Ubiquitin_E2C_Modeler.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
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// (c) members of the Rosetta Commons. For more information, see
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/// @file Ubiquitin_E2C_Modeler.hh
/// @brief Build model for di-ubiquitin and e2c enzyme complex
/// @detailed
///
///
/// @author Aroop Sircar


#ifndef INCLUDED_protocols_antibody_Ubiquitin_E2C_Modeler_hh
#define INCLUDED_protocols_antibody_Ubiquitin_E2C_Modeler_hh
#include <core/types.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <core/pack/task/TaskFactory.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>

#include <protocols/antibody/Ubiquitin_E2C_Modeler.fwd.hh>
#include <protocols/moves/Mover.hh>

#include <utility/vector1.hh>

namespace protocols {
namespace ub_e2c {

class ubi_e2c_modeler: public moves::Mover {
public:

  // default constructor
  ubi_e2c_modeler();

  // default destructor
  ~ubi_e2c_modeler();

  void set_default();

  virtual void apply( core::pose::Pose & pose_in );
  virtual std::string get_name() const;

  virtual protocols::moves::MoverOP clone() const;

  // find out domain ends and center of masses
  void
  setup_key_residues( const core::pose::Pose & pose_in );

  void setup_move_maps();

  void setup_complex_fold_tree(
    core::pose::Pose & pose_in,
    bool trim = false );

  void initial_cter_perturbation( core::pose::Pose & pose_in );

  void setup_simple_fold_tree(
    core::Size jumppoint1,
    core::Size cutpoint,
    core::Size jumppoint2,
    core::Size nres,
    core::pose::Pose & pose_in );

  void trim_cter( core::pose::Pose & pose_in );

  void restore_cter(
    core::pose::Pose & pose_in,
    core::pose::Pose without_cter );

  void init_k48r_perturbation( core::pose::Pose & pose_in );

  void init_d77_perturbation( core::pose::Pose & pose_in );

  core::Real initial_perturbation( core::pose::Pose & pose_in );

  core::Real centroid_mode_perturbation( core::pose::Pose & pose_in );

  core::Real fullatom_mode_perturbation( core::pose::Pose & pose_in );

  void initial_repack( core::pose::Pose & pose_in );

  void setup_packer_task( core::pose::Pose & pose_in );

  void restrict_to_interfacial_loop_packing( core::pose::Pose & pose_in );

  void set_e2g2_diubi_fold_tree( core::pose::Pose & pose_in );

  core::Real calc_interaction_energy(
    const core::pose::Pose & pose_in,
    bool dimer = true );

  core::Real CSP_fraction(
    const core::pose::Pose & pose_in,
    bool non_CSP = false,
    bool trim = false,
    bool swap = false );

  bool centroid_filter( core::pose::Pose & pose_in );

  bool fullatom_filter( core::pose::Pose & pose_in );

  core::Real
  calc_Lrmsd(
    const core::pose::Pose & pose_in,
    const core::pose::Pose & native_pose,
    core::Size ubiquitin );

  void evaluate_native( core::pose::Pose & pose_in );

  void optimize_cov_bond( core::pose::Pose & pose_in );

private:

  void compute_trim_CSPs();

  void compute_swap_trim_CSPs();

  void assign_CSPs( const core::pose::Pose & pose_in );

  void assign_non_CSPs( const core::pose::Pose & pose_in );

  core::Size e2_ctr_of_mass_;
  core::Size k48r_ctr_of_mass_;
  core::Size d77_ctr_of_mass_;
  core::Size e2_end_;
  core::Size k48r_end_;
  core::Size d77_end_;
  core::Size k48r_48_lys_;
  core::Size d77_48_lys_;
  core::Size k48r_trim_end_;
  core::Size d77_trim_end_;
  core::Size d77_trim_ctr_mass_;

  bool k48r_swap_;

  // move maps
  core::kinematics::MoveMapOP k48r_docking_map_;
  core::kinematics::MoveMapOP d77_docking_map_;
  core::kinematics::MoveMapOP docking_map_;
  core::kinematics::MoveMapOP flex_cter_map_;
  core::kinematics::MoveMapOP all_dof_map_;
  core::kinematics::MoveMapOP init_k48r_docking_map_;
  core::kinematics::MoveMapOP init_d77_docking_map_;
  core::kinematics::MoveMapOP init_docking_map_;
  core::kinematics::MoveMapOP init_flex_cter_map_;
  core::kinematics::MoveMapOP init_all_dof_map_;


  // jump between E2 G2 and UbK48R
  core::Size const e2_k48r_jump_;
  // jump between E2 G2 and UbD77
  core::Size const e2_d77_jump_;
  core::Real const max_k48_cter_dist_;
  core::Real const temperature_;
  std::map < std::string, core::Real > score_map_;
  // number of flexible c-terminal residues in Ubiquitin
  // actually its one more than flex_cter residues
  // so if flex_cter equals 3, then 4 residues are flexible
  core::Size const flex_cter_;
  // CA atom index
  core::Size const CA;
  // If a decoy does not pass the filters in fullatom perturbation
  // how many attempts to make before failure
  core::Size const max_repeats_;
  // strict constraint cutoffs for fullatom
  // 0.25 per constraint
  core::Real fullatom_constraint_cutoff_; // depends on mode
  // CSP Satisfaction Factor
  core::Real const centroid_allowed_CSP_fraction_;
  core::Real const fullatom_allowed_CSP_fraction_;
  // CSP score weights
  core::Real const centroid_CSP_weight_;
  core::Real const centroid_non_CSP_weight_;
  core::Real const fullatom_CSP_weight_;
  core::Real const fullatom_non_CSP_weight_;
  // weighting terms
  core::Real const cen_vdw_;
  core::Real const cen_constraint_;
  core::Real const full_vdw_;
  core::Real full_constraint_; // depends on which mode being run
  // mode
  bool const refinement_mode_;
  bool const cov_bond_only_flag_;
  bool const monoub_mode_;
  bool const higher_d77_pert_mode_;
  // MTSL PRE Tags
  core::Size k48r_48k_mtsl_ ;
  core::Size d77_75g_mtsl_;
  // filters
  bool passed_centroid_filter_;
  bool passed_fullatom_filter_;
  // Applied Full Atom Perturbation
  bool applied_fullatom_pert_;
  //packer task
  core::pack::task::TaskFactoryOP tf_;
  core::pack::task::TaskFactoryOP init_task_factory_;

  //sets up minimization parameters
  core::Real min_tolerance_;
  std::string min_type_;
  bool nb_list_;

  // CSPs
  utility::vector1<core::Size> CSP_;
  utility::vector1<core::Size> CSP_trim_;
  utility::vector1<core::Size> CSP_swap_trim_;

  // non_CSPs
  utility::vector1<core::Size> non_CSP_;
  utility::vector1<core::Size> non_CSP_trim_;
  utility::vector1<core::Size> non_CSP_swap_trim_;

  // score functions
  core::scoring::ScoreFunctionOP dock_lowres_scorefxn_;
  core::scoring::ScoreFunctionOP lowres_scorefxn_;
  core::scoring::ScoreFunctionOP dock_lowres_cst_scorefxn_;
  core::scoring::ScoreFunctionOP lowres_cst_scorefxn_;
  core::scoring::ScoreFunctionOP pack_scorefxn_;
  core::scoring::ScoreFunctionOP dockfa_scorefxn_;
  core::scoring::ScoreFunctionOP dockfa_cst_scorefxn_;
  core::scoring::ScoreFunctionOP dockfa_min_scorefxn_;
  core::scoring::ScoreFunctionOP dockfa_cst_min_scorefxn_;
  core::scoring::ScoreFunctionOP pack_cst_scorefxn_;
  core::scoring::ScoreFunctionOP output_cen_scorefxn_;
  core::scoring::ScoreFunctionOP output_full_scorefxn_;

  // Mono Ubiquitin Mode Variables
  void monoub_assign_CSPs(const core::pose::Pose & pose_in );

  void monoub_apply( core::pose::Pose & pose_in );

  void monoub_setup_key_residues( const core::pose::Pose & pose_in );

  void monoub_setup_move_maps();

  void monoub_fold_tree( core::pose::Pose & pose_in );

  void monoub_initial_cter_perturbation( core::pose::Pose & pose_in );

  void monoub_first_perturbation( core::pose::Pose & pose_in );

  void monoub_initial_perturbation( core::pose::Pose & pose_in );

  void monoub_centroid_mode_perturbation( core::pose::Pose & pose_in );

  void monoub_fullatom_mode_perturbation( core::pose::Pose & pose_in );

  core::Real monoub_calc_interaction_energy(
    const core::pose::Pose & pose_in );

  core::Real monoub_CSP_fraction( const core::pose::Pose & pose_in );

  bool monoub_centroid_filter( core::pose::Pose & pose_in );

  bool monoub_fullatom_filter( core::pose::Pose & pose_in );

  core::Real monoub_calc_Lrmsd (
    const core::pose::Pose & pose_in,
    const core::pose::Pose & native_pose );



  core::Size monoub_end_;
  core::Size monoub_ctr_of_mass_;

  core::kinematics::MoveMapOP monoub_all_dof_map_;
  core::kinematics::MoveMapOP monoub_docking_map_;
  core::kinematics::MoveMapOP monoub_flex_cter_map_;
  core::kinematics::MoveMapOP init_monoub_all_dof_map_;
  core::kinematics::MoveMapOP init_monoub_docking_map_;
  core::kinematics::MoveMapOP init_monoub_flex_cter_map_;

}; // class ubi_e2c_modeler


} // namespace ub_e2c
} // namespace protocols
#endif