R/320-extractDrugChiPath.R

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

#' Calculate the Kier and Hall Chi Path Indices of Orders 0 to 7
#'
#' Calculate the Kier and Hall Chi Path Indices of Orders 0 to 7
#'
#' Evaluates chi path descriptors. This function utilizes the graph isomorphism
#' code of the CDK to find fragments matching SMILES strings representing the
#' fragments corresponding to each type of chain.
#'
#' @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 16 columns,
#' The order and names of the columns returned is:
#' \itemize{
#' \item \code{SP.0, SP.1, ..., SP.7} - Simple path, orders 0 to 7
#' \item \code{VP.0, VP.1, ..., VP.7} - Valence path, orders 0 to 7
#' }
#'
#' @note These descriptors are calculated using graph isomorphism to identify
#' the various fragments. As a result calculations may be slow.
#' In addition, recent versions of Molconn-Z use simplified fragment definitions
#' (i.e., rings without branches etc.) whereas these descriptors use the older
#' more complex fragment definitions.
#'
#' @keywords extractDrugChiPath Chi Path
#'
#' @aliases extractDrugChiPath
#'
#' @author Nan Xiao <\url{https://nanx.me}>
#'
#' @export extractDrugChiPath
#'
#' @importFrom rcdk eval.desc
#'
#' @examples
#' smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')
#' \donttest{
#' mol = readMolFromSmi(smi, type = 'mol')
#' dat = extractDrugChiPath(mol)
#' head(dat)}

extractDrugChiPath = function (molecules, silent = TRUE) {

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

    return(x)

}