R/327-extractDrugHybridizationRatio.R

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

#' Descriptor that Characterizing Molecular Complexity
#' in Terms of Carbon Hybridization States
#'
#' Descriptor that Characterizing Molecular Complexity
#' in Terms of Carbon Hybridization States
#'
#' This descriptor calculates the fraction of sp3 carbons to sp2 carbons.
#' Note that it only considers carbon atoms and rather than use a simple
#' ratio it reports the value of Nsp3/(Nsp3 + Nsp2).
#' The original form of the descriptor (i.e., simple ratio)
#' has been used to characterize molecular complexity,
#' especially in the are of natural products,
#' which usually have a high value of the sp3 to sp2 ratio.
#'
#' @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{HybRatio}.
#'
#' @keywords extractDrugHybridizationRatio Hybridization Ratio
#'
#' @aliases extractDrugHybridizationRatio
#'
#' @author Nan Xiao <\url{https://nanx.me}>
#'
#' @export extractDrugHybridizationRatio
#'
#' @importFrom rcdk eval.desc
#'
#' @examples
#' smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')
#' \donttest{
#' mol = readMolFromSmi(smi, type = 'mol')
#' dat = extractDrugHybridizationRatio(mol)
#' head(dat)}

extractDrugHybridizationRatio = function (molecules, silent = TRUE) {

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

    return(x)

}