biggr.models ============ .. py:module:: biggr.models .. autoapi-nested-parse:: Module to mimic the cobradb models Attributes ---------- .. autoapisummary:: biggr.models.OBJECT_CACHE biggr.models.LAZY_LOADING biggr.models.T biggr.models.ForeignKey biggr.models.UniqueConstraint biggr.models.Enum biggr.models.mapped_column biggr.models.relationship biggr.models.String biggr.models.DateTime biggr.models.HASH_STR_MAX_LEN biggr.models.custom_enums biggr.models.COMPOUND_TYPE_TO_SBO Classes ------- .. autoapisummary:: biggr.models.Mapped biggr.models.PropertyNotLoaded biggr.models.ORMDummy biggr.models.DeclarativeMeta biggr.models.DeclarativeBase biggr.models.Base biggr.models.BiGGBase biggr.models.InChI biggr.models.TaxonomicRank biggr.models.Taxon biggr.models.ModelCollection biggr.models.Genome biggr.models.Chromosome biggr.models.GenomeRegion biggr.models.ReferenceCompound biggr.models.UniversalComponent biggr.models.Component biggr.models.ComponentReferenceMapping biggr.models.UniversalComponentReferenceMapping biggr.models.DataSource biggr.models.Annotation biggr.models.AnnotationProperty biggr.models.AnnotationLink biggr.models.ComponentAnnotationMapping biggr.models.ReactionAnnotationMapping biggr.models.ReferenceCompoundAnnotationMapping biggr.models.ReferenceReactionAnnotationMapping biggr.models.Synonym biggr.models.Publication biggr.models.PublicationModel biggr.models.OldIDSynonym biggr.models.GenomeRegionMap biggr.models.DeprecatedID biggr.models.Model biggr.models.ModelGene biggr.models.ModelReaction biggr.models.GeneReactionMatrix biggr.models.UniversalCompartmentalizedComponent biggr.models.CompartmentalizedComponent biggr.models.ModelCompartmentalizedComponent biggr.models.Compartment biggr.models.EscherMap biggr.models.EscherMapMatrix biggr.models.ModelCount biggr.models.Gene biggr.models.ReferenceReactivePart biggr.models.ReferenceReactivePartMatrix biggr.models.ReferenceReaction biggr.models.ReferenceReactionParticipant biggr.models.UniversalReaction biggr.models.Reaction biggr.models.UniversalReactionMatrix biggr.models.ReactionMatrix biggr.models.ComponentIDMapping biggr.models.MemoteTest biggr.models.MemoteResult biggr.models.EscherModule biggr.models.ModelReactionEscherMapping Functions --------- .. autoapisummary:: biggr.models.dummy_col_f biggr.models.dummy_f biggr.models.hybrid_property Module Contents --------------- .. py:data:: OBJECT_CACHE .. py:data:: LAZY_LOADING :value: True .. py:data:: T .. py:class:: Mapped Bases: :py:obj:`Generic`\ [\ :py:obj:`T`\ ] Makes it easier to reuse cobradb/sqlalchemy code. .. py:class:: PropertyNotLoaded .. py:class:: ORMDummy(*args, **kwargs) .. py:attribute:: args :value: () .. py:attribute:: kwargs .. py:data:: ForeignKey .. py:data:: UniqueConstraint .. py:data:: Enum .. py:function:: dummy_col_f(*args, obj_type: Type[T] = str, **kwargs) -> Mapped[T] .. py:function:: dummy_f(*args, **kwargs) .. py:function:: hybrid_property(f) .. py:data:: mapped_column .. py:data:: relationship .. py:data:: String .. py:data:: DateTime .. py:data:: HASH_STR_MAX_LEN :value: 5000 .. py:data:: custom_enums .. py:data:: COMPOUND_TYPE_TO_SBO .. py:class:: DeclarativeMeta Bases: :py:obj:`type` .. py:class:: DeclarativeBase(**kwargs) .. py:class:: Base(**kwargs) Bases: :py:obj:`DeclarativeBase` .. py:method:: from_dict(d) :classmethod: .. py:class:: BiGGBase .. py:attribute:: id :type: Mapped[int] .. py:attribute:: bigg_id :type: Mapped[str] .. py:class:: InChI(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: formula :type: Mapped[str] .. py:attribute:: c :type: Mapped[Optional[str]] .. py:attribute:: h :type: Mapped[Optional[str]] .. py:attribute:: q :type: Mapped[Optional[str]] .. py:attribute:: p :type: Mapped[Optional[str]] .. py:attribute:: b :type: Mapped[Optional[str]] .. py:attribute:: t :type: Mapped[Optional[str]] .. py:attribute:: m :type: Mapped[Optional[str]] .. py:attribute:: s :type: Mapped[Optional[str]] .. py:attribute:: key_major :type: Mapped[str] .. py:attribute:: key_minor :type: Mapped[str] .. py:attribute:: key_proton :type: Mapped[str] .. py:attribute:: reference_compounds :type: Mapped[List[ReferenceCompound]] .. py:attribute:: reference_reactive_parts :type: Mapped[List[ReferenceReactivePart]] .. py:method:: key() .. py:method:: n_protons() .. py:method:: charge() .. py:class:: TaxonomicRank(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: name :type: Mapped[str] .. py:attribute:: taxons :type: Mapped[List[Taxon]] .. py:class:: Taxon(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: parent_id :type: Mapped[Optional[int]] .. py:attribute:: parent :type: Mapped[Optional[Taxon]] .. py:attribute:: children :type: Mapped[List[Taxon]] .. py:attribute:: name :type: Mapped[Optional[str]] .. py:attribute:: rank_id :type: Mapped[int] .. py:attribute:: rank :type: Mapped[TaxonomicRank] .. py:attribute:: genomes :type: Mapped[List[Genome]] .. py:attribute:: models :type: Mapped[List[Model]] .. py:attribute:: collections :type: Mapped[List[ModelCollection]] .. py:class:: ModelCollection(**kwargs) Bases: :py:obj:`Base`, :py:obj:`BiGGBase` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: bigg_id :type: Mapped[str] .. py:attribute:: oneliner :type: Mapped[Optional[str]] .. py:attribute:: description :type: Mapped[Optional[str]] .. py:attribute:: publication_id :type: Mapped[Optional[int]] .. py:attribute:: publication :type: Mapped[Optional[Publication]] .. py:attribute:: taxon_id :type: Mapped[Optional[int]] .. py:attribute:: taxon :type: Mapped[Optional[Taxon]] .. py:attribute:: models :type: Mapped[List[Model]] .. py:attribute:: collection_namespace_components :type: Mapped[List[Component]] .. py:attribute:: collection_namespace_universal_components :type: Mapped[List[UniversalComponent]] .. py:attribute:: collection_namespace_universal_reactions :type: Mapped[List[UniversalReaction]] .. py:attribute:: collection_namespace_reactions :type: Mapped[List[Reaction]] .. py:class:: Genome(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: accession_type :type: Mapped[str] .. py:attribute:: accession_value :type: Mapped[str] .. py:attribute:: organism :type: Mapped[Optional[str]] .. py:attribute:: taxon_id :type: Mapped[Optional[int]] .. py:attribute:: taxon :type: Mapped[Optional[Taxon]] .. py:attribute:: strain :type: Mapped[Optional[str]] .. py:attribute:: ncbi_assembly_id :type: Mapped[Optional[str]] .. py:attribute:: chromosomes :type: Mapped[List[Chromosome]] .. py:attribute:: models :type: Mapped[List[Model]] .. py:class:: Chromosome(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: ncbi_accession :type: Mapped[str] .. py:attribute:: genome_id :type: Mapped[int] .. py:attribute:: genome :type: Mapped[Genome] .. py:attribute:: genome_regions :type: Mapped[List[GenomeRegion]] .. py:class:: GenomeRegion(**kwargs) Bases: :py:obj:`Base`, :py:obj:`BiGGBase` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: bigg_id :type: Mapped[str] .. py:attribute:: chromosome_id :type: Mapped[Optional[int]] .. py:attribute:: chromosome :type: Mapped[Optional[Chromosome]] .. py:attribute:: leftpos :type: Mapped[Optional[int]] .. py:attribute:: rightpos :type: Mapped[Optional[int]] .. py:attribute:: strand :type: Mapped[Optional[str]] .. py:attribute:: type :type: Mapped[str] .. py:attribute:: dna_sequence :type: Mapped[Optional[str]] .. py:attribute:: protein_sequence :type: Mapped[Optional[str]] .. py:class:: ReferenceCompound(**kwargs) Bases: :py:obj:`Base`, :py:obj:`BiGGBase` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: bigg_id :type: Mapped[str] .. py:attribute:: name :type: Mapped[str] .. py:attribute:: html_name :type: Mapped[Optional[str]] .. py:attribute:: compound_type .. py:attribute:: charge :type: Mapped[Optional[str]] .. py:attribute:: formula :type: Mapped[Optional[str]] .. py:attribute:: inchi_id :type: Mapped[Optional[int]] .. py:attribute:: inchi :type: Mapped[Optional[InChI]] .. py:attribute:: reactive_part_matrix :type: Mapped[List[ReferenceReactivePartMatrix]] .. py:attribute:: reaction_participants :type: Mapped[List[ReferenceReactionParticipant]] .. py:attribute:: reference_mappings :type: Mapped[List[ComponentReferenceMapping]] .. py:attribute:: annotation_mappings :type: Mapped[List[ReferenceCompoundAnnotationMapping]] .. py:method:: get_sbo() .. py:class:: UniversalComponent(**kwargs) Bases: :py:obj:`Base`, :py:obj:`BiGGBase` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: bigg_id :type: Mapped[str] .. py:attribute:: default_component_id :type: Mapped[Optional[int]] .. py:attribute:: default_component :type: Mapped[Optional[Component]] .. py:attribute:: allow_flexible_variants :type: Mapped[bool] .. py:attribute:: name :type: Mapped[Optional[str]] .. py:attribute:: components :type: Mapped[List[Component]] .. py:attribute:: reference_mapping :type: Mapped[UniversalComponentReferenceMapping] .. py:attribute:: collection_id :type: Mapped[Optional[int]] .. py:attribute:: collection :type: Mapped[Optional[ModelCollection]] .. py:attribute:: universal_compartmentalized_components :type: Mapped[List[UniversalCompartmentalizedComponent]] .. py:attribute:: old_bigg_ids :type: Mapped[List[ComponentIDMapping]] .. py:attribute:: reference_mappings :type: Mapped[List[ComponentReferenceMapping]] .. py:class:: Component(**kwargs) Bases: :py:obj:`Base`, :py:obj:`BiGGBase` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: bigg_id :type: Mapped[str] .. py:attribute:: universal_component_id :type: Mapped[int] .. py:attribute:: universal_component :type: Mapped[UniversalComponent] .. py:attribute:: name :type: Mapped[Optional[str]] .. py:attribute:: formula :type: Mapped[Optional[str]] .. py:attribute:: charge :type: Mapped[int] .. py:attribute:: variant :type: Mapped[int] .. py:attribute:: collection_id :type: Mapped[Optional[int]] .. py:attribute:: collection :type: Mapped[Optional[ModelCollection]] .. py:attribute:: compartmentalized_components :type: Mapped[List[CompartmentalizedComponent]] .. py:attribute:: reference_mappings :type: Mapped[List[ComponentReferenceMapping]] .. py:attribute:: annotation_mappings :type: Mapped[List[ComponentAnnotationMapping]] .. py:method:: charge_to_string(coefficient) :staticmethod: .. py:class:: ComponentReferenceMapping(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: component_id :type: Mapped[int] .. py:attribute:: component :type: Mapped[Component] .. py:attribute:: universal_component_id :type: Mapped[int] .. py:attribute:: universal_component :type: Mapped[UniversalComponent] .. py:attribute:: reference_compound_id :type: Mapped[int] .. py:attribute:: reference_compound :type: Mapped[ReferenceCompound] .. py:attribute:: reference_n :type: Mapped[Optional[int]] .. py:attribute:: reference_formula_delta :type: Mapped[Optional[str]] .. py:attribute:: universal_component_reference_mapping :type: Mapped[Optional[UniversalComponentReferenceMapping]] .. py:class:: UniversalComponentReferenceMapping(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: universal_component :type: Mapped[UniversalComponent] .. py:attribute:: mapping_id :type: Mapped[int] .. py:attribute:: mapping :type: Mapped[ComponentReferenceMapping] .. py:class:: DataSource(**kwargs) Bases: :py:obj:`Base`, :py:obj:`BiGGBase` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: bigg_id :type: Mapped[str] .. py:attribute:: name :type: Mapped[Optional[str]] .. py:attribute:: url_prefix :type: Mapped[Optional[str]] .. py:attribute:: synonyms :type: Mapped[List[Synonym]] .. py:attribute:: annotations :type: Mapped[List[Annotation]] .. py:attribute:: annotation_links :type: Mapped[List[AnnotationLink]] .. py:class:: Annotation(**kwargs) Bases: :py:obj:`Base`, :py:obj:`BiGGBase` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: bigg_id :type: Mapped[str] .. py:attribute:: type .. py:attribute:: default_data_source_id :type: Mapped[int] .. py:attribute:: default_data_source :type: Mapped[DataSource] .. py:attribute:: is_obsolete :type: Mapped[bool] .. py:attribute:: properties :type: Mapped[List[AnnotationProperty]] .. py:attribute:: links :type: Mapped[List[AnnotationLink]] .. py:attribute:: component_mappings :type: Mapped[List[ComponentAnnotationMapping]] .. py:attribute:: reaction_mappings :type: Mapped[List[ReactionAnnotationMapping]] .. py:attribute:: reference_compound_mappings :type: Mapped[List[ReferenceCompoundAnnotationMapping]] .. py:attribute:: reference_reaction_mappings :type: Mapped[List[ReferenceReactionAnnotationMapping]] .. py:class:: AnnotationProperty(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: key :type: Mapped[str] .. py:attribute:: value_str :type: Mapped[Optional[str]] .. py:attribute:: value_int :type: Mapped[Optional[int]] .. py:attribute:: value_float :type: Mapped[Optional[float]] .. py:attribute:: type .. py:attribute:: annotation_id :type: Mapped[int] .. py:attribute:: annotation :type: Mapped[Annotation] .. py:method:: value() .. py:class:: AnnotationLink(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: identifier :type: Mapped[str] .. py:attribute:: data_source_id :type: Mapped[int] .. py:attribute:: data_source :type: Mapped[DataSource] .. py:attribute:: annotation_id :type: Mapped[int] .. py:attribute:: annotation :type: Mapped[Annotation] .. py:class:: ComponentAnnotationMapping(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: component_id :type: Mapped[int] .. py:attribute:: component :type: Mapped[Component] .. py:attribute:: annotation_id :type: Mapped[int] .. py:attribute:: annotation :type: Mapped[Annotation] .. py:attribute:: reference_match :type: Mapped[bool] .. py:attribute:: bigg_id_match :type: Mapped[Optional[bool]] .. py:attribute:: inchi_match :type: Mapped[Optional[bool]] .. py:class:: ReactionAnnotationMapping(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: reaction_id :type: Mapped[int] .. py:attribute:: reaction :type: Mapped[Reaction] .. py:attribute:: annotation_id :type: Mapped[int] .. py:attribute:: annotation :type: Mapped[Annotation] .. py:attribute:: bigg_id_match :type: Mapped[Optional[bool]] .. py:attribute:: pattern_match :type: Mapped[Optional[bool]] .. py:class:: ReferenceCompoundAnnotationMapping(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: reference_compound_id :type: Mapped[int] .. py:attribute:: reference_compound :type: Mapped[ReferenceCompound] .. py:attribute:: annotation_id :type: Mapped[int] .. py:attribute:: annotation :type: Mapped[Annotation] .. py:class:: ReferenceReactionAnnotationMapping(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: reference_reaction_id :type: Mapped[int] .. py:attribute:: reference_reaction :type: Mapped[ReferenceReaction] .. py:attribute:: annotation_id :type: Mapped[int] .. py:attribute:: annotation :type: Mapped[Annotation] .. py:class:: Synonym(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: ome_id :type: Mapped[int] .. py:attribute:: synonym :type: Mapped[str] .. py:attribute:: type .. py:attribute:: data_source_id :type: Mapped[int] .. py:attribute:: data_source :type: Mapped[DataSource] .. py:class:: Publication(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: reference_type .. py:attribute:: reference_id :type: Mapped[str] .. py:attribute:: publication_models :type: Mapped[List[PublicationModel]] .. py:attribute:: collections :type: Mapped[List[ModelCollection]] .. py:class:: PublicationModel(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: model_id :type: Mapped[int] .. py:attribute:: model :type: Mapped[Model] .. py:attribute:: publication_id :type: Mapped[int] .. py:attribute:: publication :type: Mapped[Publication] .. py:class:: OldIDSynonym(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: type .. py:attribute:: synonym_id :type: Mapped[int] .. py:attribute:: ome_id :type: Mapped[int] .. py:class:: GenomeRegionMap(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: genome_region_id_1 :type: Mapped[int] .. py:attribute:: genome_region_1 :type: Mapped[GenomeRegion] .. py:attribute:: genome_region_id_2 :type: Mapped[int] .. py:attribute:: genome_region_2 :type: Mapped[GenomeRegion] .. py:attribute:: distance :type: Mapped[int] .. py:class:: DeprecatedID(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: type .. py:attribute:: deprecated_id :type: Mapped[str] .. py:attribute:: ome_id :type: Mapped[int] .. py:class:: Model(**kwargs) Bases: :py:obj:`Base`, :py:obj:`BiGGBase` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: bigg_id :type: Mapped[str] .. py:attribute:: collection_id :type: Mapped[int] .. py:attribute:: collection :type: Mapped[ModelCollection] .. py:attribute:: base_filename :type: Mapped[Optional[str]] .. py:attribute:: genome_id :type: Mapped[int] .. py:attribute:: genome :type: Mapped[Genome] .. py:attribute:: organism :type: Mapped[Optional[str]] .. py:attribute:: taxon_id :type: Mapped[Optional[int]] .. py:attribute:: taxon :type: Mapped[Optional[Taxon]] .. py:attribute:: published_filename :type: Mapped[Optional[str]] .. py:attribute:: date_modified :type: Mapped[datetime.datetime] .. py:attribute:: model_genes :type: Mapped[List[ModelGene]] .. py:attribute:: model_reactions :type: Mapped[List[ModelReaction]] .. py:attribute:: model_compartmentalized_components :type: Mapped[List[ModelCompartmentalizedComponent]] .. py:attribute:: model_count :type: Mapped[Optional[ModelCount]] .. py:attribute:: publication_models :type: Mapped[List[PublicationModel]] .. py:attribute:: escher_maps :type: Mapped[List[EscherMap]] .. py:attribute:: memote_results :type: Mapped[List[MemoteResult]] .. py:class:: ModelGene(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: model_id :type: Mapped[int] .. py:attribute:: model :type: Mapped[Model] .. py:attribute:: gene_id :type: Mapped[int] .. py:attribute:: gene :type: Mapped[Gene] .. py:attribute:: reaction_matrix :type: Mapped[List[GeneReactionMatrix]] .. py:attribute:: memote_results :type: Mapped[List[MemoteResult]] .. py:class:: ModelReaction(**kwargs) Bases: :py:obj:`Base`, :py:obj:`BiGGBase` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: bigg_id :type: Mapped[str] .. py:attribute:: id_in_original_model :type: Mapped[str] .. py:attribute:: reaction_id :type: Mapped[int] .. py:attribute:: reaction :type: Mapped[Reaction] .. py:attribute:: reversed :type: Mapped[bool] .. py:attribute:: model_id :type: Mapped[int] .. py:attribute:: model :type: Mapped[Model] .. py:attribute:: copy_number :type: Mapped[int] .. py:attribute:: objective_coefficient :type: Mapped[float] .. py:attribute:: lower_bound :type: Mapped[float] .. py:attribute:: upper_bound :type: Mapped[float] .. py:attribute:: gene_reaction_rule :type: Mapped[str] .. py:attribute:: original_gene_reaction_rule :type: Mapped[Optional[str]] .. py:attribute:: subsystem :type: Mapped[Optional[str]] .. py:attribute:: reaction_matrix :type: Mapped[List[GeneReactionMatrix]] .. py:attribute:: memote_results :type: Mapped[List[MemoteResult]] .. py:attribute:: escher_mappings :type: Mapped[List[ModelReactionEscherMapping]] .. py:method:: create_id(model_id, universal_reaction_id, copy_number) :staticmethod: .. py:method:: interpret_id(bigg_id) :staticmethod: .. py:class:: GeneReactionMatrix(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: model_gene_id :type: Mapped[int] .. py:attribute:: model_gene :type: Mapped[ModelGene] .. py:attribute:: model_reaction_id :type: Mapped[int] .. py:attribute:: model_reaction :type: Mapped[ModelReaction] .. py:class:: UniversalCompartmentalizedComponent(**kwargs) Bases: :py:obj:`Base`, :py:obj:`BiGGBase` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: bigg_id :type: Mapped[str] .. py:attribute:: universal_component_id :type: Mapped[int] .. py:attribute:: universal_component :type: Mapped[UniversalComponent] .. py:attribute:: compartment_id :type: Mapped[int] .. py:attribute:: compartment :type: Mapped[Compartment] .. py:attribute:: compartmentalized_components :type: Mapped[List[CompartmentalizedComponent]] .. py:attribute:: matrix :type: Mapped[List[UniversalReactionMatrix]] .. py:class:: CompartmentalizedComponent(**kwargs) Bases: :py:obj:`Base`, :py:obj:`BiGGBase` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: bigg_id :type: Mapped[str] .. py:attribute:: component_id :type: Mapped[int] .. py:attribute:: component :type: Mapped[Component] .. py:attribute:: compartment_id :type: Mapped[int] .. py:attribute:: compartment :type: Mapped[Compartment] .. py:attribute:: universal_compartmentalized_component_id :type: Mapped[int] .. py:attribute:: universal_compartmentalized_component :type: Mapped[UniversalCompartmentalizedComponent] .. py:attribute:: model_compartmentalized_components :type: Mapped[List[ModelCompartmentalizedComponent]] .. py:attribute:: matrix :type: Mapped[List[ReactionMatrix]] .. py:class:: ModelCompartmentalizedComponent(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: bigg_id :type: Mapped[str] .. py:attribute:: id_in_original_model :type: Mapped[str] .. py:attribute:: model_id :type: Mapped[int] .. py:attribute:: model :type: Mapped[Model] .. py:attribute:: compartmentalized_component_id :type: Mapped[int] .. py:attribute:: compartmentalized_component :type: Mapped[CompartmentalizedComponent] .. py:attribute:: memote_results :type: Mapped[List[MemoteResult]] .. py:class:: Compartment(**kwargs) Bases: :py:obj:`Base`, :py:obj:`BiGGBase` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: bigg_id :type: Mapped[str] .. py:attribute:: name :type: Mapped[str] .. py:attribute:: universal_compartmentalized_components :type: Mapped[List[UniversalCompartmentalizedComponent]] .. py:attribute:: compartmentalized_components :type: Mapped[List[CompartmentalizedComponent]] .. py:class:: EscherMap(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: map_name :type: Mapped[str] .. py:attribute:: map_data :type: Mapped[str] .. py:attribute:: model_id :type: Mapped[int] .. py:attribute:: model :type: Mapped[Model] .. py:attribute:: priority :type: Mapped[int] .. py:attribute:: matrix :type: Mapped[List[EscherMapMatrix]] .. py:class:: EscherMapMatrix(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: ome_id :type: Mapped[int] .. py:attribute:: type .. py:attribute:: escher_map_id :type: Mapped[int] .. py:attribute:: escher_map :type: Mapped[EscherMap] .. py:attribute:: escher_map_element_id :type: Mapped[str] .. py:class:: ModelCount(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: model_id :type: Mapped[int] .. py:attribute:: model :type: Mapped[Model] .. py:attribute:: reaction_count :type: Mapped[int] .. py:attribute:: gene_count :type: Mapped[int] .. py:attribute:: metabolite_count :type: Mapped[int] .. py:class:: Gene(**kwargs) Bases: :py:obj:`GenomeRegion` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: name :type: Mapped[Optional[str]] .. py:attribute:: locus_tag :type: Mapped[Optional[str]] .. py:attribute:: mapped_to_genbank :type: Mapped[bool] .. py:attribute:: alternative_transcript_id :type: Mapped[Optional[int]] .. py:attribute:: alternative_transcript_of :type: Mapped[Optional[Gene]] .. py:attribute:: model_genes :type: Mapped[List[ModelGene]] .. py:class:: ReferenceReactivePart(**kwargs) Bases: :py:obj:`Base`, :py:obj:`BiGGBase` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: bigg_id :type: Mapped[str] .. py:attribute:: name :type: Mapped[str] .. py:attribute:: html_name :type: Mapped[Optional[str]] .. py:attribute:: formula :type: Mapped[Optional[str]] .. py:attribute:: charge :type: Mapped[Optional[str]] .. py:attribute:: inchi_id :type: Mapped[Optional[int]] .. py:attribute:: inchi :type: Mapped[Optional[InChI]] .. py:attribute:: matrix :type: Mapped[List[ReferenceReactivePartMatrix]] .. py:class:: ReferenceReactivePartMatrix(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: compound_id :type: Mapped[int] .. py:attribute:: compound :type: Mapped[ReferenceCompound] .. py:attribute:: reactive_part_id :type: Mapped[int] .. py:attribute:: reactive_part :type: Mapped[ReferenceReactivePart] .. py:class:: ReferenceReaction(**kwargs) Bases: :py:obj:`Base`, :py:obj:`BiGGBase` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: bigg_id :type: Mapped[str] .. py:attribute:: name :type: Mapped[Optional[str]] .. py:attribute:: equation :type: Mapped[Optional[str]] .. py:attribute:: hash :type: Mapped[str] .. py:attribute:: reaction_participants :type: Mapped[List[ReferenceReactionParticipant]] .. py:attribute:: universal_reactions :type: Mapped[List[UniversalReaction]] .. py:attribute:: annotation_mappings :type: Mapped[List[ReferenceReactionAnnotationMapping]] .. py:method:: generate_hash(participants, pattern=False) :staticmethod: .. py:method:: update_hash() .. py:class:: ReferenceReactionParticipant(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: reaction_id :type: Mapped[int] .. py:attribute:: reaction :type: Mapped[ReferenceReaction] .. py:attribute:: compound_id :type: Mapped[int] .. py:attribute:: compound :type: Mapped[ReferenceCompound] .. py:attribute:: side .. py:attribute:: coefficient :type: Mapped[str] .. py:attribute:: compartment :type: Mapped[str] .. py:attribute:: universal_reaction_matrix :type: Mapped[List[UniversalReactionMatrix]] .. py:class:: UniversalReaction(**kwargs) Bases: :py:obj:`Base`, :py:obj:`BiGGBase` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: bigg_id :type: Mapped[str] .. py:attribute:: hash :type: Mapped[str] .. py:attribute:: name :type: Mapped[Optional[str]] .. py:attribute:: is_exchange :type: Mapped[bool] .. py:attribute:: is_transport :type: Mapped[bool] .. py:attribute:: is_pseudo :type: Mapped[bool] .. py:attribute:: collection_id :type: Mapped[Optional[int]] .. py:attribute:: collection :type: Mapped[Optional[ModelCollection]] .. py:attribute:: reference_id :type: Mapped[Optional[int]] .. py:attribute:: reference :type: Mapped[Optional[ReferenceReaction]] .. py:attribute:: reactions :type: Mapped[List[Reaction]] .. py:attribute:: matrix :type: Mapped[List[UniversalReactionMatrix]] .. py:method:: get_sbo(reference) .. py:method:: generate_hash(components) :staticmethod: .. py:class:: Reaction(**kwargs) Bases: :py:obj:`Base`, :py:obj:`BiGGBase` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: bigg_id :type: Mapped[str] .. py:attribute:: hash :type: Mapped[str] .. py:attribute:: collection_id :type: Mapped[Optional[int]] .. py:attribute:: collection :type: Mapped[Optional[ModelCollection]] .. py:attribute:: copy_number :type: Mapped[int] .. py:attribute:: universal_reaction_id :type: Mapped[int] .. py:attribute:: universal_reaction :type: Mapped[UniversalReaction] .. py:attribute:: matrix :type: Mapped[List[ReactionMatrix]] .. py:attribute:: model_reactions :type: Mapped[List[ModelReaction]] .. py:attribute:: annotation_mappings :type: Mapped[List[ReactionAnnotationMapping]] .. py:method:: create_id(universal_id, copy_number) :staticmethod: .. py:method:: coefficient_to_string(coefficient) :staticmethod: .. py:method:: generate_hash(components) :staticmethod: .. py:class:: UniversalReactionMatrix(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: universal_reaction_id :type: Mapped[Optional[int]] .. py:attribute:: universal_reaction :type: Mapped[Optional[UniversalReaction]] .. py:attribute:: reference_reaction_participant_id :type: Mapped[Optional[int]] .. py:attribute:: reference_reaction_participant :type: Mapped[Optional[ReferenceReactionParticipant]] .. py:attribute:: universal_compartmentalized_component_id :type: Mapped[int] .. py:attribute:: universal_compartmentalized_component :type: Mapped[UniversalCompartmentalizedComponent] .. py:attribute:: coefficient :type: Mapped[float] .. py:attribute:: reaction_matrices :type: Mapped[List[ReactionMatrix]] .. py:class:: ReactionMatrix(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: reaction_id :type: Mapped[int] .. py:attribute:: reaction :type: Mapped[Reaction] .. py:attribute:: universal_reaction_matrix_id :type: Mapped[int] .. py:attribute:: universal_reaction_matrix :type: Mapped[UniversalReactionMatrix] .. py:attribute:: compartmentalized_component_id :type: Mapped[int] .. py:attribute:: compartmentalized_component :type: Mapped[CompartmentalizedComponent] .. py:class:: ComponentIDMapping(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: old_bigg_id :type: Mapped[str] .. py:attribute:: new_id :type: Mapped[int] .. py:attribute:: new_universal_component :type: Mapped[UniversalComponent] .. py:class:: MemoteTest(**kwargs) Bases: :py:obj:`Base`, :py:obj:`BiGGBase` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: bigg_id :type: Mapped[str] .. py:attribute:: name :type: Mapped[str] .. py:attribute:: summary :type: Mapped[Optional[str]] .. py:attribute:: format_type :type: Mapped[str] .. py:attribute:: invert :type: Mapped[Optional[bool]] .. py:attribute:: invert_result :type: Mapped[Optional[bool]] .. py:attribute:: field :type: Mapped[Optional[str]] .. py:attribute:: results :type: Mapped[List[MemoteResult]] .. py:class:: MemoteResult(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: model_id :type: Mapped[int] .. py:attribute:: model :type: Mapped[Model] .. py:attribute:: test_id :type: Mapped[int] .. py:attribute:: test :type: Mapped[MemoteTest] .. py:attribute:: model_reaction_id :type: Mapped[Optional[int]] .. py:attribute:: model_reaction :type: Mapped[Optional[ModelReaction]] .. py:attribute:: model_compartmentalized_component_id :type: Mapped[Optional[int]] .. py:attribute:: model_compartmentalized_component :type: Mapped[Optional[ModelCompartmentalizedComponent]] .. py:attribute:: model_gene_id :type: Mapped[Optional[int]] .. py:attribute:: model_gene :type: Mapped[Optional[ModelGene]] .. py:attribute:: message :type: Mapped[Optional[str]] .. py:attribute:: data :type: Mapped[Optional[float]] .. py:attribute:: duration :type: Mapped[Optional[float]] .. py:attribute:: metric :type: Mapped[Optional[float]] .. py:attribute:: result .. py:attribute:: data_count :type: Mapped[Optional[int]] .. py:class:: EscherModule(**kwargs) Bases: :py:obj:`Base`, :py:obj:`BiGGBase` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: bigg_id :type: Mapped[str] .. py:attribute:: name :type: Mapped[str] .. py:attribute:: description :type: Mapped[str] .. py:attribute:: model_reaction_mappings :type: Mapped[List[ModelReactionEscherMapping]] .. py:class:: ModelReactionEscherMapping(**kwargs) Bases: :py:obj:`Base` .. py:attribute:: id :type: Mapped[int] .. py:attribute:: model_reaction_id :type: Mapped[int] .. py:attribute:: model_reaction :type: Mapped[ModelReaction] .. py:attribute:: escher_module_id :type: Mapped[int] .. py:attribute:: escher_module :type: Mapped[EscherModule]