diff --git a/base/core/src/main/java/org/openscience/cdk/CDKConstants.java b/base/core/src/main/java/org/openscience/cdk/CDKConstants.java
index 16a7a451cd1..7716712fb6c 100644
--- a/base/core/src/main/java/org/openscience/cdk/CDKConstants.java
+++ b/base/core/src/main/java/org/openscience/cdk/CDKConstants.java
@@ -285,6 +285,22 @@ public class CDKConstants {
*/
public static final String RELEVANT_RINGS = "cdk:RelevantRings";
+ /**
+ * Property used for reactions when converted to/from molecules. It defines what role and atom
+ * has an a reaction.
+ *
+ * Used in. ReactionManipulator.toMolecule and ReactionManipulator.toReaction.
+ */
+ public static final String REACTION_ROLE = "cdk:ReactionRole";
+
+ /**
+ * Property used for reactions when converted to/from molecules. It defines fragment grouping, for example
+ * when handling ionic components.
+ *
+ * Used in. ReactionManipulator.toMolecule and ReactionManipulator.toReaction.
+ */
+ public static final String REACTION_GROUP = "cdk:ReactionGroup";
+
/* **************************************
* Some predefined property names for * Atoms *
* **************************************
diff --git a/base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ReactionManipulator.java b/base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ReactionManipulator.java
index 5461331a49b..afaa6c20b3d 100644
--- a/base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ReactionManipulator.java
+++ b/base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ReactionManipulator.java
@@ -22,17 +22,26 @@
* */
package org.openscience.cdk.tools.manipulator;
+import org.openscience.cdk.CDKConstants;
+import org.openscience.cdk.ReactionRole;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObject;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
+import org.openscience.cdk.interfaces.IDoubleBondStereochemistry;
import org.openscience.cdk.interfaces.IElectronContainer;
import org.openscience.cdk.interfaces.IMapping;
import org.openscience.cdk.interfaces.IReaction;
+import org.openscience.cdk.interfaces.IStereoElement;
+import org.openscience.cdk.interfaces.ITetrahedralChirality;
+import org.openscience.cdk.stereo.ExtendedTetrahedral;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.List;
+import java.util.Map;
/**
* @cdk.module standard
@@ -257,4 +266,135 @@ public static IChemObject getMappedChemObject(IReaction reaction, IChemObject ch
return null;
}
+ /**
+ * Assigns a reaction role and group id to all atoms in a molecule.
+ *
+ * @param mol molecule
+ * @param role role to assign
+ * @param grpId group id
+ */
+ private static void assignRoleAndGrp(IAtomContainer mol, ReactionRole role, int grpId) {
+ for (IAtom atom : mol.atoms()) {
+ atom.setProperty(CDKConstants.REACTION_ROLE, role);
+ atom.setProperty(CDKConstants.REACTION_GROUP, grpId);
+ }
+ }
+
+ /**
+ * Converts a reaction to an 'inlined' reaction stored as a molecule. All
+ * reactants, agents, products are added to the molecule as disconnected
+ * components with atoms flagged as to their role {@link ReactionRole} and
+ * component group.
+ *
+ * The inlined reaction, stored in a molecule can be converted back to an explicit
+ * reaction with {@link #toReaction}. Data stored on the individual components (e.g.
+ * titles is lost in the conversion).
+ *
+ *
+ * @param rxn reaction to convert
+ * @return inlined reaction stored in a molecule
+ * @see #toReaction
+ */
+ public static IAtomContainer toMolecule(IReaction rxn) {
+ if (rxn == null)
+ throw new IllegalArgumentException("Null reaction provided");
+ final IChemObjectBuilder bldr = rxn.getBuilder();
+ final IAtomContainer mol = bldr.newInstance(IAtomContainer.class);
+ mol.setProperties(rxn.getProperties());
+ mol.setID(rxn.getID());
+ int grpId = 0;
+ for (IAtomContainer comp : rxn.getReactants().atomContainers()) {
+ assignRoleAndGrp(comp, ReactionRole.Reactant, ++grpId);
+ mol.add(comp);
+ }
+ for (IAtomContainer comp : rxn.getAgents().atomContainers()) {
+ assignRoleAndGrp(comp, ReactionRole.Agent, ++grpId);
+ mol.add(comp);
+ }
+ for (IAtomContainer comp : rxn.getProducts().atomContainers()) {
+ assignRoleAndGrp(comp, ReactionRole.Product, ++grpId);
+ mol.add(comp);
+ }
+ return mol;
+ }
+
+ /**
+ * Converts an 'inlined' reaction stored in a molecule back to a reaction.
+ *
+ * @param mol molecule to convert
+ * @return reaction
+ * @see #toMolecule(IReaction)
+ */
+ public static IReaction toReaction(IAtomContainer mol) {
+ if (mol == null)
+ throw new IllegalArgumentException("Null molecule provided");
+ final IChemObjectBuilder bldr = mol.getBuilder();
+ final IReaction rxn = bldr.newInstance(IReaction.class);
+ rxn.setProperties(mol.getProperties());
+ rxn.setID(mol.getID());
+
+ Map components = new HashMap<>();
+
+ // split atoms
+ for (IAtom atom : mol.atoms()) {
+ ReactionRole role = atom.getProperty(CDKConstants.REACTION_ROLE);
+ Integer grpIdx = atom.getProperty(CDKConstants.REACTION_GROUP);
+
+ if (role == null || role == ReactionRole.None)
+ throw new IllegalArgumentException("Atom " + mol.getAtomNumber(atom) + " had undefined role");
+ if (grpIdx == null)
+ throw new IllegalArgumentException("Atom " + mol.getAtomNumber(atom) + " had no reaction group id");
+
+ IAtomContainer comp = components.get(grpIdx);
+
+ // new component, and add to appropriate role
+ if (comp == null) {
+ components.put(grpIdx, comp = bldr.newInstance(IAtomContainer.class, 20, 20, 0, 0));
+ switch (role) {
+ case Reactant:
+ rxn.addReactant(comp);
+ break;
+ case Product:
+ rxn.addProduct(comp);
+ break;
+ case Agent:
+ rxn.addAgent(comp);
+ break;
+ }
+ }
+
+ comp.addAtom(atom);
+ }
+
+ // split bonds
+ for (IBond bond : mol.bonds()) {
+ IAtom beg = bond.getAtom(0);
+ IAtom end = bond.getAtom(1);
+ Integer begIdx = beg.getProperty(CDKConstants.REACTION_GROUP);
+ Integer endIdx = end.getProperty(CDKConstants.REACTION_GROUP);
+ if (begIdx == null || endIdx == null)
+ throw new IllegalArgumentException("Bond " + mol.getBondNumber(bond) + " had atoms with no reaction group id");
+ if (!begIdx.equals(endIdx))
+ throw new IllegalArgumentException("Bond " + mol.getBondNumber(bond) + " had atoms with different reaction group id");
+ components.get(begIdx).addBond(bond);
+ }
+
+ // split stereochemistry
+ for (IStereoElement se : mol.stereoElements()) {
+ IAtom focus = null;
+ if (se instanceof ITetrahedralChirality) {
+ focus = ((ITetrahedralChirality) se).getChiralAtom();
+ } else if (se instanceof IDoubleBondStereochemistry) {
+ focus = ((IDoubleBondStereochemistry) se).getStereoBond().getAtom(0);
+ } else if (se instanceof ExtendedTetrahedral) {
+ focus = ((ExtendedTetrahedral) se).focus();
+ }
+ if (focus == null)
+ throw new IllegalArgumentException("Stereochemistry had no focus");
+ Integer grpIdx = focus.getProperty(CDKConstants.REACTION_GROUP);
+ components.get(grpIdx).addStereoElement(se);
+ }
+
+ return rxn;
+ }
}
diff --git a/base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/ReactionManipulatorTest.java b/base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/ReactionManipulatorTest.java
index 2c029d2aee3..a3bcf85740c 100644
--- a/base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/ReactionManipulatorTest.java
+++ b/base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/ReactionManipulatorTest.java
@@ -32,6 +32,7 @@
import org.openscience.cdk.Reaction;
import org.openscience.cdk.ReactionSet;
import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.exception.InvalidSmilesException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
@@ -41,8 +42,13 @@
import org.openscience.cdk.interfaces.IMapping;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.io.MDLRXNReader;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
+import org.openscience.cdk.smiles.SmilesGenerator;
import org.openscience.cdk.smiles.SmilesParser;
+import static org.hamcrest.CoreMatchers.is;
+import static org.junit.Assert.assertThat;
+
/**
* @cdk.module test-standard
*
@@ -291,4 +297,17 @@ public void testGetAllReactants_IReaction() {
Assert.assertEquals(2, ReactionManipulator.getAllProducts(reaction).getAtomContainerCount());
}
+ @Test public void inliningReactions() throws CDKException {
+ IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
+ SmilesParser smipar = new SmilesParser(bldr);
+ IReaction reaction = smipar.parseReactionSmiles("CCO.CC(=O)O>[H+]>CCOC(=O)C.O ethyl esterification");
+ SmilesGenerator smigen = SmilesGenerator.isomeric();
+ // convert to molecule
+ IAtomContainer mol = ReactionManipulator.toMolecule(reaction);
+ assertThat(smigen.create(mol),
+ is("CCO.CC(=O)O.[H+].CCOC(=O)C.O"));
+ assertThat(smigen.createReactionSMILES(ReactionManipulator.toReaction(mol)),
+ is("CCO.CC(=O)O>[H+]>CCOC(=O)C.O"));
+ }
+
}