Representation of reactions


Chemical reactions take place between two or more molecules called reactants, and results other molecules called products. Sometimes other molecule may participate in the reaction, the agent. Similarly, the chemaxon.struc.RxnMolecule class that represents the chemical reactions, embeddes two or more molecules.


Build an RxnMolecule

The RxnMolecule.addComponent(Molecule, int) method adds the reactant, agent and result Molecule object to the RxnMolecule. In the argument of the method Molecule is molecule object to be added, while the integer flag specifies the type of the component. The constants of the RxnMolecule class can be used:

  • RxnMolecule.REACTANTS

  • RxnMolecule.AGENTS

  • RxnMolecule.PRODUCTS

  • RxnMolecule.RGROUPED - to add R-groups to the reaction

Reaction arrows

To change the type of the reaction arrow, use the RxnMolecule.setReactionArrowType(int). You can use the predefined constants:

  • RxnMolecule.REGULAR_SINGLE


  • RxnMolecule.REGULAR_DOUBLE


  • RxnMolecule.RESONANCE


  • RxnMolecule.EQUILIBRIUM

Example for building a simple reaction
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package chemaxon.examples.strucrep;
import chemaxon.calculations.clean.Cleaner;
import chemaxon.formats.MolExporter;
import chemaxon.formats.MolImporter;
import chemaxon.struc.Molecule;
import chemaxon.struc.RxnMolecule;
* Example class. Creates a basic RxnMolecule.
* @author Janos Kendi
public class BuildRxnMolecule {
public static void main(String[] args) throws IOException {
// Create an empty reaction
RxnMolecule mol = new RxnMolecule();
// Create the components
Molecule reactant1 = MolImporter.importMol("CC(=C)C");
Molecule reactant2 = MolImporter.importMol("Cl");
Molecule agent = MolImporter.importMol("CCOCC");
Molecule product = MolImporter.importMol("C(Cl)(C)(C)C");
// Add the components
mol.addComponent(reactant1, RxnMolecule.REACTANTS);
mol.addComponent(reactant2, RxnMolecule.REACTANTS);
mol.addComponent(agent, RxnMolecule.AGENTS);
mol.addComponent(product, RxnMolecule.PRODUCTS);
// Calculate coordinates.
Cleaner.clean(mol, 2, null);
// Change the reaction arrow type.
System.out.println(MolExporter.exportToFormat(mol, "mrv:P"));
Reaction of aromatic nitration
package chemaxon.examples.strucrep
import chemaxon.struc.*;
import chemaxon.formats.MolImporter;
import chemaxon.formats.MolFormatException;
* Example class for structure manipulation.
* Creates a simple reaction.
* @author Andras Volford
public class AromaticNitration {
public static void main(String[] args) {
// create an empty Molecule
RxnMolecule m = new RxnMolecule();
Molecule reactant = MolImporter.importMol("c1ccccc1");
Molecule agent = MolImporter.importMol("N(O)(=O)=O.S(O)(O)(=O)=O");
Molecule product = MolImporter.importMol("c1ccccc1N(=O)=O");
m.addComponent(reactant, RxnMolecule.REACTANTS);
m.addComponent(agent, RxnMolecule.AGENTS);
m.addComponent(product, RxnMolecule.PRODUCTS);
m.addComponent(MolImporter.importMol("O"), RxnMolecule.PRODUCTS);
} catch (MolFormatException e) {
System.err.println("Format not recognised.");