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Compound property lookup via pubchem

Source: R/pubchem_property_lookup_class.R
pubchem_property_lookup.Rd

Uses the PubChem API to search for CID based onthe input annotation column and returns property information.

Usage

pubchem_property_lookup(
  query_column,
  search_by,
  suffix = "_pubchem",
  property = "InChIKey",
  ...
)

Arguments

query_column

(character) The column name to use as the reference for searching the database e.g. "HMBD_ID".

search_by

(character) The PubChem domain to search for matches to the annotation_column.

suffix

(character) A suffix appended to all column names in the returned result. The default is "_pubchem".

property

(character) A comma separated list of properties to return from the pubchem database. (see https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest#section=Compound-Property-Tables for details). Keyword ".all" will return all properties. The default is "InChIKey".

...

Additional slots and values passed to struct_class.

Value

A pubchem_property_lookup object with the following output slots:

updated(annotation_source) The annotation_source after adding data returned by the API.

Inheritance

A pubchem_property_lookup object inherits the following struct classes:

[pubchem_property_lookup] -> [pubchem_compound_lookup] -> [rest_api] -> [model] -> [struct_class]

Examples

M = pubchem_property_lookup( search_by = "cid", property =
"InChIKey", output = "cids", records = "best", base_url =
"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound", url_template =
"<base_url>/<search_by>/<query_column>/property/<property>/JSON",
query_column = character(0), cache = NULL, status_codes = list(),
delay = 0.5, suffix = "_rest_api")