R/319-extractDrugChiPathCluster.R

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

#' Calculate the Kier and Hall Chi Path Cluster Indices of Orders 4, 5 and 6
#'
#' Calculate the Kier and Hall Chi Path Cluster Indices of Orders 4, 5 and 6
#'
#' Evaluates chi path cluster descriptors.
#' The code currently evluates the simple and
#' valence chi chain descriptors of orders 4, 5 and 6.
#' It 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 6 columns named
#' \code{SPC.4}, \code{SPC.5}, \code{SPC.6},
#' \code{VPC.4}, \code{VPC.5}, \code{VPC.6}:
#' \itemize{
#' \item \code{SPC.4} - Simple path cluster, order 4
#' \item \code{SPC.5} - Simple path cluster, order 5
#' \item \code{SPC.6} - Simple path cluster, order 6
#' \item \code{VPC.4} - Valence path cluster, order 4
#' \item \code{VPC.5} - Valence path cluster, order 5
#' \item \code{VPC.6} - Valence path cluster, order 6
#' }
#'
#' @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.
#'
#' @export extractDrugChiPathCluster
#'
#' @examples
#' smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')
#' \donttest{
#' mol = readMolFromSmi(smi, type = 'mol')
#' dat = extractDrugChiPathCluster(mol)
#' head(dat)}

extractDrugChiPathCluster = function (molecules, silent = TRUE) {
    evaluateDescriptor(molecules, type = 'ChiPathClusterDescriptor', silent = silent)
}