util.hh File Reference

#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 <core/id/AtomID.fwd.hh>
#include <utility/vector1.fwd.hh>
#include <utility/io/ozstream.fwd.hh>
#include <protocols/toolbox/AllowInsert.fwd.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::farna

Typedefs
typedef numeric::xyzVector < core::Length >	protocols::farna::Vector

Functions
void	protocols::farna::figure_out_secstruct (pose::Pose &pose)
void	protocols::farna::get_base_pairing_info (core::pose::Pose const &pose, core::Size const &seqpos, char &secstruct, ObjexxFCL::FArray1D< bool > &edge_is_base_pairing)
void	protocols::farna::get_base_pairing_list (core::pose::Pose &pose, utility::vector1< std::pair< core::Size, core::Size > > &base_pairing_list)
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< 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::farna::check_base_pair (core::pose::Pose &pose, ObjexxFCL::FArray1D_int &struct_type)
void	protocols::farna::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	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::print_internal_coords (core::pose::Pose const &pose)
void	protocols::farna::remove_cutpoint_closed (pose::Pose &pose, Size const i)
void	protocols::farna::remove_cutpoints_closed (pose::Pose &pose)
bool	protocols::farna::possible_root (core::kinematics::FoldTree const &f, core::Size const &n)
bool	protocols::farna::is_num_in_list (core::Size const i, utility::vector1< core::Size > const &list)
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)
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

Detailed:

Author

Rhiju Das