Documentation

• Connecting to a Database
  • get_query_handler()
  • Connecting to the Public Database
    • connect_public
  • Hosting a Local database
    • connect_local_docker
    • connect_local_docker_dev
  • Connecting to an arbitrary PostgreSQL endpoint
    • connect()
    • Params
  • Extending the database
• Querying the Database
  • Query Functions
    • find_entry()
    • find_compound_entry()
    • find_reaction_entry()
    • find_enzyme_entry()
    • find_structure_representation_entry()
    • find_aam_representation_entry()
    • find_structure_entry()
    • find_aam_entry()
    • get_relations_from_entry()
    • get_all_relations()
  • Advanced Queries with Query Handlers
    • QueryHandler
    • PopulateQueryHandler
• Entries and Relations
  • Overview
    • Entries
    • Relations
  • Entries
    • Source Entries
    • Structural Entries
  • Relations
    • Compound Relations
    • Reaction Relations
    • Enzyme Relations
    • Molecular Structure Representation Relations
    • Atom-to-Atom Map Representation Relations
    • Molecular Structure Relations
    • Atom-to-Atom Map Relations
    • Entry Graph Relations
• Identifier Types
  • IdentifierType
    • IdentifierType.enum_type
    • IdentifierType.id_org_prefix
    • IdentifierType.name
    • IdentifierType.shortname
    • IdentifierType.alt_names
    • IdentifierType.stdfunc
    • IdentifierType.recogniser
    • IdentifierType.std_identifier()
    • IdentifierType.trim()
  • Compound Identifier Types
    • IdTypeCompoundEnum
  • Reaction Identifier Types
    • IdTypeReactionEnum
  • Enzyme Identifier Types
    • IdTypeEnzymeEnum
  • MolStructureRepr Identifier Types
    • IdTypeStructureRepresentationEnum
  • AAM Identifier Types
    • IdTypeAAMEnum
• Entry Graphs
  • EntryGraph
    • EntryGraph.get_vertex_index_by_recon_id()
    • EntryGraph.get_vertex_by_entry()
    • EntryGraph.get_vertex_by_vertex_index()
    • EntryGraph.get_out_edges_of_vertex()
    • EntryGraph.vertices()
    • EntryGraph.edges()
    • EntryGraph.add_vertex()
    • EntryGraph.add_edge()
    • EntryGraph.add_vertex_from()
    • EntryGraph.draw()
    • EntryGraph.show()
  • Vertex
    • Vertex.vertex_index
    • Vertex.entry
    • Vertex.recon_id
    • Vertex.generation
  • Edge
    • Edge.edge_index
    • Edge.relation
    • Edge.recon_id_1
    • Edge.recon_id_2
• Expanding Entry Graphs
  • Exploring Entry Graphs
    • explore()
  • Exploration Protocols
  • Pre-defined Exploration Protocols
    • protocol_compound_structure
  • Defining Custom Exploration Protocols
    • ExplorationProtocol
    • Direction
• Scoring
  • Scorer
    • Scorer.__init__()
    • Scorer.__call__()
• Hosting the Database locally
• Building and Expanding the Database