AntibodyModeler.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
// (c) under license. The Rosetta software is developed by the contributing
// (c) members of the Rosetta Commons. For more information, see
// (c) http://www.rosettacommons.org. Questions about this can be addressed to
// (c) University of Washington UW TechTransfer, email:license@u.washington.edu

/// @file AntibodyModeler
/// @brief Build a homology model of an antibody
/// @detailed
///
///
/// @author Aroop Sircar


#ifndef INCLUDED_protocols_antibody_AntibodyModeler_hh
#define INCLUDED_protocols_antibody_AntibodyModeler_hh

#include <core/fragment/FragSet.fwd.hh>
#include <core/fragment/FragData.fwd.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <core/pack/task/TaskFactory.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/types.hh>

#include <protocols/antibody/AntibodyClass.hh>
#include <protocols/antibody/AntibodyModeler.fwd.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/moves/Mover.hh>

#include <utility/vector1.hh>

namespace protocols {
namespace antibody {

class AntibodyModeler: public moves::Mover {
public:

  // default constructor
  AntibodyModeler();

  // default destructor
  ~AntibodyModeler();

  void set_default();

  void init_from_options();

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

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

  virtual void init_on_new_input();

  void set_snugdock_foldtree( 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 relax_cdrs();

  void all_cdr_VL_VH_fold_tree(
      core::pose::Pose & pose_in,
      const loops::Loops & loops );

  void repulsive_ramp(
    core::pose::Pose & pose_in,
    loops::Loops loops_in );

  void snugfit_MC_min (
    core::pose::Pose & pose_in,
    core::kinematics::MoveMapOP cdr_dock_map,
    core::Size cycles,
    core::Real minimization_threshold,
    core::scoring::ScoreFunctionOP scorefxn,
    core::scoring::ScoreFunctionOP pack_scorefxn,
    utility::vector1< bool> is_flexible );

  void snugfit_mcm_protocol(
    core::pose::Pose & pose_in,
    loops::Loops loops_in );

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

  core::Real global_loop_rmsd (
    const core::pose::Pose & pose_in,
    const core::pose::Pose & native_pose,
    std::string cdr_type );

  void read_and_store_fragments();

  void display_constraint_residues();


private:

  // Modeling H3 options
  bool model_h3_;
  bool snugfit_;
  bool native_present_;
  bool graft_l1_;
  bool graft_l2_;
  bool graft_l3_;
  bool graft_h1_;
  bool graft_h2_;
  bool graft_h3_;
  bool camelid_;
  bool camelid_constraints_;

  // Benchmark mode for shorter_cycles
  bool benchmark_;

  // flag for one time fragment initialization
  bool init_for_input_yet_;

  // used as a flag to enable reading in of cst files
  core::Real cst_weight_;

  std::string native_filename_;
  core::pose::Pose start_pose_;
  core::pose::Pose native_pose_;
  antibody::Antibody antibody_in_;
  utility::vector1< core::fragment::FragData > H3_base_library_;
  utility::vector1< core::fragment::FragSetOP > offset_frags_;

  //packer task
  core::pack::task::TaskFactoryOP tf_;
  core::pack::task::TaskFactoryOP init_task_factory_;

  std::map < std::string, core::Real > score_map_;

}; // class AntibodyModeler

} // namespace antibody
} // namespace protocols
#endif