ResiduePairJumpSetup.hh

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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 ResiduePairJumpSetup
/// @brief setup jumps specifically to ResiduePairJump, read in definition file
/// @detailed derived from BaseJumpSetup
/// @author Chu Wang


#ifndef INCLUDED_protocols_jumping_ResiduePairJumpSetup_hh
#define INCLUDED_protocols_jumping_ResiduePairJumpSetup_hh

// Unit Headers
#include <protocols/jumping/ResiduePairJumpSetup.fwd.hh>

// Package Headers
#include <protocols/jumping/JumpSample.hh>
#include <protocols/jumping/JumpSetup.hh>
#include <protocols/jumping/ResiduePairJump.hh>

// Project Headers

// ObjexxFCL Headers

// Utility headers

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

#include <utility/vector1.hh>



namespace protocols {
namespace jumping {

////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
/// forward declaration
class JumpSample;

////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
class ResiduePairJumpSetup : public BaseJumpSetup {
public:
  class JumpDef {
  public:
    JumpDef( Interval jump, Interval cut_reg ) :
      jump_( jump ), cut_reg_ ( cut_reg) { };

    Interval jump_;
    Interval cut_reg_;
  };

  std::string type_name() const {
    return "ResiduePairJumpSetup";
  }

public:

  typedef utility::vector1< JumpDef >::const_iterator const_iterator;
  typedef utility::vector1< JumpDef >::iterator iterator;


  //@brief c'stor
  ResiduePairJumpSetup() :
    total_residue_( 0 ), root_( 1 )
  {};

  //@brief c'stor
  ResiduePairJumpSetup( Size total_residue ) :
    total_residue_( total_residue )
  {};

  //@brief add a new jump to the list
  void
  add_jump( JumpDef const& jd ) {
    jumps_.push_back ( jd );
  }

  void
  add_jump( Interval const& jump, Interval const& cut_reg ) {
    add_jump( JumpDef( jump, cut_reg ) );
  }

  void
  add_jump( core::Size js, core::Size je, core::Size crs, core::Size cre ) {
    add_jump( JumpDef( Interval( js, je ), Interval( crs, cre ) ) );
  }

  void
  add_residue_pair_jump( ResiduePairJumpOP ptr ) {
    ResiduePairJumps_.push_back( ptr );
  }

  void
  set_root( core::Size root ) {
    runtime_assert( root >= 1 && root <= total_residue_ );
    root_ = root;
  };

  core::Size
  root() const {
    return root_;
  };

  core::Size
  size() const {
    return jumps_.size();
  };

  const_iterator
  begin() const {
    return jumps_.begin();
  };

  const_iterator
  end() const {
    return jumps_.end();
  };

  void
  read_file( std::string file );

  JumpSample
  create_jump_sample( ) const;

  virtual JumpSample
  clean_jumps( JumpSample const& js) const {
    std::cerr << "ERROR ERROR ERROR            unimplemented method!;";
    return js;
  }

  core::fragment::FragSetOP
  generate_jump_frags( JumpSample const&, core::kinematics::MoveMap const& mm) const;

  core::Size
  total_residue() const {
    return total_residue_;
  }
  void clear() {
    jumps_.clear();
  }

private:
  utility::vector1< JumpDef > jumps_;
  core::Size total_residue_;
  core::Size root_;
  utility::vector1 <ResiduePairJumpOP> ResiduePairJumps_;
};


} //jumping
} //protocols
#endif