EnzdesBaseProtocol.hh

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//
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/// @file   protocols/enzdes/EnzdesBaseProtocol.hh
///
/// @brief
/// @author Florian Richter




#ifndef INCLUDED_protocols_enzdes_EnzdesBaseProtocol_hh
#define INCLUDED_protocols_enzdes_EnzdesBaseProtocol_hh


#include <protocols/enzdes/EnzdesBaseProtocol.fwd.hh>
// AUTO-REMOVED #include <protocols/toolbox/match_enzdes_util/EnzConstraintIO.hh>

#include <protocols/ligand_docking/LigandBaseProtocol.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/EnergyMap.fwd.hh>
#include <core/id/SequenceMapping.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>

#include <utility/vector1.hh>



namespace protocols {
namespace enzdes {


class EnzdesBaseProtocol : public protocols::ligand_docking::LigandBaseProtocol
{

public:

  EnzdesBaseProtocol();
  virtual std::string get_name() const;

  //virtual void apply( core::pose::Pose & pose) const = 0;

  //toolbox::match_enzdes_util::EnzConstraintIOOP cst_io(){ return cst_io_; }

 //catalytic res INCLUDING all ligands in pose numbering in a particular order
  utility::vector1<Size> catalytic_res( core::pose::Pose const & pose) const;

  std::set< Size > const & design_targets( core::pose::Pose const & pose ) const;

  bool
  is_catalytic_position( core::pose::Pose const & pose, core::Size const seqpos ) const;

  static void register_options();

  core::chemical::ResidueTypeSetCAP
  restype_set() const {
    return restype_set_; }

  void
  generate_explicit_ligand_rotamer_poses(
    core::pose::Pose const & orig_pose,
    utility::vector1< core::pose::PoseOP > & ligrot_poses,
    core::scoring::ScoreFunctionCOP scofx
  );

  core::scoring::ScoreFunctionCOP
  reduced_scorefxn() const;

  core::scoring::ScoreFunctionOP
  reduced_scorefxn();

  core::Real
  design_targets_score(
    core::pose::Pose const & pose
  ) const;


  virtual
  void
  remap_resid(
    core::pose::Pose const & pose,
    core::id::SequenceMapping const & smap
  );

  void
  remove_enzdes_constraints(
    core::pose::Pose & pose,
    bool keep_covalent
  ) const;

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

  void
  cst_minimize(
    core::pose::Pose & pose,
    core::pack::task::PackerTaskCOP task,
    bool cst_opt = false
  ) const;

  core::pack::task::PackerTaskOP
  create_enzdes_pack_task(
    core::pose::Pose & pose,
    bool design = true
  ); //the task

  void
  setup_sequence_recovery_cache(
    core::pose::Pose & pose,
    core::pack::task::PackerTask const & task
  ) const;

  void
  set_all_jumps_minimizable( bool const & setting ){ min_all_jumps_ = setting; }

  void
  set_minimize_options(
    bool const & min_sc,
    bool const & min_bb,
    bool const & min_rb,
    bool const & min_lig,
    bool backrub = false){
  chi_min_ = min_sc; bb_min_= min_bb; rb_min_=min_rb; minimize_ligand_torsions_=min_lig; bb_backrub_ =backrub;
  }

  void
  set_fix_cataa(
    bool const & setting){ fix_catalytic_aa_ = setting;}

  core::kinematics::MoveMapOP
  create_enzdes_movemap(
    core::pose::Pose & pose,
    core::pack::task::PackerTaskCOP task,
    bool min_all_jumps= false
  ) const;

  void
  enzdes_pack(
    core::pose::Pose & pose,
    core::pack::task::PackerTaskCOP,
    core::scoring::ScoreFunctionCOP scorefxn,
    core::Size cycles,
    bool minimize_after_packing,
    bool pack_unconstrained,
    bool favor_native
  ) const;

  void set_scorefxn( core::scoring::ScoreFunctionCOP scorefxn );

  void
  setup_bbmin_ft_and_csts(
    core::pose::Pose & pose,
    utility::vector1< bool > allow_move_bb,
    core::Size jump_id
  ) const;
protected:
  void
  setup_enzdes_constraints(
    core::pose::Pose & pose,
    bool allow_missing_remark_blocks
  ) const;

  void enable_constraint_scoreterms();

  /// @brief function to disable constraint scoring terms:
  /// @NOTE: this will leave eventual covalent connections set up by EnzConstraintIO untouched.
  void disable_constraint_scoreterms();

  bool
  exchange_ligands_in_pose(
    core::pose::Pose & pose,
    bool check_bb_clashes,
    core::scoring::ScoreFunctionCOP scofx
  );

  core::scoring::ScoreFunctionOP reduced_sfxn_;

  mutable std::set< core::Size > design_targets_;

  bool include_all_design_targets_in_design_interface_;

private:

  void
  read_ligand_superposition_file( std::string filename );

  //data

  //toolbox::match_enzdes_util::EnzConstraintIOOP cst_io_;

  core::chemical::ResidueTypeSetCAP restype_set_;
  core::scoring::EnergyMap constraint_weights_;

  core::Real bb_min_allowed_dev_;
  core::Real loop_bb_min_allowed_dev_;

  //stuff for optional ligand superposition
  bool lig_superposition_file_read_;
  std::pair< std::string, std::string > res_to_superimpose_;
  utility::vector1< std::pair< std::string, std::string > > atoms_to_superimpose_on_;
  bool chi_min_, bb_min_, rb_min_, minimize_ligand_torsions_, bb_backrub_;
  bool min_all_jumps_; // minimize protein jumps too?
  bool minimize_all_ligand_torsions_;
  core::Real lig_min_stddev_;

  bool exclude_protein_protein_hack_elec_, fix_catalytic_aa_;

}; //class EnzdesBaseProtocol


} //namespace enzdes
} //namespace protocols




#endif // INCLUDED_protocols_enzdes_EnzdesBaseProtocol_HH