/rcdk/R/visual.R

  1.packageName <- "rcdk"
  2
  3## draw.molecule <- function(molecule = NA) {
  4##   if (is.na(molecule)) {
  5##     editor <- .jnew("org/guha/rcdk/draw/Get2DStructureFromJCP")
  6##   } else {
  7##     if (attr(molecule, "jclass") != 'org/openscience/cdk/interfaces/IAtomContainer') {
  8##       stop("Supplied object should be a Java reference to an IAtomContainer")
  9##     }
 10##     editor <- .jnew("org/guha/rcdk/draw/Get2DStructureFromJCP", molecule)
 11##   }
 12##   .jcall(editor, "V", "showWindow")
 13##   molecule <- .jcall(editor, "[Lorg/openscience/cdk/interfaces/IAtomContainer;", "getMolecules")
 14##   return(molecule)
 15## }
 16
 17## script should be a valid Jmol script string
 18## view.molecule.3d <- function(molecule, ncol = 4, cellx = 200, celly = 200, script = NA) {
 19
 20##   if (class(molecule) != 'character' &&
 21##       class(molecule) != 'list' &&
 22##       class(molecule) != 'jobjRef') {
 23##     stop("Must supply a filename, single molecule object or list of molecule objects")
 24##   }
 25
 26##   if (class(molecule) == 'character') {
 27##     molecule <- load.molecules(molecule)
 28##     if (length(molecule) == 1) molecule <- molecule[[1]]
 29##   }
 30
 31##   if (class(molecule) != 'list') { ## single molecule
 32##     if (attr(molecule, "jclass") != 'org/openscience/cdk/interfaces/IAtomContainer') {
 33##       stop("Supplied object should be a Java reference to an IAtomContainer")
 34##     }
 35##     viewer <- .jnew("org/guha/rcdk/view/ViewMolecule3D", molecule)
 36##     .jcall(viewer, 'V', 'show')
 37##     if (!is.na(script)) {
 38##       .jcall(viewer, "V", "setScript", script)
 39##     }
 40##   } else { ## script is not run for the grid case
 41##     array <- .jarray(molecule, contents.class="org/openscience/cdk/interfaces/IAtomContainer")
 42##     v3d <- .jnew("org/guha/rcdk/view/ViewMolecule3DTable", array,
 43##                  as.integer(ncol), as.integer(cellx), as.integer(celly))
 44##     .jcall(v3d, 'V', 'show')    
 45##   }
 46## }
 47
 48#' get.depictor
 49#' 
 50#' return an RcdkDepictor.
 51#' 
 52#' @param width Default. \code{200}
 53#' @param height Default. \code{200}
 54#' @param zoom Default. \code{1.3}
 55#' @param style Default. \code{cow}
 56#' @param annotate Default. \code{off}
 57#' @param abbr Default. \code{on}
 58#' @param suppressh Default. \code{TRUE}
 59#' @param showTitle Default. \code{FALSE}
 60#' @param smaLimit Default. \code{100}
 61#' @param sma Default. \code{NULL}
 62#' 
 63#' @export
 64#' 
 65get.depictor <- function(width = 200, height = 200, zoom = 1.3, style = "cow", annotate = "off", abbr = "on",
 66                         suppressh = TRUE, showTitle = FALSE, smaLimit = 100, sma = NULL) {
 67  if (is.null(sma)) sma <- ""
 68  return(.jnew("org/guha/rcdk/view/RcdkDepictor",
 69               as.integer(width),
 70               as.integer(height),
 71               as.double(zoom),
 72               as.character(style),
 73               as.character(annotate),
 74               as.character(abbr),
 75               as.logical(suppressh),
 76               as.logical(showTitle),
 77               as.integer(smaLimit),
 78               as.character(sma)))
 79}
 80
 81#' view.molecule.2d
 82#' 
 83#' Create a 2D depiction of a molecule. If there are more than
 84#' one molecules supplied, return a grid woth \code{ncol} columns,.
 85#' 
 86#' @param molecule The molecule to query. Should be a `jobjRef` representing an `IAtomContainer`
 87#' @param ncol Default \code{4}
 88#' @param width Default \code{200}
 89#' @param height Default \code{200}
 90#' @param depictor Default \code{NULL}
 91#' 
 92#' @importFrom utils write.table
 93#' @export 
 94view.molecule.2d <- function(molecule, ncol = 4, width = 200, height = 200, depictor = NULL) {
 95  
 96  if (class(molecule) != 'character' &&
 97      class(molecule) != 'list' &&
 98      class(molecule) != 'jobjRef') {
 99    stop("Must supply a filename, single molecule object or list of molecule objects")
100  }
101
102  if (is.null(depictor))
103    depictor <- get.depictor()
104  
105  ## in case we're on OS X we need to prep some stuff
106  ## so we can shell out 
107  is.osx <- Sys.info()[1] == 'Darwin'
108  jarfile <- NULL
109  rcdklibs <- NULL
110  if (is.osx) { 
111    jarfile <- system.file(package='rcdk')
112    rcdklibs <- system.file(package='rcdklibs')
113  }
114
115  ## if we got a file name, lets load all the molecules
116  if (class(molecule) == 'character') {
117    molecule <- load.molecules(molecule)
118    if (length(molecule) == 1) molecule <- molecule[[1]]
119  }
120
121  if (class(molecule) != 'list') { ## single molecule
122    if (attr(molecule, "jclass") != 'org/openscience/cdk/interfaces/IAtomContainer') {
123      stop("Supplied object should be a Java reference to an IAtomContainer")
124    }
125
126    if (is.osx) {
127      smi <- get.smiles(molecule)
128      if (depictor$getSma() == "")
129        sma = "\"\""
130      else
131        sma = depictor$getSma()
132
133      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" &', rcdklibs, jarfile, smi,
134                     depictor$getWidth(), depictor$getHeight(),
135                     depictor$getZoom(), depictor$getStyle(), depictor$getAnnotate(),
136                     depictor$getAbbr(), depictor$isSuppressh(), depictor$isShowTitle(),
137                     depictor$getSmaLimit(), sma)
138      return(system(cmd))
139    } else {
140      v2d <- .jnew("org/guha/rcdk/view/ViewMolecule2D", molecule, as.integer(width), as.integer(height), depictor)
141      ret <- .jcall(v2d, "V", "draw")
142    }
143  } else { ## multiple molecules
144    if (is.osx) {
145      ## write out mols as a temp smi file
146      smi <- sapply(molecule, get.smiles, flavor = smiles.flavors(c('Isomeric')))
147      titles <- sapply(molecule, get.title)
148      tmp <- data.frame(smi, titles)
149      tf <- tempfile(pattern='rcdkv-', fileext='.smi')
150      write.table(tmp, file=tf, sep='\t', row.names=FALSE, col.names=FALSE, quote=FALSE)
151
152      if (depictor$getSma() == "") {
153        sma = "\"\""
154      } else {
155        sma = depictor$getSma()
156      }
157      cmd <- sprintf('java -cp \"%s/cont/*:%s/cont/rcdk.jar\" org.guha.rcdk.app.OSXHelper viewMolecule2Dtable "%s" %d %d %f %s %s %s %s %s %d "%s" %d &',
158                     rcdklibs, jarfile, tf,
159                     depictor$getWidth(), depictor$getHeight(),
160                     depictor$getZoom(), depictor$getStyle(), depictor$getAnnotate(),
161                     depictor$getAbbr(), depictor$isSuppressh(), depictor$isShowTitle(),
162                     depictor$getSmaLimit(), sma,
163                     ncol)
164      return(system(cmd))
165    } else {
166      array <- .jarray(molecule, contents.class="org/openscience/cdk/interfaces/IAtomContainer")
167      v2d <- .jnew("org/guha/rcdk/view/ViewMolecule2DTable", array,
168                   as.integer(ncol), depictor)
169    }
170  }
171}
172
173view.table <- function(molecules, dat, depictor = NULL) {
174
175  if (!is.list(molecules)) {
176    stop("Must provide a list of molecule objects")
177  }
178
179  if (!is.matrix(dat) && !is.data.frame(dat)) {
180    stop("datatable must be a matrix or data.frame")
181  }
182
183  if (length(molecules) != nrow(dat)) {
184    stop("The number of rows in datatable must be the same as the number of molecules")
185  }
186
187  if (is.null(depictor))
188    depictor <- get.depictor()
189  
190  if (is.null(names(dat))) cnames <- c('Molecule', paste('V',1:ncol(dat)), sep='')
191  else cnames <- c('Molecule', names(dat))
192
193  ## we need to convert the R vectors to Java arrays
194  ## and the datatable data.frame to an Object[][]
195  molecules <- .jarray(molecules, "org/openscience/cdk/interfaces/IAtomContainer")
196  carr <- .jarray(cnames)
197
198  rows <- list()
199  for (i in 1:nrow(dat)) {
200    row <- list()
201    
202    ## for a given row we have to construct a Object[] and add
203    ## it to our list
204    for (j in 1:ncol(dat)) {
205      if (is.numeric(dat[i,j])) {
206        row[j] <- .jnew("java/lang/Double", dat[i,j])
207      }
208      else if (is.character(dat[i,j]) || is.factor(dat[i,j]) || is.logical(dat[i,j])) {
209        row[j] <- .jnew("java/lang/String", as.character(dat[i,j]))
210      }
211    }
212    rows[i] <- .jarray(row, "java/lang/Object")
213  }
214
215  ## now make our object table
216  xval.arr <- .jarray(rows, "[Ljava/lang/Object;")
217  obj <- .jnew("org/guha/rcdk/view/ViewMolecule2DDataTable",
218               molecules, carr, xval.arr, depictor)
219  .jcall(obj, "V", "display")
220}
221
222
223#' view.image.2d
224#' 
225#' @param molecule The molecule to display Should be a `jobjRef` representing an `IAtomContainer`
226#' @param depictor Default \code{NULL}
227#' 
228#' @export
229view.image.2d <- function(molecule, depictor = NULL) {
230  if (is.null(depictor))
231    depictor <- get.depictor()
232  if (attr(molecule,"jclass") != "org/openscience/cdk/interfaces/IAtomContainer")
233    stop("Must supply an IAtomContainer object")
234  mi <- .jnew("org/guha/rcdk/view/MoleculeImage", molecule, depictor)
235  bytes <- .jcall(mi, "[B", "getBytes", as.integer(depictor$getWidth()), as.integer(depictor$getHeight()), "png")
236  return(readPNG(bytes))
237}
238
239#' copy.image.to.clipboard
240#' 
241#' generate an image and make it available to the system
242#' clipboard.
243#' 
244#' @param molecule The molecule to query. Should be a `jobjRef` representing an `IAtomContainer`
245#' @param depictor Optional. Default \code{NULL}. Depictor from \code{get.depictor}
246#' @export
247copy.image.to.clipboard <-  function(molecule, depictor = NULL) {
248  if (is.null(depictor))
249    depictor <- get.depictor()
250
251  if (Sys.info()[1] == 'Darwin') { ## try the standalone helper
252    smi <- get.smiles(molecule)
253    jarfile <- system.file(package='rcdk')
254    rcdklibs <- system.file(package='rcdklibs')
255    if (depictor$getSma() == "") {
256      sma = "\"\""
257    } else {
258      sma = depictor$getSma()
259    }
260    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',
261                   rcdklibs, jarfile, smi,
262                   depictor$getWidth(), depictor$getHeight(),
263                   depictor$getZoom(), depictor$getStyle(), depictor$getAnnotate(),
264                   depictor$getAbbr(), depictor$isSuppressh(), depictor$isShowTitle(),
265                   depictor$getSmaLimit(), sma)
266    return(system(cmd))
267  }
268  if (attr(molecule,"jclass") != "org/openscience/cdk/interfaces/IAtomContainer")
269    stop("Must supply an IAtomContainer object")
270  .jcall('org/guha/rcdk/view/MoleculeImageToClipboard',
271         'V',
272         'copyImageToClipboard',
273         molecule, depictor);
274}