search.compounds.by.name: Client-side interface to obtain a list of chemical compounds
In kozo2/keggapi: Client-side REST access KEGG

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/KEGGREST.R

The functions provide access to KEGG LIGAND database http://www.genome.jp/kegg/ligand.html. Given a compound name, a chemical formula, a molecular weight, or a common sub-structure, one of the functions below can return a list of compounds identifiers from KEGG LIGAND database.

search.compounds.by.name(name)
search.compounds.by.composition(composition)
search.compounds.by.mol_weight(lower.limit, upper.limit)
search.compounds.by.exact_mass(exact.mass)

`name`	`name` a character string to indicate a compound name
`composition`	`composition` a character string to indicate a compound composition, usually expressed as chemical formula
`mass`	`mass`a float to indicate a molecular weight around mass
`range`	`range` a float to indicate the range of molecular weight when searching compounds by mass
`mol`	`mol`a character string to indicate a MOL formatted structural data, more in details section
`offset`	`offset` an integer
`limit`	`limit` an integer

search.compounds.by.name returns a list of compounds having the specified name;

search.compounds.by.composition returns a list of compounds containing elements indicated by the composition. Order of the elements is insensitive;

search.compounds.by.mass returns a list of compounds having the molecular weight around "mass" with some ambiguity (range);

search.compounds.by.subcomp returns a list of compounds with the alignment having common sub-structure calculated by the subcomp program. You can obtain a MOL formatted structural data of matched compounds using bget with the "-f m" option to confirm the alignment.

All the functions return a character vector of chemical compound identifiers provided by KEGG LIGAND database

Nianhua Li

http://www.genome.jp/kegg/docs/keggapi_manual.html#label:105

bget

	compounds_1 <- search.compounds.by.name("shikimic acid")
        compounds_2 <- search.compounds.by.composition("C7H10O5")
        compounds_3 <- search.compounds.by.mass(174.05, 0.1)
        mol <- bget("-f m cpd:C00111")
        compounds_4 <- search.compounds.by.subcomp(mol, 1, 5)