util.cc File Reference

protocols that are specific to RNA_FragmentMover More...

#include <protocols/farna/util.hh>
#include <protocols/farna/RNA_SecStructInfo.hh>
#include <protocols/idealize/IdealizeMover.hh>
#include <protocols/forge/methods/fold_tree_functions.hh>
#include <protocols/toolbox/AllowInsert.hh>
#include <core/conformation/Residue.hh>
#include <core/pose/rna/util.hh>
#include <core/chemical/rna/util.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/scoring/rna/RNA_ScoringInfo.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/func/FadeFunc.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <core/import_pose/import_pose.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/tree/Atom.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/util.hh>
#include <core/io/silent/RNA_SilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/id/AtomID.hh>
#include <core/id/NamedAtomID.hh>
#include <core/id/TorsionID.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/VariantType.hh>
#include <core/types.hh>
#include <basic/Tracer.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/string.functions.hh>
#include <utility/io/ozstream.hh>
#include <vector>
#include <string>
#include <sstream>
#include <fstream>
#include <protocols/farna/RNA_MatchType.hh>
#include <utility/vector1.hh>
#include <numeric/xyz.functions.hh>
#include <ObjexxFCL/format.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/rna.OptionKeys.gen.hh>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::farna

Functions
static thread_local basic::Tracer	TR ("protocols.rna.RNA_ProtocolUtil")
void	protocols::farna::get_base_pairing_info (pose::Pose const &pose, Size const &seqpos, char &secstruct, FArray1D< bool > &edge_is_base_pairing)
void	protocols::farna::get_base_pairing_list (pose::Pose &pose, utility::vector1< std::pair< Size, Size > > &base_pairing_list)
void	protocols::farna::figure_out_secstruct (pose::Pose &pose)
void	protocols::farna::create_rna_vall_torsions (pose::Pose &pose, utility::io::ozstream &torsions_out, utility::vector1< Size > const &exclude_res_list)
void	protocols::farna::create_rna_vall_torsions (pose::Pose &pose, std::string const outfile, utility::vector1< Size > const &exclude_res_list)
Real	protocols::farna::get_op2_op1_sign (pose::Pose const &pose)
Real	protocols::farna::get_op2_op1_sign (pose::Pose const &pose, Size res_num)
void	protocols::farna::assert_phosphate_nomenclature_matches_mini (pose::Pose const &pose)
void	protocols::farna::ensure_phosphate_nomenclature_matches_mini (pose::Pose &pose)
void	protocols::farna::make_phosphate_nomenclature_matches_mini (pose::Pose &pose)
void	protocols::farna::export_packer_results (utility::vector1< std::pair< Real, std::string > > &results, utility::vector1< pose::PoseOP > pose_list, scoring::ScoreFunctionOP &scorefxn, std::string const &outfile, bool const dump)
void	protocols::farna::check_base_pair (pose::Pose &pose, FArray1D_int &struct_type)
void	protocols::farna::setup_base_pair_constraints (pose::Pose &pose, utility::vector1< std::pair< Size, Size > > const &pairings, Real const suppress_factor)
void	protocols::farna::setup_coarse_chainbreak_constraints (pose::Pose &pose, Size const &n)
std::string const	protocols::farna::convert_based_on_match_type (std::string const RNA_string, Size const type)
bool	protocols::farna::compare_RNA_char (char const char1, char const char2)
bool	protocols::farna::compare_RNA_secstruct (char const char1, char const char2)
Vector	protocols::farna::get_sugar_centroid (core::conformation::Residue const &rsd)
void	protocols::farna::make_extended_coarse_pose (pose::Pose &coarse_pose, std::string const &full_sequence)
void	protocols::farna::make_coarse_pose (pose::Pose const &pose, pose::Pose &coarse_pose)
void	protocols::farna::remove_cutpoint_closed (pose::Pose &pose, Size const i)
void	protocols::farna::remove_cutpoints_closed (pose::Pose &pose)
void	protocols::farna::print_internal_coords (core::pose::Pose const &pose)
bool	protocols::farna::possible_root (core::kinematics::FoldTree const &f, core::Size const &n)
utility::vector1< Size >	protocols::farna::get_rigid_body_jumps (core::pose::Pose const &pose)
bool	protocols::farna::let_rigid_body_jumps_move (core::kinematics::MoveMap &movemap, pose::Pose const &pose, bool const move_first_rigid_body)
void	protocols::farna::translate_virtual_anchor_to_first_rigid_body (pose::Pose &pose)
bool	protocols::farna::involved_in_phosphate_torsion (std::string atomname)
void	protocols::farna::set_output_res_num (pose::Pose &extended_pose, utility::vector1< Size > const &output_res_num)
void	protocols::farna::figure_out_base_pair_partner (pose::Pose &pose, std::map< Size, Size > &partner, bool const strict)
void	protocols::farna::process_input_file (std::string const &input_file, utility::vector1< pose::PoseOP > &pose_list, bool is_pdb, bool coarse_rna)
void	protocols::farna::print_hbonds (pose::Pose &pose)
bool	protocols::farna::moveable_jump (id::AtomID const &jump_atom_id1, id::AtomID const &jump_atom_id2, protocols::toolbox::AllowInsert const &allow_insert)
bool	protocols::farna::moveable_jump (Size const jump_pos1, Size const jump_pos2, protocols::toolbox::AllowInsert const &allow_insert)
void	protocols::farna::get_default_allowed_bulge_res (utility::vector1< core::Size > &allow_bulge_res_list, core::pose::Pose const &pose, bool const verbose)
core::Size	protocols::farna::virtualize_bulges (core::pose::Pose &input_pose, utility::vector1< core::Size > const &in_allow_bulge_res_list, core::scoring::ScoreFunctionCOP const &scorefxn, std::string const &tag, bool const allow_pre_virtualize, bool const allow_consecutive_bulges, bool const verbose)

Detailed Description

protocols that are specific to RNA_FragmentMover

Detailed:

Author

Rhiju Das

Function Documentation

static thread_local basic::Tracer TR ( "protocols.rna.RNA_ProtocolUtil"  )

static

Referenced by protocols::farna::get_default_allowed_bulge_res(), protocols::farna::get_rigid_body_jumps(), protocols::farna::setup_base_pair_constraints(), and protocols::farna::virtualize_bulges().