StepWiseBetaAntiParallelJumpSampleGenerator.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 StepWiseBetaAntiParallelJumpSampleGenerator
/// @brief Subclass of StepWisePoseSampleGenerator
/// @detailed
/// @author Rhiju Das


//////////////////////////////////
#include <protocols/swa/protein/StepWiseBetaAntiParallelJumpSampleGenerator.hh>
#include <protocols/swa/protein/StepWiseProteinJumpSampleGenerator.hh>
#include <core/types.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/pose/Pose.hh>
// AUTO-REMOVED #include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <basic/database/open.hh>

// AUTO-REMOVED #include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>

#include <iostream>
#include <string>

//Auto Headers
#include <utility/vector1.hh>
#include <utility/io/mpistream.hh>



using namespace core;

namespace protocols {
namespace swa {
namespace protein {

  //////////////////////////////////////////////////////////////////////////
  //constructor!
  StepWiseBetaAntiParallelJumpSampleGenerator::StepWiseBetaAntiParallelJumpSampleGenerator(
                                     core::pose::Pose const & pose,
                                     Size const moving_residue ):
    StepWiseProteinJumpSampleGenerator( 0, jumps_ ) //generic
  {
    Size which_jump = get_antiparallel_beta_jumps( pose, moving_residue );
    initialize( which_jump, jumps_ );
  }

  Size
  StepWiseBetaAntiParallelJumpSampleGenerator::get_antiparallel_beta_jumps( pose::Pose const & pose, int const sample_res ){

    using namespace core::kinematics;
    using ObjexxFCL::strip_whitespace;

    Size which_jump = 0;
    jumps_.clear();

    // Which jump connects into the new residue ("sample_res")? We're going to figure out nice beta-pairing jumps to it.
    bool downstream( false );
    FoldTree const & f( pose.fold_tree() );

    for ( Size i = 1; i <= f.num_jump(); i++ ) {
      if ( f.upstream_jump_residue( i )   ==  sample_res  ){
        downstream = true;
        which_jump = i;  break;
      } else if (f.downstream_jump_residue( i ) == sample_res ){
        downstream = false;
        which_jump = i; break;
      }
    }
    if ( which_jump == 0 ) utility_exit_with_message( "Could not find the jump for sample_beta?!" );

    std::string atom_base, atom_sample;
    if ( downstream ){
      atom_base   = f.upstream_atom( which_jump );
      atom_sample = f.downstream_atom( which_jump );
    } else {
      atom_base   = f.downstream_atom( which_jump );
      atom_sample = f.upstream_atom( which_jump );
    }
    atom_base   = strip_whitespace( atom_base );
    atom_sample = strip_whitespace( atom_sample );

    std::string const jump_library_file( basic::database::full_name( "clustered_beta_pairs.dat" ) );
    utility::io::izstream data( jump_library_file.c_str() );
    if ( !data.good() ) utility_exit_with_message( "Unable to open file: " +jump_library_file + '\n' );

    std::string line, atom1_in, atom2_in, tag;
    Jump jump;
    while( getline(data, line) ) {
      std::istringstream is( line );
      is >> tag >> atom1_in >> atom2_in;
      is >> jump;

      std::cout << atom1_in << " " << atom_base << " " << atom2_in << " " << atom_sample << std::endl;

      if ( (atom1_in == atom_base) && (atom2_in == atom_sample ) ){
        if ( !downstream ) jump.reverse();
        jumps_.push_back( jump );
      }
    }
    data.close();

    std::cout << "FOUND " << jumps_.size() << " JUMPS!" << std::endl;

    return which_jump;

  }

}
}
}