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.packageName <- "rcdk"
## draw.molecule <- function(molecule = NA) {
## if (is.na(molecule)) {
## editor <- .jnew("org/guha/rcdk/draw/Get2DStructureFromJCP")
## } else {
## if (attr(molecule, "jclass") != 'org/openscience/cdk/interfaces/IAtomContainer') {
## stop("Supplied object should be a Java reference to an IAtomContainer")
## }
## editor <- .jnew("org/guha/rcdk/draw/Get2DStructureFromJCP", molecule)
## }
## .jcall(editor, "V", "showWindow")
## molecule <- .jcall(editor, "[Lorg/openscience/cdk/interfaces/IAtomContainer;", "getMolecules")
## return(molecule)
## }
## script should be a valid Jmol script string
## view.molecule.3d <- function(molecule, ncol = 4, cellx = 200, celly = 200, script = NA) {
## if (class(molecule) != 'character' &&
## class(molecule) != 'list' &&
## class(molecule) != 'jobjRef') {
## stop("Must supply a filename, single molecule object or list of molecule objects")
## }
## if (class(molecule) == 'character') {
## molecule <- load.molecules(molecule)
## if (length(molecule) == 1) molecule <- molecule[[1]]
## }
## if (class(molecule) != 'list') { ## single molecule
## if (attr(molecule, "jclass") != 'org/openscience/cdk/interfaces/IAtomContainer') {
## stop("Supplied object should be a Java reference to an IAtomContainer")
## }
## viewer <- .jnew("org/guha/rcdk/view/ViewMolecule3D", molecule)
## .jcall(viewer, 'V', 'show')
## if (!is.na(script)) {
## .jcall(viewer, "V", "setScript", script)
## }
## } else { ## script is not run for the grid case
## array <- .jarray(molecule, contents.class="org/openscience/cdk/interfaces/IAtomContainer")
## v3d <- .jnew("org/guha/rcdk/view/ViewMolecule3DTable", array,
## as.integer(ncol), as.integer(cellx), as.integer(celly))
## .jcall(v3d, 'V', 'show')
## }
## }
#' get.depictor
#'
#' return an RcdkDepictor.
#'
#' @param width Default. \code{200}
#' @param height Default. \code{200}
#' @param zoom Default. \code{1.3}
#' @param style Default. \code{cow}
#' @param annotate Default. \code{off}
#' @param abbr Default. \code{on}
#' @param suppressh Default. \code{TRUE}
#' @param showTitle Default. \code{FALSE}
#' @param smaLimit Default. \code{100}
#' @param sma Default. \code{NULL}
#' @param fillToFit Defailt. \code{FALSE}
#'
#' @export
#'
get.depictor <- function(width = 200, height = 200, zoom = 1.3, style = "cow", annotate = "off", abbr = "on",
suppressh = TRUE, showTitle = FALSE, smaLimit = 100, sma = NULL, fillToFit = FALSE) {
if (is.null(sma)) sma <- ""
return(.jnew("org/guha/rcdk/view/RcdkDepictor",
as.integer(width),
as.integer(height),
as.double(zoom),
as.character(style),
as.character(annotate),
as.character(abbr),
as.logical(suppressh),
as.logical(showTitle),
as.integer(smaLimit),
as.character(sma),
as.logical(fillToFit)))
}
#' view.molecule.2d
#'
#' Create a 2D depiction of a molecule. If there are more than
#' one molecules supplied, return a grid woth \code{ncol} columns,.
#'
#' @param molecule The molecule to query. Should be a `jobjRef` representing an `IAtomContainer`
#' @param ncol Default \code{4}
#' @param width Default \code{200}
#' @param height Default \code{200}
#' @param depictor Default \code{NULL}
#'
#' @importFrom utils write.table
#' @export
view.molecule.2d <- function(molecule, ncol = 4, width = 200, height = 200, depictor = NULL) {
if (!class(molecule) %in% c('character', 'list', 'jobjRef')) {
stop("Must supply a filename, single molecule object or list of molecule objects")
}
if (is.null(depictor))
depictor <- get.depictor()
## in case we're on OS X we need to prep some stuff
## so we can shell out
is.osx <- Sys.info()[1] == 'Darwin'
jarfile <- NULL
rcdklibs <- NULL
if (is.osx) {
jarfile <- system.file(package='rcdk')
rcdklibs <- system.file(package='rcdklibs')
}
## if we got a file name, lets load all the molecules
if (is(molecule, 'character')) {
molecule <- load.molecules(molecule)
if (length(molecule) == 1) molecule <- molecule[[1]]
}
if (!is(molecule, 'list')) { ## single molecule
if (attr(molecule, "jclass") != 'org/openscience/cdk/interfaces/IAtomContainer') {
stop("Supplied object should be a Java reference to an IAtomContainer")
}
if (is.osx) {
smi <- get.smiles(molecule)
if (depictor$getSma() == "")
sma = "\"\""
else
sma = depictor$getSma()
cmd <- sprintf('java -cp \"%s/cont/*:%s/cont/rcdk.jar\" org.guha.rcdk.app.OSXHelper viewMolecule2D "%s" %d %d %f %s %s %s %s %s %d "%s" %d &', rcdklibs, jarfile, smi,
depictor$getWidth(), depictor$getHeight(),
depictor$getZoom(), depictor$getStyle(), depictor$getAnnotate(),
depictor$getAbbr(), depictor$isSuppressh(), depictor$isShowTitle(),
depictor$getSmaLimit(), sma, depictor$getFillToFit())
return(system(cmd))
} else {
v2d <- .jnew("org/guha/rcdk/view/ViewMolecule2D", molecule, as.integer(width), as.integer(height), depictor)
ret <- .jcall(v2d, "V", "draw")
}
} else { ## multiple molecules
if (is.osx) {
## write out mols as a temp smi file
smi <- sapply(molecule, get.smiles, flavor = smiles.flavors(c('Isomeric')))
titles <- sapply(molecule, get.title)
tmp <- data.frame(smi, titles)
tf <- tempfile(pattern='rcdkv-', fileext='.smi')
write.table(tmp, file=tf, sep='\t', row.names=FALSE, col.names=FALSE, quote=FALSE)
if (depictor$getSma() == "") {
sma = "\"\""
} else {
sma = depictor$getSma()
}
cmd <- sprintf('java -cp \"%s/cont/*:%s/cont/rcdk.jar\" org.guha.rcdk.app.OSXHelper viewMolecule2Dtable "%s" %d %d %f %s %s %s %s %s %d "%s" %d %d &',
rcdklibs, jarfile, tf,
depictor$getWidth(), depictor$getHeight(),
depictor$getZoom(), depictor$getStyle(), depictor$getAnnotate(),
depictor$getAbbr(), depictor$isSuppressh(), depictor$isShowTitle(),
depictor$getSmaLimit(), sma, depictor$getFillToFit(),
ncol)
return(system(cmd))
} else {
array <- .jarray(molecule, contents.class="org/openscience/cdk/interfaces/IAtomContainer")
v2d <- .jnew("org/guha/rcdk/view/ViewMolecule2DTable", array,
as.integer(ncol), depictor)
}
}
}
#' view.table
#'
#' Create a tabular view of a set of molecules (in 2D) and associated data columns
#'
#' @param molecules A list of molecule objects (`jobjRef` representing an `IAtomContainer`)
#' @param dat The \code{data.frame} associated with the molecules, one per row
#' @param depictor Default \code{NULL}
#'
#' @importFrom utils write.table
#' @export
view.table <- function(molecules, dat, depictor = NULL) {
if (!is.list(molecules)) {
stop("Must provide a list of molecule objects")
}
if (!is.matrix(dat) && !is.data.frame(dat)) {
stop("datatable must be a matrix or data.frame")
}
if (length(molecules) != nrow(dat)) {
stop("The number of rows in datatable must be the same as the number of molecules")
}
if (is.null(depictor))
depictor <- get.depictor()
if (is.null(names(dat))) cnames <- c('Molecule', paste('V',1:ncol(dat)), sep='')
else cnames <- c('Molecule', names(dat))
## we need to convert the R vectors to Java arrays
## and the datatable data.frame to an Object[][]
molecules <- .jarray(molecules, "org/openscience/cdk/interfaces/IAtomContainer")
carr <- .jarray(cnames)
rows <- list()
for (i in 1:nrow(dat)) {
row <- list()
## for a given row we have to construct a Object[] and add
## it to our list
for (j in 1:ncol(dat)) {
if (is.numeric(dat[i,j])) {
row[j] <- .jnew("java/lang/Double", dat[i,j])
}
else if (is.character(dat[i,j]) || is.factor(dat[i,j]) || is.logical(dat[i,j])) {
row[j] <- .jnew("java/lang/String", as.character(dat[i,j]))
}
}
rows[i] <- .jarray(row, "java/lang/Object")
}
## now make our object table
xval.arr <- .jarray(rows, "[Ljava/lang/Object;")
obj <- .jnew("org/guha/rcdk/view/ViewMolecule2DDataTable",
molecules, carr, xval.arr, depictor)
.jcall(obj, "V", "display")
}
#' view.image.2d
#'
#' @param molecule The molecule to display Should be a `jobjRef` representing an `IAtomContainer`
#' @param depictor Default \code{NULL}
#'
#' @export
view.image.2d <- function(molecule, depictor = NULL) {
if (is.null(depictor))
depictor <- get.depictor()
if (attr(molecule,"jclass") != "org/openscience/cdk/interfaces/IAtomContainer")
stop("Must supply an IAtomContainer object")
mi <- .jnew("org/guha/rcdk/view/MoleculeImage", molecule, depictor)
bytes <- .jcall(mi, "[B", "getBytes", as.integer(depictor$getWidth()), as.integer(depictor$getHeight()), "png")
return(readPNG(bytes))
}
#' copy.image.to.clipboard
#'
#' generate an image and make it available to the system
#' clipboard.
#'
#' @param molecule The molecule to query. Should be a `jobjRef` representing an `IAtomContainer`
#' @param depictor Optional. Default \code{NULL}. Depictor from \code{get.depictor}
#' @export
copy.image.to.clipboard <- function(molecule, depictor = NULL) {
if (is.null(depictor))
depictor <- get.depictor()
if (Sys.info()[1] == 'Darwin') { ## try the standalone helper
smi <- get.smiles(molecule)
jarfile <- system.file(package='rcdk')
rcdklibs <- system.file(package='rcdklibs')
if (depictor$getSma() == "") {
sma = "\"\""
} else {
sma = depictor$getSma()
}
cmd <- sprintf('java -cp %s/cont/*:%s/cont/rcdk.jar org.guha.rcdk.app.OSXHelper copyToClipboard "%s" %d %d %f %s %s %s %s %s %d %s %d',
rcdklibs, jarfile, smi,
depictor$getWidth(), depictor$getHeight(),
depictor$getZoom(), depictor$getStyle(), depictor$getAnnotate(),
depictor$getAbbr(), depictor$isSuppressh(), depictor$isShowTitle(),
depictor$getSmaLimit(), sma, depictor$getFillToFit())
return(system(cmd))
}
if (attr(molecule,"jclass") != "org/openscience/cdk/interfaces/IAtomContainer")
stop("Must supply an IAtomContainer object")
.jcall('org/guha/rcdk/view/MoleculeImageToClipboard',
'V',
'copyImageToClipboard',
molecule, depictor);
}
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