Creating CMLReact from UsefulChem Ugi Reactions

2008-08-31T00:20:00+00:00

Cameron, Jean-Claude and I were invited to Peter’s place in Cambridge, where we are now hacking on CMLReact for the Ugi reactions Jean-Claude has been working on. I just finished a script that uses the CDK and Sam’s interface to the InChI library to convert a list of four reactants and one Ugi product into CMLReact (doi:10.1021/ci0502698). The full BeanShell script looks like:

#!/usr/bin/bsh

import java.io.File;
import java.io.FileReader;
import java.io.BufferedReader;

import org.openscience.cdk.*;
import org.openscience.cdk.exception.*;
import org.openscience.cdk.inchi.*;
import org.openscience.cdk.interfaces.*;
import org.openscience.cdk.io.CMLWriter;

import org.openscience.cdk.libio.cml.Convertor;
import org.xmlcml.cml.element.CMLReaction;

import net.sf.jniinchi.INCHI_RET;

InChIGeneratorFactory factory = new InChIGeneratorFactory();
// Get InChIToStructure

File file = new File("inchi.ugi.txt"); // five inchis expected, last being the product
BufferedReader reader = new BufferedReader(new FileReader(file));

String first = reader.readLine();
String second = reader.readLine();
String third = reader.readLine();
String fourth = reader.readLine();
String product = reader.readLine();

System.out.println("First: " + first);
IMolecule firstAC;
{
  InChIToStructure intostruct = factory.getInChIToStructure(first, DefaultChemObjectBuilder.getInstance());

  INCHI_RET ret = intostruct.getReturnStatus();
  if (ret == INCHI_RET.WARNING) {
    // Structure generated, but with warning message
    System.out.println("InChI warning: " + intostruct.getMessage());
  } else if (ret != INCHI_RET.OKAY) {
    // Structure generation failed
    throw new CDKException("Structure generation failed failed: " + ret.toString()
      + " [" + intostruct.getMessage() + "]");
  }

  firstAC = new Molecule(intostruct.getAtomContainer());
}

System.out.println("Second: " + second);
IMolecule secondAC;
{
  InChIToStructure intostruct = factory.getInChIToStructure(second, DefaultChemObjectBuilder.getInstance());

  INCHI_RET ret = intostruct.getReturnStatus();
  if (ret == INCHI_RET.WARNING) {
    // Structure generated, but with warning message
    System.out.println("InChI warning: " + intostruct.getMessage());
  } else if (ret != INCHI_RET.OKAY) {
    // Structure generation failed
    throw new CDKException("Structure generation failed failed: " + ret.toString()
      + " [" + intostruct.getMessage() + "]");
  }

  secondAC = new Molecule(intostruct.getAtomContainer());
}

System.out.println("Third: " + third);
IMolecule thirdAC;
{
  InChIToStructure intostruct = factory.getInChIToStructure(third, DefaultChemObjectBuilder.getInstance());

  INCHI_RET ret = intostruct.getReturnStatus();
  if (ret == INCHI_RET.WARNING) {
    // Structure generated, but with warning message
    System.out.println("InChI warning: " + intostruct.getMessage());
  } else if (ret != INCHI_RET.OKAY) {
    // Structure generation failed
    throw new CDKException("Structure generation failed failed: " + ret.toString()
      + " [" + intostruct.getMessage() + "]");
  }

  thirdAC = new Molecule(intostruct.getAtomContainer());
}

System.out.println("Fourth: " + fourth);
IMolecule fourthAC;
{
  InChIToStructure intostruct = factory.getInChIToStructure(fourth, DefaultChemObjectBuilder.getInstance());

  INCHI_RET ret = intostruct.getReturnStatus();
  if (ret == INCHI_RET.WARNING) {
    // Structure generated, but with warning message
    System.out.println("InChI warning: " + intostruct.getMessage());
  } else if (ret != INCHI_RET.OKAY) {
    // Structure generation failed
    throw new CDKException("Structure generation failed failed: " + ret.toString()
      + " [" + intostruct.getMessage() + "]");
  }

  fourthAC = new Molecule(intostruct.getAtomContainer());
}

System.out.println("Product: " + product);
IMolecule productAC;
{
  InChIToStructure intostruct = factory.getInChIToStructure(product, DefaultChemObjectBuilder.getInstance());

  INCHI_RET ret = intostruct.getReturnStatus();
  if (ret == INCHI_RET.WARNING) {
    // Structure generated, but with warning message
    System.out.println("InChI warning: " + intostruct.getMessage());
  } else if (ret != INCHI_RET.OKAY) {
    // Structure generation failed
    throw new CDKException("Structure generation failed failed: " + ret.toString()
      + " [" + intostruct.getMessage() + "]");
  }

  productAC = new Molecule(intostruct.getAtomContainer());
}

IReaction ugiReaction = new Reaction();
ugiReaction.addReactant(firstAC);
ugiReaction.addReactant(secondAC);
ugiReaction.addReactant(thirdAC);
ugiReaction.addReactant(fourthAC);
ugiReaction.addProduct(productAC);

StringWriter stringWriter = new StringWriter();
CMLWriter cmlWriter = new CMLWriter(stringWriter);

cmlWriter.write(ugiReaction);
cmlWriter.close();
System.out.println(stringWriter.toString());

My apologies for the code duplication, but never tried inline functions in BeanShell yet… You can monitor the efforts at Google Docs.

UgiChem2CML

2008-08-31T00:00:00+00:00

The nice thing about a hacksession, is that you have something to write about. Below a screenshot of a Ugi reaction in Bioclipse… note the source tab of the editor, which holds the CML. Now, JChemPaint can do reactions too (I did that in 2003 in Peter’s group, but seems to be offline at this moment), but this was the quick hack to do the CMLReact in Google Docs (or soon to be):

And this is us this afternoon:

chem-bla-ics

Creating CMLReact from UsefulChem Ugi Reactions

UgiChem2CML