Examples of MDLV2000Writer

Examples of org.openscience.cdk.io.MDLV2000Writer

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        public JcpSelection(IAtomContainer tocopy1) {
            IAtomContainer tocopy= tocopy1.getBuilder().newInstance(IAtomContainer.class,tocopy1);
            // MDL mol output
            StringWriter sw = new StringWriter();
            try {
        new MDLV2000Writer(sw).writeMolecule(tocopy);
      } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
      }
            this.mol=sw.toString();
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Examples of org.openscience.cdk.io.MDLV2000Writer

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          }

          cow.write(rGroupQuery);
        }
        else {
          cow = new MDLV2000Writer(new FileWriter(outFile));
            cow.write(model);
        }
         
        cow.close();
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Examples of org.openscience.cdk.io.MDLV2000Writer

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      if (theJcpp.get2DHub().getRGroupHandler()!=null) {
        RGroupQueryWriter rgw = new RGroupQueryWriter (sw);
        rgw.write(theJcpp.get2DHub().getRGroupHandler().getrGroupQuery());
      }
      else {
            MDLV2000Writer mdlwriter = new MDLV2000Writer(sw);
            mdlwriter.write(som);
      }
        return (sw.toString());
    }
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Examples of org.openscience.cdk.io.MDLV2000Writer

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        String tmpPrbFile = workingDir + tmpFileBase + PROBFILE_EXTENSION;
       
        try {

            StringWriter writer = new StringWriter();
            MDLV2000Writer mdlWriter = new MDLV2000Writer(writer);
           
            mdlWriter.write(atc);
            String mdl = writer.toString();
           
            //Write the Molfile String into a file for the generator to work on. 
            FileWriter fstream = new FileWriter(tmpMolFile);
            BufferedWriter out = new BufferedWriter(fstream);
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