Allow contractions like SnCl2.

cdk · Oct 5, 2016 · aaae48e · aaae48e
1 parent 91a92e4
commit aaae48e
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Showing 2 changed files with 16 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
@@ -24,6 +24,7 @@
 package org.openscience.cdk.depict;
 
 import com.google.common.collect.ArrayListMultimap;
+import com.google.common.collect.FluentIterable;
 import com.google.common.collect.Multimap;
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.config.Elements;
@@ -494,6 +495,7 @@ else if (attachBond.getAtom(1) == atom)
                 nbrSymbols.add(sgroup.getSubscript());
                 todelete.add(sgroup);
             }
+            int numSGrpNbrs = nbrSymbols.size();
             for (IBond bond : mol.getConnectedBondsList(attach)) {
                 if (!xbonds.contains(bond)) {
                     IAtom nbr = bond.getConnectedAtom(attach);
@@ -515,7 +517,12 @@ else if (attachBond.getAtom(1) == atom)
                 }
             }
 
-            if (newbonds.size() < 1 || newbonds.size() > 3 || nbrSymbols.isEmpty())
+            // reject if no symbols
+            // reject if no bonds (<1), except if all symbols are identical... (HashSet.size==1)
+            // reject if more that 2 bonds
+            if (nbrSymbols.isEmpty() ||
+                newbonds.size() < 1 && (new HashSet<>(nbrSymbols).size() != 1) ||
+                newbonds.size() > 2)
                 continue;
 
             // create the symbol

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
@@ -256,6 +256,14 @@ public void dontOverwriteExistingSgroups() throws Exception {
         assertThat(sgroups.get(0).getSubscript(), is("EDCI·HCl"));
     }
 
+    @Test public void SnCl2() throws Exception {
+        Abbreviations factory = new Abbreviations();
+        IAtomContainer mol = smi("Cl[Sn]Cl");
+        List<Sgroup> sgroups = factory.generate(mol);
+        assertThat(sgroups.size(), is(1));
+        assertThat(sgroups.get(0).getSubscript(), is("SnCl2"));
+    }
+
     @Test
     public void loadFromFile() throws Exception {
         Abbreviations factory = new Abbreviations();