NamedAtomPairConstraint.hh

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file
/// @brief

#ifndef INCLUDED_core_scoring_constraints_NamedAtomPairConstraint_hh
#define INCLUDED_core_scoring_constraints_NamedAtomPairConstraint_hh

#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/NamedAtomPairConstraint.fwd.hh>

#include <core/scoring/constraints/Constraint.hh>
#include <core/scoring/constraints/Func.hh>
// AUTO-REMOVED #include <core/scoring/constraints/XYZ_Func.hh>

#include <core/scoring/ScoreType.hh>
// AUTO-REMOVED #include <core/scoring/EnergyMap.hh>
#include <core/scoring/ScoreFunction.fwd.hh>


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

#include <utility/vector1.hh>



// C++ Headers
//#include <cstdlib>
//#include <iostream>
//#include <map>
//#include <utility>


namespace core {
namespace scoring {
namespace constraints {

/* this helper class may have become obsoleted by the remapped_clone() method of ConstraintSet
   but since it is still in use by abinitio::Template I haven't removed it.
*/
class Obsolet_NamedAtomPairConstraint : public utility::pointer::ReferenceCount {
  typedef core::scoring::constraints::AtomPairConstraintOP AtomPairConstraintOP;
  typedef core::id::NamedAtomID NamedAtomID;
  typedef core::id::SequenceMapping SequenceMapping;
public:
  ///@brief Automatically generated virtual destructor for class deriving directly from ReferenceCount
  virtual ~Obsolet_NamedAtomPairConstraint();
  Obsolet_NamedAtomPairConstraint( AtomPairConstraintOP, core::pose::Pose const& );
  Obsolet_NamedAtomPairConstraint( NamedAtomID const& atom1, NamedAtomID const& atom2, AtomPairConstraintOP cst );
  AtomPairConstraintOP mapto( SequenceMapping const&, core::pose::Pose const& ) const;
  Obsolet_NamedAtomPairConstraintOP mapto( SequenceMapping const& ) const;
  AtomPairConstraintOP mapto( core::pose::Pose const& ) const;

  friend std::ostream& operator<< ( std::ostream& out, Obsolet_NamedAtomPairConstraint const& cst );

  id::NamedAtomID const& atom1() {
    return atom1_;
  }

  id::NamedAtomID const& atom2() {
    return atom2_;
  }

private:

  id::NamedAtomID atom1_;
  id::NamedAtomID atom2_;
  AtomPairConstraintOP cst_;
};

class NamedAtomPairConstraint : public AtomPairConstraint {
public:
  NamedAtomPairConstraint(
    id::NamedAtomID const& a1,
    id::NamedAtomID const& a2,
    FuncOP func,
    ScoreType scoretype = atom_pair_constraint
  ) :
    AtomPairConstraint( id::AtomID( 0, a1.rsd() ), id::AtomID( 0, a2.rsd() ), func, scoretype ),
    named_atom1_( a1 ),
    named_atom2_( a2 ),
    type1_id_( 0 ),
    type2_id_( 0 )
  {}

  virtual ConstraintOP clone() const {
    return new NamedAtomPairConstraint( named_atom1_, named_atom2_, func_, score_type() );
  }

  /// @brief Copies the data from this Constraint into a new object and returns an OP
  /// atoms are mapped to atoms with the same name in dest pose ( e.g. for switch from centroid to fullatom )
  /// if a sequence_mapping is present it is used to map residue numbers .. NULL = identity mapping
  /// to the new object. Intended to be implemented by derived classes.
  virtual ConstraintOP remapped_clone( pose::Pose const& src, pose::Pose const& dest, id::SequenceMappingCOP map=NULL ) const;


  //@brief translates the atom-names into numbers
  virtual void setup_for_scoring( XYZ_Func const &, ScoreFunction const & ) const;

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

  virtual void read_def( std::istream& in, pose::Pose const& pose, FuncFactory const& func_factory );
  //  //@brief set constraint such that the pose doesn't violate it.
  //  virtual void steal( pose::Pose& );

private:
  id::NamedAtomID named_atom1_;
  id::NamedAtomID named_atom2_;
  core::Size type1_id_;
  core::Size type2_id_;
  //@brief this could contain a checksum made from the "annotated-sequence"
  Size pose_chemical_checksum_;
};


}
}
}

#endif