Merge pull request #209 from cdk/patch/cxsmi-labelescape

Minor tweak to correctly handle labels where the first character is e…
cdk · Aug 8, 2016 · 2e9d0de · 2e9d0de
2 parents f33b396 + 26ed0ab
commit 2e9d0de
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Showing 2 changed files with 16 additions and 7 deletions.
diff --git a/storage/smiles/src/main/java/org/openscience/cdk/smiles/CxSmilesParser.java b/storage/smiles/src/main/java/org/openscience/cdk/smiles/CxSmilesParser.java
@@ -76,27 +76,29 @@ private static boolean processAtomLabels(final CharIter iter, final Map<Integer,
                 // end of atom label
                 return true;
             } else {
-                final int beg = iter.pos - 1;
+                iter.pos--; // push back
+                final int beg = iter.pos;
                 int rollback = beg;
                 while (iter.hasNext()) {
-
                     // correct step over of escaped label
                     if (iter.curr() == '&') {
                         rollback = iter.pos;
                         if (iter.nextIf('&') && iter.nextIf('#') && iter.nextIfDigit()) {
                             while (iter.nextIfDigit()){} // more digits
-                            if (!iter.nextIf(';'))
+                            if (!iter.nextIf(';')) {
                                 iter.pos = rollback;
+                            } else {
+                            }
                         } else {
                             iter.pos = rollback;
                         }
                     }
-
-                    if (iter.curr() == ';')
+                    else if (iter.curr() == ';')
                         break;
-                    if (iter.curr() == '$')
+                    else if (iter.curr() == '$')
                         break;
-                    iter.next();
+                    else
+                        iter.next();
                 }
                 dest.put(atomIdx, unescape(iter.substr(beg, iter.pos)));
                 atomIdx++;

diff --git a/storage/smiles/src/test/java/org/openscience/cdk/smiles/CxSmilesParserTest.java b/storage/smiles/src/test/java/org/openscience/cdk/smiles/CxSmilesParserTest.java
@@ -53,6 +53,13 @@ public void escapedAtomLabels() {
         assertThat(state.atomLabels, hasEntry(0, "R'"));
     }
 
+    @Test
+    public void escapedAtomLabels2() {
+        CxSmilesState state = new CxSmilesState();
+        assertThat(CxSmilesParser.processCx("|$;;;&#40;C&#40;R41&#41;&#40;R41&#41;&#41;n;;R41;R41;R41;;_AP1;R41;R41;;_AP1$|", state), is(not(-1)));
+        assertThat(state.atomLabels, hasEntry(3, "(C(R41)(R41))n"));
+    }
+
     @Test
     public void atomValues() {
         CxSmilesState state = new CxSmilesState();