convertFbcToCobra.cpp

Example of converting an SBML Level 3 model using the Flux Balance Constraints package to a COBRA-style SBML Level 2 model.

/**
 * @file    convertFbcToCobra.cpp
 * @brief   Convert COBRA L2 to L3 with FBC
 * @author  Frank T. Bergmann
 *
 * <!--------------------------------------------------------------------------
 * This sample program is distributed under a different license than the rest
 * of libSBML.  This program uses the open-source MIT license, as follows:
 *
 * Copyright (c) 2013-2018 by the California Institute of Technology
 * (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
 * and the University of Heidelberg (Germany), with support from the National
 * Institutes of Health (USA) under grant R01GM070923.  All rights reserved.
 *
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the "Software"),
 * to deal in the Software without restriction, including without limitation
 * the rights to use, copy, modify, merge, publish, distribute, sublicense,
 * and/or sell copies of the Software, and to permit persons to whom the
 * Software is furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
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 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 * DEALINGS IN THE SOFTWARE.
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 * Neither the name of the California Institute of Technology (Caltech), nor
 * of the European Bioinformatics Institute (EMBL-EBI), nor of the University
 * of Heidelberg, nor the names of any contributors, may be used to endorse
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 */
 
#include <iostream>
#include <sbml/SBMLTypes.h>
#include <sbml/conversion/ConversionProperties.h>
 
using namespace std;
LIBSBML_CPP_NAMESPACE_USE
 
int
main (int argc, char* argv[])
{
  if (argc != 3)
  {
    cout << endl << "Usage: convertFbcToCobra input-filename output-filename"
         << endl << endl;
    return 2;
  }
 
  SBMLDocument *d = readSBML(argv[1]);
  if ( d->getNumErrors(LIBSBML_SEV_ERROR) > 0)
  {
    d->printErrors();
  }
  else
  {
    /* create a new conversion properties structure */
    ConversionProperties props;
 
    /* add an option that we want to strip a given package */
    props.addOption("convert fbc to cobra", true,
                    "Convert FBC model to Cobra model");
 
    /* perform the conversion */
    int result = d->convert(props);
    if (result != LIBSBML_OPERATION_SUCCESS)
    {
      cout<< "conversion failed ... " << endl;
      return 3;
    }
 
    writeSBML(d, argv[2]);
  }
 
  return 0;
}