RNA_StructureParameters.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.
/// @author Rhiju Das

#ifndef INCLUDED_protocols_rna_RNA_StructureParameters_HH
#define INCLUDED_protocols_rna_RNA_StructureParameters_HH

#include <core/pose/Pose.fwd.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <protocols/rna/RNA_JumpLibrary.fwd.hh>
#include <protocols/toolbox/AllowInsert.fwd.hh>
#include <core/kinematics/Jump.hh>
#include <core/types.hh>
#include <utility/pointer/ReferenceCount.hh>
// ObjexxFCL Headers
// AUTO-REMOVED #include <ObjexxFCL/FArray1D.hh>

// C++ Headers
#include <string>
#include <map>
#include <iostream>
#include <list>

#include <utility/vector1.hh>



namespace protocols {
namespace rna {

////////////////////////////////////////////////////////////////////////////////////////////
class RNA_Pairing {
public:
  core::Size pos1;
  core::Size pos2;
  char edge1; //W,H,S
  char edge2; //W,H,S
  char orientation; //A,P
};

typedef utility::vector1< RNA_Pairing > RNA_PairingList;

//////////////////////////////////////////////////////////////////////////////////////////////
class RNA_StructureParameters : public utility::pointer::ReferenceCount {
public:

  //constructor
  RNA_StructureParameters();
  virtual ~RNA_StructureParameters();
  void
  initialize(
    core::pose::Pose & pose,
    std::string const rna_params_file,
    std::string const jump_library_file,
    bool const ignore_secstruct );

  void
  setup_fold_tree_and_jumps_and_variants( core::pose::Pose & pose );

  bool
  random_jump_change( core::pose::Pose & pose ) const;

toolbox::AllowInsertOP
  allow_insert();

  void
  set_allow_insert(toolbox::AllowInsertOP allow_insert );

  void
  set_root_at_first_rigid_body( bool const setting ){ root_at_first_rigid_body_ = setting; }

  void
  set_suppress_bp_constraint( bool const setting ){ suppress_bp_constraint_ = setting; }

  bool
  check_base_pairs( core::pose::Pose & pose ) const;

  std::map< Size, Size >
  connections() const;

  std::list< Size >
  get_stem_residues(  core::pose::Pose const & pose ) const;

  void
  setup_base_pair_constraints( core::pose::Pose & pose );

  private:

  void
  initialize_secstruct( core::pose::Pose & pose );

  void
  override_secstruct( core::pose::Pose & pose );

  void
  append_virtual_anchor( core::pose::Pose & pose );

  void
  initialize_allow_insert( core::pose::Pose & pose  );

  void
  get_pairings_from_line(
                         std::istringstream & line_stream,
                         bool const in_stem );

  void
  read_chain_connection( std::istringstream & line_stream );

  void
  read_parameters_from_file( std::string const & pairing_file );


  void
  setup_jumps( core::pose::Pose & pose );

  void
  setup_chainbreak_variants( core::pose::Pose & pose );

  void
  setup_virtual_phosphate_variants( core::pose::Pose & pose );

  void
  setup_virtual_phosphate_variants_OLD( core::pose::Pose & pose ); //remove this by end of 2012

  void
  set_jump_library( RNA_JumpLibraryOP rna_jump_library );

  std::string const
  read_secstruct_from_file( std::string const & rna_secstruct_file );

  core::Size
  check_in_chain_connections( core::Size const & pos1, core::Size const & pos2 ) const;

  bool
  check_forward_backward(
    core::pose::Pose & pose,
    core::Size const jump_pos ) const;

  void
  add_new_RNA_jump(
    core::pose::Pose & pose,
    core::Size const & which_jump,
    bool & success ) const;

  void
  sample_alternative_chain_connection( core::pose::Pose & pose, core::Size const & which_jump ) const;

  void
  insert_base_pair_jumps( core::pose::Pose & pose, bool & success ) const;

  void
  fill_in_default_jump_atoms( core::kinematics::FoldTree & f, core::pose::Pose const & pose ) const;

private:
  RNA_JumpLibraryOP rna_jump_library_;
  RNA_PairingList rna_pairing_list_;

  utility::vector1 < utility::vector1 <core::Size > > obligate_pairing_sets_;
  utility::vector1 < utility::vector1 <core::Size > > possible_pairing_sets_;

  utility::vector1 < std::pair< utility::vector1 <core::Size >, utility::vector1 <core::Size > > > chain_connections_;

  //    int force_stems_;// deprecated.

  utility::vector1 <core::Size > cutpoints_open_;
  utility::vector1 <core::Size > cutpoints_closed_;
  utility::vector1 <core::Size > virtual_anchor_attachment_points_;

  bool secstruct_defined_;
  std::string rna_secstruct_;
  bool assume_non_stem_is_loop;

  bool add_virtual_anchor_;
  bool root_at_first_rigid_body_;
  bool suppress_bp_constraint_;

  utility::vector1 < core::Size  > allow_insert_res_;
  toolbox::AllowInsertOP allow_insert_;

};

  typedef utility::pointer::owning_ptr< RNA_StructureParameters > RNA_StructureParametersOP;

} //rna
} //protocols

#endif