StepWiseProteinLoopBridger.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 SWA_LoopBridger.hh
/// @brief
/// @detailed
///
/// @author Rhiju Das


#ifndef INCLUDED_protocols_swa_protein_StepWiseProteinLoopBridger_HH
#define INCLUDED_protocols_swa_protein_StepWiseProteinLoopBridger_HH

#include <core/pose/Pose.fwd.hh>
#include <core/scoring/Ramachandran.hh>
// AUTO-REMOVED #include <core/id/TorsionID.hh>
#include <protocols/swa/StepWiseJobParameters.fwd.hh>
// AUTO-REMOVED #include <protocols/swa/StepWisePoseSampleGenerator.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/loops/Loop.hh>
#include <utility/vector1.hh>

//Auto Headers
#include <core/id/TorsionID.fwd.hh>
#include <protocols/swa/StepWisePoseSampleGenerator.fwd.hh>


namespace protocols {
namespace swa {
namespace protein {

  /////////////////////////////////////////////////////////////////////////////////////////////////
  class StepWiseProteinLoopBridger: public protocols::moves::Mover {
  public:

    //constructor!
    StepWiseProteinLoopBridger(
                               protocols::swa::StepWisePoseSampleGeneratorOP sample_generator,
                               protocols::swa::StepWiseJobParametersOP job_parameters );

    //destructor -- necessary?
    ~StepWiseProteinLoopBridger();

    /// @brief Apply the minimizer to one pose
    virtual void apply( core::pose::Pose & pose_to_visualize );

  virtual std::string get_name() const;


    utility::vector1< utility::vector1< core::Real > > const & main_chain_torsion_set_lists() const;
    utility::vector1< core::id::TorsionID > const & which_torsions() const;

  private:

    void
    setup_torsions( core::pose::Pose const & pose );

    void
    figure_out_loop( core::pose::Pose const & pose );

    void
    output_chainTORS( utility::vector1< core::Real > const & dt_ang,
                      utility::vector1< core::Real > const & db_ang,
                      utility::vector1< core::Real > const & db_len ) const;

    void
    fill_chainTORS_info( core::pose::Pose const & pose,
                         utility::vector1<utility::vector1<core::Real> > & atoms,
                         utility::vector1<core::Real> & dt_ang,
                         utility::vector1<core::Real> & db_ang,
                         utility::vector1<core::Real> & db_len,
                         core::Size const & start_res_ ,
                         core::Size const & end_res_ ) const;

    void
    KIC_loop_close_with_perturbations( core::pose::Pose & pose );

    void
    KIC_loop_close( core::pose::Pose & pose );

    void
    grab_main_chain_torsion_set_list( core::pose::Pose const & pose );

    void save_phi_psi_offsets( core::pose::Pose const & pose );
    void fix_phi_psi_offsets( core::pose::Pose & pose ) const;

    void
    sample_omega_recursively( core::pose::Pose & pose, int const offset, utility::vector1<utility::vector1< core::Real> > & atoms, utility::vector1< core::Real> & dt_ang, utility::vector1< core::Real> & db_ang, utility::vector1< core::Real> & db_len, utility::vector1< core::Size > const & pivots, utility::vector1< core::Size > const & order );

    void
    initialize_is_fixed_res( utility::vector1< core::Size > const & fixed_res, std::string const & working_sequence );

  private:

    protocols::swa::StepWisePoseSampleGeneratorOP sample_generator_;

    utility::vector1< Size > working_bridge_res_;
    utility::vector1< bool > is_pre_proline_;
    utility::vector1< bool > is_fixed_res_;

    loops::Loop loop_;

    utility::vector1< core::id::TorsionID >  which_torsions_;

    utility::vector1< utility::vector1< core::Real > > main_chain_torsion_sets_for_moving_residues_;

    core::scoring::Ramachandran ramachandran_;

    int const num_perturb_steps_;
    core::Real const perturb_torsion_;

    core::Real const idl_CA_C_N_, idl_C_N_CA_, idl_C_N_, OMEGA_MEAN_;
    bool const use_icoor_geometry_;

    bool const verbose_;

    utility::vector1< core::Real > phi_offsets_;
    utility::vector1< core::Real > psi_offsets_;

    Size start_res_, middle_res_, end_res_, middle_offset_, seg_len_;
    Size pose_count_;

  };

} //swa
} // protocols

}
#endif