Resolve some problems with token handling and abbreviations.

cdk · Mar 26, 2017 · 2e8e586 · 2e8e586
1 parent 55c12fe
commit 2e8e586
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Showing 3 changed files with 17 additions and 4 deletions.
diff --git a/app/depict/src/main/java/org/openscience/cdk/depict/Abbreviations.java b/app/depict/src/main/java/org/openscience/cdk/depict/Abbreviations.java
@@ -542,7 +542,8 @@ public int compare(String o1, String o2) {
                 if (nbrSymbol.equals(prev)) {
                     count++;
                 } else {
-                    appendGroup(sb, prev, count, count == 0 || countUpper(prev) > 1);
+                    boolean useParen = count == 0 || countUpper(prev) > 1 || (prev != null && nbrSymbol.startsWith(prev));
+                    appendGroup(sb, prev, count, useParen);
                     prev = nbrSymbol;
                     count = 1;
                 }

diff --git a/...sic/src/main/java/org/openscience/cdk/renderer/generators/standard/AbbreviationLabel.java b/...sic/src/main/java/org/openscience/cdk/renderer/generators/standard/AbbreviationLabel.java
@@ -273,8 +273,11 @@ static void reverse(List<String> tokens) {
             String token = tokens.get(i);
             if (token.equals("(")) {
                 tokens.set(i, ")");
-                tokens.add(i+1, numbers.pop());
-                i++;
+                String num = numbers.pop();
+                if (!num.isEmpty()) {
+                    tokens.add(i + 1, num);
+                    i++;
+                }
             }
             else if (token.equals(")")) {
                 tokens.set(i, "(");
@@ -358,7 +361,7 @@ static void reduce(List<FormattedText> texts, int from, int to) {
      * @return the token is a charge label (+2, -, +, -2)
      */
     private static boolean isChargeToken(String token) {
-        return norm(token.charAt(0)) == '-' || token.charAt(0) == '+';
+        return token.length() > 0 && (norm(token.charAt(0)) == '-' || token.charAt(0) == '+');
     }
 
     /**

diff --git a/...src/test/java/org/openscience/cdk/renderer/generators/standard/AbbreviationLabelTest.java b/...src/test/java/org/openscience/cdk/renderer/generators/standard/AbbreviationLabelTest.java
@@ -133,6 +133,15 @@ public void reversingBrackets() {
         assertThat(Joiner.on("").join(tokens), is("H2C(OH2CH2C)N"));
     }
 
+    @Test
+    public void reversingFormatPOOHOEt() {
+        List<String> tokens = new ArrayList<>();
+        assertTrue(AbbreviationLabel.parse("PO(OH)OEt", tokens));
+        AbbreviationLabel.reverse(tokens);
+        AbbreviationLabel.format(tokens);
+        assertThat(Joiner.on("").join(tokens), is("EtO(HO)OP"));
+    }
+
     @Test
     public void reversingBracketsWithNumbers() {
         List<String> tokens = new ArrayList<>();