ThreadingMover.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 protocols/comparative_modeling/ThreadingMover.hh
/// @brief
/// @author James Thompson

// libRosetta headers

#ifndef INCLUDED_protocols_comparative_modeling_ThreadingMover_HH
#define INCLUDED_protocols_comparative_modeling_ThreadingMover_HH

#include <protocols/moves/Mover.hh>

#include <core/types.hh>
#include <core/pose/Pose.hh>

#include <core/id/SequenceMapping.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/fragment/FragSet.hh>
#include <core/fragment/FragSet.fwd.hh>

// C++ headers
#include <set>
#include <string>

#include <utility/vector1.hh>

namespace protocols {
namespace comparative_modeling {

class ThreadingMover : public protocols::moves::Mover {

public:

  /// @brief align describes the association between the query and template
  /// sequences, template_pose is the conformation from which to build a
  /// threading model.
  ThreadingMover(
    core::sequence::SequenceAlignment const & align,
    core::pose::Pose const & template_pose
  );

  virtual ~ThreadingMover() {}

  /// @brief Returns the index of the query sequence in SequenceAlignment
  /// object.
  core::Size query_index() const;

  /// @brief Returns the index of the template sequence in SequenceAlignment
  /// object.
  core::Size template_index() const;

  /// @brief Returns the SequenceAlignment object used in threading.
  core::sequence::SequenceAlignment alignment();

  /// @brief Sets the index of the query sequence in SequenceAlignment object.
  void query_index( core::Size new_index );

  /// @brief Sets the index of the template sequence in SequenceAlignment
  /// object.
  void template_index( core::Size new_index );

  /// @brief Sets the SequenceAlignment associated with this object.
  void alignment( core::sequence::SequenceAlignment new_align );

  void template_pose( core::pose::Pose template_pose );

  //boolean setters
  void build_loops( bool setting );

  void randomize_loop_coords( bool setting );

  void repack_query( bool setting );

  //boolean getters
  bool build_loops() const;

  bool repack_query() const;

  bool randomize_loop_coords();

  void min_loop_size( core::Size const new_size );

  Size min_loop_size() const;

  utility::vector1< core::fragment::FragSetOP > frag_libs() const;

  void frag_libs(
    utility::vector1< core::fragment::FragSetOP > new_libs
  );

  /// @brief Returns the SequenceMapping between query and template.
  core::id::SequenceMapping get_qt_mapping(
    core::pose::Pose const & query_pose
  ) const;

  /// @brief Threads the given Pose onto the template_pose with the
  /// SequenceAlignment provided.
  virtual void apply( core::pose::Pose & query_pose );

  virtual std::string get_name() const;

private: // methods

  ///
  bool atoms_are_equiv( std::string const & a1, std::string const & a2 );

  /// @brief add pair of equivalent atoms to atom_equiv_ table.
  void add_equiv_atoms( std::string const & a1, std::string const & a2 );

  /// @brief initialize table of equivalent atoms between all residues.
  void init_atom_equiv();

private: // data members

  core::Size query_index_, template_index_;
  core::pose::Pose template_pose_;
  core::sequence::SequenceAlignment align_;
  bool build_query_loops_;
  bool repack_query_;
  bool randomize_loop_coords_;
  core::Size min_loop_size_;

  //std::map< std::string, utility::vector1< std::string > > atom_equiv_;
  std::map< std::string, std::set< std::string > > atom_equiv_;
  utility::vector1< core::fragment::FragSetOP > frag_libs_;
}; // ThreadingMover

} // comparative_modeling
} // protocols

#endif