StepWisePoseSetup.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_PoseSetup.hh
/// @brief
/// @detailed
///
/// @author Rhiju Das


#ifndef INCLUDED_protocols_swa_StepWisePoseSetup_HH
#define INCLUDED_protocols_swa_StepWisePoseSetup_HH

#include <core/pose/Pose.fwd.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
// AUTO-REMOVED #include <core/import_pose/pose_stream/PoseInputStream.fwd.hh>
#include <core/id/AtomID.fwd.hh>
#include <core/id/AtomID_Map.hh>
#include <protocols/swa/StepWiseJobParameters.fwd.hh>
#include <protocols/swa/StepWisePoseSetup.fwd.hh>
#include <core/types.hh>
#include <utility/vector1.hh>
#include <protocols/moves/Mover.hh>
#include <ObjexxFCL/FArray1D.fwd.hh>
#include <ObjexxFCL/FArray1D.hh>

#include <utility/pointer/ReferenceCount.hh>
#include <utility/pointer/owning_ptr.fwd.hh>

#include <string>
#include <map>

namespace protocols {
namespace swa {

  /////////////////////////////////////////////////////////////////////////////////////////////////
  /////////////////////////////////////////////////////////////////////////////////////////////////
  class InputStreamWithResidueInfo;
  typedef utility::pointer::owning_ptr< InputStreamWithResidueInfo > InputStreamWithResidueInfoOP;
  // class definition is below.


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

    //constructor!
    StepWisePoseSetup( utility::vector1< core::Size > const & moving_res_list,
                       std::string const & desired_sequence,
                       utility::vector1< InputStreamWithResidueInfoOP > & input_streams_with_residue_info,
                       utility::vector1< core::Size > const & cutpoint_open,
                       utility::vector1< core::Size > const & cutpoint_closed );

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

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

  virtual std::string get_name() const;



    StepWiseJobParametersOP & job_parameters();

    void
    set_fixed_res(utility::vector1 < core::Size > const & fixed_res );

    void
    set_jump_res(utility::vector1 < core::Size > const & jump_res );

    void
    set_virtual_res(utility::vector1 < core::Size > const & set_virtual_res_list);

    void
    set_terminal_res(utility::vector1 < core::Size > const & terminal_res );

    void
    set_superimpose_res(utility::vector1 < core::Size > const & superimpose_res );

    void
    set_calc_rms_res(utility::vector1 < core::Size > const & calc_rms_res );

    void
    set_bulge_res(utility::vector1 < core::Size > const & bulge_res );

    void
    set_bridge_res(utility::vector1 < core::Size > const & bridge_res );

    void
    set_parin_favorite_output( bool const & setting){ parin_favorite_output_=setting ; }

    void
    set_rsd_set( core::chemical::ResidueTypeSetCAP & rsd_set );

    void
    set_cst_file( std::string const cst_file );

    void
    set_disulfide_file( std::string const disulfide_file );

    void
    set_align_file( std::string const align_file );

    void
    set_add_peptide_plane_variants( bool const & setting );

    void
    set_remove_nterminus_variant( bool const & setting ){ remove_nterminus_variant_ = setting; }

    void
    set_remove_cterminus_variant( bool const & setting ){ remove_cterminus_variant_ = setting; }

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

    bool
    ready_to_align() const;

    void
    set_dump( bool const dump );

    void
    set_secstruct( std::string const secstruct );


  private:

    void
    Import_pose( core::pose::Pose & import_pose, InputStreamWithResidueInfoOP & stream );


    void
    check_moving_res_in_chain( Size const & start_chain, Size const & end_chain,
                               Size const & num_chains, Size & which_chain_has_moving_res  );

    void
    figure_out_working_sequence_and_mapping();

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

    void
    figure_out_jump_partners();

    Size
    which_chain( Size const & i );

    bool
    already_connected( std::pair< Size, Size > const & potential_chain_partner,
                       utility::vector1< std::pair< Size, Size > > const & chain_partners ) const;

    bool
    already_connected( Size const start_chain,
                       Size const stop_chain,
                       utility::vector1< std::pair< Size, Size > > const & chain_partners,
                       utility::vector1< bool > already_checked ) const;


    void
    figure_out_cuts();

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

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

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

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

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

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

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

    void
    figure_out_gap_size_and_first_chain_break_res();

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

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

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

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

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

//    void
//    slice_native();

    //Replacement for slice_native(); Parin Jan 29, 2010
    void
    setup_working_native_pose();

    void
    get_working_pose( core::pose::Pose const & pose, core::pose::Pose & working_pose );

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

    utility::vector1< Size > const
    apply_full_to_sub_mapping( utility::vector1< Size > & res_vector) const;

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

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

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

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

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

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

    void
    save_phi_psi_offsets(
                         core::pose::Pose const & start_pose,
                         utility::vector1< core::Size > const & input_res,
                         utility::vector1< core::Size > const & slice_res );

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

    void
    copy_rna_chi( core::pose::Pose & pose,
                  core::pose::Pose const import_pose,
                  utility::vector1< core::Size > const & input_res,
                  utility::vector1< core::Size > const & slice_res );


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

    bool
    is_working_cutpoint_closed( Size const res, std::map< Size, Size > & full_to_sub ) const;

    std::string
    get_swa_jump_atom( core::conformation::Residue const & rsd );

  private:

    utility::vector1< core::Size > const & moving_res_list_;
    std::string const desired_sequence_;
    core::chemical::ResidueTypeSetCAP rsd_set_;

    utility::vector1< InputStreamWithResidueInfoOP > input_streams_with_residue_info_;

    utility::vector1< Size > const cutpoint_open_;
    utility::vector1< Size > const cutpoint_closed_;
    utility::vector1< Size > fixed_res_;
    utility::vector1< Size > virtual_res_list_;
    utility::vector1< Size > terminal_res_;
    utility::vector1< Size > superimpose_res_;
    utility::vector1< Size > calc_rms_res_;
    utility::vector1< Size > bulge_res_;
    utility::vector1< Size > jump_res_;
    utility::vector1< Size > bridge_res_;
    ObjexxFCL::FArray1D< bool > is_cutpoint_;
    std::string secstruct_;

    ObjexxFCL::FArray1D< core::Real > phi_offsets_;
    ObjexxFCL::FArray1D< core::Real > psi_offsets_;

    utility::vector1< std::pair< core::Size, core::Size > > jump_partners_;
    utility::vector1< core::Size > cuts_;

    StepWiseJobParametersOP job_parameters_;

    bool virtualize_5prime_phosphates_;
    bool add_peptide_plane_variants_;
    bool remove_nterminus_variant_;
    bool remove_cterminus_variant_;
    bool parin_favorite_output_;

    std::string cst_file_;
    std::string disulfide_file_;
    core::scoring::constraints::ConstraintSetOP cst_set_;
    core::pose::PoseOP working_native_pose;

    Size const BRIDGE_RES_;

    std::string align_file_;
    bool ready_to_align_;
    core::pose::PoseOP working_align_pose_;
    core::id::AtomID_Map< core::id::AtomID > alignment_atom_id_map_;
    bool dump_;

  };


} //swa
} // protocols

#endif