default objective function is the submodel’s dFBA objective reaction. Since SBML does not define DfbaObjReaction as a separate class, DfbaObjReactions are added to the SBML model as SBML reactions. CheckModel ensures that wc_lang DfbaObjReactions and Reactions have distinct ids.

Parameters: sbml_model (libsbml.Model) – SBML model
Returns: SBML reaction
Return type: libsbml.Reaction

id = <obj_tables.core.SlugAttribute object>[source]

identifiers = <wc_lang.core.IdentifierManyToManyAttribute object>[source]

import_from_sbml(sbml_rxn)[source]¶

Load from SBML reaction

Parameters: sbml (libsbml.Reaction) – SBML reaction

import_relations_from_sbml(sbml_rxn, objs)[source]¶

Load relationships from SBML reaction

Parameters

sbml (libsbml.Reaction) – SBML reaction
objs (dict) – dictionary that maps WC-Lang types to dictionaries that map the ids of WC-Lang objects to WC-Lang objects

model = <obj_tables.core.ManyToOneAttribute object>[source]

name = <obj_tables.core.StringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

references = <obj_tables.core.ManyToManyAttribute object>[source]

submodel = <obj_tables.core.ManyToOneAttribute object>[source]

units = <obj_tables.sci.units.UnitAttribute object>[source]

class wc_lang.core.DfbaObjSpecies(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

A dFBA objective reaction contains a list of DfbaObjSpecies instances. Distinct DfbaObjSpecies enable separate comments and references for each one.

id[source]¶

unique identifier per DfbaObjSpecies equal to dfba-net-species-{dfba_obj_reaction.id}-{species.id}

Type: str

name[source]¶

name

Type: str

model[source]¶

model

Type: Model

dfba_obj_reaction[source]¶

the dFBA objective reaction that uses the dFBA objective species

Type: DfbaObjReaction

species[source]¶

species

Type: Species

value[source]¶

the specie’s reaction coefficient

Type: float

units[source]¶

units of the value

Type: unit_registry.Unit

identifiers[source]¶

identifiers

Type: list of Identifier

evidence[source]¶

observation that supports/disputes a conclusion

Type: list of Evidence

conclusions[source]¶

conclusions

Type: list of Conclusion

comments[source]¶

comments

Type: str

references[source]¶

references

Type: list of Reference

class Meta[source]¶

Bases: obj_tables.core.Meta

attribute_order = ('id', 'name', 'dfba_obj_reaction', 'species', 'value', 'units', 'identifiers', 'evidence', 'conclusions', 'comments', 'references')[source]¶

attributes = {'comments': <wc_lang.core.CommentAttribute object>, 'conclusions': <obj_tables.core.ManyToManyAttribute object>, 'dfba_obj_reaction': <obj_tables.core.ManyToOneAttribute object>, 'evidence': <wc_lang.core.EvidenceManyToManyAttribute object>, 'id': <obj_tables.core.StringAttribute object>, 'identifiers': <wc_lang.core.IdentifierManyToManyAttribute object>, 'model': <obj_tables.core.ManyToOneAttribute object>, 'name': <obj_tables.core.StringAttribute object>, 'references': <obj_tables.core.ManyToManyAttribute object>, 'species': <obj_tables.core.ManyToOneAttribute object>, 'units': <obj_tables.sci.units.UnitAttribute object>, 'value': <obj_tables.core.FloatAttribute object>}[source]¶

child_attrs = {'sbml': ('id', 'name', 'model', 'dfba_obj_reaction', 'species', 'value', 'units', 'identifiers', 'comments'), 'wc_sim': ('id', 'model', 'dfba_obj_reaction', 'species', 'value', 'units')}[source]¶

children = {'core_model': ('dfba_obj_reaction', 'species', 'identifiers', 'evidence', 'conclusions', 'references'), 'submodel': ('dfba_obj_reaction', 'species', 'identifiers', 'evidence', 'conclusions', 'references')}[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.DfbaObjSpecies'>,)[source]¶

local_attributes = {'comments': <obj_tables.core.LocalAttribute object>, 'conclusions': <obj_tables.core.LocalAttribute object>, 'dfba_obj_reaction': <obj_tables.core.LocalAttribute object>, 'evidence': <obj_tables.core.LocalAttribute object>, 'id': <obj_tables.core.LocalAttribute object>, 'identifiers': <obj_tables.core.LocalAttribute object>, 'model': <obj_tables.core.LocalAttribute object>, 'name': <obj_tables.core.LocalAttribute object>, 'references': <obj_tables.core.LocalAttribute object>, 'species': <obj_tables.core.LocalAttribute object>, 'units': <obj_tables.core.LocalAttribute object>, 'value': <obj_tables.core.LocalAttribute object>}[source]¶

merge = 2[source]¶

ordering = ('id',)[source]¶

primary_attribute = <obj_tables.core.StringAttribute object>[source]¶

related_attributes = {}[source]¶

unique_together = ()[source]¶

verbose_name = 'dFBA objective species'[source]¶

verbose_name_plural = 'dFBA objective species'[source]¶

comments = <wc_lang.core.CommentAttribute object>[source]

conclusions = <obj_tables.core.ManyToManyAttribute object>[source]

dfba_obj_reaction = <obj_tables.core.ManyToOneAttribute object>[source]

evidence = <wc_lang.core.EvidenceManyToManyAttribute object>[source]

gen_id()[source]¶

Generate identifier equal to dfba-net-species-{dfba_obj_reaction.id}-{species.id}

Returns: identifier
Return type: str

id = <obj_tables.core.StringAttribute object>[source]

identifiers = <wc_lang.core.IdentifierManyToManyAttribute object>[source]

model = <obj_tables.core.ManyToOneAttribute object>[source]

name = <obj_tables.core.StringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

references = <obj_tables.core.ManyToManyAttribute object>[source]

species = <obj_tables.core.ManyToOneAttribute object>[source]

units = <obj_tables.sci.units.UnitAttribute object>[source]

validate()[source]¶

Validate that the dFBA objective is valid

Check if the identifier is equal to dfba-net-species-{dfba_obj_reaction.id}-{species.id}
Units consistent with units of cell size

Returns

None if the object is valid,: otherwise return a list of errors as an instance of InvalidObject

Return type

InvalidObject or None

value = <obj_tables.core.FloatAttribute object>[source]

class wc_lang.core.DfbaObjective(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

dFBA objective function

id[source]¶

identifier equal to dfba-obj-{submodel.id}

Type: str

name[source]¶

name

Type: str

model[source]¶

model

Type: Model

submodel[source]¶

the Submodel which uses this DfbaObjective

Type: Submodel

expression[source]¶

mathematical expression of the objective function

Type: DfbaObjectiveExpression

units[source]¶

units

Type: unit_registry.Unit

reaction_rate_units[source]¶

reaction rate units

Type: unit_registry.Unit

coefficient_units[source]¶

coefficient units

Type: unit_registry.Unit

identifiers[source]¶

identifiers

Type: list of Identifier

evidence[source]¶

observation that supports/disputes a conclusion

Type: list of Evidence

conclusions[source]¶

conclusions

Type: list of Conclusion

comments[source]¶

comments

Type: str

references[source]¶

references

Type: list of Reference

class Meta[source]¶

Bases: obj_tables.core.Meta, obj_tables.math.expression.ExpressionExpressionTermMeta

attribute_order = ('id', 'name', 'submodel', 'expression', 'units', 'reaction_rate_units', 'coefficient_units', 'identifiers', 'evidence', 'conclusions', 'comments', 'references')[source]¶

attributes = {'coefficient_units': <obj_tables.sci.units.UnitAttribute object>, 'comments': <wc_lang.core.CommentAttribute object>, 'conclusions': <obj_tables.core.ManyToManyAttribute object>, 'evidence': <wc_lang.core.EvidenceManyToManyAttribute object>, 'expression': <obj_tables.math.expression.OneToOneExpressionAttribute object>, 'id': <obj_tables.core.StringAttribute object>, 'identifiers': <wc_lang.core.IdentifierManyToManyAttribute object>, 'model': <obj_tables.core.ManyToOneAttribute object>, 'name': <obj_tables.core.StringAttribute object>, 'reaction_rate_units': <obj_tables.sci.units.UnitAttribute object>, 'references': <obj_tables.core.ManyToManyAttribute object>, 'submodel': <obj_tables.core.OneToOneAttribute object>, 'units': <obj_tables.sci.units.UnitAttribute object>}[source]¶

child_attrs = {'sbml': ('id', 'name', 'model', 'submodel', 'expression', 'units', 'reaction_rate_units', 'coefficient_units', 'identifiers', 'comments'), 'wc_sim': ('id', 'model', 'submodel', 'expression', 'units', 'reaction_rate_units', 'coefficient_units')}[source]¶

children = {'core_model': ('expression', 'identifiers', 'evidence', 'conclusions', 'references'), 'submodel': ('expression', 'identifiers', 'evidence', 'conclusions', 'references')}[source]¶

expression_term_model[source]¶: alias of DfbaObjectiveExpression

expression_term_units = 'units'[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.DfbaObjective'>,)[source]¶

local_attributes = {'coefficient_units': <obj_tables.core.LocalAttribute object>, 'comments': <obj_tables.core.LocalAttribute object>, 'conclusions': <obj_tables.core.LocalAttribute object>, 'evidence': <obj_tables.core.LocalAttribute object>, 'expression': <obj_tables.core.LocalAttribute object>, 'id': <obj_tables.core.LocalAttribute object>, 'identifiers': <obj_tables.core.LocalAttribute object>, 'model': <obj_tables.core.LocalAttribute object>, 'name': <obj_tables.core.LocalAttribute object>, 'reaction_rate_units': <obj_tables.core.LocalAttribute object>, 'references': <obj_tables.core.LocalAttribute object>, 'submodel': <obj_tables.core.LocalAttribute object>, 'units': <obj_tables.core.LocalAttribute object>}[source]¶

merge = 2[source]¶

ordering = ('id',)[source]¶

primary_attribute = <obj_tables.core.StringAttribute object>[source]¶

related_attributes = {}[source]¶

unique_together = ()[source]¶

verbose_name = 'dFBA objective'[source]¶

verbose_name_plural = 'dFBA objectives'[source]¶

coefficient_units = <obj_tables.sci.units.UnitAttribute object>[source]

comments = <wc_lang.core.CommentAttribute object>[source]

conclusions = <obj_tables.core.ManyToManyAttribute object>[source]

evidence = <wc_lang.core.EvidenceManyToManyAttribute object>[source]

export_relations_to_sbml(sbml_model, sbml)[source]¶

Add relationships to/from object to SBML objective.

Parameters

sbml_model (libsbml.Model) – SBML model
sbml (libsbml.Objective) – SBML objective

export_to_sbml(sbml_model)[source]¶

Add this dFBA objective to a SBML model.

This uses version 2 of the ‘Flux Balance Constraints’ extension. SBML assumes that an DfbaObjective is a linear combination of reaction fluxes.

Parameters: sbml_model (libsbml.Model) – SBML model
Returns: SBML objective
Return type: libsbml.Objective

expression = <obj_tables.math.expression.OneToOneExpressionAttribute object>[source]

gen_id()[source]¶

Generate identifier

Returns: identifier
Return type: str

get_products(_DfbaObjective__type=None, **kwargs)[source]¶

Get the species produced by this objective function

Parameters

__type (types.TypeType or tuple of types.TypeType) – subclass(es) of Model
kwargs (dict of str –> object) – dictionary of attribute name/value pairs to find matching objects

Returns

species produced by this objective function

Return type

list of Species

id = <obj_tables.core.StringAttribute object>[source]

identifiers = <wc_lang.core.IdentifierManyToManyAttribute object>[source]

import_from_sbml(sbml)[source]¶

Load from SBML objective

Parameters: sbml (libsbml.Objective) – SBML objective

import_relations_from_sbml(sbml, objs)[source]¶

Load relationships from SBML objective

Parameters

sbml (libsbml.Objective) – SBML objective
objs (dict) – dictionary that maps WC-Lang types to dictionaries that map the ids of WC-Lang objects to WC-Lang objects

model = <obj_tables.core.ManyToOneAttribute object>[source]

name = <obj_tables.core.StringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

reaction_rate_units = <obj_tables.sci.units.UnitAttribute object>[source]

references = <obj_tables.core.ManyToManyAttribute object>[source]

submodel = <obj_tables.core.OneToOneAttribute object>[source]

units = <obj_tables.sci.units.UnitAttribute object>[source]

validate()[source]¶

Validate that the dFBA objective is valid

Check if the identifier is equal to dfba-obj-{submodel.id}]

Returns

None if the object is valid,: otherwise return a list of errors as an instance of InvalidObject

Return type

InvalidObject or None

class wc_lang.core.DfbaObjectiveExpression(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, obj_tables.math.expression.Expression, wc_lang.sbml.util.SbmlModelMixin

A mathematical expression of Reactions and DfbaObjReactions

The expression used by a DfbaObjective.

expression[source]¶

mathematical expression

Type: str

_parsed_expression[source]¶

an analyzed expression; not an obj_tables.Model

Type: ParsedExpression

reactions[source]¶

reactions used by this expression

Type: list of Reaction

dfba_obj_reactions[source]¶

dFBA objective reactions used by this expression

Type: list of DfbaObjReaction

Related attributes:

dfba_obj (DfbaObjective): dFBA objective

class Meta[source]¶

Bases: obj_tables.core.Meta, obj_tables.math.expression.Meta

attribute_order = ()[source]¶

attributes = {'dfba_obj_reactions': <obj_tables.core.OneToManyAttribute object>, 'expression': <obj_tables.core.LongStringAttribute object>, 'reactions': <obj_tables.core.OneToManyAttribute object>}[source]¶

child_attrs = {'sbml': ('expression', 'reactions', 'dfba_obj_reactions'), 'wc_sim': ('expression', 'reactions', 'dfba_obj_reactions')}[source]¶

children = {'core_model': ('reactions', 'dfba_obj_reactions'), 'submodel': ('reactions', 'dfba_obj_reactions')}[source]¶

expression_term_models = ('Reaction', 'DfbaObjReaction')[source]¶

expression_unit_registry = <pint.registry.UnitRegistry object>[source]¶

expression_valid_functions = ()[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.DfbaObjectiveExpression'>,)[source]¶

local_attributes = {'dfba_obj': <obj_tables.core.LocalAttribute object>, 'dfba_obj_reactions': <obj_tables.core.LocalAttribute object>, 'expression': <obj_tables.core.LocalAttribute object>, 'reactions': <obj_tables.core.LocalAttribute object>}[source]¶

merge = 2[source]¶

ordering = ('expression',)[source]¶

primary_attribute = <obj_tables.core.LongStringAttribute object>[source]¶

related_attributes = {'dfba_obj': <obj_tables.math.expression.OneToOneExpressionAttribute object>}[source]¶

table_format = 3[source]¶

unique_together = ()[source]¶

verbose_name = 'dFBA objective expression'[source]¶

verbose_name_plural = 'dFBA objective expressions'[source]¶

classmethod deserialize(value, objects)[source]¶

Deserialize value

Parameters

value (str) – String representation
objects (dict) – dictionary of objects, grouped by model

Returns

tuple: of cleaned value and cleaning error

Return type

tuple of DfbaObjectiveExpression, InvalidAttribute or None

dfba_obj_reactions = <obj_tables.core.OneToManyAttribute object>[source]

expression = <obj_tables.core.LongStringAttribute object>[source]

merge_attrs(other, other_objs_in_self, self_objs_in_other)[source]¶

Merge attributes of two objects

Parameters

other (obj_tables.Model) – other model
other_objs_in_self (dict) – dictionary that maps instances of objects in another model to objects in a model
self_objs_in_other (dict) – dictionary that maps instances of objects in a model to objects in another model

objects = <obj_tables.core.Manager object>[source]¶

reactions = <obj_tables.core.OneToManyAttribute object>[source]

serialize()[source]¶

Generate string representation

Returns: string representation
Return type: str

validate()[source]¶

Determine if the dFBA objective expression is valid

Check that the expression is a linear function
Check if expression is a function of at least one reaction or dFBA objective reaction
Check that the reactions and dFBA objective reactions belong to the same submodel

Returns

None if the object is valid,: otherwise return a list of errors in an InvalidObject instance

Return type

InvalidObject or None

class wc_lang.core.DistributionInitConcentration(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

Distribution of the initial concentration of a species at the beginning of each cell cycle

id[source]¶

identifier equal to dist-init-conc-{species.id}

Type: str

name[source]¶

name

Type: str

model[source]¶

model

Type: Model

species[source]¶

species

Type: Species

distribution[source]¶

distribution

Type: pronto.term.Term

mean[source]¶

mean concentration in a population of single cells at the beginning of each cell cycle

Type: float

std[source]¶

standard deviation of the concentration in a population of single cells at the beginning of each cell cycle

Type: float

units[source]¶

units; default units is M

Type: unit_registry.Unit

identifiers[source]¶

identifiers

Type: list of Identifier

evidence[source]¶

observation that supports/disputes a conclusion

Type: list of Evidence

conclusions[source]¶

conclusions

Type: list of Conclusion

comments[source]¶

comments

Type: str

references[source]¶

references

Type: list of Reference

class Meta[source]¶

Bases: obj_tables.core.Meta

attribute_order = ('id', 'name', 'species', 'distribution', 'mean', 'std', 'units', 'identifiers', 'evidence', 'conclusions', 'comments', 'references')[source]¶

attributes = {'comments': <wc_lang.core.CommentAttribute object>, 'conclusions': <obj_tables.core.ManyToManyAttribute object>, 'distribution': <obj_tables.sci.onto.OntoTermAttribute object>, 'evidence': <wc_lang.core.EvidenceManyToManyAttribute object>, 'id': <obj_tables.core.StringAttribute object>, 'identifiers': <wc_lang.core.IdentifierManyToManyAttribute object>, 'mean': <obj_tables.core.FloatAttribute object>, 'model': <obj_tables.core.ManyToOneAttribute object>, 'name': <obj_tables.core.StringAttribute object>, 'references': <obj_tables.core.ManyToManyAttribute object>, 'species': <obj_tables.core.OneToOneAttribute object>, 'std': <obj_tables.core.FloatAttribute object>, 'units': <obj_tables.sci.units.UnitAttribute object>}[source]¶

child_attrs = {'sbml': ('id', 'name', 'model', 'species', 'distribution', 'mean', 'std', 'units', 'identifiers', 'comments'), 'wc_sim': ('id', 'model', 'species', 'distribution', 'mean', 'std', 'units')}[source]¶

children = {'core_model': ('species', 'identifiers', 'evidence', 'conclusions', 'references'), 'submodel': ('identifiers', 'evidence', 'conclusions', 'references')}[source]¶

frozen_columns = 1[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.DistributionInitConcentration'>,)[source]¶

local_attributes = {'comments': <obj_tables.core.LocalAttribute object>, 'conclusions': <obj_tables.core.LocalAttribute object>, 'distribution': <obj_tables.core.LocalAttribute object>, 'evidence': <obj_tables.core.LocalAttribute object>, 'id': <obj_tables.core.LocalAttribute object>, 'identifiers': <obj_tables.core.LocalAttribute object>, 'mean': <obj_tables.core.LocalAttribute object>, 'model': <obj_tables.core.LocalAttribute object>, 'name': <obj_tables.core.LocalAttribute object>, 'references': <obj_tables.core.LocalAttribute object>, 'species': <obj_tables.core.LocalAttribute object>, 'std': <obj_tables.core.LocalAttribute object>, 'units': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ('id',)[source]¶

primary_attribute = <obj_tables.core.StringAttribute object>[source]¶

related_attributes = {}[source]¶

unique_together = ()[source]¶

verbose_name = 'Init species concentration'[source]¶

verbose_name_plural = 'Init species concentrations'[source]¶

comments = <wc_lang.core.CommentAttribute object>[source]

conclusions = <obj_tables.core.ManyToManyAttribute object>[source]

distribution = <obj_tables.sci.onto.OntoTermAttribute object>[source]

evidence = <wc_lang.core.EvidenceManyToManyAttribute object>[source]

gen_id()[source]¶

Generate string representation

Returns: string representation
Return type: str

id = <obj_tables.core.StringAttribute object>[source]

identifiers = <wc_lang.core.IdentifierManyToManyAttribute object>[source]

mean = <obj_tables.core.FloatAttribute object>[source]

model = <obj_tables.core.ManyToOneAttribute object>[source]

name = <obj_tables.core.StringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

references = <obj_tables.core.ManyToManyAttribute object>[source]

species = <obj_tables.core.OneToOneAttribute object>[source]

std = <obj_tables.core.FloatAttribute object>[source]

units = <obj_tables.sci.units.UnitAttribute object>[source]

validate()[source]¶

Check that the distribution of initial concentrations at the beginning of each cell cycle is valid

Validate that identifier is equal to dist-init-conc-{species.id}]

Returns

None if the object is valid,: otherwise return a list of errors as an instance of InvalidObject

Return type

InvalidObject or None

class wc_lang.core.Environment(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

id[source]¶

unique identifier equal to ‘env’

Type: str

name[source]¶

name

Type: str

model[source]¶

model

Type: Model

temp[source]¶

temperature

Type: float

temp_units[source]¶

temperature units

Type: unit_registry.Unit

identifiers[source]¶

identifiers

Type: list of Identifier

comments[source]¶

comments

Type: str

references[source]¶

references

Type: list of Reference

class Meta[source]¶

Bases: obj_tables.core.Meta

attribute_order = ('id', 'name', 'temp', 'temp_units', 'identifiers', 'comments', 'references')[source]¶

attributes = {'comments': <wc_lang.core.CommentAttribute object>, 'id': <obj_tables.core.RegexAttribute object>, 'identifiers': <wc_lang.core.IdentifierOneToManyAttribute object>, 'model': <obj_tables.core.OneToOneAttribute object>, 'name': <obj_tables.core.StringAttribute object>, 'references': <obj_tables.core.OneToManyAttribute object>, 'temp': <obj_tables.core.FloatAttribute object>, 'temp_units': <obj_tables.sci.units.UnitAttribute object>}[source]¶

child_attrs = {'sbml': ('id', 'name', 'model', 'temp', 'temp_units', 'identifiers', 'comments'), 'wc_sim': ()}[source]¶

children = {'core_model': ('identifiers', 'references'), 'submodel': ('identifiers', 'references')}[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.Environment'>,)[source]¶

local_attributes = {'comments': <obj_tables.core.LocalAttribute object>, 'id': <obj_tables.core.LocalAttribute object>, 'identifiers': <obj_tables.core.LocalAttribute object>, 'model': <obj_tables.core.LocalAttribute object>, 'name': <obj_tables.core.LocalAttribute object>, 'references': <obj_tables.core.LocalAttribute object>, 'temp': <obj_tables.core.LocalAttribute object>, 'temp_units': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ('id',)[source]¶

primary_attribute = <obj_tables.core.RegexAttribute object>[source]¶

related_attributes = {}[source]¶

table_format = 2[source]¶

unique_together = ()[source]¶

verbose_name = 'Environment'[source]¶

verbose_name_plural = 'Environments'[source]¶

comments = <wc_lang.core.CommentAttribute object>[source]

id = <obj_tables.core.RegexAttribute object>[source]

identifiers = <wc_lang.core.IdentifierOneToManyAttribute object>[source]

model = <obj_tables.core.OneToOneAttribute object>[source]

name = <obj_tables.core.StringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

references = <obj_tables.core.OneToManyAttribute object>[source]

temp = <obj_tables.core.FloatAttribute object>[source]

temp_units = <obj_tables.sci.units.UnitAttribute object>[source]

class wc_lang.core.Evidence(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model

Observation that supports/disputes a conclusion

observation[source]¶

observation which supports the conclusion

Type: Observation

type[source]¶

how the observation supports the conclusion (e.g. supporting, inconclusive, disputing)

Type: pronto.Term

strength (: obj:`float): how much the observation supports the conclusion

quality[source]¶

the reliability of the observation

Type: float

Related attributes:

submodels (list of Submodel): submodels

dfba_objs (list of DfbaObjective): dFBA objectives

compartments (list of Compartment): compartments

species_types (list of SpeciesType): species types

species (list of Species): species

distribution_init_concentrations (list of DistributionInitConcentration): initial concentrations

observables (list of Observable): observables

functions (list of Function): functions

stop_conditions (list of StopCondition): stop conditions

reactions (list of Reaction): reactions

rate_laws (list of RateLaw): rate laws

dfba_obj_species (list of DfbaObjSpecies): dFBA objective species

dfba_obj_reactions (list of DfbaObjReaction): dFBA objective reactions

parameters (list of Parameter): parameters

conclusions (list of Conclusion): conclusions

changes (list of Change): changes

class Meta[source]¶

Bases: obj_tables.core.Meta

attribute_order = ('observation', 'type', 'strength', 'quality')[source]¶

attributes = {'observation': <obj_tables.core.ManyToOneAttribute object>, 'quality': <obj_tables.core.FloatAttribute object>, 'strength': <obj_tables.core.FloatAttribute object>, 'type': <obj_tables.sci.onto.OntoTermAttribute object>}[source]¶

child_attrs = {'sbml': (), 'wc_sim': ()}[source]¶

children = {'core_model': ('observation',), 'submodel': ('observation',)}[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.Evidence'>,)[source]¶

local_attributes = {'changes': <obj_tables.core.LocalAttribute object>, 'compartments': <obj_tables.core.LocalAttribute object>, 'conclusions': <obj_tables.core.LocalAttribute object>, 'dfba_obj_reactions': <obj_tables.core.LocalAttribute object>, 'dfba_obj_species': <obj_tables.core.LocalAttribute object>, 'dfba_objs': <obj_tables.core.LocalAttribute object>, 'distribution_init_concentrations': <obj_tables.core.LocalAttribute object>, 'functions': <obj_tables.core.LocalAttribute object>, 'observables': <obj_tables.core.LocalAttribute object>, 'observation': <obj_tables.core.LocalAttribute object>, 'parameters': <obj_tables.core.LocalAttribute object>, 'quality': <obj_tables.core.LocalAttribute object>, 'rate_laws': <obj_tables.core.LocalAttribute object>, 'reactions': <obj_tables.core.LocalAttribute object>, 'species': <obj_tables.core.LocalAttribute object>, 'species_types': <obj_tables.core.LocalAttribute object>, 'stop_conditions': <obj_tables.core.LocalAttribute object>, 'strength': <obj_tables.core.LocalAttribute object>, 'submodels': <obj_tables.core.LocalAttribute object>, 'type': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ()[source]¶

primary_attribute = None[source]¶

related_attributes = {'changes': <wc_lang.core.EvidenceManyToManyAttribute object>, 'compartments': <wc_lang.core.EvidenceManyToManyAttribute object>, 'conclusions': <wc_lang.core.EvidenceManyToManyAttribute object>, 'dfba_obj_reactions': <wc_lang.core.EvidenceManyToManyAttribute object>, 'dfba_obj_species': <wc_lang.core.EvidenceManyToManyAttribute object>, 'dfba_objs': <wc_lang.core.EvidenceManyToManyAttribute object>, 'distribution_init_concentrations': <wc_lang.core.EvidenceManyToManyAttribute object>, 'functions': <wc_lang.core.EvidenceManyToManyAttribute object>, 'observables': <wc_lang.core.EvidenceManyToManyAttribute object>, 'parameters': <wc_lang.core.EvidenceManyToManyAttribute object>, 'rate_laws': <wc_lang.core.EvidenceManyToManyAttribute object>, 'reactions': <wc_lang.core.EvidenceManyToManyAttribute object>, 'species': <wc_lang.core.EvidenceManyToManyAttribute object>, 'species_types': <wc_lang.core.EvidenceManyToManyAttribute object>, 'stop_conditions': <wc_lang.core.EvidenceManyToManyAttribute object>, 'submodels': <wc_lang.core.EvidenceManyToManyAttribute object>}[source]¶

table_format = 3[source]¶

unique_together = ()[source]¶

verbose_name = 'Evidence'[source]¶

verbose_name_plural = 'Evidences'[source]¶

objects = <obj_tables.core.Manager object>[source]¶

observation = <obj_tables.core.ManyToOneAttribute object>[source]

quality = <obj_tables.core.FloatAttribute object>[source]

serialize()[source]¶

Generate string representation

Returns: string representation
Return type: str

strength = <obj_tables.core.FloatAttribute object>[source]¶

type = <obj_tables.sci.onto.OntoTermAttribute object>[source]

class wc_lang.core.EvidenceManyToManyAttribute(related_class, grammar=None, **kwargs)[source]¶

Bases: obj_tables.grammar.ToManyGrammarAttribute, obj_tables.core.ManyToManyAttribute

Many to many attribute for evidence

class Transformer(objects)[source]¶

Bases: obj_tables.grammar.ToManyGrammarTransformer

Transforms parse trees into a list of instances of core.Model

evidence(*args)[source]¶

get_xlsx_validation(sheet_models=None, doc_metadata_model=None)[source]¶

Get Excel validation

Parameters

sheet_models (list of Model, optional) – models encoded as separate sheets
doc_metadata_model (type) – model whose worksheet contains the document metadata

Returns

validation

Return type

wc_utils.workbook.io.FieldValidation

grammar_path = '/root/project/wc_lang/grammar/evidences.lark'[source]¶

serialize(evidence, encoded=None)[source]¶

Serialize related object

Parameters

evidence (list of Evidence) – Python representation of evidence
encoded (dict, optional) – dictionary of objects that have already been encoded

Returns

simple Python representation

Return type

str

class wc_lang.core.FluxBounds(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

Flux bounds for reactions modeled by dFBA submodels

min[source]¶

minimum flux bound for solving an FBA model; negative for reversible reactions

Type: float

max[source]¶

maximum flux bound for solving an FBA model

Type: float

units[source]¶

units for the minimum and maximum fluxes

Type: unit_registry.Unit

Related attributes:

reactions (list of Reaction): reactions

class Meta[source]¶

Bases: obj_tables.core.Meta

attribute_order = ('min', 'max', 'units')[source]¶

attributes = {'max': <obj_tables.core.FloatAttribute object>, 'min': <obj_tables.core.FloatAttribute object>, 'units': <obj_tables.sci.units.UnitAttribute object>}[source]¶

child_attrs = {'sbml': ('min', 'max', 'units'), 'wc_sim': ('min', 'max', 'units')}[source]¶

children = {'core_model': (), 'submodel': ()}[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.FluxBounds'>,)[source]¶

local_attributes = {'max': <obj_tables.core.LocalAttribute object>, 'min': <obj_tables.core.LocalAttribute object>, 'reactions': <obj_tables.core.LocalAttribute object>, 'units': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ()[source]¶

primary_attribute = None[source]¶

related_attributes = {'reactions': <obj_tables.core.ManyToOneAttribute object>}[source]¶

table_format = 4[source]¶

unique_together = ()[source]¶

verbose_name = 'Flux bounds'[source]¶

verbose_name_plural = 'Flux boundss'[source]¶

max = <obj_tables.core.FloatAttribute object>[source]

min = <obj_tables.core.FloatAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

serialize()[source]¶

Generate string representation

Returns: string representation
Return type: str

units = <obj_tables.sci.units.UnitAttribute object>[source]

class wc_lang.core.Function(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlAssignmentRuleMixin

Function: a mathematical expression of Functions, Observbles, Parameters and Python functions

id[source]¶

unique id

Type: str

name[source]¶

name

Type: str

model[source]¶

model

Type: Model

expression[source]¶

mathematical expression for a Function

Type: FunctionExpression

units[source]¶

units

Type: unit_registry.Unit

identifiers[source]¶

identifiers

Type: list of Identifier

evidence[source]¶

observation that supports/disputes a conclusion

Type: list of Evidence

conclusions[source]¶

conclusions

Type: list of Conclusion

comments[source]¶

comments

Type: str

references[source]¶

references

Type: list of Reference

Related attributes:

function_expressions (list of FunctionExpression): function expressions

rate_law_expressions (list of RateLawExpression): rate law expressions

stop_condition_expressions (list of StopConditionExpression): stop condition expressions

class Meta[source]¶

Bases: obj_tables.core.Meta, obj_tables.math.expression.ExpressionExpressionTermMeta

attribute_order = ('id', 'name', 'expression', 'units', 'identifiers', 'evidence', 'conclusions', 'comments', 'references')[source]¶

attributes = {'comments': <wc_lang.core.CommentAttribute object>, 'conclusions': <obj_tables.core.ManyToManyAttribute object>, 'evidence': <wc_lang.core.EvidenceManyToManyAttribute object>, 'expression': <obj_tables.math.expression.OneToOneExpressionAttribute object>, 'id': <obj_tables.core.SlugAttribute object>, 'identifiers': <wc_lang.core.IdentifierManyToManyAttribute object>, 'model': <obj_tables.core.ManyToOneAttribute object>, 'name': <obj_tables.core.StringAttribute object>, 'references': <obj_tables.core.ManyToManyAttribute object>, 'units': <obj_tables.sci.units.UnitAttribute object>}[source]¶

child_attrs = {'sbml': ('id', 'name', 'model', 'expression', 'units', 'identifiers', 'comments'), 'wc_sim': ('id', 'model', 'expression', 'units')}[source]¶

children = {'core_model': ('expression', 'identifiers', 'evidence', 'conclusions', 'references'), 'submodel': ('expression', 'identifiers', 'evidence', 'conclusions', 'references')}[source]¶

expression_term_model[source]¶: alias of FunctionExpression

expression_term_units = 'units'[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.Function'>,)[source]¶

local_attributes = {'comments': <obj_tables.core.LocalAttribute object>, 'conclusions': <obj_tables.core.LocalAttribute object>, 'evidence': <obj_tables.core.LocalAttribute object>, 'expression': <obj_tables.core.LocalAttribute object>, 'function_expressions': <obj_tables.core.LocalAttribute object>, 'id': <obj_tables.core.LocalAttribute object>, 'identifiers': <obj_tables.core.LocalAttribute object>, 'model': <obj_tables.core.LocalAttribute object>, 'name': <obj_tables.core.LocalAttribute object>, 'rate_law_expressions': <obj_tables.core.LocalAttribute object>, 'references': <obj_tables.core.LocalAttribute object>, 'stop_condition_expressions': <obj_tables.core.LocalAttribute object>, 'units': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ('id',)[source]¶

primary_attribute = <obj_tables.core.SlugAttribute object>[source]¶

related_attributes = {'function_expressions': <obj_tables.core.ManyToManyAttribute object>, 'rate_law_expressions': <obj_tables.core.ManyToManyAttribute object>, 'stop_condition_expressions': <obj_tables.core.ManyToManyAttribute object>}[source]¶

unique_together = ()[source]¶

verbose_name = 'Function'[source]¶

verbose_name_plural = 'Functions'[source]¶

comments = <wc_lang.core.CommentAttribute object>[source]

conclusions = <obj_tables.core.ManyToManyAttribute object>[source]

evidence = <wc_lang.core.EvidenceManyToManyAttribute object>[source]

expression = <obj_tables.math.expression.OneToOneExpressionAttribute object>[source]

id = <obj_tables.core.SlugAttribute object>[source]

identifiers = <wc_lang.core.IdentifierManyToManyAttribute object>[source]

model = <obj_tables.core.ManyToOneAttribute object>[source]

name = <obj_tables.core.StringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

references = <obj_tables.core.ManyToManyAttribute object>[source]

units = <obj_tables.sci.units.UnitAttribute object>[source]

validate()[source]¶

Check that the Function is valid

Check that expression has units units

Returns

None if the object is valid,: otherwise return a list of errors as an instance of InvalidObject

Return type

InvalidObject or None

class wc_lang.core.FunctionExpression(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, obj_tables.math.expression.Expression, wc_lang.sbml.util.SbmlModelMixin

A mathematical expression of Functions, Observbles, Parameters and Python functions

The expression used by a Function.

expression[source]¶

mathematical expression for a Function

Type: str

_parsed_expression[source]¶

an analyzed expression; not an obj_tables.Model

Type: ParsedExpression

species[source]¶

Species used by this function expression

Type: list of Species

observables[source]¶

Observables used by this function expression

Type: list of Observable

parameters[source]¶

Parameters used by this function expression

Type: list of Parameter

functions[source]¶

other Functions used by this function expression

Type: list of Function

compartments[source]¶

Compartments used by this function expression

Type: list of Compartment

Related attributes:

function (Function): function

class Meta[source]¶

Bases: obj_tables.core.Meta, obj_tables.math.expression.Meta

attribute_order = ()[source]¶

attributes = {'compartments': <obj_tables.core.ManyToManyAttribute object>, 'expression': <obj_tables.core.LongStringAttribute object>, 'functions': <obj_tables.core.ManyToManyAttribute object>, 'observables': <obj_tables.core.ManyToManyAttribute object>, 'parameters': <obj_tables.core.ManyToManyAttribute object>, 'species': <obj_tables.core.ManyToManyAttribute object>}[source]¶

child_attrs = {'sbml': ('expression', 'parameters', 'species', 'observables', 'functions', 'compartments'), 'wc_sim': ('expression', 'parameters', 'species', 'observables', 'functions', 'compartments')}[source]¶

children = {'core_model': ('parameters', 'species', 'observables', 'functions', 'compartments'), 'submodel': ('parameters', 'species', 'observables', 'functions', 'compartments')}[source]¶

expression_term_models = ('Parameter', 'Species', 'Observable', 'Function', 'Compartment')[source]¶

expression_unit_registry = <pint.registry.UnitRegistry object>[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.FunctionExpression'>,)[source]¶

local_attributes = {'compartments': <obj_tables.core.LocalAttribute object>, 'expression': <obj_tables.core.LocalAttribute object>, 'function': <obj_tables.core.LocalAttribute object>, 'functions': <obj_tables.core.LocalAttribute object>, 'observables': <obj_tables.core.LocalAttribute object>, 'parameters': <obj_tables.core.LocalAttribute object>, 'species': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ('expression',)[source]¶

primary_attribute = <obj_tables.core.LongStringAttribute object>[source]¶

related_attributes = {'function': <obj_tables.math.expression.OneToOneExpressionAttribute object>}[source]¶

table_format = 3[source]¶

unique_together = ()[source]¶

verbose_name = 'Function expression'[source]¶

verbose_name_plural = 'Function expressions'[source]¶

compartments = <obj_tables.core.ManyToManyAttribute object>[source]

classmethod deserialize(value, objects)[source]¶

Deserialize value

Parameters

value (str) – String representation
objects (dict) – dictionary of objects, grouped by model

Returns

tuple of cleaned value: and cleaning error

Return type

tuple of FunctionExpression, InvalidAttribute or None

expression = <obj_tables.core.LongStringAttribute object>[source]

functions = <obj_tables.core.ManyToManyAttribute object>[source]

merge_attrs(other, other_objs_in_self, self_objs_in_other)[source]¶

Merge attributes of two objects

Parameters

other (obj_tables.Model) – other model
other_objs_in_self (dict) – dictionary that maps instances of objects in another model to objects in a model
self_objs_in_other (dict) – dictionary that maps instances of objects in a model to objects in another model

objects = <obj_tables.core.Manager object>[source]¶

observables = <obj_tables.core.ManyToManyAttribute object>[source]

parameters = <obj_tables.core.ManyToManyAttribute object>[source]

serialize()[source]¶

Generate string representation

Returns: string representation
Return type: str

species = <obj_tables.core.ManyToManyAttribute object>[source]

validate()[source]¶

Check that the function is valid

Check that the expression is a valid Python function

Returns

None if the object is valid,: otherwise return a list of errors as an instance of InvalidObject

Return type

InvalidObject or None

class wc_lang.core.Identifier(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

Reference to an entry in a namespace

namespace[source]¶

namespace name

Type: str

id[source]¶

id of entry in namespace

Type: str

Related attributes:

model (Model): model

taxon (Taxon): taxon

env (Environment): environment

submodels (list of Submodel): submodels

compartments (list of Compartment): compartments

species_types (list of SpeciesType): species types

species (list of Species): species

distribution_init_concentrations (list of DistributionInitConcentration): distributions of initial concentrations of species at the beginning of each cell cycle

observables (list of Observable): observables

functions (list of Function): functions

reactions (list of Reaction): reactions

rate_laws (list of RateLaw): rate laws

dfba_objs (list of DfbaObjective): dFBA objectives

dfba_obj_reactions (list of DfbaObjReaction): dFBA objective reactions

dfba_obj_species (list of DfbaObjSpecies): dFBA objective species

stop_conditions (list of StopCondition): stop conditions

parameters (list of Parameter): parameters

references (list of Reference): references

authors (list of Author): authors

changes (list of Change): changes

class Meta[source]¶

Bases: obj_tables.core.Meta

attribute_order = ('namespace', 'id')[source]¶

attributes = {'id': <obj_tables.core.StringAttribute object>, 'namespace': <obj_tables.core.StringAttribute object>}[source]¶

child_attrs = {'sbml': ('namespace', 'id'), 'wc_sim': ()}[source]¶

frozen_columns = 2[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.Identifier'>,)[source]¶

local_attributes = {'authors': <obj_tables.core.LocalAttribute object>, 'changes': <obj_tables.core.LocalAttribute object>, 'compartments': <obj_tables.core.LocalAttribute object>, 'conclusions': <obj_tables.core.LocalAttribute object>, 'dfba_obj_reactions': <obj_tables.core.LocalAttribute object>, 'dfba_obj_species': <obj_tables.core.LocalAttribute object>, 'dfba_objs': <obj_tables.core.LocalAttribute object>, 'distribution_init_concentrations': <obj_tables.core.LocalAttribute object>, 'env': <obj_tables.core.LocalAttribute object>, 'functions': <obj_tables.core.LocalAttribute object>, 'id': <obj_tables.core.LocalAttribute object>, 'model': <obj_tables.core.LocalAttribute object>, 'namespace': <obj_tables.core.LocalAttribute object>, 'observables': <obj_tables.core.LocalAttribute object>, 'observation_sets': <obj_tables.core.LocalAttribute object>, 'observations': <obj_tables.core.LocalAttribute object>, 'parameters': <obj_tables.core.LocalAttribute object>, 'rate_laws': <obj_tables.core.LocalAttribute object>, 'reactions': <obj_tables.core.LocalAttribute object>, 'references': <obj_tables.core.LocalAttribute object>, 'species': <obj_tables.core.LocalAttribute object>, 'species_types': <obj_tables.core.LocalAttribute object>, 'stop_conditions': <obj_tables.core.LocalAttribute object>, 'submodels': <obj_tables.core.LocalAttribute object>, 'taxon': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ('namespace', 'id')[source]¶

primary_attribute = None[source]¶

related_attributes = {'authors': <wc_lang.core.IdentifierManyToManyAttribute object>, 'changes': <wc_lang.core.IdentifierManyToManyAttribute object>, 'compartments': <wc_lang.core.IdentifierManyToManyAttribute object>, 'conclusions': <wc_lang.core.IdentifierManyToManyAttribute object>, 'dfba_obj_reactions': <wc_lang.core.IdentifierManyToManyAttribute object>, 'dfba_obj_species': <wc_lang.core.IdentifierManyToManyAttribute object>, 'dfba_objs': <wc_lang.core.IdentifierManyToManyAttribute object>, 'distribution_init_concentrations': <wc_lang.core.IdentifierManyToManyAttribute object>, 'env': <wc_lang.core.IdentifierOneToManyAttribute object>, 'functions': <wc_lang.core.IdentifierManyToManyAttribute object>, 'model': <wc_lang.core.IdentifierOneToManyAttribute object>, 'observables': <wc_lang.core.IdentifierManyToManyAttribute object>, 'observation_sets': <wc_lang.core.IdentifierManyToManyAttribute object>, 'observations': <wc_lang.core.IdentifierManyToManyAttribute object>, 'parameters': <wc_lang.core.IdentifierManyToManyAttribute object>, 'rate_laws': <wc_lang.core.IdentifierManyToManyAttribute object>, 'reactions': <wc_lang.core.IdentifierManyToManyAttribute object>, 'references': <wc_lang.core.IdentifierManyToManyAttribute object>, 'species': <wc_lang.core.IdentifierManyToManyAttribute object>, 'species_types': <wc_lang.core.IdentifierManyToManyAttribute object>, 'stop_conditions': <wc_lang.core.IdentifierManyToManyAttribute object>, 'submodels': <wc_lang.core.IdentifierManyToManyAttribute object>, 'taxon': <wc_lang.core.IdentifierOneToManyAttribute object>}[source]¶

table_format = 3[source]¶

unique_together = (('id', 'namespace'),)[source]¶

verbose_name = 'Identifier'[source]¶

verbose_name_plural = 'Identifiers'[source]¶

id = <obj_tables.core.StringAttribute object>[source]

namespace = <obj_tables.core.StringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

serialize()[source]¶

Generate string representation

Returns: value of primary attribute
Return type: str

class wc_lang.core.IdentifierManyToManyAttribute(related_name='', verbose_name='Identifiers', verbose_related_name='', description='')[source]¶: Bases: wc_lang.core.IdentifierToManyGrammarAttribute, obj_tables.core.ManyToManyAttribute

class wc_lang.core.IdentifierOneToManyAttribute(related_name='', verbose_name='Identifiers', verbose_related_name='', description='')[source]¶: Bases: wc_lang.core.IdentifierToManyGrammarAttribute, obj_tables.core.OneToManyAttribute

class wc_lang.core.IdentifierToManyGrammarAttribute(related_class, grammar=None, **kwargs)[source]¶

Bases: obj_tables.grammar.ToManyGrammarAttribute

get_xlsx_validation(sheet_models=None, doc_metadata_model=None)[source]¶

Get Excel validation

Parameters

sheet_models (list of Model, optional) – models encoded as separate sheets
doc_metadata_model (type) – model whose worksheet contains the document metadata

Returns

validation

Return type

wc_utils.workbook.io.FieldValidation

grammar_path = '/root/project/wc_lang/grammar/identifiers.lark'[source]¶

serialize(identifiers, encoded=None)[source]¶

Serialize related object

Parameters

identifiers (list of Identifier) – Python representation of identifiers
encoded (dict, optional) – dictionary of objects that have already been encoded

Returns

string representation

Return type

str

class wc_lang.core.InitVolume(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

Initial volume of a compartment

distribution[source]¶

distribution

Type: proto.Term

mean[source]¶

mean initial volume

Type: float

std[source]¶

standard deviation of the mean initial volume

Type: float

units[source]¶

units of volume

Type: unit_registry.Unit

Related attributes:

compartments (list of Compartment): compartment

class Meta[source]¶

Bases: obj_tables.core.Meta

attribute_order = ('distribution', 'mean', 'std', 'units')[source]¶

attributes = {'distribution': <obj_tables.sci.onto.OntoTermAttribute object>, 'mean': <obj_tables.core.FloatAttribute object>, 'std': <obj_tables.core.FloatAttribute object>, 'units': <obj_tables.sci.units.UnitAttribute object>}[source]¶

child_attrs = {'sbml': ('distribution', 'mean', 'std', 'units'), 'wc_sim': ('distribution', 'mean', 'std', 'units')}[source]¶

children = {'core_model': (), 'submodel': ()}[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.InitVolume'>,)[source]¶

local_attributes = {'compartments': <obj_tables.core.LocalAttribute object>, 'distribution': <obj_tables.core.LocalAttribute object>, 'mean': <obj_tables.core.LocalAttribute object>, 'std': <obj_tables.core.LocalAttribute object>, 'units': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ()[source]¶

primary_attribute = None[source]¶

related_attributes = {'compartments': <obj_tables.core.ManyToOneAttribute object>}[source]¶

table_format = 4[source]¶

unique_together = (('distribution', 'mean', 'std', 'units'),)[source]¶

verbose_name = 'Init volume'[source]¶

verbose_name_plural = 'Init volumes'[source]¶

distribution = <obj_tables.sci.onto.OntoTermAttribute object>[source]

mean = <obj_tables.core.FloatAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

serialize()[source]¶

Generate string representation

Returns: string representation
Return type: str

std = <obj_tables.core.FloatAttribute object>[source]

units = <obj_tables.sci.units.UnitAttribute object>[source]

class wc_lang.core.Model(**kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

id[source]¶

unique identifier

Type: str

name[source]¶

name

Type: str

version[source]¶

version of the model

Type: str

url[source]¶

url of the model Git repository

Type: str

branch[source]¶

branch of the model Git repository

Type: str

revision[source]¶

hash for git commit of the wc_lang version used by a model

Type: str

wc_lang_version[source]¶

version of wc_lang

Type: str

time_units[source]¶

time units

Type: unit_registry.Unit

identifiers[source]¶

identifiers

Type: list of Identifier

comments[source]¶

comments

Type: str

created[source]¶

date created

Type: datetime.datetime

updated[source]¶

date updated

Type: datetime.datetime

Related attributes:

taxon (Taxon): taxon

env (Environment): environment

submodels (list of Submodel): submodels

compartments (list of Compartment): compartments

species_types (list of SpeciesType): species types

species (list of Species): species

distribution_init_concentrations (list of DistributionInitConcentration): distributions of initial concentrations of species at the beginning of each cell cycle

observables (list of Observable): observables

functions (list of Function): functions

reactions (list of Reaction): reactions

rate_laws (list of RateLaw): rate laws

dfba_objs (list of DfbaObjective): dFBA objectives

dfba_obj_reactions (list of DfbaObjReaction): dFBA objective reactions

dfba_obj_species (list of DfbaObjSpecies): dFBA objective species

stop_conditions (list of StopCondition): stop conditions

parameters (list of Parameter): parameters

observations (list of Observation): observations

conclusions (list of Conclusion): conclusions

references (list of Reference): references

authors (list of Author): authors

changes (list of Change): changes

class Meta[source]¶

Bases: obj_tables.core.Meta

attribute_order = ('id', 'name', 'version', 'url', 'branch', 'revision', 'wc_lang_version', 'time_units', 'identifiers', 'comments', 'created', 'updated')[source]¶

attributes = {'branch': <obj_tables.core.StringAttribute object>, 'comments': <wc_lang.core.CommentAttribute object>, 'created': <obj_tables.core.DateTimeAttribute object>, 'id': <obj_tables.core.SlugAttribute object>, 'identifiers': <wc_lang.core.IdentifierOneToManyAttribute object>, 'name': <obj_tables.core.StringAttribute object>, 'revision': <obj_tables.core.StringAttribute object>, 'time_units': <obj_tables.sci.units.UnitAttribute object>, 'updated': <obj_tables.core.DateTimeAttribute object>, 'url': <obj_tables.core.UrlAttribute object>, 'version': <obj_tables.core.RegexAttribute object>, 'wc_lang_version': <obj_tables.core.RegexAttribute object>}[source]¶

child_attrs = {'sbml': ('id', 'name', 'version', 'url', 'branch', 'revision', 'wc_lang_version', 'time_units', 'identifiers', 'comments', 'updated', 'created'), 'wc_sim': ('id', 'version', 'wc_lang_version', 'time_units')}[source]¶

children = {'core_model': ('taxon', 'env', 'compartments', 'species_types', 'species', 'distribution_init_concentrations', 'observables', 'functions', 'stop_conditions'), 'submodel': ('taxon', 'env')}[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.Model'>,)[source]¶

local_attributes = {'authors': <obj_tables.core.LocalAttribute object>, 'branch': <obj_tables.core.LocalAttribute object>, 'changes': <obj_tables.core.LocalAttribute object>, 'comments': <obj_tables.core.LocalAttribute object>, 'compartments': <obj_tables.core.LocalAttribute object>, 'conclusions': <obj_tables.core.LocalAttribute object>, 'created': <obj_tables.core.LocalAttribute object>, 'dfba_obj_reactions': <obj_tables.core.LocalAttribute object>, 'dfba_obj_species': <obj_tables.core.LocalAttribute object>, 'dfba_objs': <obj_tables.core.LocalAttribute object>, 'distribution_init_concentrations': <obj_tables.core.LocalAttribute object>, 'env': <obj_tables.core.LocalAttribute object>, 'functions': <obj_tables.core.LocalAttribute object>, 'id': <obj_tables.core.LocalAttribute object>, 'identifiers': <obj_tables.core.LocalAttribute object>, 'name': <obj_tables.core.LocalAttribute object>, 'observables': <obj_tables.core.LocalAttribute object>, 'observation_sets': <obj_tables.core.LocalAttribute object>, 'observations': <obj_tables.core.LocalAttribute object>, 'parameters': <obj_tables.core.LocalAttribute object>, 'rate_laws': <obj_tables.core.LocalAttribute object>, 'reactions': <obj_tables.core.LocalAttribute object>, 'references': <obj_tables.core.LocalAttribute object>, 'revision': <obj_tables.core.LocalAttribute object>, 'species': <obj_tables.core.LocalAttribute object>, 'species_types': <obj_tables.core.LocalAttribute object>, 'stop_conditions': <obj_tables.core.LocalAttribute object>, 'submodels': <obj_tables.core.LocalAttribute object>, 'taxon': <obj_tables.core.LocalAttribute object>, 'time_units': <obj_tables.core.LocalAttribute object>, 'updated': <obj_tables.core.LocalAttribute object>, 'url': <obj_tables.core.LocalAttribute object>, 'version': <obj_tables.core.LocalAttribute object>, 'wc_lang_version': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ('id',)[source]¶

primary_attribute = <obj_tables.core.SlugAttribute object>[source]¶

related_attributes = {'authors': <obj_tables.core.ManyToOneAttribute object>, 'changes': <obj_tables.core.ManyToOneAttribute object>, 'compartments': <obj_tables.core.ManyToOneAttribute object>, 'conclusions': <obj_tables.core.ManyToOneAttribute object>, 'dfba_obj_reactions': <obj_tables.core.ManyToOneAttribute object>, 'dfba_obj_species': <obj_tables.core.ManyToOneAttribute object>, 'dfba_objs': <obj_tables.core.ManyToOneAttribute object>, 'distribution_init_concentrations': <obj_tables.core.ManyToOneAttribute object>, 'env': <obj_tables.core.OneToOneAttribute object>, 'functions': <obj_tables.core.ManyToOneAttribute object>, 'observables': <obj_tables.core.ManyToOneAttribute object>, 'observation_sets': <obj_tables.core.ManyToOneAttribute object>, 'observations': <obj_tables.core.ManyToOneAttribute object>, 'parameters': <obj_tables.core.ManyToOneAttribute object>, 'rate_laws': <obj_tables.core.ManyToOneAttribute object>, 'reactions': <obj_tables.core.ManyToOneAttribute object>, 'references': <obj_tables.core.ManyToOneAttribute object>, 'species': <obj_tables.core.ManyToOneAttribute object>, 'species_types': <obj_tables.core.ManyToOneAttribute object>, 'stop_conditions': <obj_tables.core.ManyToOneAttribute object>, 'submodels': <obj_tables.core.ManyToOneAttribute object>, 'taxon': <obj_tables.core.OneToOneAttribute object>}[source]¶

table_format = 2[source]¶

unique_together = ()[source]¶

verbose_name = 'Model'[source]¶

verbose_name_plural = 'Models'[source]¶

branch = <obj_tables.core.StringAttribute object>[source]

comments = <wc_lang.core.CommentAttribute object>[source]

created = <obj_tables.core.DateTimeAttribute object>[source]

export_relations_to_sbml(sbml_model, sbml)[source]¶

Add relationships to/from object to SBML model.

Parameters

sbml_model (libsbml.Model) – SBML model
sbml (libsbml.Model) – SBML model

export_to_sbml(sbml_model)[source]¶

Add this metadata about this model to a SBML model.

Parameters: sbml_model (libsbml.Model) – SBML model
Returns: SBML model
Return type: libsbml.Model

get_authors(_Model__type=None, **kwargs)[source]¶

Get all authors from model and children

Parameters

__type (types.TypeType or tuple of types.TypeType) – subclass(es) of Model
kwargs (dict of str –> object) – dictionary of attribute name/value pairs to find matching objects

Returns

authors

Return type

list of Author

get_changes(_Model__type=None, **kwargs)[source]¶

Get all changes from model and children

Parameters

__type (types.TypeType or tuple of types.TypeType) – subclass(es) of Model
kwargs (dict of str –> object) – dictionary of attribute name/value pairs to find matching objects

Returns

changes

Return type

list of Change

get_compartments(_Model__type=None, **kwargs)[source]¶

Get all compartments that satisfy the matching criteria

Parameters

__type (types.TypeType or tuple of types.TypeType) – subclass(es) of Model
kwargs (dict of str –> object) – dictionary of attribute name/value pairs to find matching objects

Returns

compartments

Return type

list of Compartment

get_components(_Model__type=None, **kwargs)[source]¶

Find model component of type with id

Parameters

__type (types.TypeType or tuple of types.TypeType) – subclass(es) of Model
kwargs (dict of str –> object) – dictionary of attribute name/value pairs to find matching objects

Returns

component with id, or None if there is no component with id`=`id

Return type

obj_tables.Model

get_conclusions(_Model__type=None, **kwargs)[source]¶

Get all conclusions for model

Returns: conclusions for model
Return type: list of Conclusion

get_dfba_obj_reactions(_Model__type=None, **kwargs)[source]¶

Get all dFBA objective reactions used by submodels

Parameters

__type (types.TypeType or tuple of types.TypeType) – subclass(es) of Model
kwargs (dict of str –> object) – dictionary of attribute name/value pairs to find matching objects

Returns

dFBA objective reactions

Return type

list of DfbaObjReaction

get_dfba_obj_species(_Model__type=None, **kwargs)[source]¶

Get all dFBA objective species used by submodels

Parameters

__type (types.TypeType or tuple of types.TypeType) – subclass(es) of Model
kwargs (dict of str –> object) – dictionary of attribute name/value pairs to find matching objects

Returns

dFBA objective species

Return type

list of DfbaObjSpecies

get_dfba_objs(_Model__type=None, **kwargs)[source]¶

Get all dFBA objectives

Returns: dFBA objectives
Return type: list of DfbaObjective

get_distribution_init_concentrations(_Model__type=None, **kwargs)[source]¶

Get all initial distributions of concentrations of species at the beginning of each cell cycle

Parameters

__type (types.TypeType or tuple of types.TypeType) – subclass(es) of Model
kwargs (dict of str –> object) – dictionary of attribute name/value pairs to find matching objects

Returns

initial distributions: of concentrations of species at the beginning of each cell cycle

Return type

list of DistributionInitConcentration

get_evidence(_Model__type=None, **kwargs)[source]¶

Get all evidence for model

Returns: evidence for model
Return type: list of Evidence

get_functions(_Model__type=None, **kwargs)[source]¶

Get all functions

Parameters

__type (types.TypeType or tuple of types.TypeType) – subclass(es) of Model
kwargs (dict of str –> object) – dictionary of attribute name/value pairs to find matching objects

Returns

functions

Return type

list of Function

get_observables(_Model__type=None, **kwargs)[source]¶

Get all observables

Parameters

__type (types.TypeType or tuple of types.TypeType) – subclass(es) of Model
kwargs (dict of str –> object) – dictionary of attribute name/value pairs to find matching objects

Returns

observables

Return type

list of Observables

get_observation_sets(_Model__type=None, **kwargs)[source]¶

Get all observation sets for model

Returns: observation sets for model
Return type: list of ObservationSet

get_observations(_Model__type=None, **kwargs)[source]¶

Get all observations for model

Returns: observations for model
Return type: list of Observation

get_parameters(_Model__type=None, **kwargs)[source]¶

Get all parameters from model and submodels

Parameters

__type (types.TypeType or tuple of types.TypeType) – subclass(es) of Model
kwargs (dict of str –> object) – dictionary of attribute name/value pairs to find matching objects

Returns

parameters

Return type

list of Parameter

get_rate_laws(_Model__type=None, **kwargs)[source]¶

Get all rate laws from reactions

Parameters

__type (types.TypeType or tuple of types.TypeType) – subclass(es) of Model
kwargs (dict of str –> object) – dictionary of attribute name/value pairs to find matching objects

Returns

rate laws

Return type

list of RateLaw

get_reactions(_Model__type=None, **kwargs)[source]¶

Get all reactions from submodels

Parameters

__type (types.TypeType or tuple of types.TypeType) – subclass(es) of Model
kwargs (dict of str –> object) – dictionary of attribute name/value pairs to find matching objects

Returns

reactions

Return type

list of Reaction

get_references(_Model__type=None, **kwargs)[source]¶

Get all references from model and children

Parameters

__type (types.TypeType or tuple of types.TypeType) – subclass(es) of Model
kwargs (dict of str –> object) – dictionary of attribute name/value pairs to find matching objects

Returns

references

Return type

list of Reference

get_root_compartments(_Model__type=None, **kwargs)[source]¶

Get the root compartments (compartments that either have no parent compartment or whose parent compartment is not cellular)

Returns: root compartments
Return type: list of Compartment

get_species(_Model__type=None, **kwargs)[source]¶

Get all species from submodels

Parameters

__type (types.TypeType or tuple of types.TypeType) – subclass(es) of Model
kwargs (dict of str –> object) – dictionary of attribute name/value pairs to find matching objects

Returns

species

Return type

list of Species

get_species_types(_Model__type=None, **kwargs)[source]¶

Get all species types

Parameters

__type (types.TypeType or tuple of types.TypeType) – subclass(es) of Model
kwargs (dict of str –> object) – dictionary of attribute name/value pairs to find matching objects

Returns

species types

Return type

list of SpeciesType

get_stop_conditions(_Model__type=None, **kwargs)[source]¶

Get all stop conditions

Parameters

__type (types.TypeType or tuple of types.TypeType) – subclass(es) of Model
kwargs (dict of str –> object) – dictionary of attribute name/value pairs to find matching objects

Returns

stop conditions

Return type

list of StopCondition

get_submodels(_Model__type=None, **kwargs)[source]¶

Get all submodels

Parameters

__type (types.TypeType or tuple of types.TypeType) – subclass(es) of Model
kwargs (dict of str –> object) – dictionary of attribute name/value pairs to find matching objects

Returns

submodels

Return type

list of Submodel

id = <obj_tables.core.SlugAttribute object>[source]

identifiers = <wc_lang.core.IdentifierOneToManyAttribute object>[source]

import_from_sbml(sbml)[source]¶

Load from SBML model

Parameters: sbml (libsbml.Model) – SBML model

import_relations_from_sbml(sbml, objs)[source]¶

Load relationships from SBML model

Parameters

sbml (libsbml.Model) – SBML model
objs (dict) – dictionary that maps WC-Lang types to dictionaries that map the ids of WC-Lang objects to WC-Lang objects

merge_attrs(other, other_objs_in_self, self_objs_in_other)[source]¶

Merge attributes of two objects

Parameters

other (Model) – other model
other_objs_in_self (dict) – dictionary that maps instances of objects in another model to objects in a model
self_objs_in_other (dict) – dictionary that maps instances of objects in a model to objects in another model

name = <obj_tables.core.StringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

revision = <obj_tables.core.StringAttribute object>[source]

time_units = <obj_tables.sci.units.UnitAttribute object>[source]

updated = <obj_tables.core.DateTimeAttribute object>[source]

url = <obj_tables.core.UrlAttribute object>[source]

validate()[source]¶

Determine if the model is valid

Network of compartments is rooted and acyclic
Networks of observables and functions are acyclic

Returns

None if the object is valid,: otherwise return a list of errors as an instance of InvalidObject

Return type

InvalidObject or None

version = <obj_tables.core.RegexAttribute object>[source]

wc_lang_version = <obj_tables.core.RegexAttribute object>[source]

class wc_lang.core.Observable(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlAssignmentRuleMixin

Observable: a linear function of other Observbles and Species

id[source]¶

unique id

Type: str

name[source]¶

name

Type: str

model[source]¶

model

Type: Model

expression[source]¶

mathematical expression for an Observable

Type: ObservableExpression

units[source]¶

units of expression

Type: unit_registry.Unit

identifiers[source]¶

identifiers

Type: list of Identifier

evidence[source]¶

observation that supports/disputes a conclusion

Type: list of Evidence

conclusions[source]¶

conclusions

Type: list of Conclusion

comments[source]¶

comments

Type: str

references[source]¶

references

Type: list of Reference

Related attributes:

observable_expressions (list of ObservableExpression): observable expressions

function_expressions (list of FunctionExpression): function expressions

rate_law_expressions (list of RateLawExpression): rate law expressions

stop_condition_expressions (list of StopConditionExpression): stop condition expressions

class Meta[source]¶

Bases: obj_tables.core.Meta, obj_tables.math.expression.ExpressionExpressionTermMeta

attribute_order = ('id', 'name', 'expression', 'units', 'identifiers', 'evidence', 'conclusions', 'comments', 'references')[source]¶

attributes = {'comments': <wc_lang.core.CommentAttribute object>, 'conclusions': <obj_tables.core.ManyToManyAttribute object>, 'evidence': <wc_lang.core.EvidenceManyToManyAttribute object>, 'expression': <obj_tables.math.expression.OneToOneExpressionAttribute object>, 'id': <obj_tables.core.SlugAttribute object>, 'identifiers': <wc_lang.core.IdentifierManyToManyAttribute object>, 'model': <obj_tables.core.ManyToOneAttribute object>, 'name': <obj_tables.core.StringAttribute object>, 'references': <obj_tables.core.ManyToManyAttribute object>, 'units': <obj_tables.sci.units.UnitAttribute object>}[source]¶

child_attrs = {'sbml': ('id', 'name', 'model', 'expression', 'units', 'identifiers', 'comments'), 'wc_sim': ('id', 'model', 'expression', 'units')}[source]¶

children = {'core_model': ('expression', 'identifiers', 'evidence', 'conclusions', 'references'), 'submodel': ('expression', 'identifiers', 'evidence', 'conclusions', 'references')}[source]¶

expression_term_model[source]¶: alias of ObservableExpression

expression_term_units = 'units'[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.Observable'>,)[source]¶

local_attributes = {'comments': <obj_tables.core.LocalAttribute object>, 'conclusions': <obj_tables.core.LocalAttribute object>, 'evidence': <obj_tables.core.LocalAttribute object>, 'expression': <obj_tables.core.LocalAttribute object>, 'function_expressions': <obj_tables.core.LocalAttribute object>, 'id': <obj_tables.core.LocalAttribute object>, 'identifiers': <obj_tables.core.LocalAttribute object>, 'model': <obj_tables.core.LocalAttribute object>, 'name': <obj_tables.core.LocalAttribute object>, 'observable_expressions': <obj_tables.core.LocalAttribute object>, 'rate_law_expressions': <obj_tables.core.LocalAttribute object>, 'references': <obj_tables.core.LocalAttribute object>, 'stop_condition_expressions': <obj_tables.core.LocalAttribute object>, 'units': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ('id',)[source]¶

primary_attribute = <obj_tables.core.SlugAttribute object>[source]¶

related_attributes = {'function_expressions': <obj_tables.core.ManyToManyAttribute object>, 'observable_expressions': <obj_tables.core.ManyToManyAttribute object>, 'rate_law_expressions': <obj_tables.core.ManyToManyAttribute object>, 'stop_condition_expressions': <obj_tables.core.ManyToManyAttribute object>}[source]¶

unique_together = ()[source]¶

verbose_name = 'Observable'[source]¶

verbose_name_plural = 'Observables'[source]¶

comments = <wc_lang.core.CommentAttribute object>[source]

conclusions = <obj_tables.core.ManyToManyAttribute object>[source]

evidence = <wc_lang.core.EvidenceManyToManyAttribute object>[source]

expression = <obj_tables.math.expression.OneToOneExpressionAttribute object>[source]

id = <obj_tables.core.SlugAttribute object>[source]

identifiers = <wc_lang.core.IdentifierManyToManyAttribute object>[source]

model = <obj_tables.core.ManyToOneAttribute object>[source]

name = <obj_tables.core.StringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

references = <obj_tables.core.ManyToManyAttribute object>[source]

units = <obj_tables.sci.units.UnitAttribute object>[source]

class wc_lang.core.ObservableExpression(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, obj_tables.math.expression.Expression, wc_lang.sbml.util.SbmlModelMixin

A mathematical expression of Observables and Species

The expression used by a Observable.

expression[source]¶

mathematical expression for an Observable

Type: str

_parsed_expression[source]¶

an analyzed expression; not an obj_tables.Model

Type: ParsedExpression

species[source]¶

Species used by this Observable expression

Type: list of Species

observables[source]¶

other Observables used by this Observable expression

Type: list of Observable

Related attributes:

observable (Observable): observable

class Meta[source]¶

Bases: obj_tables.core.Meta, obj_tables.math.expression.Meta

attribute_order = ()[source]¶

attributes = {'expression': <obj_tables.core.LongStringAttribute object>, 'observables': <obj_tables.core.ManyToManyAttribute object>, 'species': <obj_tables.core.ManyToManyAttribute object>}[source]¶

child_attrs = {'sbml': ('expression', 'species', 'observables'), 'wc_sim': ('expression', 'species', 'observables')}[source]¶

children = {'core_model': ('species', 'observables'), 'submodel': ('species', 'observables')}[source]¶

expression_is_linear = True[source]¶

expression_term_models = ('Species', 'Observable')[source]¶

expression_unit_registry = <pint.registry.UnitRegistry object>[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.ObservableExpression'>,)[source]¶

local_attributes = {'expression': <obj_tables.core.LocalAttribute object>, 'observable': <obj_tables.core.LocalAttribute object>, 'observables': <obj_tables.core.LocalAttribute object>, 'species': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ('expression',)[source]¶

primary_attribute = <obj_tables.core.LongStringAttribute object>[source]¶

related_attributes = {'observable': <obj_tables.math.expression.OneToOneExpressionAttribute object>}[source]¶

table_format = 3[source]¶

unique_together = ()[source]¶

verbose_name = 'Observable expression'[source]¶

verbose_name_plural = 'Observable expressions'[source]¶

classmethod deserialize(value, objects)[source]¶

Deserialize value

Parameters

value (str) – String representation
objects (dict) – dictionary of objects, grouped by model

Returns

tuple of cleaned value and cleaning error

Return type

tuple of ObservableExpression, InvalidAttribute or None

expression = <obj_tables.core.LongStringAttribute object>[source]

merge_attrs(other, other_objs_in_self, self_objs_in_other)[source]¶

Merge attributes of two objects

Parameters

other (obj_tables.Model) – other model
other_objs_in_self (dict) – dictionary that maps instances of objects in another model to objects in a model
self_objs_in_other (dict) – dictionary that maps instances of objects in a model to objects in another model

objects = <obj_tables.core.Manager object>[source]¶

observables = <obj_tables.core.ManyToManyAttribute object>[source]

serialize()[source]¶

Generate string representation

Returns: string representation
Return type: str

species = <obj_tables.core.ManyToManyAttribute object>[source]

validate()[source]¶

Check that the observable is valid

Check that the expression is a linear function

Returns

None if the object is valid,: otherwise return a list of errors as an instance of InvalidObject

Return type

InvalidObject or None

class wc_lang.core.Observation(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model

id[source]¶

unique identifier

Type: str

name[source]¶

name

Type: str

model[source]¶

model

Type: Model

value[source]¶

value

Type: str

std[source]¶

standard error of the value

Type: str

units[source]¶

units

Type: unit_registry.Unit

type[source]¶

type

Type: pronto.term.Term

genotype[source]¶

genotype

Type: ObservationGenotype

env[source]¶

environment

Type: ObservationEnv

experiment_type[source]¶

type of experiment (e.g. RNA-seq)

Type: str

experiment_design[source]¶

experimental design

Type: str

data_generation_process[source]¶

process used to measure data (e.g. deep sequencing)

Type: Process

data_analysis_process[source]¶

process used to analyze data (e.g. Cufflinks)

Type: Process

identifiers[source]¶

identifiers

Type: list of Identifier

comments[source]¶

comments

Type: str

references[source]¶

references

Type: list of Reference

Related attributes:

observation_sets (list of ObservationSet): observation sets

evidence (list of Evidence): evidence

class Meta[source]¶

Bases: obj_tables.core.Meta

attribute_order = ('id', 'name', 'value', 'std', 'units', 'type', 'genotype', 'env', 'experiment_type', 'experiment_design', 'data_generation_process', 'data_analysis_process', 'identifiers', 'comments', 'references')[source]¶

attributes = {'comments': <wc_lang.core.CommentAttribute object>, 'data_analysis_process': <obj_tables.core.ManyToOneAttribute object>, 'data_generation_process': <obj_tables.core.ManyToOneAttribute object>, 'env': <obj_tables.core.ManyToOneAttribute object>, 'experiment_design': <obj_tables.core.LongStringAttribute object>, 'experiment_type': <obj_tables.core.LongStringAttribute object>, 'genotype': <obj_tables.core.ManyToOneAttribute object>, 'id': <obj_tables.core.SlugAttribute object>, 'identifiers': <wc_lang.core.IdentifierManyToManyAttribute object>, 'model': <obj_tables.core.ManyToOneAttribute object>, 'name': <obj_tables.core.StringAttribute object>, 'references': <obj_tables.core.ManyToManyAttribute object>, 'std': <obj_tables.core.StringAttribute object>, 'type': <obj_tables.sci.onto.OntoTermAttribute object>, 'units': <obj_tables.sci.units.UnitAttribute object>, 'value': <obj_tables.core.StringAttribute object>}[source]¶

child_attrs = {'sbml': (), 'wc_sim': ()}[source]¶

children = {'core_model': ('genotype', 'env', 'data_generation_process', 'data_analysis_process', 'identifiers', 'references'), 'submodel': ('genotype', 'env', 'data_generation_process', 'data_analysis_process', 'identifiers', 'references')}[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.Observation'>,)[source]¶

local_attributes = {'comments': <obj_tables.core.LocalAttribute object>, 'data_analysis_process': <obj_tables.core.LocalAttribute object>, 'data_generation_process': <obj_tables.core.LocalAttribute object>, 'env': <obj_tables.core.LocalAttribute object>, 'evidence': <obj_tables.core.LocalAttribute object>, 'experiment_design': <obj_tables.core.LocalAttribute object>, 'experiment_type': <obj_tables.core.LocalAttribute object>, 'genotype': <obj_tables.core.LocalAttribute object>, 'id': <obj_tables.core.LocalAttribute object>, 'identifiers': <obj_tables.core.LocalAttribute object>, 'model': <obj_tables.core.LocalAttribute object>, 'name': <obj_tables.core.LocalAttribute object>, 'observation_sets': <obj_tables.core.LocalAttribute object>, 'references': <obj_tables.core.LocalAttribute object>, 'std': <obj_tables.core.LocalAttribute object>, 'type': <obj_tables.core.LocalAttribute object>, 'units': <obj_tables.core.LocalAttribute object>, 'value': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ('id',)[source]¶

primary_attribute = <obj_tables.core.SlugAttribute object>[source]¶

related_attributes = {'evidence': <obj_tables.core.ManyToOneAttribute object>, 'observation_sets': <obj_tables.core.ManyToManyAttribute object>}[source]¶

unique_together = ()[source]¶

verbose_name = 'Observation'[source]¶

verbose_name_plural = 'Observations'[source]¶

comments = <wc_lang.core.CommentAttribute object>[source]

data_analysis_process = <obj_tables.core.ManyToOneAttribute object>[source]

data_generation_process = <obj_tables.core.ManyToOneAttribute object>[source]

env = <obj_tables.core.ManyToOneAttribute object>[source]

experiment_design = <obj_tables.core.LongStringAttribute object>[source]

experiment_type = <obj_tables.core.LongStringAttribute object>[source]

genotype = <obj_tables.core.ManyToOneAttribute object>[source]

id = <obj_tables.core.SlugAttribute object>[source]

identifiers = <wc_lang.core.IdentifierManyToManyAttribute object>[source]

model = <obj_tables.core.ManyToOneAttribute object>[source]

name = <obj_tables.core.StringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

references = <obj_tables.core.ManyToManyAttribute object>[source]

std = <obj_tables.core.StringAttribute object>[source]

type = <obj_tables.sci.onto.OntoTermAttribute object>[source]

units = <obj_tables.sci.units.UnitAttribute object>[source]

value = <obj_tables.core.StringAttribute object>[source]

class wc_lang.core.ObservationEnv(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

Environment of an observation

temp[source]¶

temperature at which the observation was observed

Type: float

temp_units[source]¶

temperature units

Type: unit_registry.Unit

ph[source]¶

pH at which the observation was observed

Type: float

ph_units[source]¶

pH units

Type: unit_registry.Unit

growth_media[source]¶

growth media at which the observation was observed

Type: str

condition[source]¶

experimental conditions (e.g. control)

Type: str

Related attributes:

env_observations (list of Observation): observations

class Meta[source]¶

Bases: obj_tables.core.Meta

attribute_order = ('temp', 'temp_units', 'ph', 'ph_units', 'growth_media', 'condition')[source]¶

attributes = {'condition': <obj_tables.core.LongStringAttribute object>, 'growth_media': <obj_tables.core.LongStringAttribute object>, 'ph': <obj_tables.core.FloatAttribute object>, 'ph_units': <obj_tables.sci.units.UnitAttribute object>, 'temp': <obj_tables.core.FloatAttribute object>, 'temp_units': <obj_tables.sci.units.UnitAttribute object>}[source]¶

child_attrs = {'sbml': (), 'wc_sim': ()}[source]¶

children = {'core_model': (), 'submodel': ()}[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.ObservationEnv'>,)[source]¶

local_attributes = {'condition': <obj_tables.core.LocalAttribute object>, 'env_observations': <obj_tables.core.LocalAttribute object>, 'growth_media': <obj_tables.core.LocalAttribute object>, 'ph': <obj_tables.core.LocalAttribute object>, 'ph_units': <obj_tables.core.LocalAttribute object>, 'temp': <obj_tables.core.LocalAttribute object>, 'temp_units': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ()[source]¶

primary_attribute = None[source]¶

related_attributes = {'env_observations': <obj_tables.core.ManyToOneAttribute object>}[source]¶

table_format = 4[source]¶

unique_together = (('condition', 'growth_media', 'ph', 'ph_units', 'temp', 'temp_units'),)[source]¶

verbose_name = 'Observation env'[source]¶

verbose_name_plural = 'Observation envs'[source]¶

condition = <obj_tables.core.LongStringAttribute object>[source]

growth_media = <obj_tables.core.LongStringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

ph = <obj_tables.core.FloatAttribute object>[source]

ph_units = <obj_tables.sci.units.UnitAttribute object>[source]

serialize()[source]¶

Generate string representation

Returns: string representation
Return type: str

temp = <obj_tables.core.FloatAttribute object>[source]

temp_units = <obj_tables.sci.units.UnitAttribute object>[source]

validate()[source]¶

Determine if the environment is valid

temperature units are defined if the temperature is not None
pH units are defined if the pH is not None

Returns

None if the object is valid,: otherwise return a list of errors as an instance of InvalidObject

Return type

InvalidObject or None

class wc_lang.core.ObservationGenotype(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

Genotype of an observation

taxon[source]¶

taxon in which the observation was observed

Type: str

genetic_variant[source]¶

genetic variant in which the observation was observed

Type: str

Related attributes:

genotype_observations (list of Observation): observations

class Meta[source]¶

Bases: obj_tables.core.Meta

attribute_order = ('taxon', 'variant')[source]¶

attributes = {'taxon': <obj_tables.core.StringAttribute object>, 'variant': <obj_tables.core.StringAttribute object>}[source]¶

child_attrs = {'sbml': (), 'wc_sim': ()}[source]¶

children = {'core_model': (), 'submodel': ()}[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.ObservationGenotype'>,)[source]¶

local_attributes = {'genotype_observations': <obj_tables.core.LocalAttribute object>, 'taxon': <obj_tables.core.LocalAttribute object>, 'variant': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ()[source]¶

primary_attribute = None[source]¶

related_attributes = {'genotype_observations': <obj_tables.core.ManyToOneAttribute object>}[source]¶

table_format = 4[source]¶

unique_together = (('taxon', 'variant'),)[source]¶

verbose_name = 'Observation genotype'[source]¶

verbose_name_plural = 'Observation genotypes'[source]¶

objects = <obj_tables.core.Manager object>[source]¶

serialize()[source]¶

Generate string representation

Returns: string representation
Return type: str

taxon = <obj_tables.core.StringAttribute object>[source]

variant = <obj_tables.core.StringAttribute object>[source]¶

class wc_lang.core.ObservationSet(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

Set of co-observed observations

id[source]¶

unique identifier

Type: str

name[source]¶

name

Type: str

model[source]¶

model

Type: Model

observations[source]¶

observations

Type: list of Observation

identifiers[source]¶

identifiers

Type: list of Identifier

comments[source]¶

comments

Type: str

references[source]¶

references

Type: list of Reference

class Meta[source]¶

Bases: obj_tables.core.Meta

attribute_order = ('id', 'name', 'observations', 'identifiers', 'comments', 'references')[source]¶

attributes = {'comments': <wc_lang.core.CommentAttribute object>, 'id': <obj_tables.core.SlugAttribute object>, 'identifiers': <wc_lang.core.IdentifierManyToManyAttribute object>, 'model': <obj_tables.core.ManyToOneAttribute object>, 'name': <obj_tables.core.StringAttribute object>, 'observations': <obj_tables.core.ManyToManyAttribute object>, 'references': <obj_tables.core.ManyToManyAttribute object>}[source]¶

child_attrs = {'sbml': (), 'wc_sim': ()}[source]¶

children = {'core_model': ('observations', 'identifiers', 'references'), 'submodel': ('observations', 'identifiers', 'references')}[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.ObservationSet'>,)[source]¶

local_attributes = {'comments': <obj_tables.core.LocalAttribute object>, 'id': <obj_tables.core.LocalAttribute object>, 'identifiers': <obj_tables.core.LocalAttribute object>, 'model': <obj_tables.core.LocalAttribute object>, 'name': <obj_tables.core.LocalAttribute object>, 'observations': <obj_tables.core.LocalAttribute object>, 'references': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ('id',)[source]¶

primary_attribute = <obj_tables.core.SlugAttribute object>[source]¶

related_attributes = {}[source]¶

unique_together = ()[source]¶

verbose_name = 'Observation set'[source]¶

verbose_name_plural = 'Observation sets'[source]¶

comments = <wc_lang.core.CommentAttribute object>[source]

id = <obj_tables.core.SlugAttribute object>[source]

identifiers = <wc_lang.core.IdentifierManyToManyAttribute object>[source]

model = <obj_tables.core.ManyToOneAttribute object>[source]

name = <obj_tables.core.StringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

observations = <obj_tables.core.ManyToManyAttribute object>[source]

references = <obj_tables.core.ManyToManyAttribute object>[source]

class wc_lang.core.Parameter(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

id[source]¶

unique identifier per model/submodel

Type: str

name[source]¶

name

Type: str

model[source]¶

model

Type: Model

type[source]¶

parameter type

Type: pronto.term.Term

value[source]¶

value

Type: float

std[source]¶

standard error of the value

Type: float

units[source]¶

units of the value and standard error

Type: unit_registry.Unit

identifiers[source]¶

identifiers

Type: list of Identifier

evidence[source]¶

observation that supports/disputes a conclusion

Type: list of Evidence

conclusions[source]¶

conclusions

Type: list of Conclusion

comments[source]¶

comments

Type: str

references[source]¶

references

Type: list of Reference

Related attributes:

density_compartment (Compartment): compartments whose density is represented by the parameter

observable_expressions (list of ObservableExpression): observable expressions

function_expressions (list of FunctionExpression): function expressions

rate_law_expressions (list of RateLawExpression): rate law expressions

stop_condition_expressions (list of StopConditionExpression): stop condition expressions

class Meta[source]¶

Bases: obj_tables.core.Meta, obj_tables.math.expression.ExpressionStaticTermMeta

attribute_order = ('id', 'name', 'type', 'value', 'std', 'units', 'identifiers', 'evidence', 'conclusions', 'comments', 'references')[source]¶

attributes = {'comments': <wc_lang.core.CommentAttribute object>, 'conclusions': <obj_tables.core.ManyToManyAttribute object>, 'evidence': <wc_lang.core.EvidenceManyToManyAttribute object>, 'id': <obj_tables.core.SlugAttribute object>, 'identifiers': <wc_lang.core.IdentifierManyToManyAttribute object>, 'model': <obj_tables.core.ManyToOneAttribute object>, 'name': <obj_tables.core.StringAttribute object>, 'references': <obj_tables.core.ManyToManyAttribute object>, 'std': <obj_tables.core.FloatAttribute object>, 'type': <obj_tables.sci.onto.OntoTermAttribute object>, 'units': <obj_tables.sci.units.UnitAttribute object>, 'value': <obj_tables.core.FloatAttribute object>}[source]¶

child_attrs = {'sbml': ('id', 'name', 'model', 'type', 'value', 'std', 'units', 'identifiers', 'comments'), 'wc_sim': ('id', 'model', 'type', 'value', 'std', 'units')}[source]¶

children = {'core_model': ('identifiers', 'evidence', 'conclusions', 'references'), 'submodel': ('identifiers', 'evidence', 'conclusions', 'references')}[source]¶

expression_term_units = 'units'[source]¶

expression_term_value = 'value'[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.Parameter'>,)[source]¶

local_attributes = {'comments': <obj_tables.core.LocalAttribute object>, 'conclusions': <obj_tables.core.LocalAttribute object>, 'density_compartment': <obj_tables.core.LocalAttribute object>, 'evidence': <obj_tables.core.LocalAttribute object>, 'function_expressions': <obj_tables.core.LocalAttribute object>, 'id': <obj_tables.core.LocalAttribute object>, 'identifiers': <obj_tables.core.LocalAttribute object>, 'model': <obj_tables.core.LocalAttribute object>, 'name': <obj_tables.core.LocalAttribute object>, 'rate_law_expressions': <obj_tables.core.LocalAttribute object>, 'references': <obj_tables.core.LocalAttribute object>, 'std': <obj_tables.core.LocalAttribute object>, 'stop_condition_expressions': <obj_tables.core.LocalAttribute object>, 'type': <obj_tables.core.LocalAttribute object>, 'units': <obj_tables.core.LocalAttribute object>, 'value': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ('id',)[source]¶

primary_attribute = <obj_tables.core.SlugAttribute object>[source]¶

related_attributes = {'density_compartment': <obj_tables.core.OneToOneAttribute object>, 'function_expressions': <obj_tables.core.ManyToManyAttribute object>, 'rate_law_expressions': <obj_tables.core.ManyToManyAttribute object>, 'stop_condition_expressions': <obj_tables.core.ManyToManyAttribute object>}[source]¶

unique_together = ()[source]¶

verbose_name = 'Parameter'[source]¶

verbose_name_plural = 'Parameters'[source]¶

comments = <wc_lang.core.CommentAttribute object>[source]

conclusions = <obj_tables.core.ManyToManyAttribute object>[source]

evidence = <wc_lang.core.EvidenceManyToManyAttribute object>[source]

export_relations_to_sbml(sbml_model, sbml)[source]¶

Add relationships to/from object to SBML parameter.

Parameters

sbml_model (libsbml.Model) – SBML model
sbml (libsbml.Parameter) – SBML parameter

export_to_sbml(sbml_model)[source]¶

Add this parameter to a SBML model.

Parameters: sbml_model (libsbml.Model) – SBML model
Returns: SBML parameter
Return type: libsbml.Parameter

id = <obj_tables.core.SlugAttribute object>[source]

identifiers = <wc_lang.core.IdentifierManyToManyAttribute object>[source]

import_from_sbml(sbml)[source]¶

Load from SBML parameter

Parameters: sbml (libsbml.Parameter) – SBML parameter

import_relations_from_sbml(sbml, objs)[source]¶

Load relationships from SBML parameter

Parameters

sbml (libsbml.Parameter) – SBML parameter
objs (dict) – dictionary that maps WC-Lang types to dictionaries that map the ids of WC-Lang objects to WC-Lang objects

model = <obj_tables.core.ManyToOneAttribute object>[source]

name = <obj_tables.core.StringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

references = <obj_tables.core.ManyToManyAttribute object>[source]

std = <obj_tables.core.FloatAttribute object>[source]

type = <obj_tables.sci.onto.OntoTermAttribute object>[source]

units = <obj_tables.sci.units.UnitAttribute object>[source]

value = <obj_tables.core.FloatAttribute object>[source]

class wc_lang.core.Ph(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

pH of a compartment

distribution[source]¶

distribution

Type: proto.Term

mean[source]¶

mean initial pH

Type: float

std[source]¶

standard deviation of the mean initial pH

Type: float

units[source]¶

units of pH

Type: unit_registry.Unit

Related attributes:

compartments (list of Compartment): compartment

class Meta[source]¶

Bases: obj_tables.core.Meta

attribute_order = ('distribution', 'mean', 'std', 'units')[source]¶

attributes = {'distribution': <obj_tables.sci.onto.OntoTermAttribute object>, 'mean': <obj_tables.core.FloatAttribute object>, 'std': <obj_tables.core.FloatAttribute object>, 'units': <obj_tables.sci.units.UnitAttribute object>}[source]¶

child_attrs = {'sbml': ('distribution', 'mean', 'std', 'units'), 'wc_sim': ()}[source]¶

children = {'core_model': (), 'submodel': ()}[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.Ph'>,)[source]¶

local_attributes = {'compartments': <obj_tables.core.LocalAttribute object>, 'distribution': <obj_tables.core.LocalAttribute object>, 'mean': <obj_tables.core.LocalAttribute object>, 'std': <obj_tables.core.LocalAttribute object>, 'units': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ()[source]¶

primary_attribute = None[source]¶

related_attributes = {'compartments': <obj_tables.core.ManyToOneAttribute object>}[source]¶

table_format = 4[source]¶

unique_together = (('distribution', 'mean', 'std', 'units'),)[source]¶

verbose_name = 'Ph'[source]¶

verbose_name_plural = 'Phs'[source]¶

distribution = <obj_tables.sci.onto.OntoTermAttribute object>[source]

mean = <obj_tables.core.FloatAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

serialize()[source]¶

Generate string representation

Returns: string representation
Return type: str

std = <obj_tables.core.FloatAttribute object>[source]

units = <obj_tables.sci.units.UnitAttribute object>[source]

class wc_lang.core.Process(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

A process of an observation or conclusion

name[source]¶

procedure which produced the conclusion

Type: str

version[source]¶

version of procedure which produced the conclusion

Type: str

Related attributes:

observation_analysis (list of Observation): observation

observation_measurement (list of Observation): observation

conclusions (list of Conclusion): conclusions

class Meta[source]¶

Bases: obj_tables.core.Meta

attribute_order = ('name', 'version')[source]¶

attributes = {'name': <obj_tables.core.LongStringAttribute object>, 'version': <obj_tables.core.StringAttribute object>}[source]¶

child_attrs = {'sbml': (), 'wc_sim': ()}[source]¶

children = {'core_model': (), 'submodel': ()}[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.Process'>,)[source]¶

local_attributes = {'conclusions': <obj_tables.core.LocalAttribute object>, 'name': <obj_tables.core.LocalAttribute object>, 'observation_data_analysis': <obj_tables.core.LocalAttribute object>, 'observation_data_generation': <obj_tables.core.LocalAttribute object>, 'version': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ()[source]¶

primary_attribute = None[source]¶

related_attributes = {'conclusions': <obj_tables.core.ManyToOneAttribute object>, 'observation_data_analysis': <obj_tables.core.ManyToOneAttribute object>, 'observation_data_generation': <obj_tables.core.ManyToOneAttribute object>}[source]¶

table_format = 4[source]¶

unique_together = (('name', 'version'),)[source]¶

verbose_name = 'Process'[source]¶

verbose_name_plural = 'Processes'[source]¶

name = <obj_tables.core.LongStringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

serialize()[source]¶

Generate string representation

Returns: string representation
Return type: str

version = <obj_tables.core.StringAttribute object>[source]

class wc_lang.core.RateLaw(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

Rate law

id[source]¶

identifier equal to {reaction.id}-{direction.name}

Type: str

name[source]¶

name

Type: str

model[source]¶

model

Type: Model

reaction[source]¶

reaction

Type: Reaction

direction[source]¶

direction

Type: RateLawDirection

type[source]¶

type

Type: pronto.term.Term

expression[source]¶

expression

Type: RateLawExpression

units[source]¶

units

Type: unit_registry.Unit

identifiers[source]¶

identifiers

Type: list of Identifier

evidence[source]¶

observation that supports/disputes a conclusion

Type: list of Evidence

conclusions[source]¶

conclusions

Type: list of Conclusion

comments[source]¶

comments

Type: str

references[source]¶

references

Type: list of Reference

class Meta[source]¶

Bases: obj_tables.core.Meta, obj_tables.math.expression.ExpressionExpressionTermMeta

attribute_order = ('id', 'name', 'reaction', 'direction', 'type', 'expression', 'units', 'identifiers', 'evidence', 'conclusions', 'comments', 'references')[source]¶

attributes = {'comments': <wc_lang.core.CommentAttribute object>, 'conclusions': <obj_tables.core.ManyToManyAttribute object>, 'direction': <obj_tables.core.EnumAttribute object>, 'evidence': <wc_lang.core.EvidenceManyToManyAttribute object>, 'expression': <obj_tables.math.expression.ManyToOneExpressionAttribute object>, 'id': <obj_tables.core.StringAttribute object>, 'identifiers': <wc_lang.core.IdentifierManyToManyAttribute object>, 'model': <obj_tables.core.ManyToOneAttribute object>, 'name': <obj_tables.core.StringAttribute object>, 'reaction': <obj_tables.core.ManyToOneAttribute object>, 'references': <obj_tables.core.ManyToManyAttribute object>, 'type': <obj_tables.sci.onto.OntoTermAttribute object>, 'units': <obj_tables.sci.units.UnitAttribute object>}[source]¶

child_attrs = {'sbml': ('id', 'name', 'model', 'reaction', 'direction', 'type', 'expression', 'units', 'identifiers', 'comments'), 'wc_sim': ('id', 'model', 'reaction', 'direction', 'expression', 'units')}[source]¶

children = {'core_model': ('expression', 'identifiers', 'evidence', 'conclusions', 'references'), 'submodel': ('expression', 'identifiers', 'evidence', 'conclusions', 'references')}[source]¶

expression_term_model[source]¶: alias of RateLawExpression

expression_term_units = 'units'[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.RateLaw'>,)[source]¶

local_attributes = {'comments': <obj_tables.core.LocalAttribute object>, 'conclusions': <obj_tables.core.LocalAttribute object>, 'direction': <obj_tables.core.LocalAttribute object>, 'evidence': <obj_tables.core.LocalAttribute object>, 'expression': <obj_tables.core.LocalAttribute object>, 'id': <obj_tables.core.LocalAttribute object>, 'identifiers': <obj_tables.core.LocalAttribute object>, 'model': <obj_tables.core.LocalAttribute object>, 'name': <obj_tables.core.LocalAttribute object>, 'reaction': <obj_tables.core.LocalAttribute object>, 'references': <obj_tables.core.LocalAttribute object>, 'type': <obj_tables.core.LocalAttribute object>, 'units': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ('id',)[source]¶

primary_attribute = <obj_tables.core.StringAttribute object>[source]¶

related_attributes = {}[source]¶

unique_together = ()[source]¶

verbose_name = 'Rate law'[source]¶

verbose_name_plural = 'Rate laws'[source]¶

comments = <wc_lang.core.CommentAttribute object>[source]

conclusions = <obj_tables.core.ManyToManyAttribute object>[source]

direction = <obj_tables.core.EnumAttribute object>[source]

evidence = <wc_lang.core.EvidenceManyToManyAttribute object>[source]

export_relations_to_sbml(sbml_model, sbml)[source]¶

Add relationships to/from object to SBML kinetic law.

Parameters

sbml_model (libsbml.Model) – SBML model
sbml (libsbml.KineticLaw) – SBML kinetic law

export_to_sbml(sbml_model)[source]¶

Add this rate law to a SBML reaction.

Parameters: sbml_model (libsbml.Model) – SBML model
Returns: SBML kinetic law
Return type: libsbml.KineticLaw

expression = <obj_tables.math.expression.ManyToOneExpressionAttribute object>[source]

gen_id()[source]¶

Generate identifier

Returns: identifier
Return type: str

id = <obj_tables.core.StringAttribute object>[source]

identifiers = <wc_lang.core.IdentifierManyToManyAttribute object>[source]

import_from_sbml(sbml)[source]¶

Load from SBML kinetic law

Parameters: sbml (libsbml.KineticLaw) – SBML kinetic law

import_relations_from_sbml(sbml, objs)[source]¶

Load relationships from SBML kinetic law

Parameters

sbml (libsbml.KineticLaw) – SBML kinetic law
objs (dict) – dictionary that maps WC-Lang types to dictionaries that map the ids of WC-Lang objects to WC-Lang objects

model = <obj_tables.core.ManyToOneAttribute object>[source]

name = <obj_tables.core.StringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

reaction = <obj_tables.core.ManyToOneAttribute object>[source]

references = <obj_tables.core.ManyToManyAttribute object>[source]

type = <obj_tables.sci.onto.OntoTermAttribute object>[source]

units = <obj_tables.sci.units.UnitAttribute object>[source]

validate()[source]¶

Determine whether this RateLaw is valid

Check if identifier equal to {reaction.id}-{direction.name}

Returns

None if the object is valid,: otherwise return a list of errors in an InvalidObject instance

Return type

InvalidObject or None

class wc_lang.core.RateLawDirection[source]¶

Bases: int, wc_utils.util.enumerate.CaseInsensitiveEnum

Rate law directions

backward = -1[source]¶

forward = 1[source]¶

class wc_lang.core.RateLawExpression(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, obj_tables.math.expression.Expression, wc_lang.sbml.util.SbmlModelMixin

A mathematical expression of Parameters, Species, Observables, Functions, Compartments and Python functions

The expression used by a RateLaw.

expression[source]¶

mathematical expression of the rate law

Type: str

_parsed_expression[source]¶

an analyzed expression; not an obj_tables.Model

Type: ParsedExpression

species[source]¶

species whose dynamic concentrations are used in the rate law

Type: list of Species

parameters[source]¶

parameters whose values are used in the rate law

Type: list of Parameter

compartments[source]¶

Compartments used by this rate law expression

Type: list of Compartment

Related attributes:

rate_law (RateLaw): the RateLaw which uses this RateLawExpression

class Meta[source]¶

Bases: obj_tables.core.Meta, obj_tables.math.expression.Meta

attribute_order = ('expression', 'species', 'parameters')[source]¶

attributes = {'compartments': <obj_tables.core.ManyToManyAttribute object>, 'expression': <obj_tables.core.LongStringAttribute object>, 'functions': <obj_tables.core.ManyToManyAttribute object>, 'observables': <obj_tables.core.ManyToManyAttribute object>, 'parameters': <obj_tables.core.ManyToManyAttribute object>, 'species': <obj_tables.core.ManyToManyAttribute object>}[source]¶

child_attrs = {'sbml': ('expression', 'parameters', 'species', 'observables', 'functions', 'compartments'), 'wc_sim': ('expression', 'parameters', 'species', 'observables', 'functions', 'compartments')}[source]¶

children = {'core_model': ('parameters', 'species', 'observables', 'functions', 'compartments'), 'submodel': ('parameters', 'species', 'observables', 'functions', 'compartments')}[source]¶

expression_term_models = ('Parameter', 'Species', 'Observable', 'Function', 'Compartment')[source]¶

expression_unit_registry = <pint.registry.UnitRegistry object>[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.RateLawExpression'>,)[source]¶

local_attributes = {'compartments': <obj_tables.core.LocalAttribute object>, 'expression': <obj_tables.core.LocalAttribute object>, 'functions': <obj_tables.core.LocalAttribute object>, 'observables': <obj_tables.core.LocalAttribute object>, 'parameters': <obj_tables.core.LocalAttribute object>, 'rate_laws': <obj_tables.core.LocalAttribute object>, 'species': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ('expression',)[source]¶

primary_attribute = <obj_tables.core.LongStringAttribute object>[source]¶

related_attributes = {'rate_laws': <obj_tables.math.expression.ManyToOneExpressionAttribute object>}[source]¶

table_format = 3[source]¶

unique_together = ()[source]¶

verbose_name = 'Rate law expression'[source]¶

verbose_name_plural = 'Rate law expressions'[source]¶

compartments = <obj_tables.core.ManyToManyAttribute object>[source]

classmethod deserialize(value, objects)[source]¶

Deserialize value

Parameters

value (str) – String representation
objects (dict) – dictionary of objects, grouped by model

Returns

tuple of cleaned value: and cleaning error

Return type

tuple of RateLawExpression, InvalidAttribute or None

expression = <obj_tables.core.LongStringAttribute object>[source]

functions = <obj_tables.core.ManyToManyAttribute object>[source]¶

merge_attrs(other, other_objs_in_self, self_objs_in_other)[source]¶

Merge attributes of two objects

Parameters

other (obj_tables.Model) – other model
other_objs_in_self (dict) – dictionary that maps instances of objects in another model to objects in a model
self_objs_in_other (dict) – dictionary that maps instances of objects in a model to objects in another model

objects = <obj_tables.core.Manager object>[source]¶

observables = <obj_tables.core.ManyToManyAttribute object>[source]¶

parameters = <obj_tables.core.ManyToManyAttribute object>[source]

serialize()[source]¶

Generate string representation

Returns: value of primary attribute
Return type: str

species = <obj_tables.core.ManyToManyAttribute object>[source]

validate()[source]¶

Determine whether a RateLawExpression is valid

Check that all of the species and parameters contribute to the expression
Check that the species and parameters encompass of the named entities in the expression

Returns

None if the object is valid,: otherwise return a list of errors in an InvalidObject instance

Return type

InvalidObject or None

class wc_lang.core.Reaction(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

id[source]¶

unique identifier

Type: str

name[source]¶

name

Type: str

model[source]¶

model

Type: Model

submodel[source]¶

submodel that reaction belongs to

Type: Submodel

participants[source]¶

participants

Type: list of SpeciesCoefficient

reversible[source]¶

indicates if reaction is thermodynamically reversible

Type: bool

rate_units[source]¶

units of rate law(s)

Type: unit_registry.Unit

flux_bounds[source]¶

flux bounds

Type: FluxBounds

identifiers[source]¶

identifiers

Type: list of Identifier

evidence[source]¶

observation that supports/disputes a conclusion

Type: list of Evidence

conclusions[source]¶

conclusions

Type: list of Conclusion

comments[source]¶

comments

Type: str

references[source]¶

references

Type: list of Reference

Related attributes:

rate_laws (list of RateLaw): rate laws; if two rate laws are present, rate_laws[1] is the forward rate law, and rate_laws[0] is the backward rate law

dfba_obj_expression (DfbaObjectiveExpression): dFBA objective expression

class Meta[source]¶

Bases: obj_tables.core.Meta, obj_tables.math.expression.ExpressionDynamicTermMeta

attribute_order = ('id', 'name', 'submodel', 'participants', 'reversible', 'rate_units', 'flux_bounds', 'identifiers', 'evidence', 'conclusions', 'comments', 'references')[source]¶

attributes = {'comments': <wc_lang.core.CommentAttribute object>, 'conclusions': <obj_tables.core.ManyToManyAttribute object>, 'evidence': <wc_lang.core.EvidenceManyToManyAttribute object>, 'flux_bounds': <obj_tables.core.ManyToOneAttribute object>, 'id': <obj_tables.core.SlugAttribute object>, 'identifiers': <wc_lang.core.IdentifierManyToManyAttribute object>, 'model': <obj_tables.core.ManyToOneAttribute object>, 'name': <obj_tables.core.StringAttribute object>, 'participants': <wc_lang.core.ReactionParticipantAttribute object>, 'rate_units': <obj_tables.sci.units.UnitAttribute object>, 'references': <obj_tables.core.ManyToManyAttribute object>, 'reversible': <obj_tables.core.BooleanAttribute object>, 'submodel': <obj_tables.core.ManyToOneAttribute object>}[source]¶

child_attrs = {'sbml': ('id', 'name', 'model', 'submodel', 'participants', 'reversible', 'rate_units', 'flux_bounds', 'identifiers', 'comments'), 'wc_sim': ('id', 'model', 'submodel', 'participants', 'reversible', 'rate_units', 'flux_bounds')}[source]¶

children = {'core_model': ('participants', 'rate_laws', 'flux_bounds', 'identifiers', 'evidence', 'conclusions', 'references'), 'submodel': ('participants', 'rate_laws', 'flux_bounds', 'identifiers', 'evidence', 'conclusions', 'references')}[source]¶

expression_term_units = 'rate_units'[source]¶

indexed_attrs_tuples = (('id',),)[source]¶

inheritance = (<class 'wc_lang.core.Reaction'>,)[source]¶

local_attributes = {'comments': <obj_tables.core.LocalAttribute object>, 'conclusions': <obj_tables.core.LocalAttribute object>, 'dfba_obj_expression': <obj_tables.core.LocalAttribute object>, 'evidence': <obj_tables.core.LocalAttribute object>, 'flux_bounds': <obj_tables.core.LocalAttribute object>, 'id': <obj_tables.core.LocalAttribute object>, 'identifiers': <obj_tables.core.LocalAttribute object>, 'model': <obj_tables.core.LocalAttribute object>, 'name': <obj_tables.core.LocalAttribute object>, 'participants': <obj_tables.core.LocalAttribute object>, 'rate_laws': <obj_tables.core.LocalAttribute object>, 'rate_units': <obj_tables.core.LocalAttribute object>, 'references': <obj_tables.core.LocalAttribute object>, 'reversible': <obj_tables.core.LocalAttribute object>, 'submodel': <obj_tables.core.LocalAttribute object>}[source]¶

merge = 2[source]¶

ordering = ('id',)[source]¶

primary_attribute = <obj_tables.core.SlugAttribute object>[source]¶

related_attributes = {'dfba_obj_expression': <obj_tables.core.OneToManyAttribute object>, 'rate_laws': <obj_tables.core.ManyToOneAttribute object>}[source]¶

unique_together = ()[source]¶

verbose_name = 'Reaction'[source]¶

verbose_name_plural = 'Reactions'[source]¶

comments = <wc_lang.core.CommentAttribute object>[source]

conclusions = <obj_tables.core.ManyToManyAttribute object>[source]

evidence = <wc_lang.core.EvidenceManyToManyAttribute object>[source]

export_relations_to_sbml(sbml_model, sbml_rxn)[source]¶

Add relationships to/from object to SBML reaction.

Parameters

sbml_model (libsbml.Model) – SBML model
sbml_rxn (libsbml.Reaction) – SBML reaction

export_to_sbml(sbml_model)[source]¶

Add this reaction to a SBML model.

Parameters: sbml_model (libsbml.Model) – SBML model
Returns: SBML reaction
Return type: libsbml.Reaction
Raises: ValueError – if the reaction has a backward rate law which cannot be exported to SBML

flux_bounds = <obj_tables.core.ManyToOneAttribute object>[source]

get_modifiers(direction=<RateLawDirection.forward: 1>)[source]¶

Get species in the expression that are not reactants in the reaction

Returns: species in the expression that are not reactants in the reaction
Return type: list of Species

get_products()[source]¶

Get the species produced by the reaction

Returns: product species
Return type: list of Species

get_reactants()[source]¶

Get the species consumed by the reaction

Returns: reactant species
Return type: list of Species

get_species(_Reaction__type=None, **kwargs)[source]¶

Get species

Parameters

__type (types.TypeType or tuple of types.TypeType) – subclass(es) of Model
kwargs (dict of str –> object) – dictionary of attribute name/value pairs to find matching objects

Returns

list of Species

Return type

list

id = <obj_tables.core.SlugAttribute object>[source]

identifiers = <wc_lang.core.IdentifierManyToManyAttribute object>[source]

import_from_sbml(sbml_rxn)[source]¶

Load from SBML reaction

Parameters: sbml (libsbml.Reaction) – SBML reaction

import_relations_from_sbml(sbml_rxn, objs)[source]¶

Load relationships from SBML reaction

Parameters

sbml (libsbml.Reaction) – SBML reaction
objs (dict) – dictionary that maps WC-Lang types to dictionaries that map the ids of WC-Lang objects to WC-Lang objects

model = <obj_tables.core.ManyToOneAttribute object>[source]

name = <obj_tables.core.StringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

participants = <wc_lang.core.ReactionParticipantAttribute object>[source]

rate_units = <obj_tables.sci.units.UnitAttribute object>[source]

references = <obj_tables.core.ManyToManyAttribute object>[source]

reversible = <obj_tables.core.BooleanAttribute object>[source]

submodel = <obj_tables.core.ManyToOneAttribute object>[source]

validate()[source]¶

Check if the reaction is valid

If the submodel is ODE or SSA, check that the reaction has a forward rate law
If the submodel is ODE or SSA and the reaction is reversible, check that the reaction has a backward rate law
Check flux units are not None if flux_bounds.min or flux_bounds.max is defined
Check that flux_bounds.min <= flux_bounds.max
Check that reaction is element and charge balanced

Returns

None if the object is valid,: otherwise return a list of errors in an InvalidObject instance

Return type

InvalidObject or None

class wc_lang.core.ReactionParticipantAttribute(related_name='', verbose_name='', verbose_related_name='', description='')[source]¶

Bases: obj_tables.grammar.ToManyGrammarAttribute, obj_tables.core.ManyToManyAttribute

Reaction participants

class Transformer(objects)[source]¶

Bases: obj_tables.grammar.ToManyGrammarTransformer

Transforms parse trees into a list of instances of core.Model

gbl(*args)[source]¶

gbl_part(*args)[source]¶

gbl_parts(*args)[source]¶

lcl(*args)[source]¶

lcl_part(*args)[source]¶

lcl_parts(*args)[source]¶

start(parts)[source]¶

Collapse return into a list of related model instances

Parameters: *args (list of core.Model) – related model instances
Returns: related model instances
Return type: list of core.Model

get_xlsx_validation(sheet_models=None, doc_metadata_model=None)[source]¶

Get Excel validation

Parameters

sheet_models (list of Model, optional) – models encoded as separate sheets
doc_metadata_model (type) – model whose worksheet contains the document metadata

Returns

validation

Return type

wc_utils.workbook.io.FieldValidation

grammar_path = '/root/project/wc_lang/grammar/reaction_participants.lark'[source]¶

serialize(participants, encoded=None)[source]¶

Serialize related object

Parameters

participants (list of SpeciesCoefficient) – Python representation of reaction participants
encoded (dict, optional) – dictionary of objects that have already been encoded

Returns

simple Python representation

Return type

str

validate(obj, value, tolerance=1e-10)[source]¶

Determine if value is a valid value of the attribute

Parameters

obj (Reaction) – object being validated
value (list of SpeciesCoefficient) – value of attribute to validate
tolerance (float, optional) – error tolerance value, default value is 1E-10

Returns

None if attribute is valid, other return list of errors as an instance of InvalidAttribute

Return type

InvalidAttribute or None

class wc_lang.core.Reference(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model

id[source]¶

unique identifier

Type: str

name[source]¶

name

Type: str

model[source]¶

model

Type: Model

title[source]¶

title

Type: str

author[source]¶

author(s)

Type: str

editor[source]¶

editor(s)

Type: str

year[source]¶

year

Type: int

type[source]¶

type

Type: pronto.Term

publication[source]¶

publication title

Type: str

publisher[source]¶

publisher

Type: str

series[source]¶

series

Type: str

volume[source]¶

volume

Type: str

number[source]¶

number

Type: str

issue[source]¶

issue

Type: str

edition[source]¶

edition

Type: str

chapter[source]¶

chapter

Type: str

pages[source]¶

page range

Type: str

identifiers[source]¶

identifiers

Type: list of Identifier

comments[source]¶

comments

Type: str

Related attributes:

taxon (Taxon): taxon

env (Environment): environment

submodels (list of Submodel): submodels

compartments (list of Compartment): compartments

species_types (list of SpeciesType): species types

species (list of Species): species

distribution_init_concentrations (list of DistributionInitConcentration): distributions of initial concentrations of species at the beginning of each cell cycle

observables (list of Observable): observables

functions (list of Function): functions

reactions (list of Reaction): reactions

rate_laws (list of RateLaw): rate laws

dfba_objs (list of DfbaObjective): dFBA objectives

dfba_obj_species (list of DfbaObjSpecies): dFBA objective species

stop_conditions (list of StopCondition): stop conditions

parameters (list of Parameter): parameters

changes (list of Change): changes

class Meta[source]¶

Bases: obj_tables.core.Meta

attribute_order = ('id', 'name', 'title', 'author', 'editor', 'year', 'type', 'publication', 'publisher', 'series', 'volume', 'number', 'issue', 'edition', 'chapter', 'pages', 'identifiers', 'comments')[source]¶

attributes = {'author': <obj_tables.core.StringAttribute object>, 'chapter': <obj_tables.core.StringAttribute object>, 'comments': <wc_lang.core.CommentAttribute object>, 'edition': <obj_tables.core.StringAttribute object>, 'editor': <obj_tables.core.StringAttribute object>, 'id': <obj_tables.core.SlugAttribute object>, 'identifiers': <wc_lang.core.IdentifierManyToManyAttribute object>, 'issue': <obj_tables.core.StringAttribute object>, 'model': <obj_tables.core.ManyToOneAttribute object>, 'name': <obj_tables.core.StringAttribute object>, 'number': <obj_tables.core.StringAttribute object>, 'pages': <obj_tables.core.StringAttribute object>, 'publication': <obj_tables.core.StringAttribute object>, 'publisher': <obj_tables.core.StringAttribute object>, 'series': <obj_tables.core.StringAttribute object>, 'title': <obj_tables.core.StringAttribute object>, 'type': <obj_tables.sci.onto.OntoTermAttribute object>, 'volume': <obj_tables.core.StringAttribute object>, 'year': <obj_tables.core.PositiveIntegerAttribute object>}[source]¶

child_attrs = {'sbml': (), 'wc_sim': ()}[source]¶

children = {'core_model': ('identifiers',), 'submodel': ('identifiers',)}[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.Reference'>,)[source]¶

local_attributes = {'author': <obj_tables.core.LocalAttribute object>, 'changes': <obj_tables.core.LocalAttribute object>, 'chapter': <obj_tables.core.LocalAttribute object>, 'comments': <obj_tables.core.LocalAttribute object>, 'compartments': <obj_tables.core.LocalAttribute object>, 'conclusions': <obj_tables.core.LocalAttribute object>, 'dfba_obj_reactions': <obj_tables.core.LocalAttribute object>, 'dfba_obj_species': <obj_tables.core.LocalAttribute object>, 'dfba_objs': <obj_tables.core.LocalAttribute object>, 'distribution_init_concentrations': <obj_tables.core.LocalAttribute object>, 'edition': <obj_tables.core.LocalAttribute object>, 'editor': <obj_tables.core.LocalAttribute object>, 'env': <obj_tables.core.LocalAttribute object>, 'functions': <obj_tables.core.LocalAttribute object>, 'id': <obj_tables.core.LocalAttribute object>, 'identifiers': <obj_tables.core.LocalAttribute object>, 'issue': <obj_tables.core.LocalAttribute object>, 'model': <obj_tables.core.LocalAttribute object>, 'name': <obj_tables.core.LocalAttribute object>, 'number': <obj_tables.core.LocalAttribute object>, 'observables': <obj_tables.core.LocalAttribute object>, 'observation_sets': <obj_tables.core.LocalAttribute object>, 'observations': <obj_tables.core.LocalAttribute object>, 'pages': <obj_tables.core.LocalAttribute object>, 'parameters': <obj_tables.core.LocalAttribute object>, 'publication': <obj_tables.core.LocalAttribute object>, 'publisher': <obj_tables.core.LocalAttribute object>, 'rate_laws': <obj_tables.core.LocalAttribute object>, 'reactions': <obj_tables.core.LocalAttribute object>, 'series': <obj_tables.core.LocalAttribute object>, 'species': <obj_tables.core.LocalAttribute object>, 'species_types': <obj_tables.core.LocalAttribute object>, 'stop_conditions': <obj_tables.core.LocalAttribute object>, 'submodels': <obj_tables.core.LocalAttribute object>, 'taxon': <obj_tables.core.LocalAttribute object>, 'title': <obj_tables.core.LocalAttribute object>, 'type': <obj_tables.core.LocalAttribute object>, 'volume': <obj_tables.core.LocalAttribute object>, 'year': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ('id',)[source]¶

primary_attribute = <obj_tables.core.SlugAttribute object>[source]¶

related_attributes = {'changes': <obj_tables.core.ManyToManyAttribute object>, 'compartments': <obj_tables.core.ManyToManyAttribute object>, 'conclusions': <obj_tables.core.ManyToManyAttribute object>, 'dfba_obj_reactions': <obj_tables.core.ManyToManyAttribute object>, 'dfba_obj_species': <obj_tables.core.ManyToManyAttribute object>, 'dfba_objs': <obj_tables.core.ManyToManyAttribute object>, 'distribution_init_concentrations': <obj_tables.core.ManyToManyAttribute object>, 'env': <obj_tables.core.OneToManyAttribute object>, 'functions': <obj_tables.core.ManyToManyAttribute object>, 'observables': <obj_tables.core.ManyToManyAttribute object>, 'observation_sets': <obj_tables.core.ManyToManyAttribute object>, 'observations': <obj_tables.core.ManyToManyAttribute object>, 'parameters': <obj_tables.core.ManyToManyAttribute object>, 'rate_laws': <obj_tables.core.ManyToManyAttribute object>, 'reactions': <obj_tables.core.ManyToManyAttribute object>, 'species': <obj_tables.core.ManyToManyAttribute object>, 'species_types': <obj_tables.core.ManyToManyAttribute object>, 'stop_conditions': <obj_tables.core.ManyToManyAttribute object>, 'submodels': <obj_tables.core.ManyToManyAttribute object>, 'taxon': <obj_tables.core.OneToManyAttribute object>}[source]¶

unique_together = ()[source]¶

verbose_name = 'Reference'[source]¶

verbose_name_plural = 'References'[source]¶

author = <obj_tables.core.StringAttribute object>[source]

chapter = <obj_tables.core.StringAttribute object>[source]

comments = <wc_lang.core.CommentAttribute object>[source]

edition = <obj_tables.core.StringAttribute object>[source]

editor = <obj_tables.core.StringAttribute object>[source]

id = <obj_tables.core.SlugAttribute object>[source]

identifiers = <wc_lang.core.IdentifierManyToManyAttribute object>[source]

issue = <obj_tables.core.StringAttribute object>[source]

model = <obj_tables.core.ManyToOneAttribute object>[source]

name = <obj_tables.core.StringAttribute object>[source]

number = <obj_tables.core.StringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

pages = <obj_tables.core.StringAttribute object>[source]

publication = <obj_tables.core.StringAttribute object>[source]

publisher = <obj_tables.core.StringAttribute object>[source]

series = <obj_tables.core.StringAttribute object>[source]

title = <obj_tables.core.StringAttribute object>[source]

type = <obj_tables.sci.onto.OntoTermAttribute object>[source]

volume = <obj_tables.core.StringAttribute object>[source]

year = <obj_tables.core.PositiveIntegerAttribute object>[source]

class wc_lang.core.Species(tuple of species type, compartment)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

id[source]¶

identifier equal to {species_type.id}[{compartment.id}]

Type: str

name[source]¶

name

Type: str

model[source]¶

model

Type: Model

species_type[source]¶

species type

Type: SpeciesType

compartment[source]¶

compartment

Type: Compartment

units[source]¶

units of counts

Type: unit_registry.Unit

identifiers[source]¶

identifiers

Type: list of Identifier

evidence[source]¶

observation that supports/disputes a conclusion

Type: list of Evidence

conclusions[source]¶

conclusions

Type: list of Conclusion

comments[source]¶

comments

Type: str

references[source]¶

references

Type: list of Reference

Related attributes:

distribution_init_concentration (DistributionInitConcentration): distribution of initial concentration

species_coefficients (list of SpeciesCoefficient): participations in reactions and observables

rate_law_expressions (list of RateLawExpression): rate law expressions

observable_expressions (list of ObservableExpression): observable expressions

stop_condition_expressions (list of StopConditionExpression): stop condition expressions

function_expressions (list of FunctionExpression): function expressions

dfba_obj_species (list of DfbaObjSpecies): dFBA objective species

class Meta[source]¶

Bases: obj_tables.core.Meta, obj_tables.math.expression.ExpressionDynamicTermMeta

attribute_order = ('id', 'name', 'species_type', 'compartment', 'units', 'identifiers', 'evidence', 'conclusions', 'comments', 'references')[source]¶

attributes = {'comments': <wc_lang.core.CommentAttribute object>, 'compartment': <obj_tables.core.ManyToOneAttribute object>, 'conclusions': <obj_tables.core.ManyToManyAttribute object>, 'evidence': <wc_lang.core.EvidenceManyToManyAttribute object>, 'id': <obj_tables.core.StringAttribute object>, 'identifiers': <wc_lang.core.IdentifierManyToManyAttribute object>, 'model': <obj_tables.core.ManyToOneAttribute object>, 'name': <obj_tables.core.StringAttribute object>, 'references': <obj_tables.core.ManyToManyAttribute object>, 'species_type': <obj_tables.core.ManyToOneAttribute object>, 'units': <obj_tables.sci.units.UnitAttribute object>}[source]¶

child_attrs = {'sbml': ('id', 'name', 'model', 'species_type', 'compartment', 'units', 'identifiers', 'comments'), 'wc_sim': ('id', 'model', 'species_type', 'compartment', 'units')}[source]¶

children = {'core_model': ('species_type', 'compartment', 'distribution_init_concentration', 'identifiers', 'evidence', 'conclusions', 'references'), 'submodel': ('species_type', 'compartment', 'distribution_init_concentration', 'identifiers', 'evidence', 'conclusions', 'references')}[source]¶

expression_term_token_pattern = (1, 9, 1, 10)[source]¶

expression_term_units = 'units'[source]¶

frozen_columns = 1[source]¶

indexed_attrs_tuples = (('compartment', 'species_type'),)[source]¶

inheritance = (<class 'wc_lang.core.Species'>,)[source]¶

local_attributes = {'comments': <obj_tables.core.LocalAttribute object>, 'compartment': <obj_tables.core.LocalAttribute object>, 'conclusions': <obj_tables.core.LocalAttribute object>, 'dfba_obj_species': <obj_tables.core.LocalAttribute object>, 'distribution_init_concentration': <obj_tables.core.LocalAttribute object>, 'evidence': <obj_tables.core.LocalAttribute object>, 'function_expressions': <obj_tables.core.LocalAttribute object>, 'id': <obj_tables.core.LocalAttribute object>, 'identifiers': <obj_tables.core.LocalAttribute object>, 'model': <obj_tables.core.LocalAttribute object>, 'name': <obj_tables.core.LocalAttribute object>, 'observable_expressions': <obj_tables.core.LocalAttribute object>, 'rate_law_expressions': <obj_tables.core.LocalAttribute object>, 'references': <obj_tables.core.LocalAttribute object>, 'species_coefficients': <obj_tables.core.LocalAttribute object>, 'species_type': <obj_tables.core.LocalAttribute object>, 'stop_condition_expressions': <obj_tables.core.LocalAttribute object>, 'units': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ('id',)[source]¶

primary_attribute = <obj_tables.core.StringAttribute object>[source]¶

related_attributes = {'dfba_obj_species': <obj_tables.core.ManyToOneAttribute object>, 'distribution_init_concentration': <obj_tables.core.OneToOneAttribute object>, 'function_expressions': <obj_tables.core.ManyToManyAttribute object>, 'observable_expressions': <obj_tables.core.ManyToManyAttribute object>, 'rate_law_expressions': <obj_tables.core.ManyToManyAttribute object>, 'species_coefficients': <obj_tables.core.ManyToOneAttribute object>, 'stop_condition_expressions': <obj_tables.core.ManyToManyAttribute object>}[source]¶

unique_together = ()[source]¶

verbose_name = 'Species'[source]¶

verbose_name_plural = 'Species'[source]¶

comments = <wc_lang.core.CommentAttribute object>[source]

compartment = <obj_tables.core.ManyToOneAttribute object>[source]

conclusions = <obj_tables.core.ManyToManyAttribute object>[source]

evidence = <wc_lang.core.EvidenceManyToManyAttribute object>[source]

export_relations_to_sbml(sbml_model, sbml)[source]¶

Add relationships to/from object to SBML species.

Parameters

sbml_model (libsbml.Model) – SBML model
sbml (libsbml.Species) – SBML species

export_to_sbml(sbml_model)[source]¶

Add this species to a SBML model.

Parameters: sbml_model (libsbml.Model) – SBML model
Returns: SBML species
Return type: libsbml.Species

gen_id()[source]¶

Generate identifier

Returns: identifier
Return type: str

static get(ids, species_iterator)[source]¶

Find some Species instances

Parameters

ids (Iterator of str) – an iterator over some species identifiers
species_iterator (Iterator) – an iterator over some species

Returns

each element of the list corresponds to an element: of ids and contains either a Species with id() equal to the element in ids, or None indicating that species_iterator does not contain a matching Species

Return type

list of Species or None

id = <obj_tables.core.StringAttribute object>[source]

identifiers = <wc_lang.core.IdentifierManyToManyAttribute object>[source]

import_from_sbml(sbml)[source]¶

Load from SBML species

Parameters: sbml (libsbml.Species) – SBML species

import_relations_from_sbml(sbml, objs)[source]¶

Load relationships from SBML species

Parameters

sbml (libsbml.Species) – SBML species
objs (dict) – dictionary that maps WC-Lang types to dictionaries that map the ids of WC-Lang objects to WC-Lang objects

model = <obj_tables.core.ManyToOneAttribute object>[source]

name = <obj_tables.core.StringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

classmethod parse_id(id)[source]¶

Parameters: id (str) – identifier
Returns: species type id str: compartment id
Return type: str
Raises: ValueError – if the id does not have the format {species.id}[{compartment.id}]

references = <obj_tables.core.ManyToManyAttribute object>[source]

species_type = <obj_tables.core.ManyToOneAttribute object>[source]

units = <obj_tables.sci.units.UnitAttribute object>[source]

validate()[source]¶

Check that the species is valid

Check if the identifier is equal to {species_type.id}[{compartment.id}]

Returns

None if the object is valid,: otherwise return a list of errors as an instance of InvalidObject

Return type

InvalidObject or None

class wc_lang.core.SpeciesCoefficient(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

A tuple of a species and a coefficient

species[source]¶

species

Type: Species

coefficient[source]¶

coefficient

Type: float

Related attributes:

reaction (Reaction): reaction

observables (Observable): observables

class Meta[source]¶

Bases: obj_tables.core.Meta

attribute_order = ('species', 'coefficient')[source]¶

attributes = {'coefficient': <obj_tables.core.FloatAttribute object>, 'species': <obj_tables.core.ManyToOneAttribute object>}[source]¶

child_attrs = {'sbml': ('species', 'coefficient'), 'wc_sim': ('species', 'coefficient')}[source]¶

children = {'core_model': ('species',), 'submodel': ('species',)}[source]¶

frozen_columns = 1[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.SpeciesCoefficient'>,)[source]¶

local_attributes = {'coefficient': <obj_tables.core.LocalAttribute object>, 'reactions': <obj_tables.core.LocalAttribute object>, 'species': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ('species', 'coefficient')[source]¶

primary_attribute = None[source]¶

related_attributes = {'reactions': <wc_lang.core.ReactionParticipantAttribute object>}[source]¶

table_format = 3[source]¶

unique_together = (('coefficient', 'species'),)[source]¶

verbose_name = 'Species coefficient'[source]¶

verbose_name_plural = 'Species coefficients'[source]¶

coefficient = <obj_tables.core.FloatAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

serialize(show_compartment=True, show_coefficient_sign=True)[source]¶

Serialize related object

Parameters

show_compartment (bool, optional) – if true, show compartment
show_coefficient_sign (bool, optional) – if true, show coefficient sign

Returns

simple Python representation

Return type

str

species = <obj_tables.core.ManyToOneAttribute object>[source]

class wc_lang.core.SpeciesType(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

Species type

id[source]¶

unique identifier

Type: str

name[source]¶

name

Type: str

model[source]¶

model

Type: Model

structure[source]¶

structure (InChI for metabolites; sequence for DNA, RNA, proteins)

Type: ChemicalStructure

type[source]¶

type

Type: pronto.term.Term

identifiers[source]¶

identifiers

Type: list of Identifier

evidence[source]¶

observation that supports/disputes a conclusion

Type: list of Evidence

conclusions[source]¶

conclusions

Type: list of Conclusion

comments[source]¶

comments

Type: str

references[source]¶

references

Type: list of Reference

Related attributes:

species (list of Species): species

class Meta[source]¶

Bases: obj_tables.core.Meta

attribute_order = ('id', 'name', 'structure', 'type', 'identifiers', 'evidence', 'conclusions', 'comments', 'references')[source]¶

attributes = {'comments': <wc_lang.core.CommentAttribute object>, 'conclusions': <obj_tables.core.ManyToManyAttribute object>, 'evidence': <wc_lang.core.EvidenceManyToManyAttribute object>, 'id': <obj_tables.core.SlugAttribute object>, 'identifiers': <wc_lang.core.IdentifierManyToManyAttribute object>, 'model': <obj_tables.core.ManyToOneAttribute object>, 'name': <obj_tables.core.StringAttribute object>, 'references': <obj_tables.core.ManyToManyAttribute object>, 'structure': <obj_tables.core.ManyToOneAttribute object>, 'type': <obj_tables.sci.onto.OntoTermAttribute object>}[source]¶

child_attrs = {'sbml': ('id', 'name', 'model', 'structure', 'type', 'identifiers', 'comments'), 'wc_sim': ('id', 'model', 'structure')}[source]¶

children = {'core_model': ('structure', 'species', 'identifiers', 'evidence', 'conclusions', 'references'), 'submodel': ('structure', 'identifiers', 'evidence', 'conclusions', 'references')}[source]¶

indexed_attrs_tuples = (('id',),)[source]¶

inheritance = (<class 'wc_lang.core.SpeciesType'>,)[source]¶

local_attributes = {'comments': <obj_tables.core.LocalAttribute object>, 'conclusions': <obj_tables.core.LocalAttribute object>, 'evidence': <obj_tables.core.LocalAttribute object>, 'id': <obj_tables.core.LocalAttribute object>, 'identifiers': <obj_tables.core.LocalAttribute object>, 'model': <obj_tables.core.LocalAttribute object>, 'name': <obj_tables.core.LocalAttribute object>, 'references': <obj_tables.core.LocalAttribute object>, 'species': <obj_tables.core.LocalAttribute object>, 'structure': <obj_tables.core.LocalAttribute object>, 'type': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ('id',)[source]¶

primary_attribute = <obj_tables.core.SlugAttribute object>[source]¶

related_attributes = {'species': <obj_tables.core.ManyToOneAttribute object>}[source]¶

unique_together = ()[source]¶

verbose_name = 'Species type'[source]¶

verbose_name_plural = 'Species types'[source]¶

comments = <wc_lang.core.CommentAttribute object>[source]

conclusions = <obj_tables.core.ManyToManyAttribute object>[source]

evidence = <wc_lang.core.EvidenceManyToManyAttribute object>[source]

id = <obj_tables.core.SlugAttribute object>[source]

identifiers = <wc_lang.core.IdentifierManyToManyAttribute object>[source]

model = <obj_tables.core.ManyToOneAttribute object>[source]

name = <obj_tables.core.StringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

references = <obj_tables.core.ManyToManyAttribute object>[source]

structure = <obj_tables.core.ManyToOneAttribute object>[source]

type = <obj_tables.sci.onto.OntoTermAttribute object>[source]

class wc_lang.core.StopCondition(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model

StopCondition: Simulation of a model terminates when one of its stop conditions is true.

A Boolean expression of Functions, Observbles, Parameters and Python functions. Stop conditions are optional.

id[source]¶

unique id

Type: str

name[source]¶

name

Type: str

model[source]¶

model

Type: Model

expression[source]¶

mathematical expression for a StopCondition

Type: StopConditionExpression

units[source]¶

units, which must be dimensionless

Type: unit_registry.Unit

identifiers[source]¶

identifiers

Type: list of Identifier

evidence[source]¶

observation that supports/disputes a conclusion

Type: list of Evidence

conclusions[source]¶

conclusions

Type: list of Conclusion

comments[source]¶

comments

Type: str

references[source]¶

references

Type: list of Reference

Related attributes:

expressions (Expressions): expressions

class Meta[source]¶

Bases: obj_tables.core.Meta, obj_tables.math.expression.ExpressionExpressionTermMeta

attribute_order = ('id', 'name', 'expression', 'units', 'identifiers', 'evidence', 'conclusions', 'comments', 'references')[source]¶

attributes = {'comments': <wc_lang.core.CommentAttribute object>, 'conclusions': <obj_tables.core.ManyToManyAttribute object>, 'evidence': <wc_lang.core.EvidenceManyToManyAttribute object>, 'expression': <obj_tables.math.expression.OneToOneExpressionAttribute object>, 'id': <obj_tables.core.SlugAttribute object>, 'identifiers': <wc_lang.core.IdentifierManyToManyAttribute object>, 'model': <obj_tables.core.ManyToOneAttribute object>, 'name': <obj_tables.core.StringAttribute object>, 'references': <obj_tables.core.ManyToManyAttribute object>, 'units': <obj_tables.sci.units.UnitAttribute object>}[source]¶

child_attrs = {'sbml': (), 'wc_sim': ('id', 'model', 'expression', 'units')}[source]¶

children = {'core_model': ('expression', 'identifiers', 'evidence', 'conclusions', 'references'), 'submodel': ('expression', 'identifiers', 'evidence', 'conclusions', 'references')}[source]¶

expression_term_model[source]¶: alias of StopConditionExpression

expression_term_units = 'units'[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.StopCondition'>,)[source]¶

local_attributes = {'comments': <obj_tables.core.LocalAttribute object>, 'conclusions': <obj_tables.core.LocalAttribute object>, 'evidence': <obj_tables.core.LocalAttribute object>, 'expression': <obj_tables.core.LocalAttribute object>, 'id': <obj_tables.core.LocalAttribute object>, 'identifiers': <obj_tables.core.LocalAttribute object>, 'model': <obj_tables.core.LocalAttribute object>, 'name': <obj_tables.core.LocalAttribute object>, 'references': <obj_tables.core.LocalAttribute object>, 'units': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ('id',)[source]¶

primary_attribute = <obj_tables.core.SlugAttribute object>[source]¶

related_attributes = {}[source]¶

unique_together = ()[source]¶

verbose_name = 'Stop condition'[source]¶

verbose_name_plural = 'Stop conditions'[source]¶

comments = <wc_lang.core.CommentAttribute object>[source]

conclusions = <obj_tables.core.ManyToManyAttribute object>[source]

evidence = <wc_lang.core.EvidenceManyToManyAttribute object>[source]

expression = <obj_tables.math.expression.OneToOneExpressionAttribute object>[source]

id = <obj_tables.core.SlugAttribute object>[source]

identifiers = <wc_lang.core.IdentifierManyToManyAttribute object>[source]

model = <obj_tables.core.ManyToOneAttribute object>[source]

name = <obj_tables.core.StringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

references = <obj_tables.core.ManyToManyAttribute object>[source]

units = <obj_tables.sci.units.UnitAttribute object>[source]

validate()[source]¶

Check that the stop condition is valid

Check that expression has units units

Returns

None if the object is valid,: otherwise return a list of errors as an instance of InvalidObject

Return type

InvalidObject or None

class wc_lang.core.StopConditionExpression(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, obj_tables.math.expression.Expression

A mathematical expression of Functions, Observables, Parameters and Python functions

The expression used by a StopCondition.

expression[source]¶

mathematical expression for a StopCondition

Type: str

_parsed_expression[source]¶

an analyzed expression; not an obj_tables.Model

Type: ParsedExpression

species[source]¶

Species used by this stop condition expression

Type: list of Species

observables[source]¶

Observables used by this stop condition expression

Type: list of Observable

parameters[source]¶

Parameters used by this stop condition expression

Type: list of Parameter

functions[source]¶

Functions used by this stop condition expression

Type: list of Function

compartments[source]¶

Compartments used by this stop condition expression

Type: list of Compartment

Related attributes:

stop_condition (StopCondition): stop condition

class Meta[source]¶

Bases: obj_tables.core.Meta, obj_tables.math.expression.Meta

attribute_order = ()[source]¶

attributes = {'compartments': <obj_tables.core.ManyToManyAttribute object>, 'expression': <obj_tables.core.LongStringAttribute object>, 'functions': <obj_tables.core.ManyToManyAttribute object>, 'observables': <obj_tables.core.ManyToManyAttribute object>, 'parameters': <obj_tables.core.ManyToManyAttribute object>, 'species': <obj_tables.core.ManyToManyAttribute object>}[source]¶

child_attrs = {'sbml': (), 'wc_sim': ('expression', 'parameters', 'species', 'observables', 'functions', 'compartments')}[source]¶

children = {'core_model': ('parameters', 'species', 'observables', 'functions', 'compartments'), 'submodel': ('parameters', 'species', 'observables', 'functions', 'compartments')}[source]¶

expression_term_models = ('Parameter', 'Species', 'Observable', 'Function', 'Compartment')[source]¶

expression_type[source]¶: alias of builtins.bool

expression_unit_registry = <pint.registry.UnitRegistry object>[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.StopConditionExpression'>,)[source]¶

local_attributes = {'compartments': <obj_tables.core.LocalAttribute object>, 'expression': <obj_tables.core.LocalAttribute object>, 'functions': <obj_tables.core.LocalAttribute object>, 'observables': <obj_tables.core.LocalAttribute object>, 'parameters': <obj_tables.core.LocalAttribute object>, 'species': <obj_tables.core.LocalAttribute object>, 'stop_condition': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ('expression',)[source]¶

primary_attribute = <obj_tables.core.LongStringAttribute object>[source]¶

related_attributes = {'stop_condition': <obj_tables.math.expression.OneToOneExpressionAttribute object>}[source]¶

table_format = 3[source]¶

unique_together = ()[source]¶

verbose_name = 'Stop condition expression'[source]¶

verbose_name_plural = 'Stop condition expressions'[source]¶

compartments = <obj_tables.core.ManyToManyAttribute object>[source]

classmethod deserialize(value, objects)[source]¶

Deserialize value

Parameters

value (str) – String representation
objects (dict) – dictionary of objects, grouped by model

Returns

tuple of: cleaned value and cleaning error

Return type

tuple of StopConditionExpression, InvalidAttribute or None

expression = <obj_tables.core.LongStringAttribute object>[source]

functions = <obj_tables.core.ManyToManyAttribute object>[source]

merge_attrs(other, other_objs_in_self, self_objs_in_other)[source]¶

Merge attributes of two objects

Parameters

other (obj_tables.Model) – other model
other_objs_in_self (dict) – dictionary that maps instances of objects in another model to objects in a model
self_objs_in_other (dict) – dictionary that maps instances of objects in a model to objects in another model

objects = <obj_tables.core.Manager object>[source]¶

observables = <obj_tables.core.ManyToManyAttribute object>[source]

parameters = <obj_tables.core.ManyToManyAttribute object>[source]

serialize()[source]¶

Generate string representation

Returns: string representation
Return type: str

species = <obj_tables.core.ManyToManyAttribute object>[source]

validate()[source]¶

Check that the stop condition is valid

Check that the expression is a Boolean function

Returns

None if the object is valid,: otherwise return a list of errors as an instance of InvalidObject

Return type

InvalidObject or None

class wc_lang.core.Submodel(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

id[source]¶

unique identifier

Type: str

name[source]¶

name

Type: str

model[source]¶

model

Type: Model

framework[source]¶

modeling integration framework (e.g. SSA, ODE or dFBA)

Type: pronto.term.Term

identifiers[source]¶

identifiers

Type: list of Identifier

evidence[source]¶

observation that supports/disputes a conclusion

Type: list of Evidence

conclusions[source]¶

conclusions

Type: list of Conclusion

comments[source]¶

comments

Type: str

references[source]¶

references

Type: list of Reference

Related attributes:

reactions (list of Reaction): reactions

dfba_obj (DfbaObjective): objective function for a dFBA submodel; if not initialized, then dfba_obj_reactions is used as the objective function

dfba_obj_reactions (list of DfbaObjReaction): the growth reaction for a dFBA submodel

changes (list of Change): changes

class Meta[source]¶

Bases: obj_tables.core.Meta

attribute_order = ('id', 'name', 'framework', 'identifiers', 'evidence', 'conclusions', 'comments', 'references')[source]¶

attributes = {'comments': <wc_lang.core.CommentAttribute object>, 'conclusions': <obj_tables.core.ManyToManyAttribute object>, 'evidence': <wc_lang.core.EvidenceManyToManyAttribute object>, 'framework': <obj_tables.sci.onto.OntoTermAttribute object>, 'id': <obj_tables.core.SlugAttribute object>, 'identifiers': <wc_lang.core.IdentifierManyToManyAttribute object>, 'model': <obj_tables.core.ManyToOneAttribute object>, 'name': <obj_tables.core.StringAttribute object>, 'references': <obj_tables.core.ManyToManyAttribute object>}[source]¶

child_attrs = {'sbml': ('id', 'name', 'model', 'framework', 'identifiers', 'comments'), 'wc_sim': ('id', 'model', 'framework')}[source]¶

children = {'submodel': ('model', 'reactions', 'dfba_obj', 'dfba_obj_reactions', 'identifiers', 'evidence', 'conclusions', 'references', 'changes')}[source]¶

indexed_attrs_tuples = (('id',),)[source]¶

inheritance = (<class 'wc_lang.core.Submodel'>,)[source]¶

local_attributes = {'changes': <obj_tables.core.LocalAttribute object>, 'comments': <obj_tables.core.LocalAttribute object>, 'conclusions': <obj_tables.core.LocalAttribute object>, 'dfba_obj': <obj_tables.core.LocalAttribute object>, 'dfba_obj_reactions': <obj_tables.core.LocalAttribute object>, 'evidence': <obj_tables.core.LocalAttribute object>, 'framework': <obj_tables.core.LocalAttribute object>, 'id': <obj_tables.core.LocalAttribute object>, 'identifiers': <obj_tables.core.LocalAttribute object>, 'model': <obj_tables.core.LocalAttribute object>, 'name': <obj_tables.core.LocalAttribute object>, 'reactions': <obj_tables.core.LocalAttribute object>, 'references': <obj_tables.core.LocalAttribute object>}[source]¶

merge = 2[source]¶

ordering = ('id',)[source]¶

primary_attribute = <obj_tables.core.SlugAttribute object>[source]¶

related_attributes = {'changes': <obj_tables.core.ManyToOneAttribute object>, 'dfba_obj': <obj_tables.core.OneToOneAttribute object>, 'dfba_obj_reactions': <obj_tables.core.ManyToOneAttribute object>, 'reactions': <obj_tables.core.ManyToOneAttribute object>}[source]¶

unique_together = ()[source]¶

verbose_name = 'Submodel'[source]¶

verbose_name_plural = 'Submodels'[source]¶

comments = <wc_lang.core.CommentAttribute object>[source]

conclusions = <obj_tables.core.ManyToManyAttribute object>[source]

evidence = <wc_lang.core.EvidenceManyToManyAttribute object>[source]

export_relations_to_sbml(sbml_model, sbml)[source]¶

Add relationships to/from object to SBML model.

Parameters

sbml_model (libsbml.Model) – SBML model
sbml (libsbml.Model) – SBML model

export_to_sbml(sbml_model)[source]¶

Add metadata about the submodel to a SBML model.

Parameters: sbml_model (libsbml.Model) – SBML model
Returns: SBML model
Return type: libsbml.Model

framework = <obj_tables.sci.onto.OntoTermAttribute object>[source]

get_children(kind=None, _Submodel__type=None, recursive=True, _Submodel__include_stop_conditions=True, **kwargs)[source]¶

Get a kind of children.

If kind is None, children are defined to be the values of the related attributes defined in each class.

Parameters

kind (str, optional) – kind of children to get
__type (types.TypeType or tuple of types.TypeType) – subclass(es) of Model
recursive (bool, optional) – if True, get children recursively
kwargs (dict of str –> object) – dictionary of attribute name/value pairs

Returns

children

Return type

list of Model

get_immediate_children(kind=None, _Submodel__type=None, _Submodel__include_stop_conditions=True, **kwargs)[source]¶

Get a kind of children.

If kind is None, children are defined to be the values of the related attributes defined in each class.

Parameters

kind (str, optional) – kind of children to get
__type (types.TypeType or tuple of types.TypeType) – subclass(es) of Model
kwargs (dict of str –> object) – dictionary of attribute name/value pairs

Returns

children

Return type

list of Model

id = <obj_tables.core.SlugAttribute object>[source]

identifiers = <wc_lang.core.IdentifierManyToManyAttribute object>[source]

import_from_sbml(sbml)[source]¶

Load from SBML model

Parameters: sbml (libsbml.Model) – SBML model

import_relations_from_sbml(sbml, objs)[source]¶

Load relationships from SBML model

Parameters

sbml (libsbml.Model) – SBML model
objs (dict) – dictionary that maps WC-Lang types to dictionaries that map the ids of WC-Lang objects to WC-Lang objects

model = <obj_tables.core.ManyToOneAttribute object>[source]

name = <obj_tables.core.StringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

references = <obj_tables.core.ManyToManyAttribute object>[source]

validate()[source]¶

Determine if the submodel is valid

dFBA submodel has an objective

Returns

None if the object is valid,: otherwise return a list of errors as an instance of InvalidObject

Return type

InvalidObject or None

class wc_lang.core.SubmodelsToModelRelatedManager(object, attribute)[source]¶

Bases: obj_tables.core.ManyToOneRelatedManager

Submodels to model related manager

gen_models()[source]¶

Generate separate models for each submodel, as well as a “core” model which contains the model integration framework (compartments, species types, species, observables, functions, stop conditions, etc.) and all model objects that are not associated with at least 1 submodel.

Returns

model with objects that (a) form the model integration framework or (b) are: not associated with any submodel

list of Model: one model for each submodel

Return type

Model

class wc_lang.core.Taxon(_comments=None, **kwargs)[source]¶

Bases: obj_tables.core.Model, wc_lang.sbml.util.SbmlModelMixin

Biological taxon (e.g. family, genus, species, strain, etc.)

id[source]¶

unique identifier equal to ‘taxon’

Type: str

name[source]¶

name

Type: str

model[source]¶

model

Type: Model

rank[source]¶

rank

Type: TaxonRank

identifiers[source]¶

identifiers

Type: list of Identifier

comments[source]¶

comments

Type: str

references[source]¶

references

Type: list of Reference

class Meta[source]¶

Bases: obj_tables.core.Meta

attribute_order = ('id', 'name', 'rank', 'identifiers', 'comments', 'references')[source]¶

attributes = {'comments': <wc_lang.core.CommentAttribute object>, 'id': <obj_tables.core.RegexAttribute object>, 'identifiers': <wc_lang.core.IdentifierOneToManyAttribute object>, 'model': <obj_tables.core.OneToOneAttribute object>, 'name': <obj_tables.core.StringAttribute object>, 'rank': <obj_tables.core.EnumAttribute object>, 'references': <obj_tables.core.OneToManyAttribute object>}[source]¶

child_attrs = {'sbml': ('id', 'name', 'model', 'rank', 'identifiers', 'comments'), 'wc_sim': ()}[source]¶

children = {'core_model': ('identifiers', 'references'), 'submodel': ('identifiers', 'references')}[source]¶

indexed_attrs_tuples = ()[source]¶

inheritance = (<class 'wc_lang.core.Taxon'>,)[source]¶

local_attributes = {'comments': <obj_tables.core.LocalAttribute object>, 'id': <obj_tables.core.LocalAttribute object>, 'identifiers': <obj_tables.core.LocalAttribute object>, 'model': <obj_tables.core.LocalAttribute object>, 'name': <obj_tables.core.LocalAttribute object>, 'rank': <obj_tables.core.LocalAttribute object>, 'references': <obj_tables.core.LocalAttribute object>}[source]¶

ordering = ('id',)[source]¶

primary_attribute = <obj_tables.core.RegexAttribute object>[source]¶

related_attributes = {}[source]¶

table_format = 2[source]¶

unique_together = ()[source]¶

verbose_name = 'Taxon'[source]¶

verbose_name_plural = 'Taxons'[source]¶

comments = <wc_lang.core.CommentAttribute object>[source]

id = <obj_tables.core.RegexAttribute object>[source]

identifiers = <wc_lang.core.IdentifierOneToManyAttribute object>[source]

model = <obj_tables.core.OneToOneAttribute object>[source]

name = <obj_tables.core.StringAttribute object>[source]

objects = <obj_tables.core.Manager object>[source]¶

rank = <obj_tables.core.EnumAttribute object>[source]

references = <obj_tables.core.OneToManyAttribute object>[source]

class wc_lang.core.TaxonRank[source]¶

Bases: int, enum.Enum

Taxonomic ranks

classis = 4[source]¶

domain = 1[source]¶

family = 6[source]¶

genus = 8[source]¶

kingdom = 2[source]¶

order = 5[source]¶

phylum = 3[source]¶

species = 9[source]¶

tribe = 7[source]¶

variety = 10[source]¶

class wc_lang.core.TaxonRankMeta[source]¶

Bases: wc_utils.util.enumerate.CaseInsensitiveEnumMeta

__getattr__(name)[source]¶

Get value by name

Parameters: name (str) – attribute name
Returns: taxonomic rank
Return type: TaxonRank

__getitem__(name)[source]¶

Get value by name

Parameters: name (str) – attribute name
Returns: taxonomic rank
Return type: TaxonRank

class wc_lang.core.Validator[source]¶

Bases: obj_tables.core.Validator

run(model, get_related=True)[source]¶

Validate a model and return its errors

Parameters

model (Model) – model
get_related (bool, optional) – if true, get all related objects

Returns

list of invalid objects/models and their errors

Return type

InvalidObjectSet or None

exception wc_lang.core.WcLangWarning[source]¶

Bases: UserWarning

WC-Lang warning

4.1.6. wc_lang.io module¶

Reading and writing models to/from files.

Supported file types:

Comma separated values (.csv)
Excel (.xlsx)
Tab separated values (.tsv)

Author: Jonathan Karr <karr@mssm.edu>
Author: Arthur Goldberg <Arthur.Goldberg@mssm.edu>
Date: 2016-12-05
License: MIT

class wc_lang.io.Reader[source]¶

Bases: obj_tables.io.Reader

Read model from file(s)

MODELS = (<class 'wc_lang.core.Model'>, <class 'wc_lang.core.Taxon'>, <class 'wc_lang.core.Environment'>, <class 'wc_lang.core.Submodel'>, <class 'wc_lang.core.Compartment'>, <class 'wc_lang.core.SpeciesType'>, <class 'wc_lang.core.Species'>, <class 'wc_lang.core.DistributionInitConcentration'>, <class 'wc_lang.core.Observable'>, <class 'wc_lang.core.Function'>, <class 'wc_lang.core.Reaction'>, <class 'wc_lang.core.RateLaw'>, <class 'wc_lang.core.DfbaObjective'>, <class 'wc_lang.core.DfbaObjReaction'>, <class 'wc_lang.core.DfbaObjSpecies'>, <class 'wc_lang.core.Parameter'>, <class 'wc_lang.core.StopCondition'>, <class 'wc_lang.core.Observation'>, <class 'wc_lang.core.ObservationSet'>, <class 'wc_lang.core.Conclusion'>, <class 'wc_lang.core.Reference'>, <class 'wc_lang.core.Author'>, <class 'wc_lang.core.Change'>)[source]¶

run(path, models=None, ignore_missing_models=None, ignore_extra_models=None, ignore_sheet_order=None, include_all_attributes=False, ignore_missing_attributes=None, ignore_extra_attributes=None, ignore_attribute_order=None, validate=None)[source]¶

Read a list of model objects from file(s) and, optionally, validate them

Parameters

path (str) – path to file(s)
models (types.TypeType or list of types.TypeType, optional) – type of object to read or list of types of objects to read
ignore_missing_models (bool, optional) – if False, report an error if a worksheet/ file is missing for one or more models
ignore_extra_models (bool, optional) – if True and all models are found, ignore other worksheets or files
ignore_sheet_order (bool, optional) – if True, do not require the sheets to be provided in the canonical order
include_all_attributes (bool, optional) – if True, export all attributes including those not explictly included in Model.Meta.attribute_order
ignore_missing_attributes (bool, optional) – if False, report an error if a worksheet/file doesn’t contain all of attributes in a model in models
ignore_extra_attributes (bool, optional) – if True, do not report errors if attributes in the data are not in the model
ignore_attribute_order (bool) – if True, do not require the attributes to be provided in the canonical order
validate (bool, optional) – if True, validate the data

Returns

model objects grouped by obj_tables.Model class

Return type

dict

Raises

ValueError – if the file defines zero or multiple models or the model defined in the file(s) is invalid

class wc_lang.io.Writer[source]¶

Bases: obj_tables.io.Writer

Write model to file(s)

MODELS = (<class 'wc_lang.core.Model'>, <class 'wc_lang.core.Taxon'>, <class 'wc_lang.core.Environment'>, <class 'wc_lang.core.Submodel'>, <class 'wc_lang.core.Compartment'>, <class 'wc_lang.core.SpeciesType'>, <class 'wc_lang.core.Species'>, <class 'wc_lang.core.DistributionInitConcentration'>, <class 'wc_lang.core.Observable'>, <class 'wc_lang.core.Function'>, <class 'wc_lang.core.Reaction'>, <class 'wc_lang.core.RateLaw'>, <class 'wc_lang.core.DfbaObjective'>, <class 'wc_lang.core.DfbaObjReaction'>, <class 'wc_lang.core.DfbaObjSpecies'>, <class 'wc_lang.core.Parameter'>, <class 'wc_lang.core.StopCondition'>, <class 'wc_lang.core.Observation'>, <class 'wc_lang.core.ObservationSet'>, <class 'wc_lang.core.Conclusion'>, <class 'wc_lang.core.Reference'>, <class 'wc_lang.core.Author'>, <class 'wc_lang.core.Change'>)[source]¶

run(path, model, models=None, get_related=True, include_all_attributes=False, validate=None, title=None, description=None, keywords=None, version=None, language=None, creator=None, write_schema=False, write_toc=True, extra_entries=0, data_repo_metadata=False, schema_package=None, protected=True)[source]¶

Write a list of model classes to an Excel file, with one worksheet for each model, or to: a set of .csv or .tsv files, with one file for each model.

Parameters

path (str) – path to write file(s)
model (type) – a wc_lang Model that’s a subclass of obj_tables.Model
models (list of Model, optional) – models in the order that they should appear as worksheets; all models which are not in models will follow in alphabetical order
get_related (bool, optional) – if True, write object and all related objects
include_all_attributes (bool, optional) – if True, export all attributes including those not explictly included in Model.Meta.attribute_order
validate (bool, optional) – if True, validate the data
title (str, optional) – title
description (str, optional) – description
keywords (str, optional) – keywords
version (str, optional) – version
language (str, optional) – language
creator (str, optional) – creator
write_schema (bool, optional) – if True, include additional worksheet with schema
write_toc (bool, optional) – if True, include additional worksheet with table of contents
extra_entries (int, optional) – additional entries to display
data_repo_metadata (bool, optional) – if True, try to write metadata information about the file’s Git repo; the repo must be current with origin, except for the file
schema_package (str, optional) – the package which defines the obj_tables schema used by the file; if not None, try to write metadata information about the the schema’s Git repository: the repo must be current with origin
protected (bool, optional) – if True, protect the worksheet

classmethod validate_implicit_relationships(root_model)[source]¶

Check that relationships to root_model do not need to be explicitly exported because: they can be inferred by Reader.run. This is necessary to enable the relationships to root_model to not be exported in workbooks, and instead added by Reader.run.

Raises: Exception – if there are relationships from core.Model or one-to-many or many-to-many relationships to root_model

validate_implicit_relationships_are_set(model, root_model)[source]¶

Check that there is only one instance of root_model and that each relationship to root_model is set. This is necessary to enable the relationships to root_model to not be exported in workbooks, and instead added by Reader.run.

Parameters

model (obj_tables.Model) – the root model instance
root_model (type) – the type of model, a subclass of obj_tables.Model

Raises

ValueError – if there are multiple instances of root_model in the object graph

wc_lang.io.convert(source, destination, protected=True)[source]¶

Convert among Excel (.xlsx), comma separated (.csv), and tab separated (.tsv) file formats

Read a model from the source files(s) and write it to the destination files(s). A path to a delimiter separated set of models must be represented by a Unix glob pattern (with a *) that matches all delimiter separated files.

Parameters

source (str) – path to source file(s)
destination (str) – path to save converted file
protected (bool, optional) – if True, protect the worksheet

wc_lang.io.create_template(path, write_schema=False, write_toc=True, extra_entries=10, data_repo_metadata=True, protected=True)[source]¶

Create file with model template, including row and column headings

Parameters

path (str) – path to file(s)
write_schema (bool, optional) – if True, include additional worksheet with schema
write_toc (bool, optional) – if True, include additional worksheet with table of contents
extra_entries (int, optional) – additional entries to display
data_repo_metadata (bool, optional) – if True, try to write metadata information about the file’s Git repo
protected (bool, optional) – if True, protect the worksheet

wc_lang.io.get_root_model(models)[source]¶

Get a root model class from an iterator over obj_tables.Model classes

The root model is obtained by name, rather than from core.Model, because models may have been obtained from obj_tables migration, which loads other versions of wc_lang.core in private imports.

Parameters: models (iterator) – subclasses of obj_tables.Model being read or written
Returns: a subclass of obj_tables.Model whose name is root_model_name
Return type: type

4.1.7. wc_lang.util module¶

Utilities

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

wc_lang.util.gen_ids(model)[source]¶

Generate ids for model objects

Parameters: model (core.Model) – model

wc_lang.util.get_model_size(model)[source]¶

Get numbers of model components

Parameters: model (core.Model) – model
Returns: dictionary with numbers of each type of model component
Return type: dict

wc_lang.util.get_model_summary(model)[source]¶

Get textual summary of a model

Parameters: model (core.Model) – model
Returns: textual summary of the model
Return type: str

wc_lang.util.get_models(inline=True)[source]¶

Get list of models :param inline: if true, return inline models :type inline: bool, optional

Returns: list of models
Return type: list of class

4.1. wc_lang package¶

4.1.1. Subpackages¶

4.1.2. Submodules¶

4.1.3. wc_lang.__main__ module¶

4.1.4. wc_lang._version module¶

4.1.5. wc_lang.core module¶

4.1.6. wc_lang.io module¶

4.1.7. wc_lang.util module¶

4.1.8. Module contents¶

4.1.3. wc_lang.main module¶