AllowInsert.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:
//  CVS information:
//  $Revision: 1.1.2.1 $
//  $Date: 2005/11/07 21:05:35 $
//  $Author: rhiju $
// (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.

#ifndef INCLUDED_protocols_toolbox_AllowInsert_HH
#define INCLUDED_protocols_toolbox_AllowInsert_HH

#include <protocols/toolbox/AllowInsert.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/conformation/Conformation.fwd.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <core/id/AtomID.fwd.hh>
#include <core/id/NamedAtomID.fwd.hh>
#include <core/id/TorsionID.fwd.hh>
#include <core/types.hh>
#include <utility/pointer/ReferenceCount.hh>
#include <utility/vector1.hh>

//XRW2 suggestion: refactor to protocols/toolbox

// C++ Headers
#include <map>

#ifdef WIN32
  #include <core/id/AtomID.hh>
#endif


namespace protocols {
namespace toolbox {

//////////////////////////////////////////////////////////////////////////////////////////////
//
// Contains a map of each atom to a "domain":
//   0      = no domain, can move this atom if you want
//   1,2... = domain occupied by a predefined "chunk". Don't shift relative atom
//              positions within each domain.
//   999    = (FIXED) part of a user-defined fixed domain.

extern core::Size const FIXED_DOMAIN;

class AllowInsert : public utility::pointer::ReferenceCount {
public:

  //constructor
  AllowInsert( core::pose::Pose const & pose );
  virtual ~AllowInsert();

  AllowInsert &
  operator=( AllowInsert const & src );

  AllowInsert( AllowInsert const & src );

  virtual AllowInsertOP clone() const;

public:

  bool
  get( Size const & i ) const;

  bool
  get( core::id::AtomID const & atom_id  ) const;

  bool
  get( core::id::TorsionID const & torsion_id, core::conformation::Conformation const & conformation ) const;

  Size
  get_domain( Size const & i ) const;

  bool
  has_domain( core::id::AtomID const & atom_id  ) const;

  Size
  get_domain( core::id::AtomID const & atom_id  ) const;

  void
  set_domain( Size const & i, Size const & setting  );

  void
  set_domain( core::id::AtomID const & atom_id, Size const & setting  );

  void
  set_domain( Size const & setting  );

  void
  and_allow_insert(AllowInsertOP allow_insert_in );

  core::Size nres(){ return nres_;}

  void
  set_phosphate_domain( core::Size const & i,
                        core::pose::Pose const & pose,
                        Size const & setting );
  void
  set_phosphate( core::Size const & i,
                 core::pose::Pose const & pose,
                 bool const & setting );

  void
  set( Size const & i, bool const & setting  );

  void
  set( core::id::AtomID const & atom_id, bool const & setting  );

  void
  set( bool const & setting  );

  void
  show();

  std::map< core::id::AtomID, Size > const &
  calculated_atom_id_domain_map();

  std::map< core::id::AtomID, Size > const &
  calculate_atom_id_domain_map( core::pose::Pose const & pose );

  void
  renumber_after_variant_changes( core::pose::Pose const & pose );

  void
  calculate_atom_id_map(
                        core::pose::Pose const & pose,
                        std::map< core::Size, core::Size > const & res_map,
                        core::kinematics::FoldTree const & scratch_fold_tree,
                        std::map< core::id::AtomID, core::id::AtomID > & atom_id_map );

  void
  set_force_ideal_chainbreak( bool const & setting ){ force_ideal_chainbreak_ = setting; }

  void
  append_residue( core::pose::Pose const & pose,
                  Size const & i,
                  bool const & setting );

private:
  void
  initialize( core::pose::Pose const & pose );

private:

  std::map< core::id::AtomID, Size > allow_insert_;
  std::map< core::id::NamedAtomID, core::id::AtomID > named_atom_id_map_;
  utility::vector1< utility::vector1< core::id::AtomID > > atom_ids_in_res_;

  std::map< core::id::AtomID, Size > calculated_atom_id_domain_map_;

  std::map< core::id::AtomID, core::id::AtomID > map_to_original_;

  core::Size nres_;

  bool force_ideal_chainbreak_;
};


} //rna
} //protocols

#endif