R/325-extractDrugHBondAcceptorCount.R

In Rcpi: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

#' Number of Hydrogen Bond Acceptors
#'
#' Number of Hydrogen Bond Acceptors
#'
#' This descriptor calculates the number of hydrogen bond acceptors
#' using a slightly simplified version of the PHACIR atom types.
#' The following groups are counted as hydrogen bond acceptors:
#' any oxygen where the formal charge of the oxygen is
#' non-positive (i.e. formal charge <= 0) except
#' \enumerate{
#' \item an aromatic ether oxygen (i.e. an ether oxygen that is
#' adjacent to at least one aromatic carbon)
#' \item an oxygen that is adjacent to a nitrogen
#' }
#' and any nitrogen where the formal charge of the nitrogen is
#' non-positive (i.e. formal charge <= 0) except a nitrogen
#' that is adjacent to an oxygen.
#'
#' @param molecules Parsed molucule object.
#' @param silent Logical. Whether the calculating process
#' should be shown or not, default is \code{TRUE}.
#'
#' @return A data frame, each row represents one of the molecules,
#' each column represents one feature.
#' This function returns one column named \code{nHBAcc}.
#'
#' @keywords extractDrugHBondAcceptorCount HBond Acceptor Count
#'
#' @aliases extractDrugHBondAcceptorCount
#'
#' @author Nan Xiao <\url{https://nanx.me}>
#'
#' @export extractDrugHBondAcceptorCount
#'
#' @importFrom rcdk eval.desc
#'
#' @examples
#' smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')
#' \donttest{
#' mol = readMolFromSmi(smi, type = 'mol')
#' dat = extractDrugHBondAcceptorCount(mol)
#' head(dat)}

extractDrugHBondAcceptorCount = function (molecules, silent = TRUE) {

    x = eval.desc(
        molecules,
        'org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor',
        verbose = !silent)

    return(x)

}