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util.hh File Reference
#include <core/types.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/pose/rna/BasePair.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/id/AtomID.fwd.hh>
#include <utility/vector1.fwd.hh>
#include <utility/io/ozstream.fwd.hh>
#include <core/pose/toolbox/AtomLevelDomainMap.fwd.hh>
#include <core/pose/rna/BasePairStep.fwd.hh>
#include <core/pose/rna/RNA_BaseDoubletClasses.hh>
#include <string>
#include <map>
#include <utility/vector1.hh>
#include <ObjexxFCL/FArray1D.fwd.hh>

Namespaces

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

Typedefs

typedef numeric::xyzVector
< core::Length
protocols::rna::denovo::Vector
 

Functions

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< 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 protocols::rna::denovo::check_base_pair (core::pose::Pose &pose, ObjexxFCL::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::is_num_in_list (core::Size const i, utility::vector1< core::Size > const &list)
 
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)
 
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::Sizeprotocols::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::Sizeprotocols::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)