% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/330-extractDrugKierHallSmarts.R
\name{extractDrugKierHallSmarts}
\alias{extractDrugKierHallSmarts}
\title{Descriptor that Counts the Number of Occurrences of the E-State Fragments}
\usage{
extractDrugKierHallSmarts(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 79 columns:
\tabular{ccc}{
ID \tab Name \tab Pattern\cr
\code{0} \tab \code{khs.sLi} \tab \code{[LiD1]-*}\cr
\code{1} \tab \code{khs.ssBe} \tab \code{[BeD2](-*)-*}\cr
\code{2} \tab \code{khs.ssssBe} \tab \code{[BeD4](-*)(-*)(-*)-*}\cr
\code{3} \tab \code{khs.ssBH} \tab \code{[BD2H](-*)-*}\cr
\code{4} \tab \code{khs.sssB} \tab \code{[BD3](-*)(-*)-*}\cr
\code{5} \tab \code{khs.ssssB} \tab \code{[BD4](-*)(-*)(-*)-*}\cr
\code{6} \tab \code{khs.sCH3} \tab \code{[CD1H3]-*}\cr
\code{7} \tab \code{khs.dCH2} \tab \code{[CD1H2]=*}\cr
\code{8} \tab \code{khs.ssCH2} \tab \code{[CD2H2](-*)-*}\cr
\code{9} \tab \code{khs.tCH} \tab \code{[CD1H]#*}\cr
\code{10} \tab \code{khs.dsCH} \tab \code{[CD2H](=*)-*}\cr
\code{11} \tab \code{khs.aaCH} \tab \code{[C,c;D2H](:*):*}\cr
\code{12} \tab \code{khs.sssCH} \tab \code{[CD3H](-*)(-*)-*}\cr
\code{13} \tab \code{khs.ddC} \tab \code{[CD2H0](=*)=*}\cr
\code{14} \tab \code{khs.tsC} \tab \code{[CD2H0](#*)-*}\cr
\code{15} \tab \code{khs.dssC} \tab \code{[CD3H0](=*)(-*)-*}\cr
\code{16} \tab \code{khs.aasC} \tab \code{[C,c;D3H0](:*)(:*)-*}\cr
\code{17} \tab \code{khs.aaaC} \tab \code{[C,c;D3H0](:*)(:*):*}\cr
\code{18} \tab \code{khs.ssssC} \tab \code{[CD4H0](-*)(-*)(-*)-*}\cr
\code{19} \tab \code{khs.sNH3} \tab \code{[ND1H3]-*}\cr
\code{20} \tab \code{khs.sNH2} \tab \code{[ND1H2]-*}\cr
\code{21} \tab \code{khs.ssNH2} \tab \code{[ND2H2](-*)-*}\cr
\code{22} \tab \code{khs.dNH} \tab \code{[ND1H]=*}\cr
\code{23} \tab \code{khs.ssNH} \tab \code{[ND2H](-*)-*}\cr
\code{24} \tab \code{khs.aaNH} \tab \code{[N,nD2H](:*):*}\cr
\code{25} \tab \code{khs.tN} \tab \code{[ND1H0]#*}\cr
\code{26} \tab \code{khs.sssNH} \tab \code{[ND3H](-*)(-*)-*}\cr
\code{27} \tab \code{khs.dsN} \tab \code{[ND2H0](=*)-*}\cr
\code{28} \tab \code{khs.aaN} \tab \code{[N,nD2H0](:*):*}\cr
\code{29} \tab \code{khs.sssN} \tab \code{[ND3H0](-*)(-*)-*}\cr
\code{30} \tab \code{khs.ddsN} \tab \code{[ND3H0](~[OD1H0])(~[OD1H0])-,:*}\cr
\code{31} \tab \code{khs.aasN} \tab \code{[N,nD3H0](:*)(:*)-,:*}\cr
\code{32} \tab \code{khs.ssssN} \tab \code{[ND4H0](-*)(-*)(-*)-*}\cr
\code{33} \tab \code{khs.sOH} \tab \code{[OD1H]-*}\cr
\code{34} \tab \code{khs.dO} \tab \code{[OD1H0]=*}\cr
\code{35} \tab \code{khs.ssO} \tab \code{[OD2H0](-*)-*}\cr
\code{36} \tab \code{khs.aaO} \tab \code{[O,oD2H0](:*):*}\cr
\code{37} \tab \code{khs.sF} \tab \code{[FD1]-*}\cr
\code{38} \tab \code{khs.sSiH3} \tab \code{[SiD1H3]-*}\cr
\code{39} \tab \code{khs.ssSiH2} \tab \code{[SiD2H2](-*)-*}\cr
\code{40} \tab \code{khs.sssSiH} \tab \code{[SiD3H1](-*)(-*)-*}\cr
\code{41} \tab \code{khs.ssssSi} \tab \code{[SiD4H0](-*)(-*)(-*)-*}\cr
\code{42} \tab \code{khs.sPH2} \tab \code{[PD1H2]-*}\cr
\code{43} \tab \code{khs.ssPH} \tab \code{[PD2H1](-*)-*}\cr
\code{44} \tab \code{khs.sssP} \tab \code{[PD3H0](-*)(-*)-*}\cr
\code{45} \tab \code{khs.dsssP} \tab \code{[PD4H0](=*)(-*)(-*)-*}\cr
\code{46} \tab \code{khs.sssssP} \tab \code{[PD5H0](-*)(-*)(-*)(-*)-*}\cr
\code{47} \tab \code{khs.sSH} \tab \code{[SD1H1]-*}\cr
\code{48} \tab \code{khs.dS} \tab \code{[SD1H0]=*}\cr
\code{49} \tab \code{khs.ssS} \tab \code{[SD2H0](-*)-*}\cr
\code{50} \tab \code{khs.aaS} \tab \code{[S,sD2H0](:*):*}\cr
\code{51} \tab \code{khs.dssS} \tab \code{[SD3H0](=*)(-*)-*}\cr
\code{52} \tab \code{khs.ddssS} \tab \code{[SD4H0](~[OD1H0])(~[OD1H0])(-*)-*}\cr
\code{53} \tab \code{khs.sCl} \tab \code{[ClD1]-*}\cr
\code{54} \tab \code{khs.sGeH3} \tab \code{[GeD1H3](-*)}\cr
\code{55} \tab \code{khs.ssGeH2} \tab \code{[GeD2H2](-*)-*}\cr
\code{56} \tab \code{khs.sssGeH} \tab \code{[GeD3H1](-*)(-*)-*}\cr
\code{57} \tab \code{khs.ssssGe} \tab \code{[GeD4H0](-*)(-*)(-*)-*}\cr
\code{58} \tab \code{khs.sAsH2} \tab \code{[AsD1H2]-*}\cr
\code{59} \tab \code{khs.ssAsH} \tab \code{[AsD2H1](-*)-*}\cr
\code{60} \tab \code{khs.sssAs} \tab \code{[AsD3H0](-*)(-*)-*}\cr
\code{61} \tab \code{khs.sssdAs} \tab \code{[AsD4H0](=*)(-*)(-*)-*}\cr
\code{62} \tab \code{khs.sssssAs} \tab \code{[AsD5H0](-*)(-*)(-*)(-*)-*}\cr
\code{63} \tab \code{khs.sSeH} \tab \code{[SeD1H1]-*}\cr
\code{64} \tab \code{khs.dSe} \tab \code{[SeD1H0]=*}\cr
\code{65} \tab \code{khs.ssSe} \tab \code{[SeD2H0](-*)-*}\cr
\code{66} \tab \code{khs.aaSe} \tab \code{[SeD2H0](:*):*}\cr
\code{67} \tab \code{khs.dssSe} \tab \code{[SeD3H0](=*)(-*)-*}\cr
\code{68} \tab \code{khs.ddssSe} \tab \code{[SeD4H0](=*)(=*)(-*)-*}\cr
\code{69} \tab \code{khs.sBr} \tab \code{[BrD1]-*}\cr
\code{70} \tab \code{khs.sSnH3} \tab \code{[SnD1H3]-*}\cr
\code{71} \tab \code{khs.ssSnH2} \tab \code{[SnD2H2](-*)-*}\cr
\code{72} \tab \code{khs.sssSnH} \tab \code{[SnD3H1](-*)(-*)-*}\cr
\code{73} \tab \code{khs.ssssSn} \tab \code{[SnD4H0](-*)(-*)(-*)-*}\cr
\code{74} \tab \code{khs.sI} \tab \code{[ID1]-*}\cr
\code{75} \tab \code{khs.sPbH3} \tab \code{[PbD1H3]-*}\cr
\code{76} \tab \code{khs.ssPbH2} \tab \code{[PbD2H2](-*)-*}\cr
\code{77} \tab \code{khs.sssPbH} \tab \code{[PbD3H1](-*)(-*)-*}\cr
\code{78} \tab \code{khs.ssssPb} \tab \code{[PbD4H0](-*)(-*)(-*)-*}
}
}
\description{
Descriptor that Counts the Number of Occurrences of the E-State Fragments
}
\details{
A fragment count descriptor that uses e-state fragments.
Traditionally the e-state descriptors identify the relevant
fragments and then evaluate the actual e-state value.
However it has been shown in Butina et al.
that simply using the counts of the e-state fragments can
lead to QSAR models that exhibit similar performance to those
built using the actual e-state indices.

Atom typing and aromaticity perception should be
performed prior to calling this descriptor.
The atom type definitions are taken from Hall et al.
The SMARTS definitions were obtained from RDKit.
}
\examples{
smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')
\donttest{
mol = readMolFromSmi(smi, type = 'mol')
dat = extractDrugKierHallSmarts(mol)
head(dat)}
}
\references{
Butina, D. ,
Performance of Kier-Hall E-state Descriptors
in Quantitative Structure Activity Relationship (QSAR)
Studies of Multifunctional Molecules,
Molecules, 2004, 9:1004-1009.

Hall, L.H. and Kier, L.B. ,
Electrotopological State Indices for Atom Types:
A Novel Combination of Electronic, Topological,
and Valence State Information,
Journal of Chemical Information and Computer Science, 1995, 35:1039-1045.
}
\author{
Nan Xiao <\url{https://nanx.me}>
}
\keyword{Hall}
\keyword{Kier}
\keyword{Smarts}
\keyword{extractDrugKierHallSmarts}
