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.