Watch out for ambiguity, we cannot collapse "N" "iPr" to "NiPr" as it…

… is ambiguous with "Ni", "Pr".
cdk · Dec 3, 2018 · 9e7cb8f · 9e7cb8f
1 parent 6cfa36a
commit 9e7cb8f
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Showing 2 changed files with 21 additions and 1 deletion.
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
@@ -448,6 +448,7 @@ else if (attachBond.getEnd().equals(atom))
             return newSgroups;
 
         // now collapse
+        collapse:
         for (IAtom attach : mol.atoms()) {
             if (usedAtoms.contains(attach))
                 continue;
@@ -470,8 +471,16 @@ else if (attachBond.getEnd().equals(atom))
             for (Sgroup sgroup : sgroupAdjs.get(attach)) {
                 if (containsChargeChar(sgroup.getSubscript()))
                     continue;
-                xbonds.addAll(sgroup.getBonds());
+                if (sgroup.getBonds().size() != 1)
+                    continue;
+                IBond xbond = sgroup.getBonds().iterator().next();
+                xbonds.add(xbond);
                 xatoms.addAll(sgroup.getAtoms());
+                if (attach.getSymbol().length() == 1 &&
+                    Character.isLowerCase(sgroup.getSubscript().charAt(0))) {
+                    if (Elements.ofString(attach.getSymbol() + sgroup.getSubscript().charAt(0)) != Elements.Unknown)
+                        continue collapse;
+                }
                 nbrSymbols.add(sgroup.getSubscript());
                 todelete.add(sgroup);
             }

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
@@ -294,6 +294,17 @@ public void dontOverwriteExistingSgroups() throws Exception {
         assertThat(sgroups.get(0).getSubscript(), is("Pd(dppf)Cl2"));
     }
 
+    // Don't generate NiPr
+    @Test public void avoidAmbiguity() throws Exception {
+        String smi = "C1CCCCC1=NC(C)C";
+        Abbreviations factory = new Abbreviations();
+        factory.add("*C(C)C iPr");
+        IAtomContainer mol = smi(smi);
+        List<Sgroup> sgroups = factory.generate(mol);
+        assertThat(sgroups.size(), is(1));
+        assertThat(sgroups.get(0).getSubscript(), is("iPr"));
+    }
+
     @Test
     public void loadFromFile() throws Exception {
         Abbreviations factory = new Abbreviations();