search.compounds.by.name {KEGGSOAP} | R Documentation |
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.mass(mass, range) search.compounds.by.subcomp(mol, offset, limit)
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
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)