StepWiseRNA_ResidueInfo.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 StepWiseRNA_ResidueInfo.hh
/// @brief
/// @detailed
///
/// @author Parin Sripakdeevong


#ifndef INCLUDED_protocols_swa_rna_StepWiseRNA_ResidueInfo_HH
#define INCLUDED_protocols_swa_rna_StepWiseRNA_ResidueInfo_HH


#include <core/types.hh>
#include <core/pose/Pose.fwd.hh>
#include <utility/vector1.hh>
#include <string>
#include <map>


namespace protocols {
namespace swa {
namespace rna {

  struct Residue_info{
    std::string name;
    core::Size seq_num; //Full_pose_sequence_num
  };

  void
  Print_torsion_info(core::pose::Pose const & pose, core::Size const seq_num, core::Size const rna_torsion_number, std::string const type);

  utility::vector1 <Residue_info>
  Convert_rebuild_residue_string_to_list(std::string const & rebuild_residue_string);

  void
  Output_residue_struct(Residue_info const & residue);

  std::string
  Get_one_letter_name(std::string const & three_letter_name);

  std::string
  Get_three_letter_name(std::string const & one_letter_name);

  core::Size
  get_max_seq_num_from_res_map(std::map< core::Size, core::Size > const & my_map);


  void
  output_res_map(std::map< core::Size, core::Size > const & my_map, core::Size const max_seq_num);

  // Undefined, commenting out to fix PyRosetta build  void output_is_prepend_map(std::map< core::Size, bool > const & my_map, core::Size const max_seq_num);

  void
  Output_residue_list(utility::vector1<Residue_info> residue_list);

  utility::vector1< Residue_info >
  Get_residue_list_from_fasta(std::string const full_fasta_sequence);

  Residue_info
  Get_residue_from_seq_num(core::Size const & seq_num, utility::vector1 <Residue_info> const & residue_list);

  bool
  Contain_residue_at_seq_num(core::Size seq_num, utility::vector1 <Residue_info> const & residue_list);

  utility::vector1 < utility::vector1 <Residue_info> >
  Create_strand_list(utility::vector1 <Residue_info> const & residue_list);

  utility::vector1 <Residue_info>
  Set_Difference(utility::vector1 <Residue_info> const & residue_list_1, utility::vector1 <Residue_info> const & residue_list_2);

  utility::vector1 <Residue_info>
  Set_Union(utility::vector1 <Residue_info> const & residue_list_1, utility::vector1 <Residue_info> const & residue_list_2);

  bool
  residue_list_sort_citeria(Residue_info residue_info_1, Residue_info residue_info_2);

  void
  sort_residue_list(utility::vector1<Residue_info>& residue_list);


}
}
}

#endif