R/342-extractDrugTPSA.R

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

#' Descriptor of Topological Polar Surface Area Based on
#' Fragment Contributions (TPSA)
#'
#' Descriptor of Topological Polar Surface Area Based on
#' Fragment Contributions (TPSA)
#'
#' Calculate the descriptor of topological polar surface area
#' based on fragment contributions (TPSA).
#'
#' @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{TopoPSA}.
#'
#' @keywords extractDrugTPSA Topological Polar Surface Area
#'
#' @aliases extractDrugTPSA
#'
#' @author Nan Xiao <\url{https://nanx.me}>
#'
#' @export extractDrugTPSA
#'
#' @importFrom rcdk eval.desc
#'
#' @references
#' Ertl, P., Rohde, B., & Selzer, P. (2000).
#' Fast calculation of molecular polar surface area as a sum of
#' fragment-based contributions and its application to the prediction
#' of drug transport properties.
#' Journal of medicinal chemistry, 43(20), 3714-3717.
#'
#' @examples
#' smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')
#' \donttest{
#' mol = readMolFromSmi(smi, type = 'mol')
#' dat = extractDrugTPSA(mol)
#' head(dat)}

extractDrugTPSA = function (molecules, silent = TRUE) {

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

    return(x)

}