SequenceCoupling1BDConstraint.hh

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//
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/// @file   protocols/constraints_additional/SequenceCoupling1BDConstraint.hh
/// @brief  This is a constraint that refers to a core::sequence::SequenceCoupling1BD? 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 ashworth

#ifndef INCLUDED_protocols_constraints_additional_SequenceCoupling1BDConstraint_hh
#define INCLUDED_protocols_constraints_additional_SequenceCoupling1BDConstraint_hh

#include <protocols/constraints_additional/SequenceCoupling1BDConstraint.fwd.hh>
#include <core/scoring/constraints/SequenceProfileConstraint.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.fwd.hh>
#include <utility/vector1.hh>


namespace protocols {
namespace constraints_additional {

///@brief
class SequenceCoupling1BDConstraint : public core::scoring::constraints::SequenceProfileConstraint {
public:
  typedef core::sequence::SequenceCoupling SequenceCoupling;
  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:

  SequenceCoupling1BDConstraint();

  SequenceCoupling1BDConstraint(
    Pose const &,
    core::Size,
    SequenceProfileCOP profile
  );

  SequenceCoupling1BDConstraint(
    core::Size,
    SequenceProfileCOP profile
  );

  virtual ~SequenceCoupling1BDConstraint();

  virtual ConstraintOP clone() const;

  virtual std::string type() const { return "SequenceCoupling1BD"; }

  ///@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( std::ostream & out ) 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;

};


} // namespace constraints_additional
} // namespace protocols

#endif // INCLUDED_protocols_constraints_additional_SequenceCoupling1BDConstraint_hh