RNA_ProtocolUtil.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 RNA_ProtocolUtil.hh
/// @brief
/// @detailed
///
/// @author Rhiju Das


#ifndef INCLUDED_protocols_rna_RNA_ProtocolUtil_HH
#define INCLUDED_protocols_rna_RNA_ProtocolUtil_HH

#include <core/types.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <utility/vector1.fwd.hh>
#include <utility/io/ozstream.fwd.hh>

// Utility headers

// ObjexxFCL headers

//// C++ headers
#include <string>
#include <utility/vector1.hh>
#include <ObjexxFCL/FArray1D.fwd.hh>



namespace protocols {
namespace rna {

typedef  numeric::xyzVector< core::Real >  Vector;

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

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

void
get_base_pairing_info( core::pose::Pose const & pose,
                       core::Size const & seqpos,
                       char & secstruct,
                       ObjexxFCL::FArray1D <bool> & edge_is_base_pairing );

void
get_base_pairing_list( core::pose::Pose & pose,
                       utility::vector1< std::pair< core::Size, core::Size> > & base_pairing_list );

void
create_rna_vall_torsions( core::pose::Pose & pose,
                          utility::io::ozstream & torsions_out,
                          utility::vector1 <core::Size> const & exclude_res_list );

void
create_rna_vall_torsions( core::pose::Pose & pose,
                          std::string const outfile,
                          utility::vector1 <core::Size> const & exclude_res_list );

core::Real
get_o1p_o2p_sign( core::pose::Pose const & pose );

core::Real
get_o1p_o2p_sign( core::pose::Pose const & pose , core::Size res_num);

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

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

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

void
export_packer_results(
  utility::vector1< std::pair< core::Real, std::string > > & results,
  utility::vector1< core::pose::PoseOP > pose_list,
  core::scoring::ScoreFunctionOP & scorefxn,
  std::string const & outfile,
  bool const dumo = false );

void
check_base_pair( core::pose::Pose & pose, ObjexxFCL::FArray1D_int & struct_type );

void
setup_base_pair_constraints(
                            core::pose::Pose & pose,
                            utility::vector1< std::pair< core::Size, core::Size > > const &  pairings,
                            core::Real const suppress_factor = 1.0 );

void
setup_coarse_chainbreak_constraints( core::pose::Pose & pose, core::Size const & n );

std::string const
convert_based_on_match_type( std::string const RNA_string, core::Size const type );

bool
compare_RNA_char( char const char1, char const char2 );

bool
compare_RNA_secstruct( char const char1, char const char2 );

Vector
get_sugar_centroid( core::conformation::Residue const & rsd );

void
make_extended_coarse_pose( core::pose::Pose & coarse_pose, std::string const & full_sequence );

void
make_coarse_pose( core::pose::Pose const & pose, core::pose::Pose & coarse_pose );

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

void
remove_cutpoint_closed( core::pose::Pose & pose, core::Size const i );

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

void
virtualize_5prime_phosphates( core::pose::Pose & pose );

bool
possible_root( core::kinematics::FoldTree const & f, core::Size const & n );

inline bool is_num_in_list ( core::Size const i,
                             utility::vector1 <core::Size> const & list )
{
  return std::find(list.begin(), list.end(), i)!=list.end();
}

utility::vector1< core::Size >
get_rigid_body_jumps( core::pose::Pose const & pose );

bool
let_rigid_body_jumps_move( core::kinematics::MoveMap & movemap,
                           core::pose::Pose const & pose,
                           bool const move_first_rigid_body  = false );

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

} //rna
} // protocols

#endif