Unified reaction SMILES API with the molecule and make it so reaction…

…s can be canonicalised.
cdk · Aug 16, 2016 · fc5e945 · fc5e945
1 parent c2b88b4
commit fc5e945
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diff --git a/storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesGenerator.java b/storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesGenerator.java
@@ -35,6 +35,7 @@
 import org.openscience.cdk.interfaces.ISingleElectron;
 import org.openscience.cdk.sgroup.Sgroup;
 import org.openscience.cdk.sgroup.SgroupKey;
+import org.openscience.cdk.tools.manipulator.ReactionManipulator;
 import uk.ac.ebi.beam.Functions;
 import uk.ac.ebi.beam.Graph;
 
@@ -431,39 +432,62 @@ public String create(IAtomContainer molecule, int[] order) throws CDKException {
         }
     }
 
+    @Deprecated
+    public String createReactionSMILES(IReaction reaction) throws CDKException {
+        return create(reaction);
+    }
+
+    public String create(IReaction reaction) throws CDKException {
+        return create(reaction, new int[ReactionManipulator.getAtomCount(reaction)]);
+    }
+
     /**
      * Generate a SMILES for the given <code>Reaction</code>.
      *
      * @param reaction the reaction in question
      * @return the SMILES representation of the reaction
      * @throws org.openscience.cdk.exception.CDKException if there is an error during SMILES generation
      */
-    public String createReactionSMILES(IReaction reaction) throws CDKException {
-        StringBuffer reactionSMILES = new StringBuffer();
+    public String create(IReaction reaction, int[] ordering) throws CDKException {
+
         IAtomContainerSet reactants = reaction.getReactants();
+        IAtomContainerSet agents    = reaction.getAgents();
+        IAtomContainerSet products  = reaction.getProducts();
+
+        IAtomContainer    reactantPart = reaction.getBuilder().newInstance(IAtomContainer.class);
+        IAtomContainer    agentPart    = reaction.getBuilder().newInstance(IAtomContainer.class);
+        IAtomContainer    productPart  = reaction.getBuilder().newInstance(IAtomContainer.class);
+
         for (int i = 0; i < reactants.getAtomContainerCount(); i++) {
-            reactionSMILES.append(create(reactants.getAtomContainer(i)));
-            if (i + 1 < reactants.getAtomContainerCount()) {
-                reactionSMILES.append('.');
-            }
+            reactantPart.add(reactants.getAtomContainer(i));
         }
-        reactionSMILES.append('>');
-        IAtomContainerSet agents = reaction.getAgents();
         for (int i = 0; i < agents.getAtomContainerCount(); i++) {
-            reactionSMILES.append(create(agents.getAtomContainer(i)));
-            if (i + 1 < agents.getAtomContainerCount()) {
-                reactionSMILES.append('.');
-            }
+            agentPart.add(agents.getAtomContainer(i));
         }
-        reactionSMILES.append('>');
-        IAtomContainerSet products = reaction.getProducts();
         for (int i = 0; i < products.getAtomContainerCount(); i++) {
-            reactionSMILES.append(create(products.getAtomContainer(i)));
-            if (i + 1 < products.getAtomContainerCount()) {
-                reactionSMILES.append('.');
-            }
+            productPart.add(products.getAtomContainer(i));
         }
-        return reactionSMILES.toString();
+
+        int[] reactantOrder = new int[reactantPart.getAtomCount()];
+        int[] agentOrder    = new int[agentPart.getAtomCount()];
+        int[] productOrder  = new int[productPart.getAtomCount()];
+
+        final int expectedSize = reactantOrder.length + agentOrder.length + productOrder.length;
+        if (expectedSize != ordering.length) {
+            throw new CDKException("Output ordering array does not have correct amount of space: " + ordering.length +
+                                   " expected: " + expectedSize);
+        }
+
+        String smi = create(reactantPart, reactantOrder) + ">" +
+                           create(agentPart, agentOrder) + ">" +
+                           create(productPart, productOrder);
+
+        // copy ordering back to unified array
+        System.arraycopy(reactantOrder, 0, ordering, 0, reactantOrder.length);
+        System.arraycopy(agentOrder, 0, ordering, reactantOrder.length, agentOrder.length);
+        System.arraycopy(productOrder, 0, ordering, reactantOrder.length + agentOrder.length, productOrder.length);
+
+        return smi;
     }
 
     /**

diff --git a/storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesGeneratorTest.java b/storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesGeneratorTest.java
@@ -62,6 +62,7 @@
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IChemSequence;
 import org.openscience.cdk.interfaces.IDoubleBondStereochemistry;
+import org.openscience.cdk.interfaces.IReaction;
 import org.openscience.cdk.interfaces.IStereoElement;
 import org.openscience.cdk.interfaces.ITetrahedralChirality;
 import org.openscience.cdk.io.CMLReader;
@@ -674,7 +675,7 @@ public void testReactionSMILES() throws Exception {
         gold.getAtom(0).setImplicitHydrogenCount(0);
 
         SmilesGenerator sg = new SmilesGenerator();
-        String smiles = sg.createReactionSMILES(reaction);
+        String smiles = sg.create(reaction);
         //logger.debug("Generated SMILES: " + smiles);
         Assert.assertEquals("C>*>[Au]", smiles);
     }
@@ -1218,6 +1219,16 @@ public void assignDbStereo() throws Exception {
         Assert.assertEquals("C(\\N)=C/C=C/1\\N=C1", SmilesGenerator.isomeric().create(mol));
     }
 
+    @Test public void canonicalReactions() throws Exception {
+        SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
+        IReaction r1 = smipar.parseReactionSmiles("CC(C)C1=CC=CC=C1.C(CC(=O)Cl)CCl>[Al+3].[Cl-].[Cl-].[Cl-].C(Cl)Cl>CC(C)C1=CC=C(C=C1)C(=O)CCCCl");
+        IReaction r2 = smipar.parseReactionSmiles("C(CC(=O)Cl)CCl.CC(C)C1=CC=CC=C1>[Al+3].[Cl-].[Cl-].[Cl-].C(Cl)Cl>CC(C)C1=CC=C(C=C1)C(=O)CCCCl");
+        IReaction r3 = smipar.parseReactionSmiles("CC(C)C1=CC=CC=C1.C(CC(=O)Cl)CCl>C(Cl)Cl.[Al+3].[Cl-].[Cl-].[Cl-]>CC(C)C1=CC=C(C=C1)C(=O)CCCCl");
+        SmilesGenerator smigen = new SmilesGenerator(SmiOpt.Canonical);
+        assertThat(smigen.create(r1), is(smigen.create(r2)));
+        assertThat(smigen.create(r2), is(smigen.create(r3)));
+    }
+
     static ITetrahedralChirality anticlockwise(IAtomContainer container, int central, int a1, int a2, int a3, int a4) {
         return new TetrahedralChirality(container.getAtom(central), new IAtom[]{container.getAtom(a1),
                                                                                 container.getAtom(a2), container.getAtom(a3), container.getAtom(a4)},