- update highlight function (#16)

- add a few more examples

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: depict
 Type: Package
 Title: Draw Beautiful Molecular Structures
-Version: 0.3.0
+Version: 0.3.1
 Authors@R: c(person('Zachary', 'Charlop-Powers', role=c('cre','aut',"cph"), email='[email protected]'))
 Description: Generate images of molecules using the Depiction API of  the 'Chemistry Development Kit'. 
     CDK's Depict Api
@@ -14,7 +14,7 @@ Depends:
 Imports:
     png,
     magrittr
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.2
 Suggests: 
     knitr,
     rmarkdown,

NEWS.md

@@ -1,3 +1,7 @@
+# depict 0.3.1-dev
+
+* extend match_smarts to work on collections of IAtomContainers 
+
 # depict 0.3.0
 
 * modify `match_smarts` to use `toChemObjects` methodinstead of `toAtomBondMap` due to an issue with Java reflection.

R/selection_functions.R

@@ -3,7 +3,7 @@
 #' Find matches to a given molecule using a SMARTs pattern.
 #'
 #' @param smarts a SMARTS string
-#' @param mol a CDK IAtomContainer
+#' @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}
@@ -14,22 +14,44 @@
 #'
 #' 
 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)
 
-  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()
-
-  # somewhat convoluted code to get all of the matching atoms
-  highlight <- new(hashset)
+  # 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()
+
+    # somewhat convoluted code to get all of the matching atoms
+    highlight <- new(hashset)
+
+    for (l in as.list(atombonds)) {
+      highlight$add(l)
+    }
 
-  for (l in as.list(atombonds)) {
-    highlight$add(l)
+  # then handle the array list of atom containers
+  } else {
+
+    # somewhat convoluted code to get all of the matching atoms
+    highlight <- new(hashset)
+
+    for (atmcont in as.list(mol)) {
+      matches <- spattern$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()$toChemObjects()
+      for (l in as.list(atombonds)) {
+        highlight$add(l)
+      }
+    }
   }
 
   highlight

vignettes/Basic-Use.Rmd

@@ -103,6 +103,46 @@ depiction() %>%
 ```
 
 
+##  SMARTS for highlighting mutiple containers
+
+```{r}
+
+small_highlight <- match_smarts("C1CCC1", many_containers)
+
+depiction() %>%
+  highlight_atoms(small_highlight, color$RED) %>%
+  set_size(400, 400) %>%
+  set_zoom(3) %>%
+  outerglow() %>%
+  add_title() %>%
+  depict(many_containers) %>%
+  get_image() %>%
+  grid::grid.raster()
+```
+
+## Multiple Colors
+
+```{r}
+mol       <- parse_smiles(paste("CC(n1c(C)ncc1c1ccnc(n1)Nc1ccc(cc1)S(=O)(=O)C)C", 
+                                "CMGC:CDC2:6gu3:A:FB8", sep=" "))
+
+# imid      <- 'c1cnc[nH]1'  #1H-imidazole
+highlight_imid <- match_smarts("c1cncn1", mol)
+highlight_2    <- match_smarts("n1cccnc1Nc2ccccc2", mol)
+
+color <- J("java.awt.Color")
+
+depiction() |>
+  highlight_atoms(highlight_imid, color$GREEN) |>
+  highlight_atoms(highlight_2, color$RED) |>
+  set_size(400, 400) |>
+  set_zoom(4) |>
+  outerglow() |>
+  add_title() |>
+  depict(mol) |>
+  get_image() |>
+  grid::grid.raster()
+```
 
 ## A Larger Example