R/436-extractDrugMannholdLogP.R

In BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions

#' Descriptor that Calculates the LogP Based on a Simple Equation 
#' Using the Number of Carbons and Hetero Atoms
#'
#' Descriptor that Calculates the LogP Based on a Simple Equation 
#' Using the Number of Carbons and Hetero Atoms
#' 
#' This descriptor calculates the LogP based on a simple equation using 
#' the number of carbons and hetero atoms. 
#' The implemented equation was proposed in Mannhold 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 one column named \code{MLogP}.
#' 
#' @keywords extrDrugMannholdLogP Mannhold LogP
#'
#' @aliases extrDrugMannholdLogP
#' 
#' @author Min-feng Zhu <\email{wind2zhu@@163.com}>, 
#'         Nan Xiao <\url{http://r2s.name}>
#' 
#' @export extrDrugMannholdLogP
#' 
#' @importFrom rcdk eval.desc
#' 
#' @references
#' Mannhold, R., Poda, G. I., Ostermann, C., & Tetko, I. V. (2009). 
#' Calculation of molecular lipophilicity: State-of-the-art and 
#' comparison of log P methods on more than 96,000 compounds. 
#' Journal of pharmaceutical sciences, 98(3), 861-893.
#' 
#' @examples
#' smi = system.file('vignettedata/FDAMDD.smi', package = 'BioMedR')
#' mol = readMolFromSmi(smi, type = 'mol')
#' dat = extrDrugMannholdLogP(mol)
#' head(dat)
#' 

extrDrugMannholdLogP = function (molecules, silent = TRUE) {

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

    return(x)

}