Chirality (Sulfoxide) got removed when added as reactant

code:

...

System.out.println(reactant.toFormat("smiles"));

reactor.setReactant(reactant);

System.out.println(reactant.toFormat("smiles"));

output:

[javaWrapper] CC(=O)NC(C)=O
[javaWrapper] CC(=O)NCS(C)=O

for other chiral molecules, it is ok:

[javaWrapper] CC[C@](C)(O)CNC(C)=O
[javaWrapper] CC[C@](C)(O)CNC(C)=O

Hi,

We cannot reproduce the error.

This code:

public static void main(String[] args) throws Exception {
	Reactor reactor = new Reactor();
	reactor.setReactionString("CC>>CO");
	Molecule reactant = MolImporter.importMol("CC(=O)NC(C)=O");	
	System.out.println(reactant.toFormat("smiles"));
	reactor.setReactant(reactant);
	System.out.println(reactant.toFormat("smiles"));	
}

Generates this output:

CC(=O)NC(C)=O
CC(=O)NC(C)=O

They are the same.

Which version of JChem are you using?

Zsolt

It seems the problem is from the reactant, if I regenerate the reactant using the reactant's smiles using:

reactant = MolImporter.importMol(mol.toFormat("smiles"));

reactor.setReactant(reactant);

instead of

reactant = mol;

reactor.setReactant(reactant);

the problem is solved.

There must be some properties within that molecule object causing the conversion.

Please try this code, if a molecule is cleaned, this problem will pop up.

import chemaxon.formats.MolImporter;
import chemaxon.reaction.Reactor;
import chemaxon.struc.Molecule;
import chemaxon.struc.RxnMolecule;

/**
 * Created by IntelliJ IDEA.
 * User: feng
 * Date: 9/16/11
 * Time: 10:35 AM
 * To change this template use File | Settings | File Templates.
 */
public class test {
    public static void main(String[] args) throws Exception {
        Reactor reactor = new Reactor();
        Molecule mol = MolImporter.importMol("C[NH:1][C:4](C)=O>>C[C:4]([OH:6])=O.C[NH2:1]");
        RxnMolecule rxnMolecule = RxnMolecule.getReaction(mol);
        rxnMolecule.aromatize(true);
        reactor.setReaction(rxnMolecule);
        Molecule molecule = MolImporter.importMol("CC(=O)NC(C)=O");
        molecule.clean(2,null);
        System.out.println(molecule.toFormat("smiles"));
        reactor.setReactant(molecule);
        System.out.println(molecule.toFormat("smiles"));
    }
}

import chemaxon.formats.MolImporter;
import chemaxon.reaction.Reactor;
import chemaxon.struc.Molecule;
import chemaxon.struc.RxnMolecule;

/**
 * Created by IntelliJ IDEA.
 * User: feng
 * Date: 9/16/11
 * Time: 10:35 AM
 * To change this template use File | Settings | File Templates.
 */
public class test {
    public static void main(String[] args) throws Exception {
        Reactor reactor = new Reactor();
        Molecule mol = MolImporter.importMol("C[NH:1][C:4](C)=O>>C[C:4]([OH:6])=O.C[NH2:1]");
        RxnMolecule rxnMolecule = RxnMolecule.getReaction(mol);
        rxnMolecule.aromatize(true);
        reactor.setReaction(rxnMolecule);
        Molecule molecule = MolImporter.importMol("CC(=O)NC(C)=O");
        molecule.clean(2,null);
        System.out.println(molecule.toFormat("smiles"));
        reactor.setReactant(molecule);
        System.out.println(molecule.toFormat("smiles"));
    }
}

We cannot reproduce the error using the code above.

Which version of JChem are you using?

Zsolt

jchem 5.4.0.1

We can reproduce the error with JChem 5.4.0.1.

Please upgrade your JChem version to 5.5.1.0 or later, it will fix the issue.

Zsolt