Help with JChem molconvert

Hi,

I have a simple question:

I want to convert a smiles string to a 3d mol file.

What is the appropriate opt settings that I can use? --> mol -3:S{fast}
Can it only read in a file or can I send it a molecule object?
      MolConverter.Options opts = new MolConverter.Options();
     opts.addInput("input.smiles", "");
     opts.setOutput("out.mol", "mol");
     opts.setOutputFlags(MolExporter.TEXT);
     MolConverter mc = new MolConverter(opts);
     while(mc.convert());
     mc.close();

Thanks,
Guy

I have moved the topic to the proper forum, the relevant asnwers will answer soon.

Best regards,

Szilard

Dear Guy,

What is the appropriate opt settings that I can use? --> mol -3:S{fast}

I would recommend to use the default setting: mol -3

Can it only read in a file or can I send it a molecule object?

According to the API docs (see http://chemaxon.com/marvin/help/developer/beans/api/chemaxon/formats/MolConverter.html ) it processes streams or files, however it can be launched from command line:

molconvert mol -3 input.smiles > output.mol

In this case using the Molecule.clean() API method may be more convenient:

Molecule m = MolImporter.importMol("CCCCC");
m.clean(3,"");
System.out.print( m.toFormat("mol") );

If you have any further questions, please do not hesitate to ask them

Regards,

Gabor

Hi Gimre,

Thanks for the tip. The clean method worked great. I didn't realize that I could use clean to generate the 3d mol file.

But for future edification, how would I set the opts in the jchem molconvert api to go from a 2d sdf file to a 3d mol file?

I tried the following but it threw an error.

     opts.addInput("input.sdf", "sdf");
     opts.setOutput("out.mol", "mol -3");

Please note: I know how to do this with the command line molconvert but I am missing something in the API.

Thanks for the help.

Regards,
Guy

Dear Guy,

 

Please note: I know how to do this with the command line molconvert.

You can use MolConverter.mainWithoutExit() in this case:

import chemaxon.formats.MolConverter;

public class MolConverterExample {
public static void main(String[] args) throws Exception {
  try {
    MolConverter.mainWithoutExit(
      new String [] { "mol", "input.sdf", "-3", "-o", "output.mol" } );
    } catch ( RuntimeException e ) {
      if ( e.getMessage().startsWith("molconvert exit:") ) {
       // molconvert exited
      } else {
        throw e;
      }
    }
  }
}

But for future edification, how would I set the opts in the jchem molconvert api to go from a 2d sdf file to a 3d mol file?

I will assign this question to the developer responsible for MolConverter.

 

Regards,

Gabor

Dear Guy,

 

Currently 3D coordinate generation functionality in MolConverter API is only available through the main()/mainWithoutExit() methods.

 

Regards,

Gabor

Created MolConverter.Builder.clean methods. The following should work, starting from Marvin 5.2.4:

MolConverter.Builder opts = new MolConverter.Builder();
opts.addInput("input", "sdf");
opts.setOutput("out.mol", "mol");
opts.clean(3);
MolConverter mc = opts.build();