Ensure component grouping is correctly initialised for reaction queries.

cdk · Sep 9, 2016 · 7518992 · 7518992
1 parent 35d5741
commit 7518992
Show file tree

Hide file tree

Showing 2 changed files with 13 additions and 2 deletions.
diff --git a/tool/smarts/src/main/java/org/openscience/cdk/smiles/smarts/parser/SmartsQueryVisitor.java b/tool/smarts/src/main/java/org/openscience/cdk/smiles/smarts/parser/SmartsQueryVisitor.java
@@ -275,8 +275,13 @@ public Object visit(ASTGroup node, Object data) {
             fullQuery = new QueryAtomContainer(builder);
 
         // keeps track of component grouping
-        int[] components = new int[0];
+        int[] components = fullQuery.getProperty(ComponentGrouping.KEY) != null ? fullQuery.getProperty(ComponentGrouping.KEY, int[].class)
+                                                                                : new int[0];
         int maxId = 0;
+        if (components.length > 0) {
+            for (int id : components)
+                if (id > maxId) maxId = id;
+        }
 
         for (int i = 0; i < node.jjtGetNumChildren(); i++) {
             ASTSmarts smarts = (ASTSmarts) node.jjtGetChild(i);
@@ -286,7 +291,7 @@ public Object visit(ASTGroup node, Object data) {
             smarts.jjtAccept(this, null);
 
             // update component info
-            if (smarts.componentId() > 0) {
+            if (components.length > 0 || smarts.componentId() > 0) {
                 components = Arrays.copyOf(components, 1 + fullQuery.getAtomCount() + query.getAtomCount());
                 int id = smarts.componentId();
                 Arrays.fill(components, fullQuery.getAtomCount(), components.length, id);

diff --git a/tool/smarts/src/test/java/org/openscience/cdk/smiles/smarts/SmartsPatternTest.java b/tool/smarts/src/test/java/org/openscience/cdk/smiles/smarts/SmartsPatternTest.java
@@ -183,6 +183,12 @@ public void mismatchedQueryMapsIgnored() throws Exception {
                    is(2));
     }
 
+    @Test public void CCBondForming() throws Exception {
+        assertThat(SmartsPattern.create("([C:1]).([C:2])>>[C:1][C:2]", null)
+                                .matchAll(rsmi("[C-:13]#[N:14].[K+].[CH:3]1=[CH:4][C:5](=[CH:11][CH:12]=[C:2]1[CH2:1]Br)[C:6](=[O:10])[CH:7]2[CH2:8][CH2:9]2>>[CH:3]1=[CH:4][C:5](=[CH:11][CH:12]=[C:2]1[CH2:1][C:13]#[N:14])[C:6](=[O:10])[CH:7]2[CH2:8][CH2:9]2 |f:0.1|")).count(),
+                   is(2));
+    }
+
     @Test
     public void stereo_ring_closures() throws Exception {
         Pattern ptrn = SmartsPattern.create("[C@@]1(O[C@@]([C@@]([C@]([C@]1(C)O)(C)O)(O)C)(O)C)(O)C");