metabolike package

Subpackages

• metabolike.api package
  • Subpackages
    • metabolike.api.core package
      • Submodules
      • metabolike.api.core.config module
      • metabolike.api.core.db module
      • Module contents
    • metabolike.api.routers package
      • Submodules
      • metabolike.api.routers.pathways module
      • Module contents
  • Submodules
  • metabolike.api.main module
  • Module contents
• metabolike.db package
  • Submodules
  • metabolike.db.metacyc module
    • MetacycClient
      • MetacycClient.add_props_to_nodes()
      • MetacycClient.get_all_compounds()
      • MetacycClient.get_all_nodes()
      • MetacycClient.merge_nodes()
      • MetacycClient.metacyc_default_cyphers
      • MetacycClient.metacyc_to_graph()
  • metabolike.db.neo4j module
    • Neo4jClient
      • Neo4jClient.driver
      • Neo4jClient.database
      • Neo4jClient.close()
      • Neo4jClient.create()
      • Neo4jClient.read()
      • Neo4jClient.read_tx()
      • Neo4jClient.write()
  • metabolike.db.sbml module
    • SBMLClient
      • SBMLClient.driver
      • SBMLClient.database
      • SBMLClient.available_node_labels
      • SBMLClient.create_nodes()
      • SBMLClient.default_cyphers
      • SBMLClient.sbml_to_graph()
  • Module contents
• metabolike.parser package
  • Submodules
  • metabolike.parser.bkms_react module
    • get_bkms_tarball()
    • read_bkms()
  • metabolike.parser.brenda module
    • parse_brenda()
  • metabolike.parser.brenda_transformer module
    • BaseTransformer
      • BaseTransformer.NUM_ID()
      • BaseTransformer.TOKEN()
      • BaseTransformer.protein_id()
      • BaseTransformer.ref_id()
    • CommentaryOnlyTreeTransformer
      • CommentaryOnlyTreeTransformer.description()
      • CommentaryOnlyTreeTransformer.entry()
    • GenericTreeTransformer
      • GenericTreeTransformer.commentary()
      • GenericTreeTransformer.content()
      • GenericTreeTransformer.description()
      • GenericTreeTransformer.entry()
    • ReactionTreeTransformer
      • ReactionTreeTransformer.commentary()
      • ReactionTreeTransformer.entry()
      • ReactionTreeTransformer.more_commentary()
      • ReactionTreeTransformer.reaction()
      • ReactionTreeTransformer.reversibility()
    • RefTreeTransformer
      • RefTreeTransformer.citation()
      • RefTreeTransformer.entry()
      • RefTreeTransformer.paper_stat()
      • RefTreeTransformer.pubmed()
      • RefTreeTransformer.ref_id()
    • SpecificInfoTreeTransformer
      • SpecificInfoTreeTransformer.substrate()
  • metabolike.parser.metacyc module
    • MetacycParser
      • MetacycParser.sbml_file
      • MetacycParser.input_files
      • MetacycParser.missing_ids
      • MetacycParser.collect_atom_mapping_dat_nodes()
      • MetacycParser.collect_citation_dat_nodes()
      • MetacycParser.collect_classes_dat_nodes()
      • MetacycParser.collect_compounds_dat_nodes()
      • MetacycParser.collect_pathways_dat_nodes()
      • MetacycParser.collect_reactions_dat_nodes()
      • MetacycParser.fix_pathway_nodes()
      • MetacycParser.read_dat_file()
      • MetacycParser.read_smiles_dat()
      • MetacycParser.report_missing_ids()
  • metabolike.parser.sbml module
    • SBMLParser
      • SBMLParser.db
      • SBMLParser.sbml_file
      • SBMLParser.collect_compartments()
      • SBMLParser.collect_compounds()
      • SBMLParser.collect_gene_products()
      • SBMLParser.collect_groups()
      • SBMLParser.collect_reaction_gene_product_links()
      • SBMLParser.collect_reactions()
      • SBMLParser.read_sbml()
  • Module contents

Submodules

metabolike.config module

class metabolike.config.BrendaConfig(**data)

Bases: BaseModel

bkms_react_file: str

brenda_file: str

class metabolike.config.Config(**data)

Bases: BaseModel

brenda: Optional[BrendaConfig]

metacyc: MetacycConfig

neo4j: Neo4jConfig

class metabolike.config.MetacycConfig(**data)

Bases: BaseModel

atom_mapping: Optional[str]

classes: Optional[str]

compounds: Optional[str]

pathways: Optional[str]

publications: Optional[str]

reactions: Optional[str]

sbml: str

class metabolike.config.Neo4jConfig(**data)

Bases: BaseModel

database: str

password: SecretStr

uri: str

user: str

metabolike.config.load_config(config_file)

Return type

Config

metabolike.main module

metabolike.main.serve()

Serves an API to the graph database.

The command uses the following environment variables to configure the database connection: METABOLIKE_DB_URI, METABOLIKE_DB_USER, METABOLIKE_DB_PASSWORD, and METABOLIKE_DB_NAME.

Alternatively, you may save the variables in a file named “metabolike.env” in the current directory.

metabolike.main.setup(config_file=<typer.models.OptionInfo object>, create_db=<typer.models.OptionInfo object>, drop_if_exists=<typer.models.OptionInfo object>)

metabolike.utils module

metabolike.utils.add_kv_to_dict(d, k, v, as_list=False)

Add a key-value pair to a dictionary.

Parameters

• d (Dict[str, Any]) – Dictionary to add the key-value pair to.

• k (str) – Key to add.

• v (Any) – Value to add.

• as_list (bool) – If True, the value is appended to the list identified by k.

Return type

Dict[str, Any]

Returns

Dictionary with the key-value pair added. If the key already exists, the value is saved as a list.

metabolike.utils.chunk(itr, chunk_size)

Chunk an iterator into chunks of size chunk_size.

Ref: https://stackoverflow.com/a/71572942/5925357

Return type

Iterable

metabolike.utils.generate_gene_reaction_rule(genes)

metabolike.utils.snake_to_camel(s, sep='-')

Convert snake_case to CamelCase.

Parameters

• s (str) – String to convert.

• sep (str) – Separator to use.

Return type

str

Returns

camelCase string.

metabolike.utils.validate_path(filepath: Union[str, Path]) → Path

metabolike.utils.validate_path(filepath: None) → None

Return type

Optional[Path]

Module contents

Build graph database from BRENDA and BioCyc for studying reprogrammed metabolisms.