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.
// (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.

#ifndef INCLUDED_protocols_forge_remodel_RemodelWorkingSet_hh
#define INCLUDED_protocols_forge_remodel_RemodelWorkingSet_hh


#include <protocols/loops/Loops.hh>
#include <core/pose/Pose.hh>
#include <protocols/forge/build/BuildManager.hh>
#include <core/pack/task/PackerTask.hh>
#include <protocols/forge/remodel/RemodelData.hh>

// AUTO-REMOVED #include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray2D.hh>

#include <utility/vector1.hh>



namespace protocols{
namespace forge{
namespace remodel{

       class WorkingRemodelSet // 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
        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;
          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;

          WorkingRemodelSet(){
            hasInsertion = false;
            buildDisulfide = false;
          };

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

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

          ~WorkingRemodelSet(){};
        };

        class Segment
        {
        public:
          std::vector<int> residues;
        };

}
}
}

#endif