SVG and (#17)

* move from magrittr to base r * fix imports and add url * update docs and Description * style pkgdown * add orcid * rename * update depict for rxn check * add rxn smiles test * style pass * update allowable classes * add a get_svg_string function * add icon * update to use SVG strings directly * use cat to get cleaner vignette --------- Co-authored-by: Zachary Charlop-Powers <[email protected]>
CDK-R · Mar 3, 2024 · 5c2b5e0 · 5c2b5e0
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,22 +1,26 @@
 Package: depict
 Type: Package
 Title: Draw Beautiful Molecular Structures
-Version: 0.3.1
-Authors@R: c(person('Zachary', 'Charlop-Powers', role=c('cre','aut',"cph"), email='[email protected]'))
+Version: 0.4.0
+Authors@R: c(
+  person('Zachary', 'Charlop-Powers', ,'[email protected]',role=c('cre'), 
+      comment = c(ORCID = "0000-0001-8816-4680")))
 Description: Generate images of molecules using the Depiction API of  the 'Chemistry Development Kit'. 
     CDK's Depict Api
 License: LGPL
 LazyData: TRUE
 Depends:
-    rJava (>= 1.0-6),
+    rJava (>= 1.0-11),
     rcdk (>= 3.7),
     rcdklibs (>= 2.8)
 Imports:
-    png,
-    magrittr
-RoxygenNote: 7.2.2
+    png
+RoxygenNote: 7.3.1
+Encoding: UTF-8
+URL: https://cdk-r.github.io/depict/
 Suggests: 
     knitr,
+    magrittr,
     rmarkdown,
-    testthat
+    testthat,
 VignetteBuilder: knitr
diff --git a/NAMESPACE b/NAMESPACE
@@ -8,6 +8,7 @@ export(color_atoms)
 export(depict)
 export(depiction)
 export(get_image)
+export(get_svg_string)
 export(highlight_atoms)
 export(match_smarts)
 export(outerglow)

diff --git a/R/IO.R b/R/IO.R
@@ -8,27 +8,25 @@
 #' @param kekulise Optional. Boolean. Default \code{TRUE}
 #' @export
 #'
-parse_smiles <- function(smi, generatecoords=TRUE, kekulise=TRUE) {
-
+parse_smiles <- function(smi, generatecoords = TRUE, kekulise = TRUE) {
   SmilesParser <- J("org.openscience.cdk.smiles.SmilesParser")
   SChemObjectBuilder <- J("org.openscience.cdk.silent.SilentChemObjectBuilder")
   StructureDiagramGenerator <- J("org.openscience.cdk.layout.StructureDiagramGenerator")
 
   sinst <- SChemObjectBuilder$getInstance()
-  sp    <- new(SmilesParser, sinst)
+  sp <- new(SmilesParser, sinst)
   sp$kekulise(kekulise)
-  
-  mol   <- sp$parseSmiles(smi)
+
+  mol <- sp$parseSmiles(smi)
 
   if (generatecoords) {
-    sdg   <- new(StructureDiagramGenerator)
+    sdg <- new(StructureDiagramGenerator)
     sdg$setMolecule(mol)
     sdg$generateCoordinates()
     mol <- sdg$getMolecule()
   }
 
   mol
-
 }
 
 #' read_mol
@@ -39,16 +37,13 @@ parse_smiles <- function(smi, generatecoords=TRUE, kekulise=TRUE) {
 #' @return an AtomContainer
 #' @export
 read_mol <- function(molfile) {
-
   jAtomContainer <- J("org.openscience.cdk.AtomContainer")
 
-  jfileobj   <- .jnew("java.io.File", molfile)
+  jfileobj <- .jnew("java.io.File", molfile)
   jreaderobj <- .jnew("java.io.FileReader", jfileobj)
   jmolreader <- .jnew("org.openscience.cdk.io.MDLV2000Reader")
-  AC         <- .jnew("org.openscience.cdk.AtomContainer")
+  AC <- .jnew("org.openscience.cdk.AtomContainer")
 
   jmolreader$setReader(jreaderobj)
   jmolreader$read(AC)
-
 }
-
diff --git a/R/depict.R b/R/depict.R
@@ -10,7 +10,7 @@ depiction <- function() {
 #' color atoms
 #'
 #' set the atom color
-#' 
+#'
 #' @param dg a CDK DepictionGenerator
 #' @seealso \url{https://cdk.github.io/cdk/latest/docs/api/org/openscience/cdk/depict/DepictionGenerator.html}
 #' @export
@@ -45,7 +45,7 @@ set_size <- function(dg, width, height) {
     stop("set_size requires a Depiction Generator")
   }
 
-  dg$withSize(width,height)
+  dg$withSize(width, height)
 }
 
 #' add_title
@@ -54,7 +54,6 @@ set_size <- function(dg, width, height) {
 #' @seealso \url{https://cdk.github.io/cdk/latest/docs/api/org/openscience/cdk/depict/DepictionGenerator.html}
 #' @export
 add_title <- function(dg) {
-
   if (!checkJavaClass(dg, "org/openscience/cdk/depict/DepictionGenerator")) {
     stop("add_title requires a Depiction Generator")
   }
@@ -86,24 +85,30 @@ add_terminal_carbons <- function(dg) {
 #' @param mol Required. An AtomContainer
 #' @seealso \url{https://cdk.github.io/cdk/latest/docs/api/org/openscience/cdk/depict/DepictionGenerator.html}
 #' @seealso \url{https://cdk.github.io/cdk/latest/docs/api/org/openscience/cdk/AtomContainer.html}
-#' 
+#'
 #' @export
 depict <- function(dg, mol) {
   if (!checkJavaClass(dg, "org/openscience/cdk/depict/DepictionGenerator")) {
+    print(.jclass(dg))
     stop("depict requires a Depiction Generator")
   }
 
-  if (!checkJavaClass(mol, c("org/openscience/cdk/AtomContainer",
-                             "org/openscience/cdk/AtomContainer2",
-                             "org/openscience/cdk/silent/AtomContainer",
-                             "org/openscience/cdk/silent/AtomContainer2",
-                             "org/openscience/cdk/silent/IAtomContainer",
-                             "java/util/ArrayList"
-                             ))) {
-    stop("depict requires an AtomContainer or an ArrayList of them")
-  } 
-
-  #.jcall(dg, "Lorg/openscience/cdk/depict/Depiction;", "depict", mol)
+  if (!checkJavaClass(mol, c(
+    "org/openscience/cdk/AtomContainer",
+    "org/openscience/cdk/AtomContainer2",
+    "org/openscience/cdk/Reaction",
+    "org/openscience/cdk/ReactionSet",
+    "org/openscience/cdk/silent/AtomContainer",
+    "org/openscience/cdk/silent/AtomContainer2",
+    "org/openscience/cdk/silent/IAtomContainer",
+    "org/openscience/cdk/silent/Reaction",
+    "org/openscience/cdk/silent/ReactionSet",
+    "java/util/ArrayList"
+  ))) {
+    stop("depict requires an AtomContainer, Reaction, ReactionSet, or an ArrayList of them")
+  }
+
+  # .jcall(dg, "Lorg/openscience/cdk/depict/Depiction;", "depict", mol)
   dg$depict(mol)
 }
 
@@ -131,7 +136,10 @@ highlight_atoms <- function(dg, atoms, color) {
 #' @param outfile Required. Filepath to the output
 #' @export
 save_image <- function(molgrid, filepath) {
-  if (!checkJavaClass(molgrid, "org/openscience/cdk/depict/MolGridDepiction")) {
+  if (!checkJavaClass(molgrid, c(
+    "org/openscience/cdk/depict/MolGridDepiction",
+    "org/openscience/cdk/depict/ReactionDepiction"
+  ))) {
     stop("highlight_atoms requires a Depiction Generator")
   }
   molgrid$writeTo(filepath)
@@ -148,13 +156,17 @@ save_image <- function(molgrid, filepath) {
 #' @export
 #'
 get_image <- function(molgrid) {
-  if (!checkJavaClass(molgrid, "org/openscience/cdk/depict/MolGridDepiction")) {
-    stop("highlight_atoms requires a Depiction Generator")
+  if (!checkJavaClass(molgrid, c(
+    "org/openscience/cdk/depict/MolGridDepiction",
+    "org/openscience/cdk/depict/ReactionDepiction"
+  ))) {
+    print(.jclass(molgrid))
+    stop("get_image requires a Depiction")
   }
 
   # CDK apends a ".png" to the name
-  output  <- paste(tempfile(),"png")
-  output1 <- paste0(output,".png")
+  output <- paste(tempfile(), "png")
+  output1 <- paste0(output, ".png")
 
   molgrid$writeTo("png", output)
   img <- readPNG(output1)
@@ -165,6 +177,31 @@ get_image <- function(molgrid) {
   img
 }
 
+#' get_svg_string
+#'
+#' @param molgrid Required. A MolGridDepiction. Usually obtained from
+#' the \code{depict} function.
+#' @returns an SVG string literal
+#' @export
+get_svg_string <- function(molgrid) {
+  if (!checkJavaClass(molgrid, c(
+    "org/openscience/cdk/depict/MolGridDepiction",
+    "org/openscience/cdk/depict/ReactionDepiction"
+  ))) {
+    print(.jclass(molgrid))
+    stop("get_image requires a Depiction")
+  }
+
+  # svg_str <- grid$toSvgStr()
+  svg_str <- .jcall(molgrid, 'S' ,'toSvgStr')
+
+  svg_list <- strsplit(svg_str, "\n")[[1]]
+
+  # return the svg without the two header lines
+  paste(svg_list[3:length(svg_list)], collapse="\n")
+}
+
+
 #' set_zoom
 #'
 #' set_zoom
@@ -173,7 +210,7 @@ get_image <- function(molgrid) {
 #' @param zoom Optional. Default \code{1}
 #' @export
 #'
-set_zoom <- function(dg, zoom=1) {
+set_zoom <- function(dg, zoom = 1) {
   if (!checkJavaClass(dg, "org/openscience/cdk/depict/DepictionGenerator")) {
     stop("highlight_atoms requires a Depiction Generator")
   }

diff --git a/R/selection_functions.R b/R/selection_functions.R
@@ -1,58 +1,54 @@
 #' match_smarts
-#' 
+#'
 #' Find matches to a given molecule using a SMARTs pattern.
 #'
 #' @param smarts a SMARTS string
 #' @param mol a CDK IAtomContainer or a java.util.Arraylist of them
 #' @param limit limit of the number of matches
-#' 
+#'
 #' @seealso \url{https://cdk.github.io/cdk/latest/docs/api/org/openscience/cdk/isomorphism/Mappings.html}
 #' @seealso \url{https://cdk.github.io/cdk/latest/docs/api/org/openscience/cdk/smiles/smarts/SmartsPattern.html}
-#' 
+#'
 #' @return a hashset of atoms and bonds
 #' @export
 #'
-#' 
-match_smarts <- function(smarts, mol, limit=10) {
-
-
-  hashset       <- J("java/util/HashSet")
+#'
+match_smarts <- function(smarts, mol, limit = 10) {
+  hashset <- J("java/util/HashSet")
   smartspattern <- J("org/openscience/cdk/smiles/smarts/SmartsPattern")
-  spattern      <- smartspattern$create(smarts, NULL)
+  spattern <- smartspattern$create(smarts, NULL)
 
   # handle the base case first
   if (!.jclass(mol) == "java.util.ArrayList") {
-
     matches <- spattern$matchAll(mol)
     matches <- matches$limit(as.integer(limit))
     # Note: switching below to chemobjects due to reflection access with the atom-bond map
     # atombondmap <- matches$uniqueAtoms()$toAtomBondMap()
-    atombonds   <- matches$uniqueAtoms()$toChemObjects()
-    
+    atombonds <- matches$uniqueAtoms()$toChemObjects()
+
     # somewhat convoluted code to get all of the matching atoms
     highlight <- new(hashset)
-    
+
     for (l in as.list(atombonds)) {
       highlight$add(l)
     }
-  
-  # then handle the array list of atom containers
+
+    # then handle the array list of atom containers
   } else {
-
     # somewhat convoluted code to get all of the matching atoms
     highlight <- new(hashset)
-    
+
     for (atmcont in as.list(mol)) {
       matches <- spattern$matchAll(atmcont)
       matches <- matches$limit(as.integer(limit))
       # Note: switching below to chemobjects due to reflection access with the atom-bond map
       # atombondmap <- matches$uniqueAtoms()$toAtomBondMap()
-      atombonds   <- matches$uniqueAtoms()$toChemObjects()
+      atombonds <- matches$uniqueAtoms()$toChemObjects()
       for (l in as.list(atombonds)) {
         highlight$add(l)
       }
     }
   }
-  
+
   highlight
 }
diff --git a/R/smarts.R b/R/smarts.R
@@ -6,22 +6,20 @@
 #' @seealso \url{http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html}
 #' @seealso \url{http://www.daylight.com/dayhtml_tutorials/languages/smarts/index.html}
 #' @export
-#' 
+#'
 #'
 amino_acids <- function() {
   list(
     # Generic amino acid: low specificity.
-    amino_acids="[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", #For use w/ non-standard a.a. search. hits pro but not gly. Hits acids and conjugate bases. Hits single a.a.s and specific residues w/in polypeptides (internal, or terminal).
+    amino_acids = "[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]", # For use w/ non-standard a.a. search. hits pro but not gly. Hits acids and conjugate bases. Hits single a.a.s and specific residues w/in polypeptides (internal, or terminal).
 
     # A.A. Template for 20 standard a.a.s
-    amino_acids20="[$([$([NX3H,NX4H2+]),$([NX3](C)(C)(C))]1[CX4H]([CH2][CH2][CH2]1)[CX3](=[OX1])[OX2H,OX1-,N]),
+    amino_acids20 = "[$([$([NX3H,NX4H2+]),$([NX3](C)(C)(C))]1[CX4H]([CH2][CH2][CH2]1)[CX3](=[OX1])[OX2H,OX1-,N]),
     $([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H2][CX3](=[OX1])[OX2H,OX1-,N]),$([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([*])[CX3](=[OX1])[OX2H,OX1-,N])]",
-
-    proline="[$([NX3H,NX4H2+]),$([NX3](C)(C)(C))]1[CX4H]([CH2][CH2][CH2]1)[CX3](=[OX1])[OX2H,OX1-,N]",
-    glycine="[$([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H2][CX3](=[OX1])[OX2H,OX1-,N])]",
-    amino_acids18="[$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([*])[CX3](=[OX1])[OX2H,OX1-,N]",
-
-    alanine="[$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([CH3X4])[CX3](=[OX1])[OX2H,OX1-,N]",
+    proline = "[$([NX3H,NX4H2+]),$([NX3](C)(C)(C))]1[CX4H]([CH2][CH2][CH2]1)[CX3](=[OX1])[OX2H,OX1-,N]",
+    glycine = "[$([$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H2][CX3](=[OX1])[OX2H,OX1-,N])]",
+    amino_acids18 = "[$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([*])[CX3](=[OX1])[OX2H,OX1-,N]",
+    alanine = "[$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([CH3X4])[CX3](=[OX1])[OX2H,OX1-,N]",
 
     # $([CH2X4][CX3](=[OX1])[NX3H2]),
     # $([CH2X4][CX3](=[OX1])[OH0-,OH]),
@@ -38,6 +36,6 @@ amino_acids <- function() {
     #   $([CH2X4][cX3]1[cX3H][nX3H][cX3]2[cX3H][cX3H][cX3H][cX3H][cX3]12),
     #   $([CH2X4][cX3]1[cX3H][cX3H][cX3]([OHX2,OH0X1-])[cX3H][cX3H]1),
     #   $([CHX4]([CH3X4])[CH3X4])
-    amino_acids18="[$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([*])[CX3](=[OX1])[OX2H,OX1-,N]"
-    )
+    amino_acids18 = "[$([NX3H2,NX4H3+]),$([NX3H](C)(C))][CX4H]([*])[CX3](=[OX1])[OX2H,OX1-,N]"
+  )
 }
diff --git a/R/utilities.R b/R/utilities.R
@@ -5,11 +5,11 @@
 #' @param jobj Required. A Java Object
 #' @param klass Required. A string defining a java class
 #' @return Boolean
-checkJavaClass <- function(jobj, klass ) {
+checkJavaClass <- function(jobj, klass) {
   if (is.null(attr(jobj, 'jclass'))) stop("this is not a Java Object")
 
-  for (k in klass ) {
-    if (attr(jobj, "jclass") == k) {
+  for (kl in klass) {
+    if (attr(jobj, "jclass") == kl) {
       return(TRUE)
     }
   }
@@ -40,8 +40,7 @@ checkJavaClass <- function(jobj, klass ) {
 atomcontainer_list_to_jarray <- function(atomcontainers) {
 
   new_array <-  .jnew('java.util.ArrayList')
-
-  for (atmcntnr in atomcontainers) {
+  for (atmcntnr in as.list(atomcontainers)) {
     new_array$add(atmcntnr)
   }
 

diff --git a/_pkgdown.yml b/_pkgdown.yml
diff --git a/man/figures/logo.png b/man/figures/logo.png
diff --git a/man/get_svg_string.Rd b/man/get_svg_string.Rd