CIRgetR: R interface for chemical identifier translation through the...

In dgrapov/CIRgetR: R interface for chemical identifier translation through the Chemical Identifier Resolver (CIR)

Description

Based on ID for structure (smiles, InchI) translate to Database identifiers (PubChem, ChemSpider, etc.) and more.

Usage

CIRgetR(id, to = c("pubchem_sid"), return.all = TRUE, progress = TRUE)

Arguments

id	character, matrix or data.frame containing InchIKey, InchI code or smiles (see Details)
to	value to translate "to""
return.all	limit results to single (first) output for each id
progress	show progress for translations

Details

This is an interface to the Chemical Identifier Resolver (CIR, http://cactus.nci.nih.gov/chemical/structure).

Value

comp1

data.frame containing the results of the translation

Author(s)

Dmitry Grapov

References

https://github.com/dgrapov/CIRgetR

Examples

#test
id<- c("C[N+](C)(C)[O-]", "CC(=O)Oc1ccccc1C(=O)O")      
opts<-c("smiles", "names", "iupac_name", "cas", "inchi", "stdinchi", "inchikey", "stdinchikey",
        "ficts", "ficus", "uuuuu", "image", "file", "mw", "monoisotopic_mass","chemspider_id",
        "pubchem_sid", "chemnavigator_sid", "formula", "chemnavigator_sid")     

translations<-sapply(1:length(opts), function(i)
    {
        CIRgetR(id=id,to=opts[i],return.all=FALSE)
    })
colnames(translations)<-opts    

#image test
CIRgetR(id,to="image")

dgrapov/CIRgetR documentation built on May 15, 2019, 7:21 a.m.