import java.util.ArrayList;

import chemaxon.reaction.*;
import chemaxon.formats.*;
import chemaxon.struc.*;

public class ReactorDemo {
    static public void main(String[] args) throws Exception {
	if (args.length < 3) {
	    System.err.println("Usage: ");
	    System.err.println("  java ReactorDemo <reaction> <reactant1> <reactant2>");
	    return;
	}

	// read reaction
	MolImporter importer = new MolImporter(args[0]);
	Molecule rmol = importer.read();
	importer.close();

	// read reactants
	Molecule mol = null;
	MolImporter importer1 = new MolImporter(args[1]);
	ArrayList r1 = new ArrayList();
	while ((mol = importer1.read()) != null) {
	    r1.add(mol);
	}
	importer1.close();
	Molecule[] reactants1 = new Molecule[r1.size()];
	r1.toArray(reactants1);
	MolImporter importer2 = new MolImporter(args[2]);
	ArrayList r2 = new ArrayList();
	while ((mol = importer2.read()) != null) {
	    r2.add(mol);
	}
	importer2.close();
	Molecule[] reactants2 = new Molecule[r2.size()];
	r2.toArray(reactants2);

	// rules - now not needed because included in reaction definition
	//String reactivity = "!match(ratom(3), \"[#6][N,O,S:1][N,O,S:2]\", 1) && !match(ratom(3), \"[N,O,S:1][C,P,S]=[N,O,S]\", 1)";
	

	// main part
	// process reaction in combinatorial mode

	// create Reactor
	Reactor reactor = new Reactor();

	// set reaction, 
	// using rules in tags if rules are not specified
	//reactor.setReaction(rmol, reactivity);

	// now rules are included in reaction definition
	reactor.setReaction(rmol);

	Molecule[] reactants = new Molecule[2];
	Molecule[] products = null;
	for (int i=0; i < reactants1.length; ++i) {

	    // the first reactant
	    reactants[0] = reactants1[i];
	    for (int j=0; j < reactants2.length; ++j) {

		// the second reactant
		reactants[1] = reactants2[j];

		// set reactants
		reactor.setReactants(reactants);

		// process reaction
		while ((products = reactor.react()) != null) {
		    System.err.println("Reactants:");
		    System.err.println(reactants[0].toFormat("smiles"));
		    System.err.println(reactants[1].toFormat("smiles"));
		    System.err.println("Products:");
		    for (int k=0; k < products.length; ++k) {
			System.err.println(products[k].toFormat("smiles"));
		    }
		    RxnMolecule result = reactor.createReaction(products);
		    System.err.println("Reaction form:");
		    System.out.println(result.toFormat("smiles"));
		    System.err.println();
		}
	    }
	}
    }
}