LigandDockProtocol.hh

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// vi: set ts=2 noet:
//
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/// @file   protocols/ligand_docking/LigandDockProtocol.hh
///
/// @brief
/// @author Ian W. Davis


#ifndef INCLUDED_protocols_ligand_docking_LigandDockProtocol_hh
#define INCLUDED_protocols_ligand_docking_LigandDockProtocol_hh

#include <protocols/ligand_docking/LigandDockProtocol.fwd.hh>

// AUTO-REMOVED #include <core/grid/CartGrid.fwd.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
// AUTO-REMOVED #include <protocols/enzdes/EnzConstraintIO.hh> //for adding constraints if demanded by user
#include <protocols/ligand_docking/LigandBaseProtocol.hh>
#include <protocols/ligand_docking/ResidueTorsionRestraints.fwd.hh>
#include <protocols/moves/MonteCarlo.fwd.hh>
#include <protocols/moves/Mover.hh>
// AUTO-REMOVED #include <utility/vector1.hh>

#include <map>

#include <protocols/toolbox/match_enzdes_util/EnzConstraintIO.fwd.hh>
#include <utility/vector1.hh>


#ifdef WIN32
  #include <protocols/ligand_docking/ResidueTorsionRestraints.hh>
  #include <protocols/ligand_docking/MinimizeLigand.hh>
#endif

namespace protocols {
namespace ligand_docking {


///@brief
///
///@details
///
class LigandDockProtocol : public protocols::ligand_docking::LigandBaseProtocol
{
public:

  LigandDockProtocol();

  LigandDockProtocol(
      std::string const protocol,
      bool const minimize_ligand,
      bool const minimize_backbone,
      bool const tether_ligand,
      bool const mutate_same_name3,
      core::Real const ligand_chi_stddev_deg,
      core::Real const protein_CA_stddev_Ang,
      core::Real const ligand_tether_stddev_Ang_=-1,
      core::Size const ligand_shear_moves=0
  );

  virtual ~LigandDockProtocol();

  void add_start_from(core::Real x, core::Real y, core::Real z);

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

  void
  append_ligand_docking_scores(
    core::pose::Pose const & before,
    core::pose::Pose const & after,
    core::scoring::ScoreFunctionCOP scorefxn,
    std::map< std::string, core::Real > & scores, //< appended to for output
    protocols::toolbox::match_enzdes_util::EnzConstraintIOCOP constraint_io = NULL
  ) const;

private:

  LigandDockProtocol(LigandDockProtocol const & that);

  void
  classic_protocol(
    core::pose::Pose & pose,
    int jump_id,
    core::scoring::ScoreFunctionOP scorefxn,
    protocols::moves::MonteCarloOP monteCarlo,
    core::Size num_cycles,
    core::Size repack_every_Nth
  ) const;

  void
  shear_min_protocol(
    core::pose::Pose & pose,
    int jump_id,
    core::scoring::ScoreFunctionOP scorefxn,
    protocols::moves::MonteCarloOP monteCarlo,
    core::Size num_cycles
  ) const;

  void
  optimize_orientation3(
    core::pose::Pose & pose,
    int jump_id,
    core::Size lig_id
  );

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

  protocols::moves::MoverOP
  make_dockmcm_mover(
    core::pose::Pose const & pose,
    int jump_id,
    protocols::moves::MoverOP repack_mover,
    protocols::moves::MoverOP rigbod_mover,
    core::kinematics::MoveMapOP movemap, //< would be COP but MinMover wants OP
    core::scoring::ScoreFunctionOP scorefxn,
    protocols::moves::MonteCarloOP monteCarlo
  ) const;

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

private:
  std::string protocol_; // i.e. 50 cycles instead of just 5
  bool minimize_ligand_;
  bool minimize_backbone_;
  bool tether_ligand_;
  bool ligand_protonation_;
  core::Real ligand_chi_stddev_deg_;
  core::Real protein_CA_stddev_Ang_;
  core::Real ligand_tether_stddev_Ang_;
  core::Size ligand_shear_moves_;
  bool minimize_all_rsds_;
  bool repack_all_rsds_;
  bool rottrials_all_rsds_;
  bool minimize_water_;
  utility::vector1< core::Vector > start_from_pts_; // may be empty
  utility::vector1< protocols::ligand_docking::ResidueTorsionRestraintsOP > ligand_torsion_restraints_;

}; // class LigandDockProtocol


} // namespace ligand_docking
} // namespace protocols

#endif // INCLUDED_protocols_ligand_docking_LigandDockProtocol_HH