R/322-extractDrugFMF.R

In road2stat/Rcpi: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

#' Calculate the FMF Descriptor
#'
#' Calculate the FMF Descriptor
#'
#' Calculates the FMF descriptor characterizing molecular complexity
#' in terms of its Murcko framework. This descriptor is the ratio of
#' heavy atoms in the framework to the total number of heavy atoms
#' in the molecule. By definition, acyclic molecules which have no frameworks,
#' will have a value of 0. Note that the authors consider an isolated ring
#' system to be a framework (even though there is no linker).
#'
#' @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{FMF}.
#'
#' @export extractDrugFMF
#'
#' @references
#' Yang, Y., Chen, H., Nilsson, I., Muresan, S., & Engkvist, O. (2010).
#' Investigation of the relationship between topology and selectivity
#' for druglike molecules. Journal of medicinal chemistry,
#' 53(21), 7709-7714.
#'
#' @examples
#' smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')
#' \donttest{
#' mol = readMolFromSmi(smi, type = 'mol')
#' dat = extractDrugFMF(mol)
#' head(dat)}

extractDrugFMF = function (molecules, silent = TRUE) {
    evaluateDescriptor(molecules, type = 'FMFDescriptor', silent = silent)
}