AmbiguousNMRDistanceConstraint.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_AmbiguousNMRDistanceConstraint_hh
#define INCLUDED_core_scoring_constraints_AmbiguousNMRDistanceConstraint_hh

#include <core/scoring/constraints/AmbiguousNMRDistanceConstraint.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/pose/Pose.fwd.hh>
#include <core/conformation/Conformation.fwd.hh>
#include <core/kinematics/ShortestPathInFoldTree.fwd.hh>
#include <core/id/AtomID.hh>
#include <core/id/NamedAtomID.hh>
#include <core/chemical/AA.hh>

#include <utility/vector1.hh>



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


namespace core {
namespace scoring {
namespace constraints {


///

class AmbiguousNMRDistanceConstraint : public Constraint {
public:
  typedef utility::vector1< AtomID > Atoms;
  ///c-tor
  AmbiguousNMRDistanceConstraint(
    Atoms const & a1,
    Atoms const & a2,
    FuncOP func,
    ScoreType scoretype = atom_pair_constraint
  ):
    Constraint( scoretype ),
    atoms1_(a1),
    atoms2_(a2),
    func_( func )
  {}

  AmbiguousNMRDistanceConstraint(
    id::NamedAtomID const & a1, //digests names like "QG1"
    id::NamedAtomID const & a2,
    core::pose::Pose const&,
    FuncOP func,
    ScoreType scoretype = atom_pair_constraint
  );

  AmbiguousNMRDistanceConstraint() :
    Constraint( atom_pair_constraint ),
    func_( NULL )
  {}

  virtual ConstraintOP clone() const {
    return new AmbiguousNMRDistanceConstraint( atoms1_, atoms2_, func_, score_type() );
  }

  ///
  virtual
  ConstraintOP clone( FuncOP func ) const {
    return new AmbiguousNMRDistanceConstraint( atoms1_, atoms2_, 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;

  ///returns AtomPairConstraint or AmbigousNMRDistanceConstraint (e.g. for GLY HA1-HA2 ... )
  ConstraintOP map_to_CEN( pose::Pose const& src, pose::Pose const& centroid, core::Size& nr_mapped, std::string const& map_atom ) const;

  ///
  void
  score( XYZ_Func const & xyz, EnergyMap const &, EnergyMap & emap ) const;

  ///
  core::Real
  inv_dist6( XYZ_Func const & xyz ) const;


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

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

  ///
  Size
  natoms() const
  {
    return atoms1_.size() + atoms2_.size();
  }

  ///
  Size
  natoms( core::Size i ) const
  {
    return i==1 ? atoms1_.size() : atoms2_.size();
  }

  Size
  multiplicity() const {
    return atoms1_.size()*atoms2_.size();
  }

  ///@brief return residue number: i=1,2
  Size
  resid( core::Size i ) const {
    return i == 1 ? atoms1_[ 1 ].rsd() : atoms2_[ 1 ].rsd();
  }

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

  ///
  AtomID const &
  atom( Size const n ) const
  {
    if ( n > natoms() ) {
      utility_exit_with_message( "AmbiguousNMRDistanceConstraint::atom() bad argument" );
    }
    if ( n <= atoms1_.size() ) {
      return atoms1_[ n ];
    } else return atoms2_[ n - atoms1_.size() ];
  }

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

  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& );

  Real dist( pose::Pose const & pose ) const;
  Real dist( XYZ_Func const & xyz ) const;


  //Real inv_dist6( conformation::Conformation const& pose ) const;
  // ^^^^ Undefined, commenting out to make PyRosetta compile.

  using Constraint::score;

  Real score( pose::Pose const& pose ) const {
    return func_->func( dist( pose ) );
  }

  virtual Size show_violations( std::ostream& out, pose::Pose const& pose, Size verbose_level, Real threshold = 1 ) const;

  virtual Func const& get_func() const {
    return *func_;
  }

  virtual
  core::Size effective_sequence_separation( core::kinematics::ShortestPathInFoldTree const& sp ) const;

private:
  // functions
  Real
  func( Real const theta ) const
  {
    return func_->func( theta );
  }

  // deriv
  Real
  dfunc( Real const theta ) const
  {
    return func_->dfunc( theta );
  }

protected:
  // data -- write accessed by NamedAmbiguousNMRDistanceConstraint

  Atoms atoms1_, atoms2_;
  FuncOP func_;
}; // class AmbiguousNMRDistanceConstraint

typedef utility::vector1< core::id::NamedAtomID > NamedAtoms;
void parse_NMR_name( std::string name, core::Size res, core::chemical::AA aa, NamedAtoms& );

} // constraints
} // scoring
} // core

#endif