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R/sd2gram3Dpharma.R
In Rchemcpp: Similarity measures for chemical compounds
Defines functions
sd2gram3Dpharma
Documented in
sd2gram3Dpharma
#' @title sd2gram3Dpharma - Similarity of molecules by the exact pharmacophore
#' kernel.
#'
#' @description This tool implements the (exact version of) pharmacophore kernel for 3D
#' structures of molecules (\cite{Mahe, 2006}).
#'
#'
#' @param sdf File containing the molecules. Must be in MDL file format
#' (MOL and SDF files). For more information on the file format see
#' http://en.wikipedia.org/wiki/Chemical_table_file.
#' @param sdf2 A second file containing molecules. Must also be in SDF format.
#' If specified the molecules of the first file will be compared with the
#' molecules of this second file. Default = "missing".
#' @param chargesFileName A character with the name of the file containing
#' the atom charges. Default = missing.
#' @param chargesFileName2 A character with the name of the file containing
#' the atom charges. Default = missing.
#' @param edgeKernelType Options to specify the kernel function comparing
#' distances between atoms. Choices are "RBF" or "triangular". Default = "RBF".
#' @param edgeKernelParameter Specifies the parameter associated to these
#' kernels. Either the bandwith of the RBF kernel or the cut-off of the
#' triangular kernel. Default = 1.
#' @param atomKernelMatrix A string that sets the similarity measure between
#' atoms that should be used. Default = "missing".
#' @param flagRemoveH A logical that indicates whether H-atoms should be
#' removed or not. Default = FALSE.
#' @param morganOrder The order of the DeMorgan Indices to be used. If set to
#' zero no DeMorgan Indices are used. The higher the order the more
#' types of atoms exist and consequently the more dissimilar will be the molecules.
#' Default = 0.
#' @param morganChargesThreshold specifies a threshold above which partial
#' Morgan charges are considered as positive/negative.
#' By default this threshold is zero, and every positive (resp. negative)
#' partial charge is seen as a positive (resp. negative) charge.
#' However, it might be interesting to consider a threshold of 0.2 for
#' example, in which case only partial charges greater than 0.2
#' (resp. smaller than -0.2) would be seen as positive (resp. negative).
#' Default = 0.
#' @param silentMode Whether or not the program should print progress reports
#' to the standart output. Default = TRUE.
#' @param returnNormalized A logical specifying whether a normalized kernel
#' matrix should be returned. Default = TRUE.
#' @param detectArom Whether aromatic rings should be detected and aromatic
#' bonds should a special bond type. If large molecules are in the data set
#' the detection of aromatic rings can be very time-consuming. (Default = FALSE).
#' @examples
#' sdfolder <- system.file("extdata",package="Rchemcpp")
#' sdf <- list.files(sdfolder,full.names=TRUE,pattern="tiny")
#' K <- sd2gram3Dpharma(sdf)
#' @return A numeric matrix containing the similarity values between the
#' molecules.
#' @author Michael Mahr <rchemcpp@@bioinf.jku.at>
#' c++ function written by Jean-Luc Perret and Pierre Mahe
#' @references (Mahe, 2006) -- P. Mahe, L. Ralaivola, V. Stoven, and J.-P. Vert.
#' The pharmacophore kernel for virtual screening
#' with support vector machines. Technical Report, HAL:ccsd-00020066, Ecole des
#' Mines de Paris, March 2006.
#'
#' @export
sd2gram3Dpharma = function(sdf, sdf2, chargesFileName = "",
chargesFileName2 = "", edgeKernelType = c("RBF", "triangular"),
edgeKernelParameter = 1, atomKernelMatrix = "", flagRemoveH = FALSE,
morganOrder = as.integer(0), morganChargesThreshold = 0, silentMode = FALSE,
returnNormalized = TRUE, detectArom=FALSE)
{
if(!is.character(chargesFileName)) stop("chargesFileName must be string")
if(!is.character(chargesFileName2)) stop("chargesFileName2 must be string")
if(!is.character(edgeKernelType)) stop("edgeKernelType must be a string")
if(!is.numeric(edgeKernelParameter)) stop("edgeKernelParameter must be numeric")
if(!is.character(atomKernelMatrix)) stop("atomKernelMatrix must be string")
if(!is.logical(flagRemoveH)) stop("flagRemoveH must be logical")
if(!is.numeric(morganOrder)) stop("morganOrder must be integer")
morganOrder <- as.integer(morganOrder)
if(!is.numeric(morganChargesThreshold)) stop("morganchargesThreshold must be numeric")
if(!is.logical(silentMode)) stop("silentMode must be logical")
if(!is.logical(returnNormalized)) stop("returnNormalized must be logical")
if (missing(edgeKernelType)) {edgeKernelType = edgeKernelType[1]}
edgeKernelType = match.arg(edgeKernelType)
#--
if((missing(sdf2)) && (chargesFileName2 != ""))
print("chargesFilename2 is useless")
if((missing(sdf2)) && (chargesFileName == "") && (chargesFileName2 != ""))
stop("both chargesFileNames have to be specified")
if((missing(sdf2)) && (chargesFileName != "") && (chargesFileName2 == ""))
stop("both chargesFileNames have to be specified")
if( atomKernelMatrix != "" ){
loadGramAtoms( atomKernelMatrix ); # atomKernelMatrix is set by the
}
if(inherits(sdf,"SDFset")){
datablock(sdf) <- lapply(1:length(sdf),function(x) return(""))
aSet <- SDFsetToRmoleculeset(sdf,detectArom=detectArom)[[1]]
molnames <- ChemmineR::sdfid(sdf)
molnames2 <- molnames
if (!missing(sdf2)){
if (inherits(sdf2,"SDFset")){
datablock(sdf2) <- lapply(1:length(sdf2),function(x) return(""))
aSet2 <- SDFsetToRmoleculeset(sdf2,detectArom=detectArom)[[1]]
molnames2 <- ChemmineR::sdfid(sdf2)
} else
stop("Input must be existing SDF files or \"SDFset\" objects.")
}
inputMode <- "SDFset"
} else if (inherits(sdf,"Rcpp_Rmoleculeset")) {
aSet <- sdf
molnames <- NULL
molnames2 <- NULL
if (!missing(sdf2)){
if (inherits(sdf2,"Rcpp_Rmoleculeset")){
aSet2 <- sdf2
} else
stop("Input must be existing SDF files or \"SDFset\" objects.")
}
inputMode <- "Rmoleculeset"
} else if (is.character(sdf) & file.exists(sdf)) {
aSetList <- readRmoleculeset(sdf,detectArom=detectArom)
aSet <- aSetList[[1]]
molnames <- aSetList[[3]]
molnames2 <- aSetList[[3]]
if (!missing(sdf2)){
if (is.character(sdf2) & file.exists(sdf2)){
aSetList2 <- readRmoleculeset(sdf2,detectArom=detectArom)
aSet2 <- aSetList2[[1]]
molnames2 <- aSetList2[[3]]
} else
stop("Input must be existing SDF files or \"SDFset\" objects.")
}
inputMode <- "fileName"
} else {
stop("Input must be existing SDF files or \"SDFset\" objects.")
}
if(!missing(sdf2)){ # i.e., test set version.
# read partial charges if specified on command line
if(chargesFileName != ""){
if( !silentMode ){
print("reading partial charges");
}
aSet$readPartialCharges(chargesFileName);
aSet2$readPartialCharges(chargesFileName2);
}
# remove hydrogens
if( flagRemoveH == TRUE ){
if( !silentMode ){
print("removing hydrogens");
}
aSet$hideHydrogens();
aSet2$hideHydrogens();
}
# set morgan labels
if( !silentMode )
print(paste("setting morgan labels ", morganOrder));
aSet$setMorganLabels( morganOrder );
aSet2$setMorganLabels( morganOrder );
# introduce partial charges in Morgan labels if specified on command line
if(chargesFileName != ""){
if( !silentMode ){
print("setting partial charges");
}
aSet$setMorganChargesLabels(morganChargesThreshold);
aSet2$setMorganChargesLabels(morganChargesThreshold);
}
# compute gram matrix
aSet$setComparisonSetCopy( aSet2 );
if( atomKernelMatrix != "" ){
if( !silentMode ){
print("using external atomKernel");
}
if (edgeKernelType == "RBF"){
# --> RBF edge kernel
aSet$gramCompute3D (edgeKernelParameter, silentMode, TRUE, TRUE) #external,rbf
}else if (edgeKernelType == "triangular"){
# --> triangular edge kernel
aSet$gramCompute3D (edgeKernelParameter, silentMode, TRUE, FALSE) #external,triangular
}
}
else{
if (edgeKernelType == "RBF"){
# --> RBF edge kernel
aSet$gramCompute3D (edgeKernelParameter, silentMode, FALSE, TRUE) #morgan,rbf
}else if (edgeKernelType == "triangular"){
# --> triangular edge kernel
aSet$gramCompute3D (edgeKernelParameter, silentMode, FALSE, FALSE) #morgan,triangular
}
}
if( !silentMode ){
print("gram matrix computation OK");
}
# write the gram matrix to a file (raw and normalized matrices)
#aSet$writeGramMatrix( outputDir + baseName, false, false, silentMode);
#aSet$writeGramMatrix( outputDir + baseName, true, false, silentMode);
# --> write self kernel values
if (returnNormalized == FALSE)
{
K <- do.call(rbind,aSet$getGram() )
}
else
{
K <- do.call(rbind,aSet$getGramNormal() )
}
#aSet$writeSelfKernelList( outputDir + baseName + "_test", silentMode );
#aSet2$writeSelfKernelList( outputDir + baseName + "_train", silentMode );
# and exit
#aSet$deleteAll(); should be done by destructor
#aSet2$deleteAll(); should be done by destructor
}
else{ # self-set version
# read partial charges if specified on command line
if(chargesFileName != ""){
if( !silentMode )
print("reading partial charges");
aSet$readPartialCharges(chargesFileName);
}
# remove hydrogens
if( flagRemoveH == TRUE ) {
if( !silentMode ){
print("removing Hydrogens");
}
aSet$hideHydrogens();
}
# set morgan labels
if( !silentMode ){
print(paste("setting morgan labels ", morganOrder));
}
aSet$setMorganLabels(morganOrder);
if( !silentMode ){
print("setting morgan labels OK");
}
# introduce partial charges in Morgan labels if specified on command line
if(chargesFileName != ""){
if( !silentMode ){
print("setting partial charges");
}
aSet$setMorganChargesLabels(morganChargesThreshold);
}
# compute gram matrix
aSet$setComparisonSetSelf();
if( atomKernelMatrix != "" ){
if( !silentMode ) {
print("using external atomKernel");
}
if (edgeKernelType == "RBF"){
# --> RBF edge kernel
aSet$gramCompute3D (edgeKernelParameter, silentMode, TRUE, TRUE) #external,rbf
}else if (edgeKernelType == "triangular"){
# --> triangular edge kernel
aSet$gramCompute3D (edgeKernelParameter, silentMode, TRUE, FALSE) #external,triangular
}
}
else{
if (edgeKernelType == "RBF"){
# --> RBF edge kernel
aSet$gramCompute3D (edgeKernelParameter, silentMode, FALSE, TRUE) #morgan,rbf
}else if (edgeKernelType == "triangular"){
# --> triangular edge kernel
aSet$gramCompute3D (edgeKernelParameter, silentMode, FALSE, FALSE) #morgan,triangular
}
}
if( !silentMode )
{
print("gram matrix computation OK");
}
if (returnNormalized == FALSE)
{
K <- do.call(rbind,aSet$getGram() )
}
else
{
K <- do.call(rbind,aSet$getGramNormal() )
}
# write the gram matrix to a file (raw and normalized matrices)
#aSet$writeGramMatrix( outputDir + baseName, false, false, silentMode);
#aSet$writeGramMatrix( outputDir + baseName, true, false, silentMode);
# --> write self kernel values
#aSet$writeSelfKernelList( outputDir + baseName + "_train", false);
# and exit
#aSet$deleteAll(); should be done by destructor
}
if (inputMode == "fileName" | inputMode == "SDFset"){
aSet$deleteAll()
if (exists("aSet2"))
aSet2$deleteAll()
}
try({
rownames(K) <- molnames
colnames(K) <- molnames2
})
return ( K )
}
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Rchemcpp documentation built on May 6, 2019, 4:58 a.m.
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Defines functions sd2gram3Dpharma
Documented in sd2gram3Dpharma
#' @title sd2gram3Dpharma - Similarity of molecules by the exact pharmacophore
#' kernel.
#'
#' @description This tool implements the (exact version of) pharmacophore kernel for 3D
#' structures of molecules (\cite{Mahe, 2006}).
#'
#'
#' @param sdf File containing the molecules. Must be in MDL file format
#' (MOL and SDF files). For more information on the file format see
#' http://en.wikipedia.org/wiki/Chemical_table_file.
#' @param sdf2 A second file containing molecules. Must also be in SDF format.
#' If specified the molecules of the first file will be compared with the
#' molecules of this second file. Default = "missing".
#' @param chargesFileName A character with the name of the file containing
#' the atom charges. Default = missing.
#' @param chargesFileName2 A character with the name of the file containing
#' the atom charges. Default = missing.
#' @param edgeKernelType Options to specify the kernel function comparing
#' distances between atoms. Choices are "RBF" or "triangular". Default = "RBF".
#' @param edgeKernelParameter Specifies the parameter associated to these
#' kernels. Either the bandwith of the RBF kernel or the cut-off of the
#' triangular kernel. Default = 1.
#' @param atomKernelMatrix A string that sets the similarity measure between
#' atoms that should be used. Default = "missing".
#' @param flagRemoveH A logical that indicates whether H-atoms should be
#' removed or not. Default = FALSE.
#' @param morganOrder The order of the DeMorgan Indices to be used. If set to
#' zero no DeMorgan Indices are used. The higher the order the more
#' types of atoms exist and consequently the more dissimilar will be the molecules.
#' Default = 0.
#' @param morganChargesThreshold specifies a threshold above which partial
#' Morgan charges are considered as positive/negative.
#' By default this threshold is zero, and every positive (resp. negative)
#' partial charge is seen as a positive (resp. negative) charge.
#' However, it might be interesting to consider a threshold of 0.2 for
#' example, in which case only partial charges greater than 0.2
#' (resp. smaller than -0.2) would be seen as positive (resp. negative).
#' Default = 0.
#' @param silentMode Whether or not the program should print progress reports
#' to the standart output. Default = TRUE.
#' @param returnNormalized A logical specifying whether a normalized kernel
#' matrix should be returned. Default = TRUE.
#' @param detectArom Whether aromatic rings should be detected and aromatic
#' bonds should a special bond type. If large molecules are in the data set
#' the detection of aromatic rings can be very time-consuming. (Default = FALSE).
#' @examples
#' sdfolder <- system.file("extdata",package="Rchemcpp")
#' sdf <- list.files(sdfolder,full.names=TRUE,pattern="tiny")
#' K <- sd2gram3Dpharma(sdf)
#' @return A numeric matrix containing the similarity values between the
#' molecules.
#' @author Michael Mahr <rchemcpp@@bioinf.jku.at>
#' c++ function written by Jean-Luc Perret and Pierre Mahe
#' @references (Mahe, 2006) -- P. Mahe, L. Ralaivola, V. Stoven, and J.-P. Vert.
#' The pharmacophore kernel for virtual screening
#' with support vector machines. Technical Report, HAL:ccsd-00020066, Ecole des
#' Mines de Paris, March 2006.
#'
#' @export
sd2gram3Dpharma = function(sdf, sdf2, chargesFileName = "",
chargesFileName2 = "", edgeKernelType = c("RBF", "triangular"),
edgeKernelParameter = 1, atomKernelMatrix = "", flagRemoveH = FALSE,
morganOrder = as.integer(0), morganChargesThreshold = 0, silentMode = FALSE,
returnNormalized = TRUE, detectArom=FALSE)
{
if(!is.character(chargesFileName)) stop("chargesFileName must be string")
if(!is.character(chargesFileName2)) stop("chargesFileName2 must be string")
if(!is.character(edgeKernelType)) stop("edgeKernelType must be a string")
if(!is.numeric(edgeKernelParameter)) stop("edgeKernelParameter must be numeric")
if(!is.character(atomKernelMatrix)) stop("atomKernelMatrix must be string")
if(!is.logical(flagRemoveH)) stop("flagRemoveH must be logical")
if(!is.numeric(morganOrder)) stop("morganOrder must be integer")
morganOrder <- as.integer(morganOrder)
if(!is.numeric(morganChargesThreshold)) stop("morganchargesThreshold must be numeric")
if(!is.logical(silentMode)) stop("silentMode must be logical")
if(!is.logical(returnNormalized)) stop("returnNormalized must be logical")
if (missing(edgeKernelType)) {edgeKernelType = edgeKernelType[1]}
edgeKernelType = match.arg(edgeKernelType)
#--
if((missing(sdf2)) && (chargesFileName2 != ""))
print("chargesFilename2 is useless")
if((missing(sdf2)) && (chargesFileName == "") && (chargesFileName2 != ""))
stop("both chargesFileNames have to be specified")
if((missing(sdf2)) && (chargesFileName != "") && (chargesFileName2 == ""))
stop("both chargesFileNames have to be specified")
if( atomKernelMatrix != "" ){
loadGramAtoms( atomKernelMatrix ); # atomKernelMatrix is set by the
}
if(inherits(sdf,"SDFset")){
datablock(sdf) <- lapply(1:length(sdf),function(x) return(""))
aSet <- SDFsetToRmoleculeset(sdf,detectArom=detectArom)[[1]]
molnames <- ChemmineR::sdfid(sdf)
molnames2 <- molnames
if (!missing(sdf2)){
if (inherits(sdf2,"SDFset")){
datablock(sdf2) <- lapply(1:length(sdf2),function(x) return(""))
aSet2 <- SDFsetToRmoleculeset(sdf2,detectArom=detectArom)[[1]]
molnames2 <- ChemmineR::sdfid(sdf2)
} else
stop("Input must be existing SDF files or \"SDFset\" objects.")
}
inputMode <- "SDFset"
} else if (inherits(sdf,"Rcpp_Rmoleculeset")) {
aSet <- sdf
molnames <- NULL
molnames2 <- NULL
if (!missing(sdf2)){
if (inherits(sdf2,"Rcpp_Rmoleculeset")){
aSet2 <- sdf2
} else
stop("Input must be existing SDF files or \"SDFset\" objects.")
}
inputMode <- "Rmoleculeset"
} else if (is.character(sdf) & file.exists(sdf)) {
aSetList <- readRmoleculeset(sdf,detectArom=detectArom)
aSet <- aSetList[[1]]
molnames <- aSetList[[3]]
molnames2 <- aSetList[[3]]
if (!missing(sdf2)){
if (is.character(sdf2) & file.exists(sdf2)){
aSetList2 <- readRmoleculeset(sdf2,detectArom=detectArom)
aSet2 <- aSetList2[[1]]
molnames2 <- aSetList2[[3]]
} else
stop("Input must be existing SDF files or \"SDFset\" objects.")
}
inputMode <- "fileName"
} else {
stop("Input must be existing SDF files or \"SDFset\" objects.")
}
if(!missing(sdf2)){ # i.e., test set version.
# read partial charges if specified on command line
if(chargesFileName != ""){
if( !silentMode ){
print("reading partial charges");
}
aSet$readPartialCharges(chargesFileName);
aSet2$readPartialCharges(chargesFileName2);
}
# remove hydrogens
if( flagRemoveH == TRUE ){
if( !silentMode ){
print("removing hydrogens");
}
aSet$hideHydrogens();
aSet2$hideHydrogens();
}
# set morgan labels
if( !silentMode )
print(paste("setting morgan labels ", morganOrder));
aSet$setMorganLabels( morganOrder );
aSet2$setMorganLabels( morganOrder );
# introduce partial charges in Morgan labels if specified on command line
if(chargesFileName != ""){
if( !silentMode ){
print("setting partial charges");
}
aSet$setMorganChargesLabels(morganChargesThreshold);
aSet2$setMorganChargesLabels(morganChargesThreshold);
}
# compute gram matrix
aSet$setComparisonSetCopy( aSet2 );
if( atomKernelMatrix != "" ){
if( !silentMode ){
print("using external atomKernel");
}
if (edgeKernelType == "RBF"){
# --> RBF edge kernel
aSet$gramCompute3D (edgeKernelParameter, silentMode, TRUE, TRUE) #external,rbf
}else if (edgeKernelType == "triangular"){
# --> triangular edge kernel
aSet$gramCompute3D (edgeKernelParameter, silentMode, TRUE, FALSE) #external,triangular
}
}
else{
if (edgeKernelType == "RBF"){
# --> RBF edge kernel
aSet$gramCompute3D (edgeKernelParameter, silentMode, FALSE, TRUE) #morgan,rbf
}else if (edgeKernelType == "triangular"){
# --> triangular edge kernel
aSet$gramCompute3D (edgeKernelParameter, silentMode, FALSE, FALSE) #morgan,triangular
}
}
if( !silentMode ){
print("gram matrix computation OK");
}
# write the gram matrix to a file (raw and normalized matrices)
#aSet$writeGramMatrix( outputDir + baseName, false, false, silentMode);
#aSet$writeGramMatrix( outputDir + baseName, true, false, silentMode);
# --> write self kernel values
if (returnNormalized == FALSE)
{
K <- do.call(rbind,aSet$getGram() )
}
else
{
K <- do.call(rbind,aSet$getGramNormal() )
}
#aSet$writeSelfKernelList( outputDir + baseName + "_test", silentMode );
#aSet2$writeSelfKernelList( outputDir + baseName + "_train", silentMode );
# and exit
#aSet$deleteAll(); should be done by destructor
#aSet2$deleteAll(); should be done by destructor
}
else{ # self-set version
# read partial charges if specified on command line
if(chargesFileName != ""){
if( !silentMode )
print("reading partial charges");
aSet$readPartialCharges(chargesFileName);
}
# remove hydrogens
if( flagRemoveH == TRUE ) {
if( !silentMode ){
print("removing Hydrogens");
}
aSet$hideHydrogens();
}
# set morgan labels
if( !silentMode ){
print(paste("setting morgan labels ", morganOrder));
}
aSet$setMorganLabels(morganOrder);
if( !silentMode ){
print("setting morgan labels OK");
}
# introduce partial charges in Morgan labels if specified on command line
if(chargesFileName != ""){
if( !silentMode ){
print("setting partial charges");
}
aSet$setMorganChargesLabels(morganChargesThreshold);
}
# compute gram matrix
aSet$setComparisonSetSelf();
if( atomKernelMatrix != "" ){
if( !silentMode ) {
print("using external atomKernel");
}
if (edgeKernelType == "RBF"){
# --> RBF edge kernel
aSet$gramCompute3D (edgeKernelParameter, silentMode, TRUE, TRUE) #external,rbf
}else if (edgeKernelType == "triangular"){
# --> triangular edge kernel
aSet$gramCompute3D (edgeKernelParameter, silentMode, TRUE, FALSE) #external,triangular
}
}
else{
if (edgeKernelType == "RBF"){
# --> RBF edge kernel
aSet$gramCompute3D (edgeKernelParameter, silentMode, FALSE, TRUE) #morgan,rbf
}else if (edgeKernelType == "triangular"){
# --> triangular edge kernel
aSet$gramCompute3D (edgeKernelParameter, silentMode, FALSE, FALSE) #morgan,triangular
}
}
if( !silentMode )
{
print("gram matrix computation OK");
}
if (returnNormalized == FALSE)
{
K <- do.call(rbind,aSet$getGram() )
}
else
{
K <- do.call(rbind,aSet$getGramNormal() )
}
# write the gram matrix to a file (raw and normalized matrices)
#aSet$writeGramMatrix( outputDir + baseName, false, false, silentMode);
#aSet$writeGramMatrix( outputDir + baseName, true, false, silentMode);
# --> write self kernel values
#aSet$writeSelfKernelList( outputDir + baseName + "_train", false);
# and exit
#aSet$deleteAll(); should be done by destructor
}
if (inputMode == "fileName" | inputMode == "SDFset"){
aSet$deleteAll()
if (exists("aSet2"))
aSet2$deleteAll()
}
try({
rownames(K) <- molnames
colnames(K) <- molnames2
})
return ( K )
}
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