R/324-extractDrugGravitationalIndex.R

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

#' Descriptor Characterizing the Mass Distribution of the Molecule.
#'
#' Descriptor Characterizing the Mass Distribution of the Molecule.
#'
#' Descriptor characterizing the mass distribution of the molecule described by
#' Katritzky et al. For modelling purposes the value of the descriptor is
#' calculated both with and without H atoms.
#' Furthermore the square and cube roots of the descriptor
#' are also generated as described by Wessel et al.
#'
#' @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 9 columns:
#' \itemize{
#' \item \code{GRAV.1} - gravitational index of heavy atoms
#' \item \code{GRAV.2} - square root of gravitational index of heavy atoms
#' \item \code{GRAV.3} - cube root of gravitational index of heavy atoms
#' \item \code{GRAVH.1} - gravitational index - hydrogens included
#' \item \code{GRAVH.2} - square root of hydrogen-included gravitational index
#' \item \code{GRAVH.3} - cube root of hydrogen-included gravitational index
#' \item \code{GRAV.4} - grav1 for all pairs of atoms (not just bonded pairs)
#' \item \code{GRAV.5} - grav2 for all pairs of atoms (not just bonded pairs)
#' \item \code{GRAV.6} - grav3 for all pairs of atoms (not just bonded pairs)
#' }
#'
#' @export extractDrugGravitationalIndex
#'
#' @references
#' Katritzky, A.R. and Mu, L. and Lobanov, V.S. and Karelson, M.,
#' Correlation of Boiling Points With Molecular Structure.
#' 1. A Training Set of 298 Diverse Organics and a
#' Test Set of 9 Simple Inorganics,
#' J. Phys. Chem., 1996, 100:10400-10407.
#'
#' Wessel, M.D. and Jurs, P.C. and Tolan, J.W. and Muskal, S.M. ,
#' Prediction of Human Intestinal Absorption of Drug Compounds
#' From Molecular Structure,
#' Journal of Chemical Information and Computer Sciences, 1998, 38:726-735.
#'
#' @examples
#' sdf = system.file('sysdata/OptAA3d.sdf', package = 'Rcpi')
#' \donttest{
#' mol = readMolFromSDF(sdf)
#' dat = extractDrugGravitationalIndex(mol)
#' head(dat)}

extractDrugGravitationalIndex = function (molecules, silent = TRUE) {
    evaluateDescriptor(molecules, type = 'GravitationalIndexDescriptor', silent = silent)
}