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Clean function randomly changes the structure.
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binzhou

Joined: 27 Jun 2006
Posts: 26

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Link to postPosted: Mon Oct 18, 2010 7:59 pmPost subject: Clean function randomly changes the structure. Reply with quote

It seems that Clean function changes the structure somehow.  The following codes randomly breaks at "clean" branch, if I uncomment dearomatize and aromatize, then it will break at "deromatize".  The two smiles are not same,  I tested them in cartridge.

Thanks

Bin

      public static void smiles2sdf(String[] args) throws Exception {

            int count = 0;

            String original = "CN1C2=CC=CC=C2C2(N\\C(=N\\S(C)(=O)=O)[C@@]1(C)N2S(C)(=O)=O)C1=CC=CC=C1";

            String changed =  "CN1C2=CC=CC=C2C2(NC(=NS(C)(=O)=O)[C@@]1(C)N2S(C)(=O)=O)C1=CC=CC=C1";

            while (true) {

                  count++;

                  System.out.println(count);

                  MolHandler mh = new MolHandler(original);

                  Molecule mol = mh.getMolecule();

//                mol.dearomatize();

//                mol.aromatize();

                  boolean error = mol.clean(2, null);

                  System.out.println(error);

                  if (mol.toFormat("smiles").equals(changed)) {

                        System.out.println("clean");

                        break;

                  }

                  mol.dearomatize();

                  if (mol.toFormat("smiles").equals(changed)) {

                        System.out.println("dearomatize");

                        break;

                  }

            }

      }

Szilard
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Joined: 21 May 2004
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Link to postPosted: Mon Oct 18, 2010 10:30 pmPost subject: Reply with quote

Hi Bin,

 

Could you let us know the JChem  version you are using ?

Also could you copy any error message or stack trace you are getting ?

 

Best regards,

 

Szilard

binzhou

Joined: 27 Jun 2006
Posts: 26

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Link to postPosted: Mon Oct 18, 2010 10:37 pmPost subject: Reply with quote

System.out.println(VersionInfo.JCHEM_VERSION);
 The above code returns 5.1.0

No error message.

Szilard wrote:

Hi Bin,

 

Could you let us know the JChem  version you are using ?

Also could you copy any error message or stack trace you are getting ?

 

Best regards,

 

Szilard

 

Szilard
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Joined: 21 May 2004
Posts: 1552

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Link to postPosted: Mon Oct 18, 2010 11:26 pmPost subject: Reply with quote

Hi Bin,

5.1.0 is more than two years old and there are no planned bugfix releases for the 5.1.x versions.

I have only tested with MarvinSketch so far, but it seems we do not have issues with the structure in the latest version.

So I suggest to upgrade to the latest stable version, if possible.

 

Best regards,

Szilard

 

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