util.cc File Reference

#include <protocols/stepwise/legacy/modeler/rna/util.hh>
#include <protocols/stepwise/modeler/working_parameters/StepWiseWorkingParameters.hh>
#include <protocols/stepwise/modeler/rna/util.hh>
#include <protocols/stepwise/modeler/output_util.hh>
#include <protocols/stepwise/modeler/util.hh>
#include <core/chemical/rna/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/conformation/Residue.hh>
#include <core/pose/Pose.hh>
#include <core/pose/rna/util.hh>
#include <core/chemical/rna/RNA_FittedTorsionInfo.hh>
#include <core/sequence/util.hh>
#include <ObjexxFCL/format.hh>
#include <basic/Tracer.hh>

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

Functions
static basic::Tracer	TR ("protocols.stepwise.legacy.modeler.rna.util")
bool	protocols::stepwise::legacy::modeler::rna::check_can_prepend (utility::vector1< core::Size > const &seq_num_list)
bool	protocols::stepwise::legacy::modeler::rna::check_can_append (utility::vector1< core::Size > const &seq_num_list)
bool	protocols::stepwise::legacy::modeler::rna::pair_sort_criterion (std::pair< core::Size, core::Size > pair_one, std::pair< core::Size, core::Size > pair_two)
void	protocols::stepwise::legacy::modeler::rna::sort_pair_list (utility::vector1< std::pair< core::Size, core::Size > > pair_list)
void	protocols::stepwise::legacy::modeler::rna::output_pair_size (std::pair< core::Size, core::Size > const &pair_size, std::ostream &outstream)
void	protocols::stepwise::legacy::modeler::rna::output_pair_size (utility::vector1< std::pair< core::Size, core::Size > > const &pair_size_vector, std::string const &output_string, std::ostream &outstream, core::Size const spacing)
void	protocols::stepwise::legacy::modeler::rna::output_is_prepend_map (std::string const &tag, std::map< core::Size, bool > const &my_map, core::Size const max_seq_num, std::ostream &outstream, core::Size const tag_spacing)
void	protocols::stepwise::legacy::modeler::rna::output_bool_list (std::string const &tag, utility::vector1< core::Size > const &size_list, std::ostream &outstream, core::Size const spacing)
void	protocols::stepwise::legacy::modeler::rna::output_bool_list (std::string const &tag, utility::vector1< bool > const &bool_list, std::ostream &outstream, core::Size const spacing)
void	protocols::stepwise::legacy::modeler::rna::output_size_list (std::string const &tag, utility::vector1< core::Size > const &size_list, std::ostream &outstream, core::Size const spacing)
void	protocols::stepwise::legacy::modeler::rna::output_fold_tree_info (kinematics::FoldTree const &fold_tree, std::string const &pose_name, std::ostream &outstream)
void	protocols::stepwise::legacy::modeler::rna::output_fold_tree_info (pose::Pose const &pose, std::string pose_name, std::ostream &outstream)
core::Real	protocols::stepwise::legacy::modeler::rna::full_length_rmsd_over_residue_list (pose::Pose const &pose1, pose::Pose const &pose2, utility::vector1< core::Size > const &residue_list, std::string const &full_sequence, bool const verbose, bool const ignore_virtual_atom)
void	protocols::stepwise::legacy::modeler::rna::print_backbone_torsions (pose::Pose const &pose, core::Size const five_prime_chainbreak)
core::Size	protocols::stepwise::legacy::modeler::rna::setup_chain_break_jump_point (core::pose::Pose &pose, core::Size const moving_res, core::Size const reference_res)
void	protocols::stepwise::legacy::modeler::rna::remove_chain_break_jump_point (core::pose::Pose &pose, core::Size const moving_res, core::Size const reference_res)
core::Size	protocols::stepwise::legacy::modeler::rna::setup_bulge_jump_point (pose::Pose &pose, core::Size const &moving_base, core::Size const &reference_base, bool const verbose)
void	protocols::stepwise::legacy::modeler::rna::apply_rotamer (pose::Pose &pose, utility::vector1< Torsion_Info > const &rotamer_list)
bool	protocols::stepwise::legacy::modeler::rna::is_same_sugar_pucker (core::pose::Pose const &current_pose, core::pose::Pose const &cluster_center_pose, core::Size const seq_num)
void	protocols::stepwise::legacy::modeler::rna::setup_simple_fold_tree (core::pose::Pose &pose)
void	protocols::stepwise::legacy::modeler::rna::import_pose_from_silent_file (core::pose::Pose &import_pose, std::string const &silent_file, std::string const &input_tag)
std::string	protocols::stepwise::legacy::modeler::rna::get_tag_from_pdb_filename (std::string const &pdb_filename)
void	protocols::stepwise::legacy::modeler::rna::print_WorkingParameters_info (working_parameters::StepWiseWorkingParametersCOP const &const_WP, std::string const &WP_name, std::ostream &outstream, bool const is_simple_full_length_WP)
void	protocols::stepwise::legacy::modeler::rna::print_WorkingParameters_info (working_parameters::StepWiseWorkingParametersOP const &WP, std::string const &WP_name, std::ostream &outstream, bool const is_simple_full_length_WP)
void	protocols::stepwise::legacy::modeler::rna::set_nucleotide_to_A_form (pose::Pose &pose, core::Size const seq_num)
std::string	protocols::stepwise::legacy::modeler::rna::path_basename (std::string const &full_path)

Detailed Description

Author

Rhiju Das, rhiju.nosp@m.@sta.nosp@m.nford.nosp@m..edu

Function Documentation

static basic::Tracer TR ( "protocols.stepwise.legacy.modeler.rna.util"  )

static