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handle .jcall unexpected error #120

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Merged
rajarshi merged 1 commit into from
Jul 3, 2021
Merged

handle .jcall unexpected error #120

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68 changes: 36 additions & 32 deletions rcdk/R/desc.R
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Original file line number Diff line number Diff line change
Expand Up @@ -5,17 +5,21 @@
if (is.null(dval) || is.na(dval)) return(NA)
}

exception <- .jcall(dval, "Ljava/lang/Exception;", "getException")
exception <- tryCatch({
.jcall(dval, "Ljava/lang/Exception;", "getException")},
error = function(e) {
e
})
if (!is.null(exception)) {
warning(exception$getMessage())
return(rep(NA, nexpected))
}

nval <- numeric()
if (!inherits(dval,'jobjRef') && is.na(dval)) {
return(NA)
}

result <- .jcall(dval, "Lorg/openscience/cdk/qsar/result/IDescriptorResult;", "getValue")
methods <- .jmethods(result)

Expand All @@ -24,18 +28,18 @@
len <- .jcall(result, "I", "length")
for (i in 1:len) nval[i] <- .jcall(result, "D", "get", as.integer(i-1))
} else if ("public int org.openscience.cdk.qsar.result.IntegerArrayResult.get(int)" %in% methods) {
result <- .jcast(result, "org/openscience/cdk/qsar/result/IntegerArrayResult")
result <- .jcast(result, "org/openscience/cdk/qsar/result/IntegerArrayResult")
len <- .jcall(result, "I", "length")
for (i in 1:len) nval[i] <- .jcall(result, "I", "get", as.integer(i-1))
for (i in 1:len) nval[i] <- .jcall(result, "I", "get", as.integer(i-1))
} else if ("public int org.openscience.cdk.qsar.result.IntegerResult.intValue()" %in% methods) {
result <- .jcast(result, "org/openscience/cdk/qsar/result/IntegerResult")
result <- .jcast(result, "org/openscience/cdk/qsar/result/IntegerResult")
nval <- .jcall(result, "I", "intValue")
} else if ("public double org.openscience.cdk.qsar.result.DoubleResult.doubleValue()" %in% methods) {
result <- .jcast(result, "org/openscience/cdk/qsar/result/DoubleResult")
nval <- .jcall(result, "D", "doubleValue")
result <- .jcast(result, "org/openscience/cdk/qsar/result/DoubleResult")
nval <- .jcall(result, "D", "doubleValue")
} else if ("public boolean org.openscience.cdk.qsar.result.BooleanResult.booleanValue()" %in% methods) {
result <- .jcast(result, "org/openscience/cdk/qsar/result/BooleanResult")
nval <- .jcall(result, "Z", "booleanValue")
result <- .jcast(result, "org/openscience/cdk/qsar/result/BooleanResult")
nval <- .jcall(result, "Z", "booleanValue")
}

return(nval)
Expand All @@ -50,9 +54,9 @@
if (type == 'molecular') {
interface <- J("org.openscience.cdk.qsar.IMolecularDescriptor")
} else if (type == 'atomic') {
interface <- J("org.openscience.cdk.qsar.IAtomicDescriptor")
interface <- J("org.openscience.cdk.qsar.IAtomicDescriptor")
} else if (type == 'bond') {
interface <- J("org.openscience.cdk.qsar.IBondDescriptor")
interface <- J("org.openscience.cdk.qsar.IBondDescriptor")
}
dklass <- interface@jobj
dcob <- get.chem.object.builder()
Expand All @@ -79,7 +83,7 @@
}

#' Get descriptor class names
#'
#'
#' @param type A string indicating which class of descriptors to return. Specifying
#' `"all"` will return class names for all molecular descriptors. Options include
#' * topological
Expand Down Expand Up @@ -108,8 +112,8 @@ get.desc.names <- function(type = "all") {
}

#' List available descriptor categories
#'
#' @return A character vector listing available descriptor categories. This can be
#'
#' @return A character vector listing available descriptor categories. This can be
#' used in \link{get.desc.names}
#' @seealso \link{get.desc.names}
#' @author Rajarshi Guha (\email{rajarshi.guha@@gmail.com})
Expand All @@ -121,7 +125,7 @@ get.desc.categories <- function() {
}

#' Compute descriptor values for a set of molecules
#'
#'
#' @param molecules A `list` of molecule objects
#' @param which.desc A character vector listing descriptor class names
#' @param verbose If `TRUE`, verbose output
Expand All @@ -144,14 +148,14 @@ eval.desc <- function(molecules, which.desc, verbose = FALSE) {
}

dcob <- get.chem.object.builder()

if (length(which.desc) == 1) {
desc <- .jnew(which.desc)
.jcall(desc, "V", "initialise", dcob)

dnames <- .jcall(desc, "[Ljava/lang/String;", "getDescriptorNames")
dnames <- gsub('-', '.', dnames)

descvals <- lapply(molecules, function(a,b) {
val <- tryCatch({.jcall(b, "Lorg/openscience/cdk/qsar/DescriptorValue;", "calculate", a)},
warning = function(e) return(NA),
Expand All @@ -161,7 +165,7 @@ eval.desc <- function(molecules, which.desc, verbose = FALSE) {

vals <- lapply(descvals, .get.desc.values, nexpected = length(dnames))
vals <- data.frame(do.call('rbind', vals))
names(vals) <- dnames
names(vals) <- dnames
return(vals)
} else {
counter <- 1
Expand All @@ -172,7 +176,7 @@ eval.desc <- function(molecules, which.desc, verbose = FALSE) {
, "\n") }
desc <- .jnew(desc)
.jcall(desc, "V", "initialise", dcob)

dnames <- .jcall(desc, "[Ljava/lang/String;", "getDescriptorNames")
dnames <- gsub('-', '.', dnames)

Expand All @@ -183,16 +187,16 @@ eval.desc <- function(molecules, which.desc, verbose = FALSE) {
vals <- lapply(descvals, .get.desc.values, nexpected = length(dnames))
vals <- data.frame(do.call('rbind', vals))


if (length(vals) == 1 && any(is.na(vals))) {

vals <- as.data.frame(matrix(NA, nrow=1, ncol=length(dnames)))
}

names(vals) <- dnames
## idx <- which(is.na(names(vals)))
## if (length(idx) > 0) vals <- vals[,-idx]

dl[[counter]] <- vals
counter <- counter + 1
}
Expand All @@ -201,7 +205,7 @@ eval.desc <- function(molecules, which.desc, verbose = FALSE) {
}

#' Get class names for atomic descriptors
#'
#'
#' @param type A string indicating which class of descriptors to return. Specifying
#' `"all"` will return class names for all molecular descriptors. Options include
#' * topological
Expand All @@ -220,7 +224,7 @@ get.atomic.desc.names <- function(type = "all") {
}

#' Compute descriptors for each atom in a molecule
#'
#'
#' @param molecule A molecule object
#' @param which.desc A character vector of atomic descriptor class names
#' @param verbose Optional. Default \code{FALSE}. Toggle verbosity.
Expand Down Expand Up @@ -250,20 +254,20 @@ eval.atomic.desc <- function(molecule, which.desc, verbose = FALSE) {
}
return(dval)
})

dnames <- NULL
if (inherits(descvals[[1]], "jobjRef")) {
dnames <- .jcall(descvals[[1]], "[Ljava/lang/String;", "getNames")
} else {
dnames <- gsub('org.openscience.cdk.qsar.descriptors.atomic.', '', desc)
}
if (verbose)
if (verbose)
cat("\t", "computed", length(dnames), "descriptor values\n")

vals <- lapply(descvals, .get.desc.values, nexpected=length(dnames))
vals <- data.frame(do.call('rbind', vals))
names(vals) <- dnames

dl[[counter]] <- vals
counter <- counter + 1
}
Expand Down Expand Up @@ -320,8 +324,8 @@ get.xlogp <- function(molecule) {
}

#' Compute volume of a molecule
#'
#' This method does not require 3D coordinates. As a result its an
#'
#' This method does not require 3D coordinates. As a result its an
#' approximation
#' @param molecule A molecule object
#' @return A double value representing the volume
Expand Down