import.adap.kdb {RAMClustR}

import.adap.kdb

Description

use pubchem rest and view APIs to retrieve structures, CIDs (if a name or inchikey is given), synonyms, and optionally vendor data, when available.

Usage

import.adap.kdb(
  ramclustObj = NULL,
  annotations = NULL,
  min.score = 700,
  annotate = TRUE,
  manual.name = TRUE
)

Arguments

ramclustObj

ramclustR object to be annotated.

annotations

file name/path to annotations .xlsx file. generally 'simple_export.xlsx'

min.score

700 (out of 1000) by default

annotate

logical. TRUE by default. for now please leave default

manual.name

when looking up inchikey/names, should manual input be used to fill ambiguous names? generally recommend TRUE

Details

useful for moving from chemical name to digital structure representation. greek letters are assumed to be 'UTF-8' encoded, and are converted to latin text before searching. if you are reading in your compound name list, do so with 'encoding' set to 'UTF-8'.

Value

returns a ramclustR structured object suitable for down stream processing steps.

Author(s)

Corey Broeckling