% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/315-extractDrugCPSA.R
\name{extractDrugCPSA}
\alias{extractDrugCPSA}
\title{A Variety of Descriptors Combining Surface Area and Partial Charge Information}
\usage{
extractDrugCPSA(molecules, silent = TRUE)
}
\arguments{
\item{molecules}{Parsed molucule object.}

\item{silent}{Logical. Whether the calculating process
should be shown or not, default is \code{TRUE}.}
}
\value{
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
}
}
\description{
A Variety of Descriptors Combining Surface Area and Partial Charge Information
}
\details{
Calculates 29 Charged Partial Surface Area (CPSA) descriptors.
The CPSA's were developed by Stanton et al.
}
\examples{
sdf = system.file('sysdata/OptAA3d.sdf', package = 'Rcpi')
\donttest{
mol = readMolFromSDF(sdf)
dat = extractDrugCPSA(mol)
head(dat)}
}
\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.
}
\author{
Nan Xiao <\url{https://nanx.me}>
}
\keyword{CPSA}
\keyword{extractDrugCPSA}
