SequenceProfileConstraint.hh

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// vi: set ts=2 noet:
//
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/// @file   core/scoring/constraints/SequenceProfileConstraint.hh
/// @brief  This is a constraint that refers to a core::sequence::SequenceProfile? 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_core_scoring_constraints_SequenceProfileConstraint_hh
#define INCLUDED_core_scoring_constraints_SequenceProfileConstraint_hh

#include <core/scoring/constraints/SequenceProfileConstraint.fwd.hh>
#include <core/scoring/constraints/Constraint.hh>

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

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

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


namespace core {
namespace scoring {
namespace constraints {

///@brief
class SequenceProfileConstraint : public core::scoring::constraints::Constraint {
public:
  typedef core::sequence::SequenceProfile SequenceProfile;
  typedef core::sequence::SequenceProfileCOP SequenceProfileCOP;
  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:

  SequenceProfileConstraint();

  SequenceProfileConstraint(
    Pose const &,
    core::Size,
    SequenceProfileCOP profile = NULL,
    core::id::SequenceMappingCOP mapping = NULL // current pose numbers onto profile numbers.
  );

  SequenceProfileConstraint(
    core::Size,
    SequenceProfileCOP profile = NULL,
    core::id::SequenceMappingCOP mapping = NULL // current pose numbers onto profile numbers.
  );

  virtual ~SequenceProfileConstraint();

  virtual ConstraintOP clone() const;

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

  ///@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 seqpos() const { return seqpos_; }

  //hk
  void seqpos(core::Size seqpos) {
    seqpos_=seqpos;
  }
  //hk end

  void set_sequence_profile( SequenceProfileCOP profile, core::id::SequenceMappingCOP mapping = NULL);
  SequenceProfileCOP sequence_profile() const;
  core::id::SequenceMappingCOP profile_mapping() const;

  virtual core::Size natoms() const { return 0; }
  virtual AtomID const & atom( core::Size const ) const {
    utility_exit_with_message("SequenceProfileConstraint 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 ConstraintOP remapped_clone(pose::Pose const& src, pose::Pose const& dest, id::SequenceMappingCOP map=NULL ) 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;

  void weight( core::Real const w );
  core::Real weight() const;

private:
  core::Size seqpos_;
  // COP is deliberate, as sequence profiles are typically shared amoung many constraints, and as such probably shouldn't be fiddled with
  SequenceProfileCOP sequence_profile_;
  /// @brief A mapping of current pose numbers onto profile numbers.
  core::id::SequenceMappingCOP mapping_;
  core::Real weight_; //dflt 1; allows weighting the profile's contribution according to different criteria, for instance according to whether the position is close or far from the active site
};

} // namespace constraints
} // namespace scoring
} // namespace protocols

#endif // INCLUDED_core_scoring_constraints_SequenceProfileConstraint_HH