Index

_

__eq__() (wc_lang.transform.change_value.ChangeValueTransform method) __getattr__() (wc_lang.core.TaxonRankMeta method) __getitem__() (wc_lang.core.TaxonRankMeta method) _parsed_expression (wc_lang.core.DfbaObjectiveExpression attribute) (wc_lang.core.FunctionExpression attribute) (wc_lang.core.ObservableExpression attribute) (wc_lang.core.RateLawExpression attribute) (wc_lang.core.StopConditionExpression attribute)

A

address (wc_lang.core.Author attribute), [1] alphabet (wc_lang.core.ChemicalStructure attribute), [1] App (class in wc_lang.__main__) App.Meta (class in wc_lang.__main__) arguments (wc_lang.__main__.BaseController.Meta attribute) (wc_lang.__main__.ConvertController.Meta attribute) (wc_lang.__main__.CreateTemplateController.Meta attribute) (wc_lang.__main__.CutSubmodelsController.Meta attribute) (wc_lang.__main__.DifferenceController.Meta attribute) (wc_lang.__main__.ExportController.Meta attribute) (wc_lang.__main__.ImportController.Meta attribute) (wc_lang.__main__.MergeModelsController.Meta attribute) (wc_lang.__main__.NormalizeController.Meta attribute) (wc_lang.__main__.TransformController.Meta attribute) (wc_lang.__main__.UpdateVersionMetadataController.Meta attribute) (wc_lang.__main__.ValidateController.Meta attribute) attr_path (wc_lang.transform.change_value.ChangeValueTransform attribute) attr_path_from_str() (wc_lang.transform.change_value.ChangeValueTransform static method) attr_path_to_str() (wc_lang.transform.change_value.ChangeValueTransform method) attribute_order (wc_lang.core.Author.Meta attribute) (wc_lang.core.Change.Meta attribute) (wc_lang.core.ChemicalStructure.Meta attribute) (wc_lang.core.Compartment.Meta attribute) (wc_lang.core.Conclusion.Meta attribute) (wc_lang.core.DfbaObjective.Meta attribute) (wc_lang.core.DfbaObjectiveExpression.Meta attribute) (wc_lang.core.DfbaObjReaction.Meta attribute) (wc_lang.core.DfbaObjSpecies.Meta attribute) (wc_lang.core.DistributionInitConcentration.Meta attribute) (wc_lang.core.Environment.Meta attribute) (wc_lang.core.Evidence.Meta attribute) (wc_lang.core.FluxBounds.Meta attribute) (wc_lang.core.Function.Meta attribute) (wc_lang.core.FunctionExpression.Meta attribute) (wc_lang.core.Identifier.Meta attribute) (wc_lang.core.InitVolume.Meta attribute) (wc_lang.core.Model.Meta attribute) (wc_lang.core.Observable.Meta attribute) (wc_lang.core.ObservableExpression.Meta attribute) (wc_lang.core.Observation.Meta attribute) (wc_lang.core.ObservationEnv.Meta attribute) (wc_lang.core.ObservationGenotype.Meta attribute) (wc_lang.core.ObservationSet.Meta attribute) (wc_lang.core.Parameter.Meta attribute) (wc_lang.core.Ph.Meta attribute) (wc_lang.core.Process.Meta attribute) (wc_lang.core.RateLaw.Meta attribute) (wc_lang.core.RateLawExpression.Meta attribute) (wc_lang.core.Reaction.Meta attribute) (wc_lang.core.Reference.Meta attribute) (wc_lang.core.Species.Meta attribute) (wc_lang.core.SpeciesCoefficient.Meta attribute) (wc_lang.core.SpeciesType.Meta attribute) (wc_lang.core.StopCondition.Meta attribute) (wc_lang.core.StopConditionExpression.Meta attribute) (wc_lang.core.Submodel.Meta attribute) (wc_lang.core.Taxon.Meta attribute)

attributes (wc_lang.core.Author.Meta attribute) (wc_lang.core.Change.Meta attribute) (wc_lang.core.ChemicalStructure.Meta attribute) (wc_lang.core.Compartment.Meta attribute) (wc_lang.core.Conclusion.Meta attribute) (wc_lang.core.DfbaObjective.Meta attribute) (wc_lang.core.DfbaObjectiveExpression.Meta attribute) (wc_lang.core.DfbaObjReaction.Meta attribute) (wc_lang.core.DfbaObjSpecies.Meta attribute) (wc_lang.core.DistributionInitConcentration.Meta attribute) (wc_lang.core.Environment.Meta attribute) (wc_lang.core.Evidence.Meta attribute) (wc_lang.core.FluxBounds.Meta attribute) (wc_lang.core.Function.Meta attribute) (wc_lang.core.FunctionExpression.Meta attribute) (wc_lang.core.Identifier.Meta attribute) (wc_lang.core.InitVolume.Meta attribute) (wc_lang.core.Model.Meta attribute) (wc_lang.core.Observable.Meta attribute) (wc_lang.core.ObservableExpression.Meta attribute) (wc_lang.core.Observation.Meta attribute) (wc_lang.core.ObservationEnv.Meta attribute) (wc_lang.core.ObservationGenotype.Meta attribute) (wc_lang.core.ObservationSet.Meta attribute) (wc_lang.core.Parameter.Meta attribute) (wc_lang.core.Ph.Meta attribute) (wc_lang.core.Process.Meta attribute) (wc_lang.core.RateLaw.Meta attribute) (wc_lang.core.RateLawExpression.Meta attribute) (wc_lang.core.Reaction.Meta attribute) (wc_lang.core.Reference.Meta attribute) (wc_lang.core.Species.Meta attribute) (wc_lang.core.SpeciesCoefficient.Meta attribute) (wc_lang.core.SpeciesType.Meta attribute) (wc_lang.core.StopCondition.Meta attribute) (wc_lang.core.StopConditionExpression.Meta attribute) (wc_lang.core.Submodel.Meta attribute) (wc_lang.core.Taxon.Meta attribute) attrs_to_keep (wc_lang.transform.nullify_attrs.NullifyAttrsTransform attribute) Author (class in wc_lang.core) author (wc_lang.core.Reference attribute), [1] Author.Meta (class in wc_lang.core) authors (wc_lang.core.Change attribute), [1] (wc_lang.core.Conclusion attribute), [1]

B

backward (wc_lang.core.RateLawDirection attribute) base_controller (wc_lang.__main__.App.Meta attribute) BaseController (class in wc_lang.__main__) BaseController.Meta (class in wc_lang.__main__)

bcforms (wc_lang.core.ChemicalStructureFormat attribute) biological_type (wc_lang.core.Compartment attribute), [1] bpforms (wc_lang.core.ChemicalStructureFormat attribute) branch (wc_lang.core.Model attribute), [1]

C

call_libsbml() (wc_lang.sbml.util.LibSbmlInterface class method) canonical_dna (wc_lang.core.ChemicalStructureAlphabet attribute) canonical_protein (wc_lang.core.ChemicalStructureAlphabet attribute) canonical_rna (wc_lang.core.ChemicalStructureAlphabet attribute) cell_size_units (wc_lang.core.DfbaObjReaction attribute), [1] Change (class in wc_lang.core) Change.Meta (class in wc_lang.core) ChangeValueTransform (class in wc_lang.transform.change_value) ChangeValueTransform.Meta (class in wc_lang.transform.change_value) chapter (wc_lang.core.Reference attribute), [1] charge (wc_lang.core.ChemicalStructure attribute), [1] ChemicalStructure (class in wc_lang.core) ChemicalStructure.Meta (class in wc_lang.core) ChemicalStructureAlphabet (class in wc_lang.core) ChemicalStructureFormat (class in wc_lang.core) child_attrs (wc_lang.core.Author.Meta attribute) (wc_lang.core.Change.Meta attribute) (wc_lang.core.ChemicalStructure.Meta attribute) (wc_lang.core.Compartment.Meta attribute) (wc_lang.core.Conclusion.Meta attribute) (wc_lang.core.DfbaObjective.Meta attribute) (wc_lang.core.DfbaObjectiveExpression.Meta attribute) (wc_lang.core.DfbaObjReaction.Meta attribute) (wc_lang.core.DfbaObjSpecies.Meta attribute) (wc_lang.core.DistributionInitConcentration.Meta attribute) (wc_lang.core.Environment.Meta attribute) (wc_lang.core.Evidence.Meta attribute) (wc_lang.core.FluxBounds.Meta attribute) (wc_lang.core.Function.Meta attribute) (wc_lang.core.FunctionExpression.Meta attribute) (wc_lang.core.Identifier.Meta attribute) (wc_lang.core.InitVolume.Meta attribute) (wc_lang.core.Model.Meta attribute) (wc_lang.core.Observable.Meta attribute) (wc_lang.core.ObservableExpression.Meta attribute) (wc_lang.core.Observation.Meta attribute) (wc_lang.core.ObservationEnv.Meta attribute) (wc_lang.core.ObservationGenotype.Meta attribute) (wc_lang.core.ObservationSet.Meta attribute) (wc_lang.core.Parameter.Meta attribute) (wc_lang.core.Ph.Meta attribute) (wc_lang.core.Process.Meta attribute) (wc_lang.core.RateLaw.Meta attribute) (wc_lang.core.RateLawExpression.Meta attribute) (wc_lang.core.Reaction.Meta attribute) (wc_lang.core.Reference.Meta attribute) (wc_lang.core.Species.Meta attribute) (wc_lang.core.SpeciesCoefficient.Meta attribute) (wc_lang.core.SpeciesType.Meta attribute) (wc_lang.core.StopCondition.Meta attribute) (wc_lang.core.StopConditionExpression.Meta attribute) (wc_lang.core.Submodel.Meta attribute) (wc_lang.core.Taxon.Meta attribute) children (wc_lang.core.Author.Meta attribute) (wc_lang.core.Change.Meta attribute) (wc_lang.core.ChemicalStructure.Meta attribute) (wc_lang.core.Compartment.Meta attribute) (wc_lang.core.Conclusion.Meta attribute) (wc_lang.core.DfbaObjective.Meta attribute) (wc_lang.core.DfbaObjectiveExpression.Meta attribute) (wc_lang.core.DfbaObjReaction.Meta attribute) (wc_lang.core.DfbaObjSpecies.Meta attribute) (wc_lang.core.DistributionInitConcentration.Meta attribute) (wc_lang.core.Environment.Meta attribute) (wc_lang.core.Evidence.Meta attribute) (wc_lang.core.FluxBounds.Meta attribute) (wc_lang.core.Function.Meta attribute) (wc_lang.core.FunctionExpression.Meta attribute) (wc_lang.core.InitVolume.Meta attribute) (wc_lang.core.Model.Meta attribute) (wc_lang.core.Observable.Meta attribute) (wc_lang.core.ObservableExpression.Meta attribute) (wc_lang.core.Observation.Meta attribute) (wc_lang.core.ObservationEnv.Meta attribute) (wc_lang.core.ObservationGenotype.Meta attribute) (wc_lang.core.ObservationSet.Meta attribute) (wc_lang.core.Parameter.Meta attribute) (wc_lang.core.Ph.Meta attribute) (wc_lang.core.Process.Meta attribute) (wc_lang.core.RateLaw.Meta attribute) (wc_lang.core.RateLawExpression.Meta attribute) (wc_lang.core.Reaction.Meta attribute) (wc_lang.core.Reference.Meta attribute) (wc_lang.core.Species.Meta attribute) (wc_lang.core.SpeciesCoefficient.Meta attribute) (wc_lang.core.SpeciesType.Meta attribute) (wc_lang.core.StopCondition.Meta attribute) (wc_lang.core.StopConditionExpression.Meta attribute) (wc_lang.core.Submodel.Meta attribute) (wc_lang.core.Taxon.Meta attribute)

classis (wc_lang.core.TaxonRank attribute) coefficient (wc_lang.core.SpeciesCoefficient attribute), [1] coefficient_units (wc_lang.core.DfbaObjective attribute), [1] CommentAttribute (class in wc_lang.core) comments (wc_lang.core.Author attribute), [1] (wc_lang.core.Change attribute), [1] (wc_lang.core.Compartment attribute), [1] (wc_lang.core.Conclusion attribute), [1] (wc_lang.core.DfbaObjective attribute), [1] (wc_lang.core.DfbaObjReaction attribute), [1] (wc_lang.core.DfbaObjSpecies attribute), [1] (wc_lang.core.DistributionInitConcentration attribute), [1] (wc_lang.core.Environment attribute), [1] (wc_lang.core.Function attribute), [1] (wc_lang.core.Model attribute), [1] (wc_lang.core.Observable attribute), [1] (wc_lang.core.Observation attribute), [1] (wc_lang.core.ObservationSet attribute), [1] (wc_lang.core.Parameter attribute), [1] (wc_lang.core.RateLaw attribute), [1] (wc_lang.core.Reaction attribute), [1] (wc_lang.core.Reference attribute), [1] (wc_lang.core.Species attribute), [1] (wc_lang.core.SpeciesType attribute), [1] (wc_lang.core.StopCondition attribute), [1] (wc_lang.core.Submodel attribute), [1] (wc_lang.core.Taxon attribute), [1] Compartment (class in wc_lang.core) compartment (wc_lang.core.Species attribute), [1] Compartment.Meta (class in wc_lang.core) compartments (wc_lang.core.FunctionExpression attribute), [1] (wc_lang.core.RateLawExpression attribute), [1] (wc_lang.core.StopConditionExpression attribute), [1] COMPONENT_TRANSFORMS (wc_lang.transform.core.CompositeTransform attribute), [1] (wc_lang.transform.prep_for_sbml.PrepForSbmlTransform attribute) (wc_lang.transform.prep_for_wc_sim.PrepForWcSimTransform attribute) CompositeTransform (class in wc_lang.transform.core) Conclusion (class in wc_lang.core) Conclusion.Meta (class in wc_lang.core) conclusions (wc_lang.core.Change attribute), [1] (wc_lang.core.Compartment attribute), [1] (wc_lang.core.DfbaObjective attribute), [1] (wc_lang.core.DfbaObjReaction attribute), [1] (wc_lang.core.DfbaObjSpecies attribute), [1] (wc_lang.core.DistributionInitConcentration attribute), [1] (wc_lang.core.Function attribute), [1] (wc_lang.core.Observable attribute), [1] (wc_lang.core.Parameter attribute), [1] (wc_lang.core.RateLaw attribute), [1] (wc_lang.core.Reaction attribute), [1] (wc_lang.core.Species attribute), [1] (wc_lang.core.SpeciesType attribute), [1] (wc_lang.core.StopCondition attribute), [1] (wc_lang.core.Submodel attribute), [1] condition (wc_lang.core.ObservationEnv attribute), [1] convert() (in module wc_lang.io) ConvertController (class in wc_lang.__main__) ConvertController.Meta (class in wc_lang.__main__) create_base_unit() (wc_lang.sbml.util.LibSbmlInterface class method) create_doc() (wc_lang.sbml.util.LibSbmlInterface class method) create_model() (wc_lang.sbml.util.LibSbmlInterface class method) create_parameter() (wc_lang.sbml.util.LibSbmlInterface class method) create_template() (in module wc_lang.io) create_unit() (wc_lang.sbml.util.LibSbmlInterface class method) create_units() (wc_lang.sbml.util.LibSbmlInterface class method) created (wc_lang.core.Model attribute), [1] CreateImplicitDfbaExchangeReactionsTransform (class in wc_lang.transform.create_implicit_dfba_ex_rxns) CreateImplicitDfbaExchangeReactionsTransform.Meta (class in wc_lang.transform.create_implicit_dfba_ex_rxns) CreateImplicitDistributionZeroInitConcentrationsTransform (class in wc_lang.transform.create_implicit_dist_zero_init_concs) CreateImplicitDistributionZeroInitConcentrationsTransform.Meta (class in wc_lang.transform.create_implicit_dist_zero_init_concs) CreateTemplateController (class in wc_lang.__main__) CreateTemplateController.Meta (class in wc_lang.__main__) CutSubmodelsController (class in wc_lang.__main__) CutSubmodelsController.Meta (class in wc_lang.__main__)

D

data_analysis_process (wc_lang.core.Observation attribute), [1] data_generation_process (wc_lang.core.Observation attribute), [1] date (wc_lang.core.Change attribute), [1] (wc_lang.core.Conclusion attribute), [1] description (wc_lang.__main__.BaseController.Meta attribute) (wc_lang.__main__.ConvertController.Meta attribute) (wc_lang.__main__.CreateTemplateController.Meta attribute) (wc_lang.__main__.CutSubmodelsController.Meta attribute) (wc_lang.__main__.DifferenceController.Meta attribute) (wc_lang.__main__.ExportController.Meta attribute) (wc_lang.__main__.ImportController.Meta attribute) (wc_lang.__main__.MergeModelsController.Meta attribute) (wc_lang.__main__.NormalizeController.Meta attribute) (wc_lang.__main__.TransformController.Meta attribute) (wc_lang.__main__.UpdateVersionMetadataController.Meta attribute) (wc_lang.__main__.ValidateController.Meta attribute) deserialize() (wc_lang.core.DfbaObjectiveExpression class method) (wc_lang.core.FunctionExpression class method) (wc_lang.core.ObservableExpression class method) (wc_lang.core.RateLawExpression class method) (wc_lang.core.StopConditionExpression class method)

dfba_framework (wc_lang.transform.prep_for_sbml.PrepForSbmlTransform attribute) dfba_obj_reaction (wc_lang.core.DfbaObjSpecies attribute), [1] dfba_obj_reactions (wc_lang.core.DfbaObjectiveExpression attribute), [1] DfbaObjective (class in wc_lang.core) DfbaObjective.Meta (class in wc_lang.core) DfbaObjectiveExpression (class in wc_lang.core) DfbaObjectiveExpression.Meta (class in wc_lang.core) DfbaObjReaction (class in wc_lang.core) DfbaObjReaction.Meta (class in wc_lang.core) DfbaObjSpecies (class in wc_lang.core) DfbaObjSpecies.Meta (class in wc_lang.core) DifferenceController (class in wc_lang.__main__) DifferenceController.Meta (class in wc_lang.__main__) direction (wc_lang.core.RateLaw attribute), [1] distribution (wc_lang.core.DistributionInitConcentration attribute), [1] (wc_lang.core.InitVolume attribute), [1] (wc_lang.core.Ph attribute), [1] DistributionInitConcentration (class in wc_lang.core) DistributionInitConcentration.Meta (class in wc_lang.core) dna (wc_lang.core.ChemicalStructureAlphabet attribute) domain (wc_lang.core.TaxonRank attribute)

E

edition (wc_lang.core.Reference attribute), [1] editor (wc_lang.core.Reference attribute), [1] email (wc_lang.core.Author attribute), [1] empirical_formula (wc_lang.core.ChemicalStructure attribute), [1] env (wc_lang.core.Observation attribute), [1] Environment (class in wc_lang.core) Environment.Meta (class in wc_lang.core) Evidence (class in wc_lang.core) evidence (wc_lang.core.Change attribute), [1] (wc_lang.core.Compartment attribute), [1] (wc_lang.core.Conclusion attribute), [1] (wc_lang.core.DfbaObjective attribute), [1] (wc_lang.core.DfbaObjReaction attribute), [1] (wc_lang.core.DfbaObjSpecies attribute), [1] (wc_lang.core.DistributionInitConcentration attribute), [1] (wc_lang.core.Function attribute), [1] (wc_lang.core.Observable attribute), [1] (wc_lang.core.Parameter attribute), [1] (wc_lang.core.RateLaw attribute), [1] (wc_lang.core.Reaction attribute), [1] (wc_lang.core.Species attribute), [1] (wc_lang.core.SpeciesType attribute), [1] (wc_lang.core.StopCondition attribute), [1] (wc_lang.core.Submodel attribute), [1] evidence() (wc_lang.core.EvidenceManyToManyAttribute.Transformer method) Evidence.Meta (class in wc_lang.core) EvidenceManyToManyAttribute (class in wc_lang.core) EvidenceManyToManyAttribute.Transformer (class in wc_lang.core) experiment_design (wc_lang.core.Observation attribute), [1] experiment_type (wc_lang.core.Observation attribute), [1] export_relations_to_sbml() (wc_lang.core.Compartment method) (wc_lang.core.DfbaObjective method) (wc_lang.core.DfbaObjReaction method) (wc_lang.core.Model method) (wc_lang.core.Parameter method) (wc_lang.core.RateLaw method) (wc_lang.core.Reaction method) (wc_lang.core.Species method) (wc_lang.core.Submodel method) (wc_lang.sbml.util.SbmlAssignmentRuleMixin method) (wc_lang.sbml.util.SbmlModelMixin method) export_to_sbml() (wc_lang.core.Compartment method) (wc_lang.core.DfbaObjective method) (wc_lang.core.DfbaObjReaction method) (wc_lang.core.Model method) (wc_lang.core.Parameter method) (wc_lang.core.RateLaw method) (wc_lang.core.Reaction method) (wc_lang.core.Species method) (wc_lang.core.Submodel method) (wc_lang.sbml.util.SbmlAssignmentRuleMixin method) (wc_lang.sbml.util.SbmlModelMixin method)

ExportController (class in wc_lang.__main__) ExportController.Meta (class in wc_lang.__main__) expression (wc_lang.core.DfbaObjective attribute), [1] (wc_lang.core.DfbaObjectiveExpression attribute), [1] (wc_lang.core.Function attribute), [1] (wc_lang.core.FunctionExpression attribute), [1] (wc_lang.core.Observable attribute), [1] (wc_lang.core.ObservableExpression attribute), [1] (wc_lang.core.RateLaw attribute), [1] (wc_lang.core.RateLawExpression attribute), [1] (wc_lang.core.StopCondition attribute), [1] (wc_lang.core.StopConditionExpression attribute), [1] expression_is_linear (wc_lang.core.ObservableExpression.Meta attribute) expression_term_model (wc_lang.core.DfbaObjective.Meta attribute) (wc_lang.core.Function.Meta attribute) (wc_lang.core.Observable.Meta attribute) (wc_lang.core.RateLaw.Meta attribute) (wc_lang.core.StopCondition.Meta attribute) expression_term_models (wc_lang.core.DfbaObjectiveExpression.Meta attribute) (wc_lang.core.FunctionExpression.Meta attribute) (wc_lang.core.ObservableExpression.Meta attribute) (wc_lang.core.RateLawExpression.Meta attribute) (wc_lang.core.StopConditionExpression.Meta attribute) expression_term_token_pattern (wc_lang.core.Species.Meta attribute) expression_term_units (wc_lang.core.Compartment.Meta attribute) (wc_lang.core.DfbaObjective.Meta attribute) (wc_lang.core.DfbaObjReaction.Meta attribute) (wc_lang.core.Function.Meta attribute) (wc_lang.core.Observable.Meta attribute) (wc_lang.core.Parameter.Meta attribute) (wc_lang.core.RateLaw.Meta attribute) (wc_lang.core.Reaction.Meta attribute) (wc_lang.core.Species.Meta attribute) (wc_lang.core.StopCondition.Meta attribute) expression_term_value (wc_lang.core.Parameter.Meta attribute) expression_type (wc_lang.core.StopConditionExpression.Meta attribute) expression_unit_registry (wc_lang.core.DfbaObjectiveExpression.Meta attribute) (wc_lang.core.FunctionExpression.Meta attribute) (wc_lang.core.ObservableExpression.Meta attribute) (wc_lang.core.RateLawExpression.Meta attribute) (wc_lang.core.StopConditionExpression.Meta attribute) expression_valid_functions (wc_lang.core.DfbaObjectiveExpression.Meta attribute)

F

family (wc_lang.core.TaxonRank attribute) first_name (wc_lang.core.Author attribute), [1] flux_bounds (wc_lang.core.Reaction attribute), [1] FluxBounds (class in wc_lang.core) FluxBounds.Meta (class in wc_lang.core) format (wc_lang.core.ChemicalStructure attribute), [1] forward (wc_lang.core.RateLawDirection attribute) framework (wc_lang.core.Submodel attribute), [1] frozen_columns (wc_lang.core.Author.Meta attribute) (wc_lang.core.DistributionInitConcentration.Meta attribute) (wc_lang.core.Identifier.Meta attribute) (wc_lang.core.Species.Meta attribute) (wc_lang.core.SpeciesCoefficient.Meta attribute)

Function (class in wc_lang.core) Function.Meta (class in wc_lang.core) FunctionExpression (class in wc_lang.core) FunctionExpression.Meta (class in wc_lang.core) functions (wc_lang.core.FunctionExpression attribute), [1] (wc_lang.core.RateLawExpression attribute) (wc_lang.core.StopConditionExpression attribute), [1]

G

gbl() (wc_lang.core.ReactionParticipantAttribute.Transformer method) gbl_part() (wc_lang.core.ReactionParticipantAttribute.Transformer method) gbl_parts() (wc_lang.core.ReactionParticipantAttribute.Transformer method) gen_annotations() (wc_lang.sbml.util.LibSbmlInterface class method) gen_authors_annotation() (wc_lang.sbml.util.LibSbmlInterface class method) gen_id() (wc_lang.core.DfbaObjective method) (wc_lang.core.DfbaObjSpecies method) (wc_lang.core.DistributionInitConcentration method) (wc_lang.core.RateLaw method) (wc_lang.core.Species method) gen_ids() (in module wc_lang.util) gen_models() (wc_lang.core.SubmodelsToModelRelatedManager method) gen_nested_attr_paths() (wc_lang.sbml.util.LibSbmlInterface static method) gen_sbml_id() (wc_lang.sbml.util.SbmlModelMixin method) gen_unit_id() (wc_lang.sbml.util.LibSbmlInterface class method) genetic_variant (wc_lang.core.ObservationGenotype attribute) genotype (wc_lang.core.Observation attribute), [1] genus (wc_lang.core.TaxonRank attribute) geometry (wc_lang.core.Compartment attribute), [1] get() (wc_lang.core.Species static method) get_annotations() (wc_lang.sbml.util.LibSbmlInterface class method) get_authors() (wc_lang.core.Model method) get_authors_annotation() (wc_lang.sbml.util.LibSbmlInterface class method) get_changes() (wc_lang.core.Model method) get_children() (wc_lang.core.Submodel method) get_commments() (wc_lang.sbml.util.LibSbmlInterface class method) get_compartments() (wc_lang.core.Model method) get_components() (wc_lang.core.Model method) get_conclusions() (wc_lang.core.Model method) get_config() (in module wc_lang.config.core) get_debug_logs_config() (in module wc_lang.config.core) get_dfba_obj_reactions() (wc_lang.core.Model method) get_dfba_obj_species() (wc_lang.core.Model method) get_dfba_objs() (wc_lang.core.Model method) get_distribution_init_concentrations() (wc_lang.core.Model method) get_errors_warnings() (wc_lang.sbml.util.LibSbmlInterface class method) get_evidence() (wc_lang.core.Model method)

get_functions() (wc_lang.core.Model method) get_identifier() (wc_lang.core.Author method) get_immediate_children() (wc_lang.core.Submodel method) get_math() (wc_lang.sbml.util.LibSbmlInterface class method) get_model_size() (in module wc_lang.util) get_model_summary() (in module wc_lang.util) get_models() (in module wc_lang.util) get_modifiers() (wc_lang.core.Reaction method) get_observables() (wc_lang.core.Model method) get_observation_sets() (wc_lang.core.Model method) get_observations() (wc_lang.core.Model method) get_parameters() (wc_lang.core.Model method) get_products() (wc_lang.core.DfbaObjective method) (wc_lang.core.Reaction method) get_rate_laws() (wc_lang.core.Model method) get_reactants() (wc_lang.core.Reaction method) get_reactions() (wc_lang.core.Model method) get_references() (wc_lang.core.Model method) get_root_compartments() (wc_lang.core.Model method) get_root_model() (in module wc_lang.io) get_species() (wc_lang.core.Model method) (wc_lang.core.Reaction method) get_species_types() (wc_lang.core.Model method) get_stop_conditions() (wc_lang.core.Model method) get_structure() (wc_lang.core.ChemicalStructure method) get_sub_compartments() (wc_lang.core.Compartment method) get_submodels() (wc_lang.core.Model method) get_tot_mean_init_volume() (wc_lang.core.Compartment method) get_transforms() (in module wc_lang.transform.core) get_unit() (wc_lang.sbml.util.LibSbmlInterface class method) get_xlsx_validation() (wc_lang.core.EvidenceManyToManyAttribute method) (wc_lang.core.IdentifierToManyGrammarAttribute method) (wc_lang.core.ReactionParticipantAttribute method) grammar_path (wc_lang.core.EvidenceManyToManyAttribute attribute) (wc_lang.core.IdentifierToManyGrammarAttribute attribute) (wc_lang.core.ReactionParticipantAttribute attribute) growth_media (wc_lang.core.ObservationEnv attribute), [1]

H

handlers (wc_lang.__main__.App.Meta attribute) has_carbon() (wc_lang.core.ChemicalStructure method) help (wc_lang.__main__.BaseController.Meta attribute) (wc_lang.__main__.ConvertController.Meta attribute) (wc_lang.__main__.CreateTemplateController.Meta attribute) (wc_lang.__main__.CutSubmodelsController.Meta attribute) (wc_lang.__main__.DifferenceController.Meta attribute) (wc_lang.__main__.ExportController.Meta attribute) (wc_lang.__main__.ImportController.Meta attribute) (wc_lang.__main__.MergeModelsController.Meta attribute) (wc_lang.__main__.NormalizeController.Meta attribute) (wc_lang.__main__.TransformController.Meta attribute) (wc_lang.__main__.UpdateVersionMetadataController.Meta attribute) (wc_lang.__main__.ValidateController.Meta attribute)

I

id (wc_lang.core.Author attribute), [1] (wc_lang.core.Change attribute), [1] (wc_lang.core.Compartment attribute), [1] (wc_lang.core.Conclusion attribute), [1] (wc_lang.core.DfbaObjective attribute), [1] (wc_lang.core.DfbaObjReaction attribute), [1] (wc_lang.core.DfbaObjSpecies attribute), [1] (wc_lang.core.DistributionInitConcentration attribute), [1] (wc_lang.core.Environment attribute), [1] (wc_lang.core.Function attribute), [1] (wc_lang.core.Identifier attribute), [1] (wc_lang.core.Model attribute), [1] (wc_lang.core.Observable attribute), [1] (wc_lang.core.Observation attribute), [1] (wc_lang.core.ObservationSet attribute), [1] (wc_lang.core.Parameter attribute), [1] (wc_lang.core.RateLaw attribute), [1] (wc_lang.core.Reaction attribute), [1] (wc_lang.core.Reference attribute), [1] (wc_lang.core.Species attribute), [1] (wc_lang.core.SpeciesType attribute), [1] (wc_lang.core.StopCondition attribute), [1] (wc_lang.core.Submodel attribute), [1] (wc_lang.core.Taxon attribute), [1] (wc_lang.transform.change_value.ChangeValueTransform.Meta attribute) (wc_lang.transform.create_implicit_dfba_ex_rxns.CreateImplicitDfbaExchangeReactionsTransform.Meta attribute) (wc_lang.transform.create_implicit_dist_zero_init_concs.CreateImplicitDistributionZeroInitConcentrationsTransform.Meta attribute) (wc_lang.transform.merge_submodels.MergeAlgorithmicallyLikeSubmodelsTransform.Meta attribute) (wc_lang.transform.nullify_attrs.NullifyAttrsTransform.Meta attribute) (wc_lang.transform.prep_for_sbml.PrepForSbmlTransform.Meta attribute) (wc_lang.transform.prep_for_wc_sim.PrepForWcSimTransform.Meta attribute) (wc_lang.transform.set_finite_dfba_flux_bounds.SetFiniteDfbaFluxBoundsTransform.Meta attribute) (wc_lang.transform.split_reversible_reactions.SplitReversibleReactionsTransform.Meta attribute) Identifier (class in wc_lang.core) Identifier.Meta (class in wc_lang.core) IdentifierManyToManyAttribute (class in wc_lang.core) IdentifierOneToManyAttribute (class in wc_lang.core) identifiers (wc_lang.core.Author attribute), [1] (wc_lang.core.Change attribute), [1] (wc_lang.core.Compartment attribute), [1] (wc_lang.core.Conclusion attribute), [1] (wc_lang.core.DfbaObjective attribute), [1] (wc_lang.core.DfbaObjReaction attribute), [1] (wc_lang.core.DfbaObjSpecies attribute), [1] (wc_lang.core.DistributionInitConcentration attribute), [1] (wc_lang.core.Environment attribute), [1] (wc_lang.core.Function attribute), [1] (wc_lang.core.Model attribute), [1] (wc_lang.core.Observable attribute), [1] (wc_lang.core.Observation attribute), [1] (wc_lang.core.ObservationSet attribute), [1] (wc_lang.core.Parameter attribute), [1] (wc_lang.core.RateLaw attribute), [1] (wc_lang.core.Reaction attribute), [1] (wc_lang.core.Reference attribute), [1] (wc_lang.core.Species attribute), [1] (wc_lang.core.SpeciesType attribute), [1] (wc_lang.core.StopCondition attribute), [1] (wc_lang.core.Submodel attribute), [1] (wc_lang.core.Taxon attribute), [1] IdentifierToManyGrammarAttribute (class in wc_lang.core) import_from_sbml() (wc_lang.core.Compartment method) (wc_lang.core.DfbaObjective method) (wc_lang.core.DfbaObjReaction method) (wc_lang.core.Model method) (wc_lang.core.Parameter method) (wc_lang.core.RateLaw method) (wc_lang.core.Reaction method) (wc_lang.core.Species method) (wc_lang.core.Submodel method) (wc_lang.sbml.util.SbmlAssignmentRuleMixin method) (wc_lang.sbml.util.SbmlModelMixin method) import_relations_from_sbml() (wc_lang.core.Compartment method) (wc_lang.core.DfbaObjective method) (wc_lang.core.DfbaObjReaction method) (wc_lang.core.Model method) (wc_lang.core.Parameter method) (wc_lang.core.RateLaw method) (wc_lang.core.Reaction method) (wc_lang.core.Species method) (wc_lang.core.Submodel method) (wc_lang.sbml.util.SbmlAssignmentRuleMixin method) (wc_lang.sbml.util.SbmlModelMixin method) ImportController (class in wc_lang.__main__)

ImportController.Meta (class in wc_lang.__main__) indexed_attrs_tuples (wc_lang.core.Author.Meta attribute) (wc_lang.core.Change.Meta attribute) (wc_lang.core.ChemicalStructure.Meta attribute) (wc_lang.core.Compartment.Meta attribute) (wc_lang.core.Conclusion.Meta attribute) (wc_lang.core.DfbaObjective.Meta attribute) (wc_lang.core.DfbaObjectiveExpression.Meta attribute) (wc_lang.core.DfbaObjReaction.Meta attribute) (wc_lang.core.DfbaObjSpecies.Meta attribute) (wc_lang.core.DistributionInitConcentration.Meta attribute) (wc_lang.core.Environment.Meta attribute) (wc_lang.core.Evidence.Meta attribute) (wc_lang.core.FluxBounds.Meta attribute) (wc_lang.core.Function.Meta attribute) (wc_lang.core.FunctionExpression.Meta attribute) (wc_lang.core.Identifier.Meta attribute) (wc_lang.core.InitVolume.Meta attribute) (wc_lang.core.Model.Meta attribute) (wc_lang.core.Observable.Meta attribute) (wc_lang.core.ObservableExpression.Meta attribute) (wc_lang.core.Observation.Meta attribute) (wc_lang.core.ObservationEnv.Meta attribute) (wc_lang.core.ObservationGenotype.Meta attribute) (wc_lang.core.ObservationSet.Meta attribute) (wc_lang.core.Parameter.Meta attribute) (wc_lang.core.Ph.Meta attribute) (wc_lang.core.Process.Meta attribute) (wc_lang.core.RateLaw.Meta attribute) (wc_lang.core.RateLawExpression.Meta attribute) (wc_lang.core.Reaction.Meta attribute) (wc_lang.core.Reference.Meta attribute) (wc_lang.core.Species.Meta attribute) (wc_lang.core.SpeciesCoefficient.Meta attribute) (wc_lang.core.SpeciesType.Meta attribute) (wc_lang.core.StopCondition.Meta attribute) (wc_lang.core.StopConditionExpression.Meta attribute) (wc_lang.core.Submodel.Meta attribute) (wc_lang.core.Taxon.Meta attribute) inheritance (wc_lang.core.Author.Meta attribute) (wc_lang.core.Change.Meta attribute) (wc_lang.core.ChemicalStructure.Meta attribute) (wc_lang.core.Compartment.Meta attribute) (wc_lang.core.Conclusion.Meta attribute) (wc_lang.core.DfbaObjective.Meta attribute) (wc_lang.core.DfbaObjectiveExpression.Meta attribute) (wc_lang.core.DfbaObjReaction.Meta attribute) (wc_lang.core.DfbaObjSpecies.Meta attribute) (wc_lang.core.DistributionInitConcentration.Meta attribute) (wc_lang.core.Environment.Meta attribute) (wc_lang.core.Evidence.Meta attribute) (wc_lang.core.FluxBounds.Meta attribute) (wc_lang.core.Function.Meta attribute) (wc_lang.core.FunctionExpression.Meta attribute) (wc_lang.core.Identifier.Meta attribute) (wc_lang.core.InitVolume.Meta attribute) (wc_lang.core.Model.Meta attribute) (wc_lang.core.Observable.Meta attribute) (wc_lang.core.ObservableExpression.Meta attribute) (wc_lang.core.Observation.Meta attribute) (wc_lang.core.ObservationEnv.Meta attribute) (wc_lang.core.ObservationGenotype.Meta attribute) (wc_lang.core.ObservationSet.Meta attribute) (wc_lang.core.Parameter.Meta attribute) (wc_lang.core.Ph.Meta attribute) (wc_lang.core.Process.Meta attribute) (wc_lang.core.RateLaw.Meta attribute) (wc_lang.core.RateLawExpression.Meta attribute) (wc_lang.core.Reaction.Meta attribute) (wc_lang.core.Reference.Meta attribute) (wc_lang.core.Species.Meta attribute) (wc_lang.core.SpeciesCoefficient.Meta attribute) (wc_lang.core.SpeciesType.Meta attribute) (wc_lang.core.StopCondition.Meta attribute) (wc_lang.core.StopConditionExpression.Meta attribute) (wc_lang.core.Submodel.Meta attribute) (wc_lang.core.Taxon.Meta attribute) init_density (wc_lang.core.Compartment attribute), [1] init_model() (wc_lang.sbml.util.LibSbmlInterface class method) init_volume (wc_lang.core.Compartment attribute), [1] InitVolume (class in wc_lang.core) InitVolume.Meta (class in wc_lang.core) intention (wc_lang.core.Change attribute), [1] intention_type (wc_lang.core.Change attribute), [1] issue (wc_lang.core.Reference attribute), [1]

K

kingdom (wc_lang.core.TaxonRank attribute)

L

label (wc_lang.__main__.App.Meta attribute) (wc_lang.__main__.BaseController.Meta attribute) (wc_lang.__main__.ConvertController.Meta attribute) (wc_lang.__main__.CreateTemplateController.Meta attribute) (wc_lang.__main__.CutSubmodelsController.Meta attribute) (wc_lang.__main__.DifferenceController.Meta attribute) (wc_lang.__main__.ExportController.Meta attribute) (wc_lang.__main__.ImportController.Meta attribute) (wc_lang.__main__.MergeModelsController.Meta attribute) (wc_lang.__main__.NormalizeController.Meta attribute) (wc_lang.__main__.TransformController.Meta attribute) (wc_lang.__main__.UpdateVersionMetadataController.Meta attribute) (wc_lang.__main__.ValidateController.Meta attribute) (wc_lang.transform.change_value.ChangeValueTransform.Meta attribute) (wc_lang.transform.create_implicit_dfba_ex_rxns.CreateImplicitDfbaExchangeReactionsTransform.Meta attribute) (wc_lang.transform.create_implicit_dist_zero_init_concs.CreateImplicitDistributionZeroInitConcentrationsTransform.Meta attribute) (wc_lang.transform.merge_submodels.MergeAlgorithmicallyLikeSubmodelsTransform.Meta attribute) (wc_lang.transform.nullify_attrs.NullifyAttrsTransform.Meta attribute) (wc_lang.transform.prep_for_sbml.PrepForSbmlTransform.Meta attribute) (wc_lang.transform.prep_for_wc_sim.PrepForWcSimTransform.Meta attribute) (wc_lang.transform.set_finite_dfba_flux_bounds.SetFiniteDfbaFluxBoundsTransform.Meta attribute) (wc_lang.transform.split_reversible_reactions.SplitReversibleReactionsTransform.Meta attribute) last_name (wc_lang.core.Author attribute), [1] lcl() (wc_lang.core.ReactionParticipantAttribute.Transformer method) lcl_part() (wc_lang.core.ReactionParticipantAttribute.Transformer method) lcl_parts() (wc_lang.core.ReactionParticipantAttribute.Transformer method) LibSbmlError LibSbmlInterface (class in wc_lang.sbml.util) local_attributes (wc_lang.core.Author.Meta attribute) (wc_lang.core.Change.Meta attribute) (wc_lang.core.ChemicalStructure.Meta attribute) (wc_lang.core.Compartment.Meta attribute) (wc_lang.core.Conclusion.Meta attribute) (wc_lang.core.DfbaObjective.Meta attribute) (wc_lang.core.DfbaObjectiveExpression.Meta attribute) (wc_lang.core.DfbaObjReaction.Meta attribute) (wc_lang.core.DfbaObjSpecies.Meta attribute) (wc_lang.core.DistributionInitConcentration.Meta attribute) (wc_lang.core.Environment.Meta attribute) (wc_lang.core.Evidence.Meta attribute) (wc_lang.core.FluxBounds.Meta attribute) (wc_lang.core.Function.Meta attribute) (wc_lang.core.FunctionExpression.Meta attribute) (wc_lang.core.Identifier.Meta attribute) (wc_lang.core.InitVolume.Meta attribute) (wc_lang.core.Model.Meta attribute) (wc_lang.core.Observable.Meta attribute) (wc_lang.core.ObservableExpression.Meta attribute) (wc_lang.core.Observation.Meta attribute) (wc_lang.core.ObservationEnv.Meta attribute) (wc_lang.core.ObservationGenotype.Meta attribute) (wc_lang.core.ObservationSet.Meta attribute) (wc_lang.core.Parameter.Meta attribute) (wc_lang.core.Ph.Meta attribute) (wc_lang.core.Process.Meta attribute) (wc_lang.core.RateLaw.Meta attribute) (wc_lang.core.RateLawExpression.Meta attribute) (wc_lang.core.Reaction.Meta attribute) (wc_lang.core.Reference.Meta attribute) (wc_lang.core.Species.Meta attribute) (wc_lang.core.SpeciesCoefficient.Meta attribute) (wc_lang.core.SpeciesType.Meta attribute) (wc_lang.core.StopCondition.Meta attribute) (wc_lang.core.StopConditionExpression.Meta attribute) (wc_lang.core.Submodel.Meta attribute) (wc_lang.core.Taxon.Meta attribute)

M

main() (in module wc_lang.__main__) mass_units (wc_lang.core.Compartment attribute), [1] max (wc_lang.core.FluxBounds attribute), [1] mean (wc_lang.core.DistributionInitConcentration attribute), [1] (wc_lang.core.InitVolume attribute), [1] (wc_lang.core.Ph attribute), [1] merge (wc_lang.core.DfbaObjective.Meta attribute) (wc_lang.core.DfbaObjectiveExpression.Meta attribute) (wc_lang.core.DfbaObjReaction.Meta attribute) (wc_lang.core.DfbaObjSpecies.Meta attribute) (wc_lang.core.Reaction.Meta attribute) (wc_lang.core.Submodel.Meta attribute) merge() (wc_lang.core.CommentAttribute method) merge_attrs() (wc_lang.core.DfbaObjectiveExpression method) (wc_lang.core.FunctionExpression method) (wc_lang.core.Model method) (wc_lang.core.ObservableExpression method) (wc_lang.core.RateLawExpression method) (wc_lang.core.StopConditionExpression method) MergeAlgorithmicallyLikeSubmodelsTransform (class in wc_lang.transform.merge_submodels) MergeAlgorithmicallyLikeSubmodelsTransform.Meta (class in wc_lang.transform.merge_submodels) MergeModelsController (class in wc_lang.__main__) MergeModelsController.Meta (class in wc_lang.__main__) middle_name (wc_lang.core.Author attribute), [1] min (wc_lang.core.FluxBounds attribute), [1] Model (class in wc_lang.core)

model (wc_lang.core.Author attribute), [1] (wc_lang.core.Change attribute), [1] (wc_lang.core.Compartment attribute), [1] (wc_lang.core.Conclusion attribute), [1] (wc_lang.core.DfbaObjective attribute), [1] (wc_lang.core.DfbaObjReaction attribute), [1] (wc_lang.core.DfbaObjSpecies attribute), [1] (wc_lang.core.DistributionInitConcentration attribute), [1] (wc_lang.core.Environment attribute), [1] (wc_lang.core.Function attribute), [1] (wc_lang.core.Observable attribute), [1] (wc_lang.core.Observation attribute), [1] (wc_lang.core.ObservationSet attribute), [1] (wc_lang.core.Parameter attribute), [1] (wc_lang.core.RateLaw attribute), [1] (wc_lang.core.Reaction attribute), [1] (wc_lang.core.Reference attribute), [1] (wc_lang.core.Species attribute), [1] (wc_lang.core.SpeciesType attribute), [1] (wc_lang.core.StopCondition attribute), [1] (wc_lang.core.Submodel attribute), [1] (wc_lang.core.Taxon attribute), [1] Model.Meta (class in wc_lang.core) MODELS (wc_lang.io.Reader attribute) (wc_lang.io.Writer attribute) molecular_weight (wc_lang.core.ChemicalStructure attribute), [1]

N

name (wc_lang.core.Author attribute), [1] (wc_lang.core.Change attribute), [1] (wc_lang.core.Compartment attribute), [1] (wc_lang.core.Conclusion attribute), [1] (wc_lang.core.DfbaObjective attribute), [1] (wc_lang.core.DfbaObjReaction attribute), [1] (wc_lang.core.DfbaObjSpecies attribute), [1] (wc_lang.core.DistributionInitConcentration attribute), [1] (wc_lang.core.Environment attribute), [1] (wc_lang.core.Function attribute), [1] (wc_lang.core.Model attribute), [1] (wc_lang.core.Observable attribute), [1] (wc_lang.core.Observation attribute), [1] (wc_lang.core.ObservationSet attribute), [1] (wc_lang.core.Parameter attribute), [1] (wc_lang.core.Process attribute), [1] (wc_lang.core.RateLaw attribute), [1] (wc_lang.core.Reaction attribute), [1] (wc_lang.core.Reference attribute), [1] (wc_lang.core.Species attribute), [1] (wc_lang.core.SpeciesType attribute), [1] (wc_lang.core.StopCondition attribute), [1] (wc_lang.core.Submodel attribute), [1] (wc_lang.core.Taxon attribute), [1]

namespace (wc_lang.core.Identifier attribute), [1] normalize_unit_kind() (wc_lang.sbml.util.LibSbmlInterface class method) NormalizeController (class in wc_lang.__main__) NormalizeController.Meta (class in wc_lang.__main__) NullifyAttrsTransform (class in wc_lang.transform.nullify_attrs) NullifyAttrsTransform.Meta (class in wc_lang.transform.nullify_attrs) number (wc_lang.core.Reference attribute), [1]

O

objects (wc_lang.core.Author attribute) (wc_lang.core.Change attribute) (wc_lang.core.ChemicalStructure attribute) (wc_lang.core.Compartment attribute) (wc_lang.core.Conclusion attribute) (wc_lang.core.DfbaObjective attribute) (wc_lang.core.DfbaObjectiveExpression attribute) (wc_lang.core.DfbaObjReaction attribute) (wc_lang.core.DfbaObjSpecies attribute) (wc_lang.core.DistributionInitConcentration attribute) (wc_lang.core.Environment attribute) (wc_lang.core.Evidence attribute) (wc_lang.core.FluxBounds attribute) (wc_lang.core.Function attribute) (wc_lang.core.FunctionExpression attribute) (wc_lang.core.Identifier attribute) (wc_lang.core.InitVolume attribute) (wc_lang.core.Model attribute) (wc_lang.core.Observable attribute) (wc_lang.core.ObservableExpression attribute) (wc_lang.core.Observation attribute) (wc_lang.core.ObservationEnv attribute) (wc_lang.core.ObservationGenotype attribute) (wc_lang.core.ObservationSet attribute) (wc_lang.core.Parameter attribute) (wc_lang.core.Ph attribute) (wc_lang.core.Process attribute) (wc_lang.core.RateLaw attribute) (wc_lang.core.RateLawExpression attribute) (wc_lang.core.Reaction attribute) (wc_lang.core.Reference attribute) (wc_lang.core.Species attribute) (wc_lang.core.SpeciesCoefficient attribute) (wc_lang.core.SpeciesType attribute) (wc_lang.core.StopCondition attribute) (wc_lang.core.StopConditionExpression attribute) (wc_lang.core.Submodel attribute) (wc_lang.core.Taxon attribute) Observable (class in wc_lang.core) Observable.Meta (class in wc_lang.core) ObservableExpression (class in wc_lang.core) ObservableExpression.Meta (class in wc_lang.core) observables (wc_lang.core.FunctionExpression attribute), [1] (wc_lang.core.ObservableExpression attribute), [1] (wc_lang.core.RateLawExpression attribute) (wc_lang.core.StopConditionExpression attribute), [1] Observation (class in wc_lang.core) observation (wc_lang.core.Evidence attribute), [1]

Observation.Meta (class in wc_lang.core) ObservationEnv (class in wc_lang.core) ObservationEnv.Meta (class in wc_lang.core) ObservationGenotype (class in wc_lang.core) ObservationGenotype.Meta (class in wc_lang.core) observations (wc_lang.core.ObservationSet attribute), [1] ObservationSet (class in wc_lang.core) ObservationSet.Meta (class in wc_lang.core) order (wc_lang.core.TaxonRank attribute) ordering (wc_lang.core.Author.Meta attribute) (wc_lang.core.Change.Meta attribute) (wc_lang.core.ChemicalStructure.Meta attribute) (wc_lang.core.Compartment.Meta attribute) (wc_lang.core.Conclusion.Meta attribute) (wc_lang.core.DfbaObjective.Meta attribute) (wc_lang.core.DfbaObjectiveExpression.Meta attribute) (wc_lang.core.DfbaObjReaction.Meta attribute) (wc_lang.core.DfbaObjSpecies.Meta attribute) (wc_lang.core.DistributionInitConcentration.Meta attribute) (wc_lang.core.Environment.Meta attribute) (wc_lang.core.Evidence.Meta attribute) (wc_lang.core.FluxBounds.Meta attribute) (wc_lang.core.Function.Meta attribute) (wc_lang.core.FunctionExpression.Meta attribute) (wc_lang.core.Identifier.Meta attribute) (wc_lang.core.InitVolume.Meta attribute) (wc_lang.core.Model.Meta attribute) (wc_lang.core.Observable.Meta attribute) (wc_lang.core.ObservableExpression.Meta attribute) (wc_lang.core.Observation.Meta attribute) (wc_lang.core.ObservationEnv.Meta attribute) (wc_lang.core.ObservationGenotype.Meta attribute) (wc_lang.core.ObservationSet.Meta attribute) (wc_lang.core.Parameter.Meta attribute) (wc_lang.core.Ph.Meta attribute) (wc_lang.core.Process.Meta attribute) (wc_lang.core.RateLaw.Meta attribute) (wc_lang.core.RateLawExpression.Meta attribute) (wc_lang.core.Reaction.Meta attribute) (wc_lang.core.Reference.Meta attribute) (wc_lang.core.Species.Meta attribute) (wc_lang.core.SpeciesCoefficient.Meta attribute) (wc_lang.core.SpeciesType.Meta attribute) (wc_lang.core.StopCondition.Meta attribute) (wc_lang.core.StopConditionExpression.Meta attribute) (wc_lang.core.Submodel.Meta attribute) (wc_lang.core.Taxon.Meta attribute) organization (wc_lang.core.Author attribute), [1]

P

pages (wc_lang.core.Reference attribute), [1] Parameter (class in wc_lang.core) Parameter.Meta (class in wc_lang.core) parameters (wc_lang.core.FunctionExpression attribute), [1] (wc_lang.core.RateLawExpression attribute), [1] (wc_lang.core.StopConditionExpression attribute), [1] parent_compartment (wc_lang.core.Compartment attribute), [1] parse_annotations() (wc_lang.sbml.util.LibSbmlInterface class method) parse_id() (wc_lang.core.Species class method) parse_parameter() (wc_lang.sbml.util.LibSbmlInterface class method) parse_sbml_id() (wc_lang.sbml.util.SbmlModelMixin class method) parse_unit_id() (wc_lang.sbml.util.LibSbmlInterface class method) parse_units() (wc_lang.sbml.util.LibSbmlInterface class method) participants (wc_lang.core.Reaction attribute), [1] Ph (class in wc_lang.core) ph (wc_lang.core.Compartment attribute), [1] (wc_lang.core.ObservationEnv attribute), [1] Ph.Meta (class in wc_lang.core) ph_units (wc_lang.core.ObservationEnv attribute), [1] phylum (wc_lang.core.TaxonRank attribute) physical_type (wc_lang.core.Compartment attribute), [1] PrepForSbmlTransform (class in wc_lang.transform.prep_for_sbml) PrepForSbmlTransform.Meta (class in wc_lang.transform.prep_for_sbml) PrepForWcSimTransform (class in wc_lang.transform.prep_for_wc_sim) PrepForWcSimTransform.Meta (class in wc_lang.transform.prep_for_wc_sim) primary_attribute (wc_lang.core.Author.Meta attribute) (wc_lang.core.Change.Meta attribute) (wc_lang.core.ChemicalStructure.Meta attribute) (wc_lang.core.Compartment.Meta attribute) (wc_lang.core.Conclusion.Meta attribute) (wc_lang.core.DfbaObjective.Meta attribute) (wc_lang.core.DfbaObjectiveExpression.Meta attribute) (wc_lang.core.DfbaObjReaction.Meta attribute) (wc_lang.core.DfbaObjSpecies.Meta attribute) (wc_lang.core.DistributionInitConcentration.Meta attribute) (wc_lang.core.Environment.Meta attribute) (wc_lang.core.Evidence.Meta attribute) (wc_lang.core.FluxBounds.Meta attribute) (wc_lang.core.Function.Meta attribute) (wc_lang.core.FunctionExpression.Meta attribute) (wc_lang.core.Identifier.Meta attribute) (wc_lang.core.InitVolume.Meta attribute) (wc_lang.core.Model.Meta attribute) (wc_lang.core.Observable.Meta attribute) (wc_lang.core.ObservableExpression.Meta attribute) (wc_lang.core.Observation.Meta attribute) (wc_lang.core.ObservationEnv.Meta attribute) (wc_lang.core.ObservationGenotype.Meta attribute) (wc_lang.core.ObservationSet.Meta attribute) (wc_lang.core.Parameter.Meta attribute) (wc_lang.core.Ph.Meta attribute) (wc_lang.core.Process.Meta attribute) (wc_lang.core.RateLaw.Meta attribute) (wc_lang.core.RateLawExpression.Meta attribute) (wc_lang.core.Reaction.Meta attribute) (wc_lang.core.Reference.Meta attribute) (wc_lang.core.Species.Meta attribute) (wc_lang.core.SpeciesCoefficient.Meta attribute) (wc_lang.core.SpeciesType.Meta attribute) (wc_lang.core.StopCondition.Meta attribute) (wc_lang.core.StopConditionExpression.Meta attribute) (wc_lang.core.Submodel.Meta attribute) (wc_lang.core.Taxon.Meta attribute)

Process (class in wc_lang.core) process (wc_lang.core.Conclusion attribute), [1] Process.Meta (class in wc_lang.core) protein (wc_lang.core.ChemicalStructureAlphabet attribute) publication (wc_lang.core.Reference attribute), [1] publisher (wc_lang.core.Reference attribute), [1]

Q

quality (wc_lang.core.Evidence attribute), [1]

R

raise_if_error() (wc_lang.sbml.util.LibSbmlInterface class method) rank (wc_lang.core.Taxon attribute), [1] rate_units (wc_lang.core.Reaction attribute), [1] RateLaw (class in wc_lang.core) RateLaw.Meta (class in wc_lang.core) RateLawDirection (class in wc_lang.core) RateLawExpression (class in wc_lang.core) RateLawExpression.Meta (class in wc_lang.core) Reaction (class in wc_lang.core) reaction (wc_lang.core.RateLaw attribute), [1] Reaction.Meta (class in wc_lang.core) reaction_rate_units (wc_lang.core.DfbaObjective attribute), [1] ReactionParticipantAttribute (class in wc_lang.core) ReactionParticipantAttribute.Transformer (class in wc_lang.core) reactions (wc_lang.core.DfbaObjectiveExpression attribute), [1] Reader (class in wc_lang.io) reason (wc_lang.core.Change attribute), [1] reason_type (wc_lang.core.Change attribute), [1] Reference (class in wc_lang.core) Reference.Meta (class in wc_lang.core) references (wc_lang.core.Change attribute), [1] (wc_lang.core.Compartment attribute), [1] (wc_lang.core.Conclusion attribute), [1] (wc_lang.core.DfbaObjective attribute), [1] (wc_lang.core.DfbaObjReaction attribute), [1] (wc_lang.core.DfbaObjSpecies attribute), [1] (wc_lang.core.DistributionInitConcentration attribute), [1] (wc_lang.core.Environment attribute), [1] (wc_lang.core.Function attribute), [1] (wc_lang.core.Observable attribute), [1] (wc_lang.core.Observation attribute), [1] (wc_lang.core.ObservationSet attribute), [1] (wc_lang.core.Parameter attribute), [1] (wc_lang.core.RateLaw attribute), [1] (wc_lang.core.Reaction attribute), [1] (wc_lang.core.Species attribute), [1] (wc_lang.core.SpeciesType attribute), [1] (wc_lang.core.StopCondition attribute), [1] (wc_lang.core.Submodel attribute), [1] (wc_lang.core.Taxon attribute), [1] related_attributes (wc_lang.core.Author.Meta attribute) (wc_lang.core.Change.Meta attribute) (wc_lang.core.ChemicalStructure.Meta attribute) (wc_lang.core.Compartment.Meta attribute) (wc_lang.core.Conclusion.Meta attribute) (wc_lang.core.DfbaObjective.Meta attribute) (wc_lang.core.DfbaObjectiveExpression.Meta attribute) (wc_lang.core.DfbaObjReaction.Meta attribute) (wc_lang.core.DfbaObjSpecies.Meta attribute) (wc_lang.core.DistributionInitConcentration.Meta attribute) (wc_lang.core.Environment.Meta attribute) (wc_lang.core.Evidence.Meta attribute) (wc_lang.core.FluxBounds.Meta attribute) (wc_lang.core.Function.Meta attribute) (wc_lang.core.FunctionExpression.Meta attribute) (wc_lang.core.Identifier.Meta attribute) (wc_lang.core.InitVolume.Meta attribute) (wc_lang.core.Model.Meta attribute) (wc_lang.core.Observable.Meta attribute) (wc_lang.core.ObservableExpression.Meta attribute) (wc_lang.core.Observation.Meta attribute) (wc_lang.core.ObservationEnv.Meta attribute) (wc_lang.core.ObservationGenotype.Meta attribute) (wc_lang.core.ObservationSet.Meta attribute) (wc_lang.core.Parameter.Meta attribute) (wc_lang.core.Ph.Meta attribute) (wc_lang.core.Process.Meta attribute) (wc_lang.core.RateLaw.Meta attribute) (wc_lang.core.RateLawExpression.Meta attribute) (wc_lang.core.Reaction.Meta attribute) (wc_lang.core.Reference.Meta attribute) (wc_lang.core.Species.Meta attribute) (wc_lang.core.SpeciesCoefficient.Meta attribute) (wc_lang.core.SpeciesType.Meta attribute) (wc_lang.core.StopCondition.Meta attribute) (wc_lang.core.StopConditionExpression.Meta attribute) (wc_lang.core.Submodel.Meta attribute) (wc_lang.core.Taxon.Meta attribute)

remove_metadata() (wc_lang.__main__.DifferenceController static method) reversible (wc_lang.core.Reaction attribute), [1] revision (wc_lang.core.Model attribute), [1] rna (wc_lang.core.ChemicalStructureAlphabet attribute) run() (wc_lang.core.Validator method) (wc_lang.io.Reader method) (wc_lang.io.Writer method) (wc_lang.sbml.io.SbmlExporter class method) (wc_lang.sbml.io.SbmlImporter class method) (wc_lang.sbml.io.SbmlReader method) (wc_lang.sbml.io.SbmlWriter method) (wc_lang.transform.change_value.ChangeValueTransform method) (wc_lang.transform.core.CompositeTransform method) (wc_lang.transform.core.Transform method) (wc_lang.transform.create_implicit_dfba_ex_rxns.CreateImplicitDfbaExchangeReactionsTransform method) (wc_lang.transform.create_implicit_dist_zero_init_concs.CreateImplicitDistributionZeroInitConcentrationsTransform method) (wc_lang.transform.merge_submodels.MergeAlgorithmicallyLikeSubmodelsTransform method) (wc_lang.transform.nullify_attrs.NullifyAttrsTransform method) (wc_lang.transform.set_finite_dfba_flux_bounds.SetFiniteDfbaFluxBoundsTransform method) (wc_lang.transform.split_reversible_reactions.SplitReversibleReactionsTransform method)

S

SbmlAssignmentRuleMixin (class in wc_lang.sbml.util) SbmlExporter (class in wc_lang.sbml.io) SbmlImporter (class in wc_lang.sbml.io) SbmlModelMixin (class in wc_lang.sbml.util) SbmlReader (class in wc_lang.sbml.io) SbmlWriter (class in wc_lang.sbml.io) SEPARATOR (wc_lang.core.CommentAttribute attribute) serialize() (wc_lang.core.ChemicalStructure method) (wc_lang.core.DfbaObjectiveExpression method) (wc_lang.core.Evidence method) (wc_lang.core.EvidenceManyToManyAttribute method) (wc_lang.core.FluxBounds method) (wc_lang.core.FunctionExpression method) (wc_lang.core.Identifier method) (wc_lang.core.IdentifierToManyGrammarAttribute method) (wc_lang.core.InitVolume method) (wc_lang.core.ObservableExpression method) (wc_lang.core.ObservationEnv method) (wc_lang.core.ObservationGenotype method) (wc_lang.core.Ph method) (wc_lang.core.Process method) (wc_lang.core.RateLawExpression method) (wc_lang.core.ReactionParticipantAttribute method) (wc_lang.core.SpeciesCoefficient method) (wc_lang.core.StopConditionExpression method) series (wc_lang.core.Reference attribute), [1] set_annotations() (wc_lang.sbml.util.LibSbmlInterface class method) set_commments() (wc_lang.sbml.util.LibSbmlInterface class method) set_math() (wc_lang.sbml.util.LibSbmlInterface class method) set_unit() (wc_lang.sbml.util.LibSbmlInterface class method) SetFiniteDfbaFluxBoundsTransform (class in wc_lang.transform.set_finite_dfba_flux_bounds) SetFiniteDfbaFluxBoundsTransform.Meta (class in wc_lang.transform.set_finite_dfba_flux_bounds) smiles (wc_lang.core.ChemicalStructureFormat attribute) Species (class in wc_lang.core) species (wc_lang.core.DfbaObjSpecies attribute), [1] (wc_lang.core.DistributionInitConcentration attribute), [1] (wc_lang.core.FunctionExpression attribute), [1] (wc_lang.core.ObservableExpression attribute), [1] (wc_lang.core.RateLawExpression attribute), [1] (wc_lang.core.SpeciesCoefficient attribute), [1] (wc_lang.core.StopConditionExpression attribute), [1] (wc_lang.core.TaxonRank attribute) Species.Meta (class in wc_lang.core) species_type (wc_lang.core.Species attribute), [1] SpeciesCoefficient (class in wc_lang.core) SpeciesCoefficient.Meta (class in wc_lang.core)

SpeciesType (class in wc_lang.core) SpeciesType.Meta (class in wc_lang.core) SplitReversibleReactionsTransform (class in wc_lang.transform.split_reversible_reactions) SplitReversibleReactionsTransform.Meta (class in wc_lang.transform.split_reversible_reactions) stacked_on (wc_lang.__main__.ConvertController.Meta attribute) (wc_lang.__main__.CreateTemplateController.Meta attribute) (wc_lang.__main__.CutSubmodelsController.Meta attribute) (wc_lang.__main__.DifferenceController.Meta attribute) (wc_lang.__main__.ExportController.Meta attribute) (wc_lang.__main__.ImportController.Meta attribute) (wc_lang.__main__.MergeModelsController.Meta attribute) (wc_lang.__main__.NormalizeController.Meta attribute) (wc_lang.__main__.TransformController.Meta attribute) (wc_lang.__main__.UpdateVersionMetadataController.Meta attribute) (wc_lang.__main__.ValidateController.Meta attribute) stacked_type (wc_lang.__main__.ConvertController.Meta attribute) (wc_lang.__main__.CreateTemplateController.Meta attribute) (wc_lang.__main__.CutSubmodelsController.Meta attribute) (wc_lang.__main__.DifferenceController.Meta attribute) (wc_lang.__main__.ExportController.Meta attribute) (wc_lang.__main__.ImportController.Meta attribute) (wc_lang.__main__.MergeModelsController.Meta attribute) (wc_lang.__main__.NormalizeController.Meta attribute) (wc_lang.__main__.TransformController.Meta attribute) (wc_lang.__main__.UpdateVersionMetadataController.Meta attribute) (wc_lang.__main__.ValidateController.Meta attribute) start() (wc_lang.core.ReactionParticipantAttribute.Transformer method) std (wc_lang.core.Conclusion attribute), [1] (wc_lang.core.DistributionInitConcentration attribute), [1] (wc_lang.core.InitVolume attribute), [1] (wc_lang.core.Observation attribute), [1] (wc_lang.core.Parameter attribute), [1] (wc_lang.core.Ph attribute), [1] StopCondition (class in wc_lang.core) StopCondition.Meta (class in wc_lang.core) StopConditionExpression (class in wc_lang.core) StopConditionExpression.Meta (class in wc_lang.core) str_from_xml_node() (wc_lang.sbml.util.LibSbmlInterface class method) str_to_xml_node() (wc_lang.sbml.util.LibSbmlInterface class method) strength (wc_lang.core.Evidence attribute) structure (wc_lang.core.SpeciesType attribute), [1] Submodel (class in wc_lang.core) submodel (wc_lang.core.DfbaObjective attribute), [1] (wc_lang.core.DfbaObjReaction attribute), [1] (wc_lang.core.Reaction attribute), [1] Submodel.Meta (class in wc_lang.core) SubmodelsToModelRelatedManager (class in wc_lang.core)

T

table_format (wc_lang.core.ChemicalStructure.Meta attribute) (wc_lang.core.DfbaObjectiveExpression.Meta attribute) (wc_lang.core.Environment.Meta attribute) (wc_lang.core.Evidence.Meta attribute) (wc_lang.core.FluxBounds.Meta attribute) (wc_lang.core.FunctionExpression.Meta attribute) (wc_lang.core.Identifier.Meta attribute) (wc_lang.core.InitVolume.Meta attribute) (wc_lang.core.Model.Meta attribute) (wc_lang.core.ObservableExpression.Meta attribute) (wc_lang.core.ObservationEnv.Meta attribute) (wc_lang.core.ObservationGenotype.Meta attribute) (wc_lang.core.Ph.Meta attribute) (wc_lang.core.Process.Meta attribute) (wc_lang.core.RateLawExpression.Meta attribute) (wc_lang.core.SpeciesCoefficient.Meta attribute) (wc_lang.core.StopConditionExpression.Meta attribute) (wc_lang.core.Taxon.Meta attribute) target (wc_lang.core.Change attribute), [1] target_submodel (wc_lang.core.Change attribute), [1] target_type (wc_lang.core.Change attribute), [1] Taxon (class in wc_lang.core)

taxon (wc_lang.core.ObservationGenotype attribute), [1] Taxon.Meta (class in wc_lang.core) TaxonRank (class in wc_lang.core) TaxonRankMeta (class in wc_lang.core) temp (wc_lang.core.Environment attribute), [1] (wc_lang.core.ObservationEnv attribute), [1] temp_units (wc_lang.core.Environment attribute), [1] (wc_lang.core.ObservationEnv attribute), [1] time_units (wc_lang.core.Model attribute), [1] title (wc_lang.core.Author attribute), [1] (wc_lang.core.Reference attribute), [1] Transform (class in wc_lang.transform.core) TransformController (class in wc_lang.__main__) TransformController.Meta (class in wc_lang.__main__) tribe (wc_lang.core.TaxonRank attribute) type (wc_lang.core.Change attribute), [1] (wc_lang.core.Conclusion attribute), [1] (wc_lang.core.Evidence attribute), [1] (wc_lang.core.Observation attribute), [1] (wc_lang.core.Parameter attribute), [1] (wc_lang.core.RateLaw attribute), [1] (wc_lang.core.Reference attribute), [1] (wc_lang.core.SpeciesType attribute), [1]

U

unique_together (wc_lang.core.Author.Meta attribute) (wc_lang.core.Change.Meta attribute) (wc_lang.core.ChemicalStructure.Meta attribute) (wc_lang.core.Compartment.Meta attribute) (wc_lang.core.Conclusion.Meta attribute) (wc_lang.core.DfbaObjective.Meta attribute) (wc_lang.core.DfbaObjectiveExpression.Meta attribute) (wc_lang.core.DfbaObjReaction.Meta attribute) (wc_lang.core.DfbaObjSpecies.Meta attribute) (wc_lang.core.DistributionInitConcentration.Meta attribute) (wc_lang.core.Environment.Meta attribute) (wc_lang.core.Evidence.Meta attribute) (wc_lang.core.FluxBounds.Meta attribute) (wc_lang.core.Function.Meta attribute) (wc_lang.core.FunctionExpression.Meta attribute) (wc_lang.core.Identifier.Meta attribute) (wc_lang.core.InitVolume.Meta attribute) (wc_lang.core.Model.Meta attribute) (wc_lang.core.Observable.Meta attribute) (wc_lang.core.ObservableExpression.Meta attribute) (wc_lang.core.Observation.Meta attribute) (wc_lang.core.ObservationEnv.Meta attribute) (wc_lang.core.ObservationGenotype.Meta attribute) (wc_lang.core.ObservationSet.Meta attribute) (wc_lang.core.Parameter.Meta attribute) (wc_lang.core.Ph.Meta attribute) (wc_lang.core.Process.Meta attribute) (wc_lang.core.RateLaw.Meta attribute) (wc_lang.core.RateLawExpression.Meta attribute) (wc_lang.core.Reaction.Meta attribute) (wc_lang.core.Reference.Meta attribute) (wc_lang.core.Species.Meta attribute) (wc_lang.core.SpeciesCoefficient.Meta attribute) (wc_lang.core.SpeciesType.Meta attribute) (wc_lang.core.StopCondition.Meta attribute) (wc_lang.core.StopConditionExpression.Meta attribute) (wc_lang.core.Submodel.Meta attribute) (wc_lang.core.Taxon.Meta attribute)

units (wc_lang.core.Conclusion attribute), [1] (wc_lang.core.DfbaObjective attribute), [1] (wc_lang.core.DfbaObjReaction attribute), [1] (wc_lang.core.DfbaObjSpecies attribute), [1] (wc_lang.core.DistributionInitConcentration attribute), [1] (wc_lang.core.FluxBounds attribute), [1] (wc_lang.core.Function attribute), [1] (wc_lang.core.InitVolume attribute), [1] (wc_lang.core.Observable attribute), [1] (wc_lang.core.Observation attribute), [1] (wc_lang.core.Parameter attribute), [1] (wc_lang.core.Ph attribute), [1] (wc_lang.core.RateLaw attribute), [1] (wc_lang.core.Species attribute), [1] (wc_lang.core.StopCondition attribute), [1] updated (wc_lang.core.Model attribute), [1] UpdateVersionMetadataController (class in wc_lang.__main__) UpdateVersionMetadataController.Meta (class in wc_lang.__main__) url (wc_lang.core.Model attribute), [1]

V

validate() (wc_lang.core.ChemicalStructure method) (wc_lang.core.Compartment method) (wc_lang.core.DfbaObjective method) (wc_lang.core.DfbaObjectiveExpression method) (wc_lang.core.DfbaObjSpecies method) (wc_lang.core.DistributionInitConcentration method) (wc_lang.core.Function method) (wc_lang.core.FunctionExpression method) (wc_lang.core.Model method) (wc_lang.core.ObservableExpression method) (wc_lang.core.ObservationEnv method) (wc_lang.core.RateLaw method) (wc_lang.core.RateLawExpression method) (wc_lang.core.Reaction method) (wc_lang.core.ReactionParticipantAttribute method) (wc_lang.core.Species method) (wc_lang.core.StopCondition method) (wc_lang.core.StopConditionExpression method) (wc_lang.core.Submodel method) validate_config() (in module wc_lang.config.core) validate_implicit_relationships() (wc_lang.io.Writer class method) validate_implicit_relationships_are_set() (wc_lang.io.Writer method) ValidateController (class in wc_lang.__main__) ValidateController.Meta (class in wc_lang.__main__) Validator (class in wc_lang.core) value (wc_lang.core.ChemicalStructure attribute), [1] (wc_lang.core.Conclusion attribute), [1] (wc_lang.core.DfbaObjSpecies attribute), [1] (wc_lang.core.Observation attribute), [1] (wc_lang.core.Parameter attribute), [1] (wc_lang.transform.change_value.ChangeValueTransform attribute) variant (wc_lang.core.ObservationGenotype attribute) variety (wc_lang.core.TaxonRank attribute) verbose_name (wc_lang.core.Author.Meta attribute) (wc_lang.core.Change.Meta attribute) (wc_lang.core.ChemicalStructure.Meta attribute) (wc_lang.core.Compartment.Meta attribute) (wc_lang.core.Conclusion.Meta attribute) (wc_lang.core.DfbaObjective.Meta attribute) (wc_lang.core.DfbaObjectiveExpression.Meta attribute) (wc_lang.core.DfbaObjReaction.Meta attribute) (wc_lang.core.DfbaObjSpecies.Meta attribute) (wc_lang.core.DistributionInitConcentration.Meta attribute) (wc_lang.core.Environment.Meta attribute) (wc_lang.core.Evidence.Meta attribute) (wc_lang.core.FluxBounds.Meta attribute) (wc_lang.core.Function.Meta attribute) (wc_lang.core.FunctionExpression.Meta attribute) (wc_lang.core.Identifier.Meta attribute) (wc_lang.core.InitVolume.Meta attribute) (wc_lang.core.Model.Meta attribute) (wc_lang.core.Observable.Meta attribute) (wc_lang.core.ObservableExpression.Meta attribute) (wc_lang.core.Observation.Meta attribute) (wc_lang.core.ObservationEnv.Meta attribute) (wc_lang.core.ObservationGenotype.Meta attribute) (wc_lang.core.ObservationSet.Meta attribute) (wc_lang.core.Parameter.Meta attribute) (wc_lang.core.Ph.Meta attribute) (wc_lang.core.Process.Meta attribute) (wc_lang.core.RateLaw.Meta attribute) (wc_lang.core.RateLawExpression.Meta attribute) (wc_lang.core.Reaction.Meta attribute) (wc_lang.core.Reference.Meta attribute) (wc_lang.core.Species.Meta attribute) (wc_lang.core.SpeciesCoefficient.Meta attribute) (wc_lang.core.SpeciesType.Meta attribute) (wc_lang.core.StopCondition.Meta attribute) (wc_lang.core.StopConditionExpression.Meta attribute) (wc_lang.core.Submodel.Meta attribute) (wc_lang.core.Taxon.Meta attribute)

verbose_name_plural (wc_lang.core.Author.Meta attribute) (wc_lang.core.Change.Meta attribute) (wc_lang.core.ChemicalStructure.Meta attribute) (wc_lang.core.Compartment.Meta attribute) (wc_lang.core.Conclusion.Meta attribute) (wc_lang.core.DfbaObjective.Meta attribute) (wc_lang.core.DfbaObjectiveExpression.Meta attribute) (wc_lang.core.DfbaObjReaction.Meta attribute) (wc_lang.core.DfbaObjSpecies.Meta attribute) (wc_lang.core.DistributionInitConcentration.Meta attribute) (wc_lang.core.Environment.Meta attribute) (wc_lang.core.Evidence.Meta attribute) (wc_lang.core.FluxBounds.Meta attribute) (wc_lang.core.Function.Meta attribute) (wc_lang.core.FunctionExpression.Meta attribute) (wc_lang.core.Identifier.Meta attribute) (wc_lang.core.InitVolume.Meta attribute) (wc_lang.core.Model.Meta attribute) (wc_lang.core.Observable.Meta attribute) (wc_lang.core.ObservableExpression.Meta attribute) (wc_lang.core.Observation.Meta attribute) (wc_lang.core.ObservationEnv.Meta attribute) (wc_lang.core.ObservationGenotype.Meta attribute) (wc_lang.core.ObservationSet.Meta attribute) (wc_lang.core.Parameter.Meta attribute) (wc_lang.core.Ph.Meta attribute) (wc_lang.core.Process.Meta attribute) (wc_lang.core.RateLaw.Meta attribute) (wc_lang.core.RateLawExpression.Meta attribute) (wc_lang.core.Reaction.Meta attribute) (wc_lang.core.Reference.Meta attribute) (wc_lang.core.Species.Meta attribute) (wc_lang.core.SpeciesCoefficient.Meta attribute) (wc_lang.core.SpeciesType.Meta attribute) (wc_lang.core.StopCondition.Meta attribute) (wc_lang.core.StopConditionExpression.Meta attribute) (wc_lang.core.Submodel.Meta attribute) (wc_lang.core.Taxon.Meta attribute) verify_doc() (wc_lang.sbml.util.LibSbmlInterface class method) verify_doc_is_compatible() (wc_lang.sbml.util.LibSbmlInterface class method) verify_doc_is_consistent() (wc_lang.sbml.util.LibSbmlInterface class method) verify_doc_is_valid_sbml() (wc_lang.sbml.util.LibSbmlInterface class method) version (wc_lang.core.Model attribute), [1] (wc_lang.core.Process attribute), [1] volume (wc_lang.core.Reference attribute), [1]

W

wc_lang (module) wc_lang.__main__ (module) wc_lang._version (module) wc_lang.config (module) wc_lang.config.core (module) wc_lang.core (module) wc_lang.io (module) wc_lang.migrations (module) wc_lang.migrations.custom_io_classes (module) wc_lang.sbml (module) wc_lang.sbml.io (module) wc_lang.sbml.util (module) wc_lang.transform (module) wc_lang.transform.change_value (module)

wc_lang.transform.core (module) wc_lang.transform.create_implicit_dfba_ex_rxns (module) wc_lang.transform.create_implicit_dist_zero_init_concs (module) wc_lang.transform.merge_submodels (module) wc_lang.transform.nullify_attrs (module) wc_lang.transform.prep_for_sbml (module) wc_lang.transform.prep_for_wc_sim (module) wc_lang.transform.set_finite_dfba_flux_bounds (module) wc_lang.transform.split_reversible_reactions (module) wc_lang.util (module) wc_lang_version (wc_lang.core.Model attribute), [1] WcLangWarning website (wc_lang.core.Author attribute), [1] Writer (class in wc_lang.io)

X

XML_NAMESPACE (wc_lang.sbml.util.LibSbmlInterface attribute)

Y

year (wc_lang.core.Reference attribute), [1]