RemodelWorkingSet.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.
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// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
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/// @file   protocols/forge/remodel/RemodelWorkingSet.hh
/// @brief
/// @author Possu Huang (possu@u.washington.edu)
/// @author Yih-En Andrew Ban (yab@u.washington.edu)

#ifndef INCLUDED_protocols_forge_remodel_RemodelWorkingSet_hh
#define INCLUDED_protocols_forge_remodel_RemodelWorkingSet_hh

#include <ObjexxFCL/FArray2D.hh>

#include <utility/vector1.hh>

#include <core/pack/task/PackerTask.hh>
#include <core/pose/Pose.hh>

#include <protocols/loops/Loops.hh>
#include <protocols/forge/build/BuildManager.hh>
#include <protocols/forge/remodel/RemodelData.hh>


namespace protocols {
namespace forge {
namespace remodel {

// this class holds all the info for the model pose
// in the future a new variable might be added to delete a certain jump
// to create domain assembly type of fold-tree
class RemodelWorkingSet {

public:

  // default constructor
  RemodelWorkingSet();

  // copy constrctor
  RemodelWorkingSet( RemodelWorkingSet const & rval );

  // copy assignment
  RemodelWorkingSet & operator = ( RemodelWorkingSet const & rval );

  ~RemodelWorkingSet(){};

  void workingSetGen( core::pose::Pose const & input_pose, protocols::forge::remodel::RemodelData const & data );
  void manualPackerTaskGen( core::pose::Pose const & built_pose, protocols::forge::remodel::RemodelData const & data );

  //void design_matrix_from_blueprint( std::vector<protocols::forge::remodel::LineObject>  blueprint ); //manual
  //void setup_auto_design_matrix( core::pose::Pose const & model_pose, std::vector<protocols::forge::remodel::LineObject> const & blueprint, bool const core, bool const boundary, bool surface );

  //void setup_repack_residues(core::pose::Pose & model_pose, std::vector<protocols::forge::remodel::LineObject> const & blueprint);
  //void createDisulfideBuildingData(core::pose::Pose const & model_pose, protocols::forge::remodel::RemodelData const & remodel_data);
  //void updatePoseWithARandomDisulfideJump(core::pose::Pose & model_pose);
  //void makeDisulfPairs(core::pose::Pose & model_pose);

  /// @brief If remodel loop setup is calling for n-terminus movement then return true, otherwise false.
  //bool moving_n_terminus() const;

  /// @brief build a fold tree for loop modeling using the defined loops
  /// @note  builds directly from internal loop data and does not randomize cutpoints,
  ///        so inside a fully stochastic loop building routine you most likely
  ///        *do not* want to use this function
  //core::kinematics::FoldTree standard_loop_fold_tree() const;


  // Revisit by Sachko 03/29/2013
  // Whey are these all public???
  ///
  protocols::loops::Loops loops;
  int safe_root_;
  std::string sequence;
  std::string ss;
  std::string abego;
  std::map<int,int> translate_index;

  std::vector<int> begin;
  std::vector<int> end;
  std::vector<int> copy_begin;
  std::vector<int> copy_end;
  std::vector<int> src_begin;
  std::vector<int> src_end;

  std::string aa; // for assigning generic type used for building.
  bool hasInsertion;

  protocols::forge::build::BuildManager manager;
  core::pack::task::PackerTaskOP task;

  // disulfide building
  core::pose::Pose rvjump_pose;
  bool buildDisulfide;
  ObjexxFCL::FArray2D_int disulfide_jump_points;
  int disulfide_cutpoint;
  std::string disulfide_ss;

  int insertionStartIndex;
  int insertionEndIndex;
  ObjexxFCL::FArray2D_bool design_matrix;

};

class Segment {

public:
  std::vector<int> residues;
};


}
}
}

#endif