/rcdk/R/iterating.R

 1hasNext <- function(obj, ...) { UseMethod("hasNext") } 
 2hasNext.iload.molecules <- function(obj, ...) obj$hasNext()
 3iload.molecules<- function(molfile, type = 'smi', aromaticity = TRUE, typing = TRUE, isotopes = TRUE, skip=TRUE) {
 4
 5  if (!file.exists(molfile) && length(grep('http://', molfile)) == 0)
 6    stop(paste(molfile, ": Does not exist", sep=''))
 7
 8  fr <- .jnew("java/io/FileReader", as.character(molfile))
 9  dcob <- .get.chem.object.builder()
10  if (type == 'smi') {
11    sreader <- .jnew("org/openscience/cdk/io/iterator/IteratingSMILESReader",.jcast(fr, "java/io/Reader"), dcob)
12  } else if (type == 'sdf') {
13    sreader <- .jnew("org/openscience/cdk/io/iterator/IteratingSDFReader",.jcast(fr, "java/io/Reader"), dcob)
14    .jcall(sreader, "V", "setSkip", skip)
15  }
16  hasNext <- NA
17  mol <- NA
18  molr <- NA
19  
20  hasNx <- function() {
21    hasNext <<- .jcall(sreader, "Z", "hasNext")
22    if (!hasNext) {
23      .jcall(sreader, "V", "close")      
24      mol <<- NA
25    }
26    return(hasNext)
27  }
28  
29  nextEl <- function() {
30    mol <<- .jcall(sreader, "Ljava/lang/Object;", "next")
31    mol <<- .jcast(mol, "org/openscience/cdk/interfaces/IAtomContainer")
32    if (aromaticity) do.aromaticity(mol)
33    if (typing) do.typing(mol)
34    if (isotopes) do.isotopes(mol)
35
36    hasNext <<- NA    
37    return(mol)
38  }
39
40  obj <- list(nextElem = nextEl, hasNext = hasNx)
41  class(obj) <- c("iload.molecules", "abstractiter", "iter")
42  obj
43}