LinearChainbreakEnergy.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   core/scoring/methods/EtableEnergy.hh
/// @brief  Etable energy method class declaration
/// @author Phil Bradley
/// @author Andrew Leaver-Fay
/// @author Christopher Miles (cmiles@uw.edu)

#ifndef INCLUDED_core_scoring_methods_LinearChainbreakEnergy_hh
#define INCLUDED_core_scoring_methods_LinearChainbreakEnergy_hh

// Unit headers
#include <core/scoring/methods/LinearChainbreakEnergy.fwd.hh>

// Package headers
#include <core/types.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/kinematics/ShortestPathInFoldTree.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/EnergyMap.fwd.hh>
#include <core/scoring/methods/WholeStructureEnergy.hh>

// Project headers

// Third-party headers
#include <boost/scoped_ptr.hpp>

// C++ headers
// AUTO-REMOVED #include <cstdlib>

#include <utility/vector1.hh>


using boost::scoped_ptr;
using core::Size;
using core::kinematics::ShortestPathInFoldTree;

namespace core {
namespace scoring {
namespace methods {

/// @brief LinearChainbreakEnergy class iterates across all residues in finalize()
/// and determines the penalty between residues i and i+1 by how much their
/// psueduo atoms do not align.
class LinearChainbreakEnergy : public WholeStructureEnergy {
public:
  typedef WholeStructureEnergy parent;

  // @brief Creates a new LinearChainbreakEnergy with the default allowable sequence
  // separation (+inf)
  LinearChainbreakEnergy();

  // @brief Create a new LinearChainbreakEnergy with the specified allowable sequence
  // separation
  explicit LinearChainbreakEnergy(Size allowable_sequence_sep);

  /// @brief The auto-generated copy constructor does not properly handle smart
  /// pointer types, so we must explicitly define our own.
  LinearChainbreakEnergy(const LinearChainbreakEnergy&);

  /// @brief The auto-generated operator=() method does not properly handle pointer types.
  LinearChainbreakEnergy& operator=(const LinearChainbreakEnergy&);

  // @brief Releases resources associated with an instance.
  ~LinearChainbreakEnergy();

  /// clone
  virtual EnergyMethodOP clone() const {
    return new LinearChainbreakEnergy(*this);
  }

  /// called at the end of energy evaluation
  virtual void finalize_total_energy(
    pose::Pose & pose,
    ScoreFunction const &,
    EnergyMap & totals) const;

  /// called during gradient-based minimization inside dfunc
  /**
  F1 and F2 are not zeroed -- contributions from this atom are
  just summed in
  **/
  virtual void eval_atom_derivative(id::AtomID const & id,
    pose::Pose const & pose,
    kinematics::DomainMap const & domain_map,
    ScoreFunction const & sfxn,
    EnergyMap const & weights,
    Vector & F1,
    Vector & F2) const;

  virtual void indicate_required_context_graphs( utility::vector1< bool > & ) const;

private:
  core::Real do_score_dev(const core::conformation::Residue& lower_rsd,
                          const core::conformation::Residue& upper_rsd,
                          const core::Size nbb) const;

  core::Real do_score_ovp(const core::conformation::Residue& lower_rsd,
                          const core::conformation::Residue& upper_rsd,
                          const core::Size nbb,
                          const core::Size cutpoint,
                          const core::pose::Pose& pose) const;

  // Initialization routine common to both constructor
  void initialize(Size allowable_sequence_sep);

  // Maximum allowable sequence separation permitted for scoring
  Size allowable_sequence_sep_;

  // Every call to finalize_total_energy() requires us to compute shortest
  // paths between the residues defining a cutpoint. The
  // ShortestPathInFoldTree object computes pair-wise shortest paths
  // between all residues in its constructor. However, it is unaware of
  // changes to the FoldTree used to initialize it. As a result, we can
  // only reuse a ShortestPathInFoldTree object if we are certain that the
  // FoldTree has not changed.
  mutable scoped_ptr<ShortestPathInFoldTree> shortest_paths_;

  // FoldTree::hash_value() provides a time- and space-efficient mechanism
  // to compare a pair of FoldTree's. Each time we are forced to recompute
  // the ShortestPathInFoldTree (either because it has yet to be
  // initialized or because the FoldTree has changed), we take note of the
  // new FoldTree's hash value.
  mutable size_t previous_hash_value_;

  virtual
  core::Size version() const;
};

} // methods
} // scoring
} // core
#endif