Modifications to required invariants for tests.

cdk · Jul 22, 2016 · 2f2ccc4 · 2f2ccc4
1 parent 1600782
commit 2f2ccc4
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Showing 3 changed files with 6 additions and 3 deletions.
diff --git a/storage/smiles/src/main/java/org/openscience/cdk/smiles/BeamToCDK.java b/storage/smiles/src/main/java/org/openscience/cdk/smiles/BeamToCDK.java
@@ -360,7 +360,6 @@ IBond toCDKBond(Edge edge, IAtom[] atoms) {
                 if (atoms[u].isAromatic() && atoms[v].isAromatic()) {
                     bond.setIsAromatic(true);
                     bond.setOrder(IBond.Order.UNSET);
-                    bond.setFlag(CDKConstants.SINGLE_OR_DOUBLE, true);
                     atoms[u].setIsAromatic(true);
                     atoms[v].setIsAromatic(true);
                 }

diff --git a/storage/smiles/src/test/java/org/openscience/cdk/smiles/DeduceBondSystemToolTest.java b/storage/smiles/src/test/java/org/openscience/cdk/smiles/DeduceBondSystemToolTest.java
@@ -75,6 +75,7 @@ public void testPyrrole() throws Exception {
         SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
         smilesParser.kekulise(false);
         IAtomContainer molecule = smilesParser.parseSmiles(smiles);
+        AtomContainerManipulator.setSingleOrDoubleFlags(molecule);
         AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
 
         molecule = dbst.fixAromaticBondOrders(molecule);
@@ -96,12 +97,13 @@ public void testPyrrole_Silent() throws Exception {
         SmilesParser smilesParser = new SmilesParser(SilentChemObjectBuilder.getInstance());
         smilesParser.kekulise(false);
         IAtomContainer molecule = smilesParser.parseSmiles(smiles);
+        AtomContainerManipulator.setSingleOrDoubleFlags(molecule);
         AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
-
         molecule = dbst.fixAromaticBondOrders(molecule);
         Assert.assertNotNull(molecule);
 
         molecule = (IAtomContainer) AtomContainerManipulator.removeHydrogens(molecule);
+
         int doubleBondCount = 0;
         for (int i = 0; i < molecule.getBondCount(); i++) {
             IBond bond = molecule.getBond(i);
@@ -164,6 +166,7 @@ public void testPyrrole_CustomRingFinder() throws Exception {
         SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
         smilesParser.kekulise(false);
         IAtomContainer molecule = smilesParser.parseSmiles(smiles);
+        AtomContainerManipulator.setSingleOrDoubleFlags(molecule);
         AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
 
         DeduceBondSystemTool dbst = new DeduceBondSystemTool(new AllRingsFinder());

diff --git a/storage/smiles/src/test/java/org/openscience/cdk/smiles/FixBondOrdersToolTest.java b/storage/smiles/src/test/java/org/openscience/cdk/smiles/FixBondOrdersToolTest.java
@@ -74,6 +74,7 @@ public void testPyrrole() throws Exception {
         SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
         smilesParser.kekulise(false);
         IAtomContainer molecule = smilesParser.parseSmiles(smiles);
+        AtomContainerManipulator.setSingleOrDoubleFlags(molecule);
         AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
 
         molecule = fbot.kekuliseAromaticRings(molecule);
@@ -95,11 +96,11 @@ public void testPyrrole_Silent() throws Exception {
         SmilesParser smilesParser = new SmilesParser(SilentChemObjectBuilder.getInstance());
         smilesParser.kekulise(false);
         IAtomContainer molecule = smilesParser.parseSmiles(smiles);
+        AtomContainerManipulator.setSingleOrDoubleFlags(molecule);
         AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
 
         molecule = fbot.kekuliseAromaticRings(molecule);
         Assert.assertNotNull(molecule);
-
         molecule = (IAtomContainer) AtomContainerManipulator.removeHydrogens(molecule);
         int doubleBondCount = 0;
         for (int i = 0; i < molecule.getBondCount(); i++) {