biotite.database.pubchem

A subpackage for searching and downloading files from the PubChem database. Although PubChem is part of NCBI Entrez, biotite.database.entrez is only capable of accessing meta-information from PubChem. This subpackage, on the other hand, supports searching PubChem compounds based on chemical information and is able to download structure records.

Queries

Query	A search query for the PubChem REST API.
NameQuery	A query that searches for compounds with the given name.
SmilesQuery	A query that searches for compounds with a given Simplified Molecular Input Line Entry Specification (SMILES) string.
InchiQuery	A query that searches for compounds with a given International Chemical Identifier (InChI) string.
InchiKeyQuery	A query that searches for compounds with a given International Chemical Identifier (InChI) key.
FormulaQuery	A query that searches for compounds with the given molecular formula.
SuperstructureQuery	A query that searches for all structures, where the given input structure is a superstructure.
SubstructureQuery	A query that searches for all structures, where the given input structure is a substructure.
SimilarityQuery	A query that searches for all structures similar to the given input structure.
IdentityQuery	A query that searches for all structures that are identical to the given input structure.

Search and fetch

search	Get all CIDs that meet the given query requirements, via the PubChem REST API.
fetch	Download structure files from PubChem in various formats.
fetch_property	Download the given property for the given CID(s).

Miscellaneous

ThrottleStatus

This class gives information about the dynamic request throttling of Pubchem.