HOOH not OHOH.

cdk · Oct 7, 2016 · 2b83fa4 · 2b83fa4
1 parent 953e611
commit 2b83fa4
Show file tree

Hide file tree

Showing 2 changed files with 25 additions and 8 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
@@ -508,7 +508,7 @@ else if (attachBond.getAtom(1) == atom)
                             hcount++;
                             xatoms.add(nbr);
                         } else if (nbr.getAtomicNumber() > 0){
-                            nbrSymbols.add(newSymbol(nbr.getAtomicNumber(), nbr.getImplicitHydrogenCount()));
+                            nbrSymbols.add(newSymbol(nbr.getAtomicNumber(), nbr.getImplicitHydrogenCount(), false));
                             xatoms.add(nbr);
                         }
                     } else {
@@ -527,7 +527,7 @@ else if (attachBond.getAtom(1) == atom)
 
             // create the symbol
             StringBuilder sb = new StringBuilder();
-            sb.append(newSymbol(attach.getAtomicNumber(), hcount));
+            sb.append(newSymbol(attach.getAtomicNumber(), hcount, newbonds.size() == 0));
             String prev  = null;
             int    count = 0;
             Collections.sort(nbrSymbols, new Comparator<String>() {
@@ -597,16 +597,25 @@ private boolean digitAtEnd(String str) {
         return Character.isDigit(str.charAt(str.length()-1));
     }
 
-    private String newSymbol(int atomnum, int hcount) {
+    private String newSymbol(int atomnum, int hcount, boolean prefix) {
         StringBuilder sb = new StringBuilder();
         Elements elem = Elements.ofNumber(atomnum);
         if (elem == Elements.Carbon && hcount == 3)
             return "Me";
-        sb.append(elem.symbol());
-        if (hcount > 0) {
-            sb.append('H');
-            if (hcount > 1)
-                sb.append(hcount);
+        if (prefix) {
+            if (hcount > 0) {
+                sb.append('H');
+                if (hcount > 1)
+                    sb.append(hcount);
+            }
+            sb.append(elem.symbol());
+        } else {
+            sb.append(elem.symbol());
+            if (hcount > 0) {
+                sb.append('H');
+                if (hcount > 1)
+                    sb.append(hcount);
+            }
         }
         return sb.toString();
     }

diff --git a/app/depict/src/test/java/org/openscience/cdk/depict/AbbreviationsTest.java b/app/depict/src/test/java/org/openscience/cdk/depict/AbbreviationsTest.java
@@ -264,6 +264,14 @@ public void dontOverwriteExistingSgroups() throws Exception {
         assertThat(sgroups.get(0).getSubscript(), is("SnCl2"));
     }
 
+    @Test public void HOOH() throws Exception {
+        Abbreviations factory = new Abbreviations();
+        IAtomContainer mol = smi("OO");
+        List<Sgroup> sgroups = factory.generate(mol);
+        assertThat(sgroups.size(), is(1));
+        assertThat(sgroups.get(0).getSubscript(), is("HOOH"));
+    }
+
     @Test
     public void loadFromFile() throws Exception {
         Abbreviations factory = new Abbreviations();