#include <protocols/stepwise/sampling/rna/StepWiseRNA_ResidueInfo.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_Classes.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_JobParameters.fwd.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/types.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <core/chemical/AA.hh>
#include <core/io/silent/RNA_SilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <numeric/angle.functions.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <core/id/AtomID_Map.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/conformation/Residue.hh>
#include <protocols/toolbox/AllowInsert.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyzVector.hh>
#include <utility/vector1.hh>
#include <ObjexxFCL/FArray.fwd.hh>
#include <string>
#include <map>

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

	protocols::stepwise

	protocols::stepwise::sampling

	protocols::stepwise::sampling::rna

Typedefs
typedef numeric::xyzMatrix < core::Real >	Matrix

Functions
bool	protocols::stepwise::sampling::rna::is_OP2_atom (std::string const &atom_name)

bool	protocols::stepwise::sampling::rna::is_OP1_atom (std::string const &atom_name)

bool	protocols::stepwise::sampling::rna::is_P_atom (std::string const &atom_name)

bool	protocols::stepwise::sampling::rna::is_O2prime_atom (std::string const &atom_name)

bool	protocols::stepwise::sampling::rna::is_O3prime_atom (std::string const &atom_name)

bool	protocols::stepwise::sampling::rna::is_O4prime_atom (std::string const &atom_name)

bool	protocols::stepwise::sampling::rna::is_O5prime_atom (std::string const &atom_name)

bool	protocols::stepwise::sampling::rna::is_C2prime_atom (std::string const &atom_name)

bool	protocols::stepwise::sampling::rna::is_C3prime_atom (std::string const &atom_name)

bool	protocols::stepwise::sampling::rna::is_C4prime_atom (std::string const &atom_name)

bool	protocols::stepwise::sampling::rna::is_C5prime_atom (std::string const &atom_name)

bool	protocols::stepwise::sampling::rna::is_1H5prime_atom (std::string const &atom_name)

bool	protocols::stepwise::sampling::rna::is_2H5prime_atom (std::string const &atom_name)

bool	protocols::stepwise::sampling::rna::is_H3prime_atom (std::string const &atom_name)

bool	protocols::stepwise::sampling::rna::is_H4prime_atom (std::string const &atom_name)

bool	protocols::stepwise::sampling::rna::is_three_prime_phosphate_atom (std::string const &atom_name)

bool	protocols::stepwise::sampling::rna::is_five_prime_phosphate_atom (std::string const &atom_name)

bool	protocols::stepwise::sampling::rna::is_phosphate_atom (std::string const &atom_name)

void	protocols::stepwise::sampling::rna::minimize_with_constraints (core::pose::Pose &pose, core::kinematics::MoveMap const &mm, core::scoring::ScoreFunctionOP const &scorefxn, core::optimization::MinimizerOptions const &options)

bool	protocols::stepwise::sampling::rna::check_can_prepend (utility::vector1< core::Size > const &seq_num_list)

bool	protocols::stepwise::sampling::rna::check_can_append (utility::vector1< core::Size > const &seq_num_list)

void	protocols::stepwise::sampling::rna::apply_protonated_H1_adenosine_variant_type (core::pose::Pose &pose, core::Size const &seq_num, bool const apply_check)

void	protocols::stepwise::sampling::rna::apply_virtual_rna_residue_variant_type (core::pose::Pose &pose, core::Size const &seq_num, bool const apply_check)

void	protocols::stepwise::sampling::rna::apply_virtual_rna_residue_variant_type (core::pose::Pose &pose, core::Size const &seq_num, utility::vector1< core::Size > const &working_cutpoint_closed_list, bool const apply_check)

void	protocols::stepwise::sampling::rna::remove_virtual_rna_residue_variant_type (pose::Pose &pose, Size const &seq_num)

bool	protocols::stepwise::sampling::rna::has_virtual_rna_residue_variant_type (pose::Pose &pose, Size const &seq_num)

void	protocols::stepwise::sampling::rna::remove_all_variant_types (pose::Pose &pose)

void	protocols::stepwise::sampling::rna::setup_suite_atom_id_map (conformation::Residue const &rsd_1, conformation::Residue const &rsd_2, id::AtomID_Map< id::AtomID > &atom_ID_map, bool const base_only)

void	protocols::stepwise::sampling::rna::setup_suite_atom_id_map (conformation::Residue const &rsd_1, conformation::Residue const &rsd_2, Size const res_num_1, Size const res_num_2, id::AtomID_Map< id::AtomID > &atom_ID_map, bool const base_only)

void	protocols::stepwise::sampling::rna::setup_suite_atom_id_map (pose::Pose const &pose_1, pose::Pose const &pose_2, Size const base_res, id::AtomID_Map< id::AtomID > &atom_ID_map, bool const base_only)

void	protocols::stepwise::sampling::rna::setup_suite_atom_id_map (pose::Pose const &pose_1, pose::Pose const &pose_2, Size const base_res_1, Size const base_res_2, id::AtomID_Map< id::AtomID > &atom_ID_map, bool const base_only)

id::AtomID_Map< id::AtomID >	protocols::stepwise::sampling::rna::create_alignment_id_map (pose::Pose &mod_pose, pose::Pose const &ref_pose, utility::vector1< core::Size > const &rmsd_residue_list, bool const base_only)

void	protocols::stepwise::sampling::rna::align_poses (core::pose::Pose &moving_pose, std::string const moving_tag, core::pose::Pose const &static_pose, std::string const static_tag, utility::vector1< core::Size > const &working_best_alignment, bool const base_only)

utility::vector1< Size >	protocols::stepwise::sampling::rna::apply_full_to_sub_mapping (utility::vector1< Size > const &res_vector, utility::vector1< core::Size > const &is_working_res, std::map< core::Size, core::Size > const &full_to_sub)

utility::vector1< Size >	protocols::stepwise::sampling::rna::apply_full_to_sub_mapping (utility::vector1< Size > const &res_vector, StepWiseRNA_JobParametersCOP job_parameters)

void	protocols::stepwise::sampling::rna::ensure_valid_full_seq_num (Size const full_seq_num, StepWiseRNA_JobParametersCOP const &job_parameters)

bool	protocols::stepwise::sampling::rna::check_is_working_res (Size const full_seq_num, StepWiseRNA_JobParametersCOP const &job_parameters)

core::Size	protocols::stepwise::sampling::rna::check_validity_and_get_working_res (Size const full_seq_num, StepWiseRNA_JobParametersCOP const &job_parameters)

utility::vector1< Size >	protocols::stepwise::sampling::rna::apply_sub_to_full_mapping (utility::vector1< Size > const &working_res_vector, StepWiseRNA_JobParametersCOP job_parameters)

std::map< core::Size, core::Size >	protocols::stepwise::sampling::rna::create_full_to_input_res_map (utility::vector1< core::Size > const &input_res_vector)

core::Size	protocols::stepwise::sampling::rna::string_to_int (std::string const input_string)

core::Real	protocols::stepwise::sampling::rna::string_to_real (std::string const input_string)

utility::vector1< std::string >	protocols::stepwise::sampling::rna::tokenize (std::string const str, std::string delimiters)

bool	protocols::stepwise::sampling::rna::is_virtual_base (conformation::Residue const &rsd)

void	protocols::stepwise::sampling::rna::output_pair_size (std::pair< Size, Size > const &pair_size, std::ostream &outstream)

void	protocols::stepwise::sampling::rna::output_pair_size (utility::vector1< std::pair< Size, Size > > const &pair_size_vector, std::string const &output_string, std::ostream &outstream, core::Size const spacing)

bool	protocols::stepwise::sampling::rna::pair_sort_criterion (std::pair< Size, Size > pair_one, std::pair< Size, Size > pair_two)

void	protocols::stepwise::sampling::rna::sort_seq_num_list (utility::vector1< core::Size > &seq_num_list)

void	protocols::stepwise::sampling::rna::output_seq_num_list (std::string const tag, utility::vector1< core::Size > const &seq_num_list, std::ostream &outstream, core::Size const spacing)

bool	protocols::stepwise::sampling::rna::is_equivalent_vector (utility::vector1< core::Size > const &seq_num_list_1, utility::vector1< core::Size > const &seq_num_list_2)

void	protocols::stepwise::sampling::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::sampling::rna::output_bool_list (std::string const tag, utility::vector1< bool > const &bool_list, std::ostream &outstream, core::Size const spacing)

void	protocols::stepwise::sampling::rna::output_bool_list (std::string const tag, utility::vector1< Size > const &size_list, std::ostream &outstream, core::Size const spacing)

void	protocols::stepwise::sampling::rna::output_size_list (std::string const tag, utility::vector1< Size > const &size_list, std::ostream &outstream, core::Size const spacing)

void	protocols::stepwise::sampling::rna::sort_pair_list (utility::vector1< std::pair< Size, Size > > pair_list)

void	protocols::stepwise::sampling::rna::output_fold_tree_info (kinematics::FoldTree const &fold_tree, std::string const pose_name, std::ostream &outstream)

void	protocols::stepwise::sampling::rna::output_fold_tree_info (pose::Pose const &pose, std::string pose_name, std::ostream &outstream)

bool	protocols::stepwise::sampling::rna::file_exists (std::string const &file_name)

void	protocols::stepwise::sampling::rna::remove_file (std::string const &file_name)

void	protocols::stepwise::sampling::rna::output_rotamer (utility::vector1< Real > &rotamer)

void	protocols::stepwise::sampling::rna::add_virtual_O2Prime_hydrogen (core::pose::Pose &pose)

bool	protocols::stepwise::sampling::rna::remove_virtual_O2Prime_hydrogen (pose::Pose &pose)

Real	protocols::stepwise::sampling::rna::suite_rmsd (pose::Pose const &pose1, pose::Pose const &pose2, Size const &moving_res_num, bool const prepend_res, bool const ignore_virtual_atom)

core::Real	protocols::stepwise::sampling::rna::full_length_rmsd_over_residue_list (pose::Pose const &pose1, pose::Pose const &pose2, utility::vector1< Size > const &residue_list, std::string const &full_sequence, bool const verbose, bool const ignore_virtual_atom)

Real	protocols::stepwise::sampling::rna::rmsd_over_residue_list (pose::Pose const &pose1, pose::Pose const &pose2, utility::vector1< Size > const &residue_list, std::map< core::Size, core::Size > const &full_to_sub, std::map< core::Size, bool > const &is_prepend_map, bool const verbose, bool const ignore_virtual_atom)

Real	protocols::stepwise::sampling::rna::rmsd_over_residue_list (pose::Pose const &pose1, pose::Pose const &pose2, StepWiseRNA_JobParametersCOP job_parameters_, bool const ignore_virtual_atom)

void	protocols::stepwise::sampling::rna::print_heavy_atoms (Size const &suite_num_1, Size const &suite_num_2, pose::Pose const &pose1, pose::Pose const &pose2)

Size	protocols::stepwise::sampling::rna::get_num_side_chain_atom_from_res_name (chemical::AA const &res_aa, bool const verbose)

void	protocols::stepwise::sampling::rna::base_atoms_square_deviation (pose::Pose const &pose1, pose::Pose const &pose2, Size const &moving_res_1, Size const &moving_res_2, Size &atom_count, Real &sum_sd, bool verbose, bool const ignore_virtual_atom)

void	protocols::stepwise::sampling::rna::phosphate_square_deviation (pose::Pose const &pose1, pose::Pose const &pose2, Size const &moving_res_1, Size const &moving_res_2, Size &atom_count, Real &sum_sd, bool verbose, bool const ignore_virtual_atom)

core::Real	protocols::stepwise::sampling::rna::phosphate_base_phosphate_rmsd (pose::Pose const &pose1, pose::Pose const &pose2, Size const &moving_res_num, bool const ignore_virtual_atom)

void	protocols::stepwise::sampling::rna::phosphate_base_phosphate_square_deviation (pose::Pose const &pose1, pose::Pose const &pose2, Size const &moving_res_1, Size const &moving_res_2, Size &atom_count, Real &sum_sd, bool verbose, bool const ignore_virtual_atom)

Real	protocols::stepwise::sampling::rna::atom_square_deviation (conformation::Residue const &rsd_1, conformation::Residue const &rsd_2, Size const &atomno_1, Size const &atomno_2, bool verbose)

void	protocols::stepwise::sampling::rna::suite_square_deviation (pose::Pose const &pose1, pose::Pose const &pose2, bool const &prepend_res, Size const &moving_res_1, Size const &moving_res_2, Size &atom_count, Real &sum_sd, bool verbose, bool const ignore_virtual_atom)

void	protocols::stepwise::sampling::rna::output_title_text (std::string const title, std::ostream &outstream)

void	protocols::stepwise::sampling::rna::Freeze_sugar_torsions (core::kinematics::MoveMap &mm, Size const total_residue)

void	protocols::stepwise::sampling::rna::output_boolean (std::string const &tag, bool boolean, std::ostream &outstream)

void	protocols::stepwise::sampling::rna::output_boolean (bool boolean, std::ostream &outstream)

void	protocols::stepwise::sampling::rna::output_movemap (kinematics::MoveMap const &mm, core::pose::Pose const &pose, std::ostream &outstream)

utility::vector1< core::Size >	protocols::stepwise::sampling::rna::get_surrounding_O2prime_hydrogen (pose::Pose const &pose, utility::vector1< core::Size > const &moving_res, bool verbose)

void	protocols::stepwise::sampling::rna::o2prime_trials (pose::Pose &pose, core::scoring::ScoreFunctionOP const &packer_scorefxn)

void	protocols::stepwise::sampling::rna::o2prime_trials (pose::Pose &pose, core::scoring::ScoreFunctionOP const &packer_scorefxn, utility::vector1< core::Size > const &O2prime_pack_seq_num)

pack::task::PackerTaskOP	protocols::stepwise::sampling::rna::create_standard_o2prime_pack_task (pose::Pose const &pose, utility::vector1< core::Size > const &O2prime_pack_seq_num)

void	protocols::stepwise::sampling::rna::print_backbone_torsions (pose::Pose const &pose, Size const five_prime_chainbreak)

void	protocols::stepwise::sampling::rna::copy_torsions_FROM_TO (core::id::TorsionID const start_torsion_ID, core::id::TorsionID const end_torsion_ID, core::pose::Pose const &template_pose, core::pose::Pose &pose)

core::Size	protocols::stepwise::sampling::rna::setup_chain_break_jump_point (core::pose::Pose &pose, core::Size const moving_res, core::Size const reference_res)

void	protocols::stepwise::sampling::rna::remove_chain_break_jump_point (core::pose::Pose &pose, core::Size const moving_res, core::Size const reference_res)

void	protocols::stepwise::sampling::rna::setup_chain_break_variants (core::pose::Pose &pose, Size const cutpoint)

void	protocols::stepwise::sampling::rna::remove_chain_break_variants (core::pose::Pose &pose, Size const &cutpoint)

core::Size	protocols::stepwise::sampling::rna::setup_bulge_jump_point (pose::Pose &pose, Size const &moving_base, Size const &reference_base, bool const verbose)

utility::vector1< bool >	protocols::stepwise::sampling::rna::get_partition_definition_floating_base (pose::Pose const &pose, Size const &moving_res)

Size	protocols::stepwise::sampling::rna::get_anchor_res (Size const rebuild_res, pose::Pose const &pose)

void	protocols::stepwise::sampling::rna::apply_rotamer (pose::Pose &pose, utility::vector1< Torsion_Info > const &rotamer_list)

bool	protocols::stepwise::sampling::rna::check_for_messed_up_structure (core::pose::Pose const &pose, std::string const &tag)

core::Size	protocols::stepwise::sampling::rna::get_residue_base_state (core::pose::Pose const &pose, Size const seq_num)

core::Size	protocols::stepwise::sampling::rna::get_residue_pucker_state (core::pose::Pose const &pose, Size const seq_num, bool const verbose)

bool	protocols::stepwise::sampling::rna::is_same_sugar_pucker (core::pose::Pose const &current_pose, core::pose::Pose const &cluster_center_pose, Size const seq_num)

void	protocols::stepwise::sampling::rna::sleep (core::Size mseconds)

void	protocols::stepwise::sampling::rna::setup_simple_fold_tree (core::pose::Pose &pose)

void	protocols::stepwise::sampling::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::sampling::rna::path_basename (std::string const full_path)

bool	protocols::stepwise::sampling::rna::is_residues_in_contact (core::Size const &res_ONE, core::pose::Pose const &pose_ONE, core::Size const &res_TWO, core::pose::Pose const &pose_TWO, core::Real const atom_atom_overlap_dist_cutoff, core::Size const num_atom_contacts_cutoff, bool const verbose)

void	protocols::stepwise::sampling::rna::set_CCD_torsions_to_zero (core::pose::Pose &pose, Size const five_prime_res)

void	protocols::stepwise::sampling::rna::get_default_allowed_bulge_res (utility::vector1< core::Size > &allow_bulge_res_list, core::pose::Pose const &pose, bool const verbose)

core::Size	protocols::stepwise::sampling::rna::virtualize_bulges (core::pose::Pose &input_pose, utility::vector1< core::Size > const &in_allow_bulge_res_list, core::scoring::ScoreFunctionOP const &scorefxn, std::string const &tag, bool const allow_pre_virtualize, bool const allow_consecutive_bulges, bool const verbose)

std::string	protocols::stepwise::sampling::rna::get_tag_from_pdb_filename (std::string const pdb_filename)

void	protocols::stepwise::sampling::rna::move_jump_atom_to_base (core::kinematics::FoldTree &fold_tree, std::string const &working_sequence)

void	protocols::stepwise::sampling::rna::print_JobParameters_info (StepWiseRNA_JobParametersOP const &JP, std::string const JP_name, std::ostream &outstream, bool const is_simple_full_length_JP)

void	protocols::stepwise::sampling::rna::print_JobParameters_info (StepWiseRNA_JobParametersCOP const &const_JP, std::string const JP_name, std::ostream &outstream, bool const is_simple_full_length_JP)

void	protocols::stepwise::sampling::rna::set_nucleotide_to_A_form (pose::Pose &pose, Size const seq_num)

void	protocols::stepwise::sampling::rna::print_atom_info (pose::Pose const &pose, Size const seq_num, std::string const pose_name)

void	protocols::stepwise::sampling::rna::print_individual_atom_info (core::conformation::Residue const &rsd, Size const atomno, std::string const rsd_name)

void	protocols::stepwise::sampling::rna::print_base_state (std::string const tag, core::Size const base_state, std::ostream &outstream)

void	protocols::stepwise::sampling::rna::print_sugar_pucker_state (std::string const tag, core::Size const pucker_state, std::ostream &outstream)

scoring::ScoreFunctionOP	protocols::stepwise::sampling::rna::get_sampling_scorefxn (scoring::ScoreFunctionCOP scorefxn)

void	protocols::stepwise::sampling::rna::initialize_common_scorefxns (core::scoring::ScoreFunctionOP const &scorefxn_, core::scoring::ScoreFunctionOP &sampling_scorefxn_, core::scoring::ScoreFunctionOP &atr_rep_screening_scorefxn_, core::scoring::ScoreFunctionOP &chainbreak_scorefxn_, core::scoring::ScoreFunctionOP &o2prime_pack_scorefxn_)

void	protocols::stepwise::sampling::rna::copy_all_o2prime_torsions (core::pose::Pose &mod_pose, core::pose::Pose const &template_pose)

core::scoring::ScoreFunctionOP	protocols::stepwise::sampling::rna::rescale_scorefxn (core::scoring::ScoreFunctionOP const &starting_scorefxn, Real const scaling_factor)

void	protocols::stepwise::sampling::rna::show_scorefxn_weight_lines (core::scoring::ScoreFunctionOP const &scorefxn, std::string const title)

void	protocols::stepwise::sampling::rna::figure_out_stepwise_rna_movemap (core::kinematics::MoveMap &mm, core::pose::Pose const &pose, utility::vector1< Size > const &minimize_res)

void	protocols::stepwise::sampling::rna::figure_out_stepwise_rna_movemap (core::kinematics::MoveMap &mm, core::pose::Pose const &pose, toolbox::AllowInsertOP const &allow_insert)

void	protocols::stepwise::sampling::rna::update_allow_insert_with_extra_minimize_res (pose::Pose const &pose, toolbox::AllowInsertOP &allow_insert, utility::vector1< core::Size > const &extra_minimize_res)

void	protocols::stepwise::sampling::rna::choose_random_if_unspecified_nucleotide (char &newrestype)

bool	protocols::stepwise::sampling::rna::mutate_res_if_allowed (pose::Pose &pose, Size const mutate_res, Real const mutation_frequency)

std::string	protocols::stepwise::sampling::rna::create_tag (std::string const &prestring, Size const i)

std::string	protocols::stepwise::sampling::rna::create_torsion_value_string (core::Real const &torsion_value)

std::string	protocols::stepwise::sampling::rna::create_rotamer_string (core::pose::Pose const &pose, Size const moving_res, bool const is_prepend)

std::string	protocols::stepwise::sampling::rna::create_rotamer_string (core::pose::Pose const &pose, Size const moving_res, Size const reference_res)

void	protocols::stepwise::sampling::rna::add_fade_chain_break_constraint_across_gap (pose::Pose &pose, Size const five_prime_res, Size const three_prime_res, Size const gap_size)

void	protocols::stepwise::sampling::rna::add_harmonic_chain_break_constraint (pose::Pose &pose, Size const five_prime_res)

void	protocols::stepwise::sampling::rna::get_possible_O3prime_C5prime_distance_range (Size const gap_size_, Distance &min_dist, Distance &max_dist)

Detailed Description

Detailed:

Author: Rhiju Das

Detailed:

Author: Parin Sripakdeevong

Typedef Documentation

typedef numeric::xyzMatrix< core::Real > Matrix

Namespaces

Typedefs

Functions

Detailed Description

Typedef Documentation