DisulfideMatchingDatabase.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 sw=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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// (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
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/// @file   core/scoring/disulfides/CentroidDisulfideDatabase.cc
/// @brief  Centroid Disulfide Energy Databases
/// @author rvernon@u.washington.edu
/// @date   02/09/10

// Unit Headers
#include <core/scoring/disulfides/DisulfideMatchingDatabase.hh>

// Project Headers
// AUTO-REMOVED #include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
// AUTO-REMOVED #include <core/chemical/ResidueTypeSet.hh>
// AUTO-REMOVED #include <core/chemical/ChemicalManager.hh>
#include <basic/database/open.hh>
// AUTO-REMOVED #include <core/scoring/constraints/util.hh>
#include <core/conformation/Atom.hh>
#include <core/kinematics/RT.hh>

// Utility Headers
#include <utility/io/izstream.hh>
#include <utility/vector1.hh>


#include <basic/Tracer.hh>

#include <core/kinematics/Jump.hh>

static basic::Tracer TR("core.scoring.disulfides.CentroidMatchingDatabase");


using namespace core;
using core::scoring::disulfides::DisulfideMatchingDatabase;
using core::conformation::Residue;
using std::string;
using utility::vector1;

namespace core {
namespace scoring {
namespace disulfides {

/**
 * Constructor
 */
DisulfideMatchingDatabase::DisulfideMatchingDatabase()
{
  db_init_ = false;
}

/**
 * Deconstructor
 */
DisulfideMatchingDatabase::~DisulfideMatchingDatabase() {}

void
DisulfideMatchingDatabase::read_disulfide_database() const{

  utility::io::izstream disulfide_database;

  basic::database::open(disulfide_database, "sampling/disulfide_jump_database_wip.dat");

  std::string line;

  utility::vector1< core::kinematics::RT > disulfides;

  getline(disulfide_database, line);
  while ( !disulfide_database.eof() ) {
    std::istringstream line_stream(line);
    std::string junk;
    core::kinematics::RT rt;

    line_stream >> junk >> junk >> junk >> junk >> junk >> junk >> junk >> junk >> junk >> rt;

    disulfides.push_back(rt);

    //std::cout << "RT " << rt << std::endl;

    getline(disulfide_database, line);
  }

  //std::cout << "READ DIS DB " << disulfides.size() << std::endl;

  db_disulfides_ = disulfides;
}

utility::vector1< core::kinematics::RT > &
DisulfideMatchingDatabase::get_all_disulfides() const {

  if (db_init_ == false) {
    //std::cout << "READING DB " << std::endl;
    read_disulfide_database();

    if (db_disulfides_.size() == 0) {
      utility_exit_with_message("Failure to Read Disulfide Database");
    }

    db_init_ = true;
  }

  return db_disulfides_;
}

} // disulfides
} // scoring
} // core