getCactus: Retrieve information from Cactus

In sneumann/RMassBank: Workflow to process tandem MS files and build MassBank records

Description

Retrieves information from the Cactus Chemical Identifier Resolver (PubChem).

Usage

getCactus(identifier, representation)

Arguments

identifier	Any identifier interpreted by the resolver, e.g. an InChI key or a SMILES code.
representation	The desired representation, as required from the resolver. e.g. stdinchikey, chemspider_id, formula... Refer to the webpage for details.

Details

It is not necessary to specify in which format the identifier is. Somehow, cactus does this automatically.

Value

The result of the query, in plain text. Can be NA, or one or multiple lines (character array) of results.

Note

Note that the InChI key is retrieved with a prefix (InChIkey=), which must be removed for most database searches in other databases (e.g. CTS).

Author(s)

Michael Stravs

References

cactus Chemical Identifier Resolver: http://cactus.nci.nih.gov/chemical/structure

See Also

getCtsRecord, getPcId

Examples

# Benzene:
getCactus("C1=CC=CC=C1", "cas")
getCactus("C1=CC=CC=C1", "stdinchikey")
getCactus("C1=CC=CC=C1", "chemspider_id")

sneumann/RMassBank documentation built on Oct. 20, 2020, 3:19 p.m.