SequenceCouplingConstraint.hh

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/// @file   protocols/constraints_additional/SequenceCouplingConstraint.hh
/// @brief  This is a constraint that refers to a core::sequence::SequenceCoupling? in order to influence the scoring of amino acid types based on multiple sequence alignments (i.e. for biasing amino acid choices during design).
/// @author HetuKamisetty

#ifndef INCLUDED_protocols_constraints_additional_SequenceCouplingConstraint_hh
#define INCLUDED_protocols_constraints_additional_SequenceCouplingConstraint_hh

#include <protocols/constraints_additional/SequenceCouplingConstraint.fwd.hh>
#include <core/scoring/constraints/Constraint.hh>

// AUTO-REMOVED #include <core/chemical/AA.hh>
// AUTO-REMOVED #include <core/sequence/SequenceCoupling.hh>

// AUTO-REMOVED #include <utility/vector1.hh>

#include <core/sequence/SequenceCoupling.hh>
#include <core/id/AtomID.hh>
#include <utility/vector1.hh>


namespace protocols {
namespace constraints_additional {

///@brief
class SequenceCouplingConstraint : public core::scoring::constraints::Constraint {
public:
  typedef core::sequence::SequenceCoupling SequenceCoupling;
  typedef core::sequence::SequenceCouplingOP SequenceCouplingOP;
  typedef core::sequence::SequenceCouplingCOP SequenceCouplingCOP;
  typedef core::id::SequenceMapping SequenceMapping;
  typedef core::pose::Pose Pose;
  typedef core::conformation::Conformation Conformation;
  typedef core::scoring::EnergyMap EnergyMap;
  typedef core::scoring::constraints::FuncFactory FuncFactory;
  typedef core::scoring::constraints::XYZ_Func XYZ_Func;
  typedef core::scoring::constraints::ConstraintOP ConstraintOP;

public:

  SequenceCouplingConstraint();

  SequenceCouplingConstraint(
    Pose const &,
    core::Size,
    core::Size,
    SequenceCouplingOP profile = NULL
  );

  SequenceCouplingConstraint(
    core::Size,
    core::Size,
    SequenceCouplingOP profile = NULL
  );

  virtual ~SequenceCouplingConstraint();

  virtual ConstraintOP clone() const;

  virtual std::string type() const { return "SequenceCoupling"; }

  ///@brief used by ConstraintIO and ConstraintFactory to construct this constraint from a input file stream (constraint file)
  virtual void
  read_def(
    std::istream &,
    Pose const &,
    FuncFactory const &
  );

  virtual void show_def( std::ostream &, Pose const & ) const;

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

  core::Size seqpos1() const { return seqpos1_; }
  core::Size seqpos2() const { return seqpos2_; }

  void set_sequence_coupling( SequenceCouplingOP );
  SequenceCouplingOP sequence_coupling();
  SequenceCouplingCOP sequence_coupling() const;

  virtual core::Size natoms() const { return 0; };
  virtual AtomID const & atom( Size const ) const { 
    utility_exit_with_message("SequenceCouplingConstraint is not atom-based!."); 
    return core::id::BOGUS_ATOM_ID;  // required for compilation on Windows
  }
  
  virtual utility::vector1< core::Size > residues() const;

  //virtual ConstraintOP remap_resid( SequenceMapping const & ) const;

  virtual void
  score(
    XYZ_Func const &,
    EnergyMap const &,
    EnergyMap &
  ) const;

  virtual void
  fill_f1_f2(
    AtomID const &,
    XYZ_Func const &,
    core::Vector &,
    core::Vector &,
    EnergyMap const &
  ) const;

private:
  core::Size seqpos1_;
  core::Size seqpos2_;
  SequenceCouplingOP sequence_coupling_;
};


} // namespace constraints_additional
} // namespace protocols

#endif // INCLUDED_protocols_constraints_additional_SequenceCouplingConstraint_HH