[Joelib-help] Canonified version?

[Andreas M. <an...@ma...>]

Hi,

with the following code I read in a SMILES, build a molecule out of it and reencode it as a string:

----------------- BEGIN CODE --------------------------------

import joelib.molecule.*;
import joelib.smiles.*;

public class SmilesCanonifier {
        
	public String canonify(String smiles) {
                JOEMol mol=new JOEMol();
                JOEMol2Smi m2s = new JOEMol2Smi(); m2s.init();
	        StringBuffer smilesb = new StringBuffer(1000);

                // create mol object out of this smiles string
                JOESmilesParser.smiToMol(mol, smiles, smiles);

	        // create mol to smiles converter
	        m2s.init();
	        // do some correction
        	m2s.correctAromaticAmineCharge(mol);

	        // String buffer to hold the canonified string
	        m2s.createSmiString(mol, smilesb);
	        return smilesb.toString();
        }

        public static void main(String args[]) {
                String smiles = args[0];
                System.out.println(smiles);
                SmilesCanonifier sc = new SmilesCanonifier();
                System.out.println(sc.canonify(smiles));
        }
}

----------------- END CODE ----------------------------------

When I try this on a SMILES s0 I get an equivalent output smiles s1.
When I try it on s1, I get an equivalent output smiles s2, which is different from s1.
When I try it on s2, I get an equivalent output smiles s3, which is the same as s1, s3=s1.
When I try it on s3=s1, I get an equivalent output smiles s4, which is the same as s2, s4=s2.

The process repeats from now on, switching between two SMILES versions.
Is there no canonical version? Otherwise, how can I get one?

Greetings,
Andi