% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/311-extractDrugBCUT.R
\name{extractDrugBCUT}
\alias{extractDrugBCUT}
\title{BCUT -- Eigenvalue Based Descriptor}
\usage{
extractDrugBCUT(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 6 columns:
\itemize{
\item \code{BCUTw-1l, BCUTw-2l ...} - n high lowest atom weighted BCUTS
\item \code{BCUTw-1h, BCUTw-2h ...} - n low highest atom weighted BCUTS
\item \code{BCUTc-1l, BCUTc-2l ...} - n high lowest partial charge weighted BCUTS
\item \code{BCUTc-1h, BCUTc-2h ...} - n low highest partial charge weighted BCUTS
\item \code{BCUTp-1l, BCUTp-2l ...} - n high lowest polarizability weighted BCUTS
\item \code{BCUTp-1h, BCUTp-2h ...} - n low highest polarizability weighted BCUTS
}
}
\description{
BCUT -- Eigenvalue Based Descriptor
}
\details{
Eigenvalue based descriptor noted for its utility in chemical diversity.
Described by Pearlman et al.
The descriptor is based on a weighted version of the Burden matrix which
takes into account both the connectivity as well as atomic properties
of a molecule. The weights are a variety of atom properties placed along
the diagonal of the Burden matrix.
Currently three weighting schemes are employed:
\itemize{
\item Atomic Weight
\item Partial Charge (Gasteiger Marsilli)
\item Polarizability (Kang et al.)
}
}
\note{
By default, the descriptor will return the highest and lowest eigenvalues
for the three classes of descriptor in a single ArrayList
(in the order shown above). However it is also possible to supply a parameter
list indicating how many of the highest and lowest eigenvalues
(for each class of descriptor) are required. The descriptor works with
the hydrogen depleted molecule.

A side effect of specifying the number of highest and lowest eigenvalues
is that it is possible to get two copies of all the eigenvalues. That is,
if a molecule has 5 heavy atoms, then specifying the 5 highest eigenvalues
returns all of them, and specifying the 5 lowest eigenvalues returns all of
them, resulting in two copies of all the eigenvalues.

Note that it is possible to specify an arbitrarily large number of
eigenvalues to be returned. However if the number (i.e., nhigh or nlow)
is larger than the number of heavy atoms, the remaining eignevalues
will be \code{NaN}.

Given the above description, if the aim is to gt all the eigenvalues for
a molecule, you should set nlow to 0 and specify the number of heavy atoms
(or some large number) for nhigh (or vice versa).
}
\examples{
smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')
\donttest{
mol = readMolFromSmi(smi, type = 'mol')
dat = extractDrugBCUT(mol)
head(dat)}
}
\references{
Pearlman, R.S. and Smith, K.M.,
Metric Validation and the Receptor-Relevant Subspace Concept,
J. Chem. Inf. Comput. Sci., 1999, 39:28-35.

Burden, F.R., Molecular identification number for substructure searches,
J. Chem. Inf. Comput. Sci., 1989, 29:225-227.

Burden, F.R., Chemically Intuitive Molecular Index,
Quant. Struct. -Act. Relat., 1997, 16:309-314

Kang, Y.K. and Jhon, M.S.,
Additivity of Atomic Static Polarizabilities and Dispersion Coefficients,
Theoretica Chimica Acta, 1982, 61:41-48
}
\author{
Nan Xiao <\url{https://nanx.me}>
}
\keyword{BCUT}
\keyword{extractDrugBCUT}
