util.cc File Reference

util functions for use in rna/denovo, i.e. fragment assembly of RNA More...

#include <protocols/rna/denovo/util.hh>
#include <core/pose/rna/secstruct_legacy/RNA_SecStructLegacyInfo.hh>
#include <protocols/idealize/IdealizeMover.hh>
#include <core/pose/toolbox/AtomLevelDomainMap.hh>
#include <core/conformation/Residue.hh>
#include <core/pose/rna/util.hh>
#include <core/chemical/rna/util.hh>
#include <core/chemical/rna/RNA_Info.hh>
#include <core/scoring/rna/RNA_ScoringInfo.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/func/FadeFunc.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/import_pose/import_pose.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/FoldTree.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/annotated_sequence.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentFileOptions.hh>
#include <core/id/AtomID.hh>
#include <core/id/TorsionID.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 <fstream>
#include <core/fragment/rna/RNA_MatchType.hh>
#include <utility/vector1.hh>
#include <ObjexxFCL/format.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/corrections.OptionKeys.gen.hh>
#include <numeric/conversions.hh>

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

Functions
static basic::Tracer	TR ("protocols.rna.denovo.util")
void	protocols::rna::denovo::create_rna_vall_torsions (pose::Pose &pose, utility::io::ozstream &torsions_out, utility::vector1< core::Size > const &exclude_res_list)
void	protocols::rna::denovo::create_rna_vall_torsions (pose::Pose &pose, std::string const &outfile, utility::vector1< core::Size > const &exclude_res_list)
void	protocols::rna::denovo::ensure_phosphate_nomenclature_matches_mini (pose::Pose &pose)
void	protocols::rna::denovo::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::rna::denovo::check_base_pair (pose::Pose &pose, FArray1D_int &struct_type)
void	protocols::rna::denovo::setup_coarse_chainbreak_constraints (pose::Pose &pose, core::Size const &n)
void	protocols::rna::denovo::print_internal_coords (core::pose::Pose const &pose)
bool	protocols::rna::denovo::possible_root (core::kinematics::FoldTree const &f, core::Size const &n)
bool	protocols::rna::denovo::let_rigid_body_jumps_move (core::kinematics::MoveMap &movemap, pose::Pose const &pose, bool const &move_first_rigid_body, bool const &allow_single_rigid_body)
void	protocols::rna::denovo::translate_virtual_anchor_to_first_rigid_body (pose::Pose &pose)
bool	protocols::rna::denovo::involved_in_phosphate_torsion (std::string const &atomname)
void	protocols::rna::denovo::figure_out_base_pair_partner (pose::Pose &pose, std::map< core::Size, core::Size > &partner, bool const strict)
utility::vector1< core::pose::rna::BasePair >	protocols::rna::denovo::classify_base_pairs_lores (pose::Pose const &pose_input)
void	protocols::rna::denovo::print_hbonds (pose::Pose &pose)
void	protocols::rna::denovo::get_default_allowed_bulge_res (utility::vector1< core::Size > &allow_bulge_res_list, core::pose::Pose const &pose, bool const verbose)
core::Size	protocols::rna::denovo::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)
core::scoring::ScoreFunctionOP	protocols::rna::denovo::get_rna_hires_scorefxn (bool const &include_protein_terms)
utility::vector1< core::Size >	protocols::rna::denovo::get_moving_res (core::pose::Pose const &pose, core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map)
void	protocols::rna::denovo::delete_non_protein_from_pose (core::pose::Pose &pose)
utility::vector1< core::Size >	protocols::rna::denovo::get_residues_within_dist_of_RNA (core::pose::Pose const &pose, core::Real const &dist_cutoff)
core::kinematics::FoldTree	protocols::rna::denovo::get_rnp_docking_fold_tree (pose::Pose const &pose, bool const &with_density)

Detailed Description

util functions for use in rna/denovo, i.e. fragment assembly of RNA

Author

Rhiju Das

Function Documentation

TR()

static basic::Tracer TR ( "protocols.rna.denovo.util"  )

static