BindingSiteConstraint.hh

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//
// (c) Copyright Rosetta Commons Member Institutions.
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/// @file
/// @brief

#ifndef INCLUDED_protocols_constraints_additional_BindingSiteConstraint_hh
#define INCLUDED_protocols_constraints_additional_BindingSiteConstraint_hh

// Package headers
#include <core/scoring/constraints/Constraint.hh>
#include <core/scoring/constraints/Func.hh>
#include <core/scoring/constraints/XYZ_Func.fwd.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/EnergyMap.fwd.hh>
#include <core/scoring/constraints/FuncFactory.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>

// Project headers
#include <core/pose/Pose.fwd.hh>
#include <core/id/AtomID.hh>

// ObjexxFCL headers
#include <ObjexxFCL/FArray2D.hh>

// C++ Headers
#include <map>

#include <utility/vector1.hh>



namespace protocols {
namespace constraints_additional {

class BindingSiteConstraint : public core::scoring::constraints::Constraint {
public:

  /// null constructor
  BindingSiteConstraint( ) :
    core::scoring::constraints::Constraint( core::scoring::atom_pair_constraint )  /// ? TO DO -- give own scoretype
  { }

  /// ctor from atom list + input pose
  BindingSiteConstraint(
    utility::vector1< AtomID > const & atms,
    core::pose::Pose const &start_pose,
    core::scoring::ScoreType scoretype = core::scoring::atom_pair_constraint   /// ? TO DO -- give own scoretype
  );

  /// ctor from a vector of atom positions (in lieu of a pose)
  BindingSiteConstraint(
    utility::vector1< AtomID > const & atms,
    ObjexxFCL::FArray2D< core::Real >  tgt_pos,
    ObjexxFCL::FArray2D< core::Real >  tgt_pos_centroid,
    core::scoring::ScoreType scoretype = core::scoring::atom_pair_constraint   /// ? TO DO -- give own scoretype
  );

  virtual core::scoring::constraints::ConstraintOP clone() const {
    return new BindingSiteConstraint( atms_, tgt_pos_, tgt_pos_centroid_ );
  }

  ///
  void
  score( core::scoring::constraints::XYZ_Func const & xyz, core::scoring::EnergyMap const &, core::scoring::EnergyMap & emap ) const;

  // do some pre-scoring calculations
  void setup_for_scoring( core::scoring::constraints::XYZ_Func const & xyz, core::scoring::ScoreFunction const &scfxn ) const;

  // align the atoms
  //   ... placing a vector  -- from each atom to the the rotated >target< atoms -- in the database
  void pre_align( utility::vector1< numeric::xyzVector< core::Real > > const & templ_atms,
                  utility::vector1< bool > const & ) const;

  // call the setup_for_derivatives for each constraint
  void setup_for_derivatives(  core::scoring::constraints::XYZ_Func const & xyz, core::scoring::ScoreFunction const &scfxn ) const;

  // atom deriv
  virtual
  void
  fill_f1_f2(
    AtomID const & atom,
    core::scoring::constraints::XYZ_Func const & xyz,
    core::Vector & F1,
    core::Vector & F2,
    core::scoring::EnergyMap const & weights
  ) const;

  std::string type() const;

  ///
  Size
  natoms() const;

  virtual
  core::scoring::constraints::ConstraintOP
  remap_resid( core::id::SequenceMapping const &seqmap ) const;

  ///
  AtomID const &
  atom( Size const n ) const;

  void show( std::ostream& out ) const;

  void show_def( std::ostream& out, core::pose::Pose const & pose ) const;
  void read_def( std::istream& in, core::pose::Pose const & pose, core::scoring::constraints::FuncFactory const & func_factory );

  Size show_violations( std::ostream & out, core::pose::Pose const & pose, core::Size verbose_level, core::Real threshold = 1.0 ) const;

protected:
  void init( core::pose::Pose const & start_pose );

private:
  // data
  utility::vector1< AtomID > atms_;
  ObjexxFCL::FArray2D< core::Real >  tgt_pos_;
  ObjexxFCL::FArray2D< core::Real >  tgt_pos_centroid_;

  // map of pos->tgt in rotated struct
  static std::map< AtomID , numeric::xyzVector< core::Real > > rot_db;

  // database mapping constraints to RB transformations
  // static std::map< AtomID , ?? > transformDB;
};

}
}

#endif