rna_suitename.cc

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file
/// @brief


// libRosetta headers
#include <core/types.hh>
#include <core/chemical/ChemicalManager.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <protocols/viewer/viewers.hh>
#include <core/pose/Pose.hh>
#include <core/pose/rna/RNA_SuiteName.hh>
#include <core/pose/rna/util.hh>
#include <core/init/init.hh>
#include <core/import_pose/import_pose.hh>
#include <core/import_pose/pose_stream/PDBPoseInputStream.hh>
#include <utility/vector1.hh>
#include <ObjexxFCL/string.functions.hh>
#include <protocols/farna/util.hh>

// C++ headers
#include <iostream>
#include <string>

// option key includes
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/full_model.OptionKeys.gen.hh>

#include <utility/excn/Exceptions.hh>

using namespace core;
using namespace basic::options::OptionKeys;
using utility::vector1;

///////////////////////////////////////////////////////////////////////////////
void
rna_suitename()
{
  using namespace basic::options;
  using namespace basic::options::OptionKeys;
  using namespace core::import_pose::pose_stream;
  using namespace core::chemical;
  using namespace core::pose::rna;
  using namespace protocols::farna;

  ResidueTypeSetCOP rsd_set;
  rsd_set = core::chemical::ChemicalManager::get_instance()->residue_type_set( FA_STANDARD );

  // input stream
  PoseInputStreamOP input;
  input = PoseInputStreamOP( new PDBPoseInputStream( option[ in::file::s ]() ) );


  pose::Pose pose;
  Size i( 0 );
  RNA_SuiteName suitename;

  while ( input->has_another_pose() ) {
    input->fill_pose( pose, *rsd_set );
    i++;

    protocols::farna::ensure_phosphate_nomenclature_matches_mini( pose );
    core::pose::rna::figure_out_reasonable_rna_fold_tree( pose );
    core::pose::rna::virtualize_5prime_phosphates( pose ); // should we have this on by deafult?

    std::cout << "-----Pose " << i << "-----" << std::endl;
    for ( Size j = 1; j <= pose.total_residue(); ++j ) {
      RNA_SuiteAssignment assignment = suitename.assign(pose, j);
      std::cout << "Residue " << j << ' ' << assignment.name << ' ' << std::setprecision(3) <<assignment.suiteness << std::endl;
    }
  }

}


///////////////////////////////////////////////////////////////
void*
my_main( void* )
{
  rna_suitename();

  protocols::viewer::clear_conformation_viewers();
  exit( 0 );
}


///////////////////////////////////////////////////////////////////////////////
int
main( int argc, char * argv [] )
{
  try {
    using namespace basic::options;

    std::cout << std::endl << "Basic usage:  " << argv[0] << "  -s <pdb file> " << std::endl;
    std::cout << std::endl << " Type -help for full slate of options." << std::endl << std::endl;

    option.add_relevant( in::file::s );

    ////////////////////////////////////////////////////////////////////////////
    // setup
    ////////////////////////////////////////////////////////////////////////////
    core::init::init(argc, argv);

    ////////////////////////////////////////////////////////////////////////////
    // end of setup
    ////////////////////////////////////////////////////////////////////////////
    protocols::viewer::viewer_main( my_main );
  } catch ( utility::excn::EXCN_Base const & e ) {
    std::cout << "caught exception " << e.msg() << std::endl;
    return -1;
  }
}