R/415-extractDrugCPSA.R

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

#' A Variety of Descriptors Combining Surface Area and Partial Charge Information
#'
#' A Variety of Descriptors Combining Surface Area and Partial Charge Information
#' 
#' Calculates 29 Charged Partial Surface Area (CPSA) descriptors. 
#' The CPSA's were developed by Stanton 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 29 columns:
#' \itemize{
#' \item \code{PPSA.1} - partial positive surface area -- 
#' sum of surface area on positive parts of molecule
#' \item \code{PPSA.2} - partial positive surface area * 
#' total positive charge on the molecule
#' \item \code{PPSA.3} - charge weighted partial positive surface area
#' \item \code{PNSA.1} - partial negative surface area -- 
#' sum of surface area on negative parts of molecule
#' \item \code{PNSA.2} - partial negative surface area * 
#' total negative charge on the molecule
#' \item \code{PNSA.3} - charge weighted partial negative surface area
#' \item \code{DPSA.1} - difference of PPSA.1 and PNSA.1
#' \item \code{DPSA.2} - difference of FPSA.2 and PNSA.2
#' \item \code{DPSA.3} - difference of PPSA.3 and PNSA.3
#' \item \code{FPSA.1} - PPSA.1 / total molecular surface area
#' \item \code{FFSA.2} - PPSA.2 / total molecular surface area
#' \item \code{FPSA.3} - PPSA.3 / total molecular surface area
#' \item \code{FNSA.1} - PNSA.1 / total molecular surface area
#' \item \code{FNSA.2} - PNSA.2 / total molecular surface area
#' \item \code{FNSA.3} - PNSA.3 / total molecular surface area
#' \item \code{WPSA.1} - PPSA.1 * total molecular surface area / 1000
#' \item \code{WPSA.2} - PPSA.2 * total molecular surface area /1000
#' \item \code{WPSA.3} - PPSA.3 * total molecular surface area / 1000
#' \item \code{WNSA.1} - PNSA.1 * total molecular surface area /1000
#' \item \code{WNSA.2} - PNSA.2 * total molecular surface area / 1000
#' \item \code{WNSA.3} - PNSA.3 * total molecular surface area / 1000
#' \item \code{RPCG} - relative positive charge -- 
#' most positive charge / total positive charge
#' \item \code{RNCG} - relative negative charge -- 
#' most negative charge / total negative charge
#' \item \code{RPCS} - relative positive charge surface area -- 
#' most positive surface area * RPCG
#' \item \code{RNCS} - relative negative charge surface area -- 
#' most negative surface area * RNCG
#' \item \code{THSA} - sum of solvent accessible surface areas of 
#' atoms with absolute value of partial charges less than 0.2
#' \item \code{TPSA} - sum of solvent accessible surface areas of 
#' atoms with absolute value of partial charges greater than or equal 0.2
#' \item \code{RHSA} - THSA / total molecular surface area
#' \item \code{RPSA} - TPSA / total molecular surface area
#' }
#' 
#' @keywords extrDrugCPSA CPSA
#'
#' @aliases extrDrugCPSA
#' 
#' @author Min-feng Zhu <\email{wind2zhu@@163.com}>, 
#'         Nan Xiao <\url{http://r2s.name}>
#' 
#' @export extrDrugCPSA
#' 
#' @importFrom rcdk eval.desc
#' 
#' @references
#' Stanton, D.T. and Jurs, P.C. , 
#' Development and Use of Charged Partial Surface 
#' Area Structural Descriptors in Computer Assissted 
#' Quantitative Structure Property Relationship Studies, 
#' Analytical Chemistry, 1990, 62:2323.2329.
#' 
#' @examples
#' sdf = system.file('sysdata/test.sdf', package = 'BioMedR')
#' mol = readMolFromSDF(sdf)
#' dat = extrDrugCPSA(mol)
#' head(dat)
#' 

extrDrugCPSA = function (molecules, silent = TRUE) {

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

    return(x)

}