Correct parsing and building of reaction SMARTS queries. Relatively s…

…imple adaption to existing parser.

tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ReactionRole.java

@@ -0,0 +1,65 @@
+/*
+ * Copyright (c) 2016 John May <jwmay@users.sf.net>
+ *
+ * Contact: cdk-devel@lists.sourceforge.net
+ *
+ * This program is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation; either version 2.1 of the License, or (at
+ * your option) any later version. All we ask is that proper credit is given
+ * for our work, which includes - but is not limited to - adding the above
+ * copyright notice to the beginning of your source code files, and to any
+ * copyright notice that you may distribute with programs based on this work.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
+ * License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U
+ */
+package org.openscience.cdk.isomorphism.matchers.smarts;
+
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
+
+/**
+ * Matches atoms with a particular role in a reaction.
+ */
+public class ReactionRole extends SMARTSAtom {
+
+    public static final int ROLE_REACTANT = 0x1;
+    public static final int ROLE_AGENT    = 0x2;
+    public static final int ROLE_PRODUCT  = 0x4;
+    public static final int ROLE_ANY      = ROLE_REACTANT | ROLE_PRODUCT | ROLE_AGENT;
+
+    private final int role;
+
+    public final static ReactionRole RoleReactant = new ReactionRole(null, ROLE_REACTANT);
+    public final static ReactionRole RoleAgent = new ReactionRole(null, ROLE_AGENT);
+    public final static ReactionRole RoleProduct = new ReactionRole(null, ROLE_PRODUCT);
+
+    public ReactionRole(IChemObjectBuilder builder, int role) {
+        super(builder);
+        this.role = role;
+    }
+
+    @Override
+    public boolean matches(IAtom atom) {
+        return true; // TODO
+    }
+
+    @Override
+    public String toString() {
+        StringBuilder sb = new StringBuilder();
+        if ((role & ROLE_REACTANT) != 0)
+            sb.append("Reactant");
+        if ((role & ROLE_AGENT) != 0)
+            sb.append("Agent");
+        if ((role & ROLE_PRODUCT) != 0)
+            sb.append("Product");
+        return "ReactionRole(" + sb.toString() + ")";
+    }
+}

tool/smarts/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTGroup.java

@@ -17,6 +17,8 @@
  */
 package org.openscience.cdk.smiles.smarts.parser;
 
+import org.openscience.cdk.isomorphism.matchers.smarts.ReactionRole;
+
 /**
  * An AST node. It represents the group notation (.) of smarts.
  *
@@ -28,6 +30,13 @@
  */
 class ASTGroup extends SimpleNode {
 
+    static final int ROLE_REACTANT = ReactionRole.ROLE_REACTANT;
+    static final int ROLE_AGENT    = ReactionRole.ROLE_AGENT;
+    static final int ROLE_PRODUCT  = ReactionRole.ROLE_PRODUCT;
+    static final int ROLE_ANY      = ReactionRole.ROLE_ANY;
+
+    private int role = ROLE_ANY;
+
     /**
      * Creates a new instance
      *
@@ -47,6 +56,14 @@ public ASTGroup(SMARTSParser p, int id) {
         super(p, id);
     }
 
+    public void setRole(int role) {
+        this.role = role;
+    }
+
+    public int getRole() {
+        return this.role;
+    }
+
     /*
      * (non-Javadoc)
      * @see

tool/smarts/src/main/java/org/openscience/cdk/smiles/smarts/parser/SmartsQueryVisitor.java

@@ -50,6 +50,7 @@
 import org.openscience.cdk.isomorphism.matchers.smarts.NonCHHeavyAtom;
 import org.openscience.cdk.isomorphism.matchers.smarts.OrderQueryBond;
 import org.openscience.cdk.isomorphism.matchers.smarts.PeriodicGroupNumberAtom;
+import org.openscience.cdk.isomorphism.matchers.smarts.ReactionRole;
 import org.openscience.cdk.isomorphism.matchers.smarts.RecursiveSmartsAtom;
 import org.openscience.cdk.isomorphism.matchers.smarts.RingBond;
 import org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom;
@@ -211,13 +212,48 @@ public Object visit(ASTStart node, Object data) {
         return node.jjtGetChild(0).jjtAccept(this, data);
     }
 
-    // TODO: No QueryReaction API
     public Object visit(ASTReaction node, Object data) {
-        return node.jjtGetChild(0).jjtAccept(this, data);
+        IAtomContainer query = new QueryAtomContainer(builder);
+        for (int grpIdx = 0; grpIdx < node.jjtGetNumChildren(); grpIdx++) {
+
+            int rollback = query.getAtomCount();
+
+            ASTGroup group = (ASTGroup) node.jjtGetChild(grpIdx);
+            group.jjtAccept(this, query);
+
+            // fill in the roles for newly create atoms
+            if (group.getRole() != ASTGroup.ROLE_ANY) {
+                IQueryAtom roleQueryAtom = null;
+
+                // use single instances
+                switch (group.getRole()) {
+                    case ASTGroup.ROLE_REACTANT:
+                        roleQueryAtom = ReactionRole.RoleReactant;
+                        break;
+                    case ASTGroup.ROLE_AGENT:
+                        roleQueryAtom = ReactionRole.RoleAgent;
+                        break;
+                    case ASTGroup.ROLE_PRODUCT:
+                        roleQueryAtom = ReactionRole.RoleProduct;
+                        break;
+                }
+
+                if (roleQueryAtom != null) {
+                    while (rollback < query.getAtomCount()) {
+                        query.setAtom(rollback, LogicalOperatorAtom.and(roleQueryAtom, (IQueryAtom) query.getAtom(rollback)));
+                        rollback++;
+                    }
+                }
+            }
+        }
+        return query;
     }
 
     public Object visit(ASTGroup node, Object data) {
-        IAtomContainer fullQuery = new QueryAtomContainer(builder);
+        IAtomContainer fullQuery = (IAtomContainer) data;
+
+        if (fullQuery == null)
+            fullQuery = new QueryAtomContainer(builder);
 
         // keeps track of component grouping
         int[] components = new int[0];

tool/smarts/src/main/jjtree/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.jjt

@@ -295,8 +295,7 @@ TOKEN_MGR_DECLS : {
 
 /**
  *                     Start ::= <ReactionExpression> <#_WS>
- *        ReactionExpression ::= <GroupExpression> (">>" <GroupExpression>)? |
- *                               ">" <GroupExpression> ">" | ">>" <GroupExpression>
+ *        ReactionExpression ::= <GroupExpression>? (">" <GroupExpression>? ">" <GroupExpression>?)?
  *           GroupExpression ::= ["("] <SmartsExpresion> [")"] ( "." ["("] <SmartsExpression> [")"] )*
  *          SmartsExpression ::= <AtomExpression> ( 
  									( [ <LowAndBond> ] ( <Digit> | <AtomExpression> ) ) |
@@ -341,11 +340,24 @@ ASTStart Start() #Start : {}
 
 void ReactionExpression() #Reaction : {}
 {
-    GroupExpression() ( ">>" [GroupExpression()] )?
-    |
-    ">" GroupExpression() ">"
-    |
-    ">>" GroupExpression()
+    [GroupExpression()]
+    (
+      ">"
+      {
+        if(jjtree.nodeArity() > 0)
+          ((ASTGroup)jjtree.peekNode()).setRole(ASTGroup.ROLE_REACTANT);
+      }
+      [
+        GroupExpression()
+        {
+          ((ASTGroup)jjtree.peekNode()).setRole(ASTGroup.ROLE_AGENT);
+        }
+      ]
+      ">"
+      [
+        GroupExpression(){((ASTGroup)jjtree.peekNode()).setRole(ASTGroup.ROLE_PRODUCT);}
+      ]
+    )?
 }
 
 void GroupExpression() #Group : {}

tool/smarts/src/test/java/org/openscience/cdk/smiles/smarts/parser/SmartsQueryVisitorTest.java

@@ -1281,4 +1281,28 @@ public void testRing() throws Exception {
         visit("[$([C;#12]=1CCCCC1)]");
     }
 
+    @Test
+    public void reaction() throws Exception {
+        visit("CCO.CC(=O)O>[H+]>CCOC(=O)C.O");
+    }
+
+    @Test
+    public void reactionNoAgents() throws Exception {
+        visit("CCO.CC(=O)O>>CCOC(=O)C.O");
+    }
+
+    @Test
+    public void reactionNoProduct() throws Exception {
+        visit("CCO.CC(=O)O>>");
+    }
+
+    @Test
+    public void reactionNoReactant() throws Exception {
+        visit(">>CCOC(=O)C.O");
+    }
+
+    @Test
+    public void reactionOnlyAgents() throws Exception {
+        visit(">>CCOC(=O)C.O");
+    }
 }