webchem (version 1.0.0)

ci_query: Retrieve information from ChemIDPlus

Description

Retrieve information from ChemIDPlus https://chem.nlm.nih.gov/chemidplus

Usage

ci_query(
  query,
  type = c("name", "rn", "inchikey"),
  match = c("best", "first", "ask", "na"),
  verbose = TRUE
)

Arguments

query

character; query string

type

character; type of query string. "rn" for registry number or "name" for common name or "inchikey" for inchikey as input.

match

character; How should multiple hits be handeled? "first" returns only the first match, "best" the best matching (by name) ID, "ask" enters an interactive mode and the user is asked for input, "na" returns NA if multiple hits are found.

verbose

logical; should a verbose output be printed on the console?

Value

A list of 8 entries: name (vector), synonyms (vector), cas (vector), inchi (vector), inchikey (vector), smiles(vector), toxicity (data.frame), physprop (data.frame) and source_url.

Examples

# NOT RUN {
# might fail if API is not available
# query common name
y1 <- ci_query(c('Formaldehyde', 'Triclosan'), type = 'name')
names(y1)
str(y1[['Triclosan']]) # lots of information inside
y1[['Triclosan']]$inchikey

# Query by CAS
y2 <- ci_query('50-00-0', type = 'rn', match = 'first')
y2[['50-00-0']]$inchikey

# query by inchikey
y3 <- ci_query('WSFSSNUMVMOOMR-UHFFFAOYSA-N', type = 'inchikey')
y3[[1]]$name

# extract lop-P
sapply(y1, function(y){
 if (length(y) == 1 && is.na(y))
   return(NA)
 y$physprop$Value[y$physprop$`Physical Property` == 'log P (octanol-water)']
 })
# }