Descriptor that Counts the Number of Occurrences of the E-State Fragments

Usage

extractDrugKierHallSmarts(molecules, silent = TRUE)

Arguments

molecules: Parsed molucule object.
silent: Logical. Whether the calculating process should be shown or not, default is TRUE.

Value

A data frame, each row represents one of the molecules, each column represents one feature. This function returns 79 columns:

ID	Name	Pattern
`0`	`khs.sLi`	`[LiD1]-*`
`1`	`khs.ssBe`	`[BeD2](-)-`
`2`	`khs.ssssBe`	`[BeD4](-)(-)(-)-`
`3`	`khs.ssBH`	`[BD2H](-)-`
`4`	`khs.sssB`	`[BD3](-)(-)-*`
`5`	`khs.ssssB`	`[BD4](-)(-)(-)-`
`6`	`khs.sCH3`	`[CD1H3]-*`
`7`	`khs.dCH2`	`[CD1H2]=*`
`8`	`khs.ssCH2`	`[CD2H2](-)-`
`9`	`khs.tCH`	`[CD1H]#*`
`10`	`khs.dsCH`	`[CD2H](=)-`
`11`	`khs.aaCH`	`[C,c;D2H](:):`
`12`	`khs.sssCH`	`[CD3H](-)(-)-*`
`13`	`khs.ddC`	`[CD2H0](=)=`
`14`	`khs.tsC`	`[CD2H0](#)-`
`15`	`khs.dssC`	`[CD3H0](=)(-)-*`
`16`	`khs.aasC`	`[C,c;D3H0](:)(:)-*`
`17`	`khs.aaaC`	`[C,c;D3H0](:)(:):*`
`18`	`khs.ssssC`	`[CD4H0](-)(-)(-)-`
`19`	`khs.sNH3`	`[ND1H3]-*`
`20`	`khs.sNH2`	`[ND1H2]-*`
`21`	`khs.ssNH2`	`[ND2H2](-)-`
`22`	`khs.dNH`	`[ND1H]=*`
`23`	`khs.ssNH`	`[ND2H](-)-`
`24`	`khs.aaNH`	`[N,nD2H](:):`
`25`	`khs.tN`	`[ND1H0]#*`
`26`	`khs.sssNH`	`[ND3H](-)(-)-*`
`27`	`khs.dsN`	`[ND2H0](=)-`
`28`	`khs.aaN`	`[N,nD2H0](:):`
`29`	`khs.sssN`	`[ND3H0](-)(-)-*`
`30`	`khs.ddsN`	`[ND3H0](~[OD1H0])(~[OD1H0])-,:*`
`31`	`khs.aasN`	`[N,nD3H0](:)(:)-,:*`
`32`	`khs.ssssN`	`[ND4H0](-)(-)(-)-`
`33`	`khs.sOH`	`[OD1H]-*`
`34`	`khs.dO`	`[OD1H0]=*`
`35`	`khs.ssO`	`[OD2H0](-)-`
`36`	`khs.aaO`	`[O,oD2H0](:):`
`37`	`khs.sF`	`[FD1]-*`
`38`	`khs.sSiH3`	`[SiD1H3]-*`
`39`	`khs.ssSiH2`	`[SiD2H2](-)-`
`40`	`khs.sssSiH`	`[SiD3H1](-)(-)-*`
`41`	`khs.ssssSi`	`[SiD4H0](-)(-)(-)-`
`42`	`khs.sPH2`	`[PD1H2]-*`
`43`	`khs.ssPH`	`[PD2H1](-)-`
`44`	`khs.sssP`	`[PD3H0](-)(-)-*`
`45`	`khs.dsssP`	`[PD4H0](=)(-)(-)-`
`46`	`khs.sssssP`	`[PD5H0](-)(-)(-)(-)-*`
`47`	`khs.sSH`	`[SD1H1]-*`
`48`	`khs.dS`	`[SD1H0]=*`
`49`	`khs.ssS`	`[SD2H0](-)-`
`50`	`khs.aaS`	`[S,sD2H0](:):`
`51`	`khs.dssS`	`[SD3H0](=)(-)-*`
`52`	`khs.ddssS`	`[SD4H0](~[OD1H0])(~[OD1H0])(-)-`
`53`	`khs.sCl`	`[ClD1]-*`
`54`	`khs.sGeH3`	`[GeD1H3](-*)`
`55`	`khs.ssGeH2`	`[GeD2H2](-)-`
`56`	`khs.sssGeH`	`[GeD3H1](-)(-)-*`
`57`	`khs.ssssGe`	`[GeD4H0](-)(-)(-)-`
`58`	`khs.sAsH2`	`[AsD1H2]-*`
`59`	`khs.ssAsH`	`[AsD2H1](-)-`
`60`	`khs.sssAs`	`[AsD3H0](-)(-)-*`
`61`	`khs.sssdAs`	`[AsD4H0](=)(-)(-)-`
`62`	`khs.sssssAs`	`[AsD5H0](-)(-)(-)(-)-*`
`63`	`khs.sSeH`	`[SeD1H1]-*`
`64`	`khs.dSe`	`[SeD1H0]=*`
`65`	`khs.ssSe`	`[SeD2H0](-)-`
`66`	`khs.aaSe`	`[SeD2H0](:):`
`67`	`khs.dssSe`	`[SeD3H0](=)(-)-*`
`68`	`khs.ddssSe`	`[SeD4H0](=)(=)(-)-`
`69`	`khs.sBr`	`[BrD1]-*`
`70`	`khs.sSnH3`	`[SnD1H3]-*`
`71`	`khs.ssSnH2`	`[SnD2H2](-)-`
`72`	`khs.sssSnH`	`[SnD3H1](-)(-)-*`
`73`	`khs.ssssSn`	`[SnD4H0](-)(-)(-)-`
`74`	`khs.sI`	`[ID1]-*`
`75`	`khs.sPbH3`	`[PbD1H3]-*`
`76`	`khs.ssPbH2`	`[PbD2H2](-)-`
`77`	`khs.sssPbH`	`[PbD3H1](-)(-)-*`
`78`	`khs.ssssPb`	`[PbD4H0](-)(-)(-)-`

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.

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.

Examples

smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')
# \donttest{
mol = readMolFromSmi(smi, type = 'mol')
#> Error in parseSmiles(smi): The package "rcdk" is required to parse SMILES
dat = extractDrugKierHallSmarts(mol)
#> Error in evaluateDescriptor(molecules, type = "KierHallSmartsDescriptor",     silent = silent): The package "rcdk" is required to compute molecular descriptors
head(dat)# }
#> Error in eval(expr, envir, enclos): object 'dat' not found