StepWiseRNA_Util.hh File Reference

#include <protocols/swa/rna/StepWiseRNA_ResidueInfo.hh>
#include <protocols/swa/rna/StepWiseRNA_Classes.hh>
#include <protocols/swa/rna/StepWiseRNA_JobParameters.fwd.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <core/io/silent/BinaryRNASilentStruct.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/types.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <utility/vector1.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyzVector.hh>
#include <string>
#include <map>
#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.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/conformation/Residue.hh>
#include <set>

Go to the source code of this file.

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

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

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

Functions
bool	protocols::swa::rna::Is_O1P_atom (std::string const &atom_name)
bool	protocols::swa::rna::Is_O2P_atom (std::string const &atom_name)
bool	protocols::swa::rna::Is_P_atom (std::string const &atom_name)
bool	protocols::swa::rna::Is_O2star_atom (std::string const &atom_name)
bool	protocols::swa::rna::Is_O3star_atom (std::string const &atom_name)
bool	protocols::swa::rna::Is_O4star_atom (std::string const &atom_name)
bool	protocols::swa::rna::Is_O5star_atom (std::string const &atom_name)
bool	protocols::swa::rna::Is_C2star_atom (std::string const &atom_name)
bool	protocols::swa::rna::Is_C3star_atom (std::string const &atom_name)
bool	protocols::swa::rna::Is_C4star_atom (std::string const &atom_name)
bool	protocols::swa::rna::Is_C5star_atom (std::string const &atom_name)
bool	protocols::swa::rna::Is_1H5star_atom (std::string const &atom_name)
bool	protocols::swa::rna::Is_2H5star_atom (std::string const &atom_name)
bool	protocols::swa::rna::Is_H3star_atom (std::string const &atom_name)
bool	protocols::swa::rna::Is_H4star_atom (std::string const &atom_name)
bool	protocols::swa::rna::Is_three_prime_phosphate_atom (std::string const &atom_name)
bool	protocols::swa::rna::Is_five_prime_phosphate_atom (std::string const &atom_name)
bool	protocols::swa::rna::Is_phosphate_atom (std::string const &atom_name)
void	protocols::swa::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::swa::rna::assert_can_prepend (utility::vector1< core::Size > const &seq_num_list)
bool	protocols::swa::rna::assert_can_append (utility::vector1< core::Size > const &seq_num_list)
void	protocols::swa::rna::apply_protonated_H1_adenosine_variant_type (core::pose::Pose &pose, core::Size const &seq_num, bool const apply_check)
void	protocols::swa::rna::apply_virtual_rna_residue_variant_type (core::pose::Pose &pose, core::Size const &seq_num, bool const apply_check)
void	protocols::swa::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::swa::rna::remove_virtual_rna_residue_variant_type (pose::Pose &pose, Size const &seq_num)
bool	protocols::swa::rna::has_virtual_rna_residue_variant_type (pose::Pose &pose, Size const &seq_num)
void	protocols::swa::rna::remove_all_variant_types (pose::Pose &pose)
void	protocols::swa::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::swa::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::swa::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::swa::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::swa::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::swa::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::swa::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::swa::rna::apply_full_to_sub_mapping (utility::vector1< Size > const &res_vector, StepWiseRNA_JobParametersCOP job_parameters)
void	protocols::swa::rna::ensure_valid_full_seq_num (Size const full_seq_num, StepWiseRNA_JobParametersCOP const &job_parameters)
bool	protocols::swa::rna::check_is_working_res (Size const full_seq_num, StepWiseRNA_JobParametersCOP const &job_parameters)
core::Size	protocols::swa::rna::check_validity_and_get_working_res (Size const full_seq_num, StepWiseRNA_JobParametersCOP const &job_parameters)
utility::vector1< Size >	protocols::swa::rna::apply_sub_to_full_mapping (utility::vector1< Size > const &working_res_vector, StepWiseRNA_JobParametersCOP job_parameters)
std::map< core::Size, core::Size >	protocols::swa::rna::create_full_to_input_res_map (utility::vector1< core::Size > const &input_res_vector)
core::Size	protocols::swa::rna::string_to_int (std::string const input_string)
core::Real	protocols::swa::rna::string_to_real (std::string const input_string)
utility::vector1< std::string >	protocols::swa::rna::Tokenize (std::string const str, std::string delimiters)
bool	protocols::swa::rna::Contain_seq_num (Size const &seq_num, utility::vector1< std::pair< core::Size, core::Size > > const &residue_pair_list)
bool	protocols::swa::rna::Contain_seq_num (Size const &seq_num, utility::vector1< core::Size > const &residue_list)
bool	protocols::swa::rna::Is_virtual_base (conformation::Residue const &rsd)
void	protocols::swa::rna::output_pair_size (std::pair< core::Size, core::Size > const &pair_size)
void	protocols::swa::rna::output_pair_size_vector (utility::vector1< std::pair< core::Size, core::Size > > const &pair_size_vector, std::string const &output_string, core::Size const spacing=40)
bool	protocols::swa::rna::pair_sort_citeria (std::pair< core::Size, core::Size > pair_one, std::pair< core::Size, core::Size > pair_two)
void	protocols::swa::rna::sort_seq_num_list (utility::vector1< core::Size > &seq_num_list)
void	protocols::swa::rna::Output_seq_num_list (std::string const tag, utility::vector1< core::Size > const &seq_num_list, core::Size const spacing)
bool	protocols::swa::rna::Is_equivalent_vector (utility::vector1< core::Size > const &seq_num_list_1, utility::vector1< core::Size > const &seq_num_list_2)
void	protocols::swa::rna::Output_is_prepend_map (std::string const tag, std::map< core::Size, bool > const &my_map, core::Size const max_seq_num, core::Size const tag_spacing)
void	protocols::swa::rna::Output_bool_list (std::string const tag, utility::vector1< bool > const &bool_list, core::Size const spacing)
void	protocols::swa::rna::Output_bool_list (std::string const tag, utility::vector1< Size > const &size_list, core::Size const spacing)
void	protocols::swa::rna::Output_size_list (std::string const tag, utility::vector1< Size > const &size_list, core::Size const spacing)
void	protocols::swa::rna::Sort_pair_list (utility::vector1< std::pair< core::Size, core::Size > > pair_list)
bool	protocols::swa::rna::Is_close_chain_break (pose::Pose const &pose)
void	protocols::swa::rna::Add_harmonic_chainbreak_constraint (pose::Pose &pose, Size const five_prime_res)
void	protocols::swa::rna::Output_fold_tree_info (kinematics::FoldTree const &fold_tree, std::string const pose_name)
void	protocols::swa::rna::Output_fold_tree_info (pose::Pose const &pose, std::string pose_name)
bool	protocols::swa::rna::file_exists (std::string const &file_name)
void	protocols::swa::rna::remove_file (std::string const &file_name)
void	protocols::swa::rna::output_rotamer (utility::vector1< Real > &rotamer)
void	protocols::swa::rna::Add_virtual_O2Star_hydrogen (core::pose::Pose &pose)
bool	protocols::swa::rna::Remove_virtual_O2Star_hydrogen (pose::Pose &pose)
Real	protocols::swa::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::swa::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::swa::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::swa::rna::rmsd_over_residue_list (pose::Pose const &pose1, pose::Pose const &pose2, StepWiseRNA_JobParametersCOP job_parameters_, bool const ignore_virtual_atom)
void	protocols::swa::rna::Print_heavy_atoms (Size const &suite_num_1, Size const &suite_num_2, pose::Pose const &pose1, pose::Pose const &pose2)
Size	protocols::swa::rna::Get_num_side_chain_atom_from_res_name (chemical::AA const &res_aa, bool const verbose)
void	protocols::swa::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::swa::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::swa::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::swa::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::swa::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::swa::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::swa::rna::Output_title_text (std::string const title)
bool	protocols::swa::rna::Check_chain_closable (numeric::xyzVector< core::Real > const &xyz_1, numeric::xyzVector< core::Real > const &xyz_2, core::Size const gap_size)
bool	protocols::swa::rna::Check_chain_closable (pose::Pose const &pose, Size const five_prime_chain_break_res, Size const gap_size)
bool	protocols::swa::rna::Check_chain_closable_floating_base (pose::Pose const &five_prime_pose, pose::Pose const &three_prime_pose, Size const five_prime_chain_break_res, Size const gap_size)
void	protocols::swa::rna::get_C4_C3_distance_range (conformation::Residue const &five_prime_rsd, conformation::Residue const &three_prime_rsd, Distance &C4_C3_dist_min, Distance &C4_C3_dist_max)
void	protocols::swa::rna::Freeze_sugar_torsions (core::kinematics::MoveMap &mm, Size const total_residue)
void	protocols::swa::rna::Output_boolean (std::string const &tag, bool boolean)
void	protocols::swa::rna::Output_boolean (bool boolean)
void	protocols::swa::rna::Output_movemap (kinematics::MoveMap const &mm, core::pose::Pose const &pose)
utility::vector1< core::Size >	protocols::swa::rna::get_surrounding_O2star_hydrogen (pose::Pose const &pose, utility::vector1< core::Size > const &moving_res, bool verbose)
void	protocols::swa::rna::o2star_minimize (pose::Pose &pose, core::scoring::ScoreFunctionOP const &packer_scorefxn)
void	protocols::swa::rna::o2star_minimize (pose::Pose &pose, core::scoring::ScoreFunctionOP const &packer_scorefxn, utility::vector1< core::Size > const &O2star_pack_seq_num)
pack::task::PackerTaskOP	protocols::swa::rna::create_standard_o2star_pack_task (pose::Pose const &pose, utility::vector1< core::Size > const &O2star_pack_seq_num)
void	protocols::swa::rna::print_backbone_torsions (pose::Pose const &pose, Size const five_prime_chainbreak)
void	protocols::swa::rna::Correctly_position_cutpoint_phosphate_torsions (pose::Pose &current_pose, Size const five_prime_chainbreak, bool verbose)
void	protocols::swa::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::swa::rna::setup_chain_break_jump_point (core::pose::Pose &pose, core::Size const jump_point_one, core::Size const jump_point_two, core::Size const five_prime_cutpoint, bool const verbose)
void	protocols::swa::rna::remove_chain_break_jump_point (core::pose::Pose &pose, core::Size const five_prime_cutpoint, core::kinematics::FoldTree const fold_tree_without_cutpoint)
core::Size	protocols::swa::rna::setup_bulge_jump_point (pose::Pose &pose, Size const &moving_base, Size const &reference_base, bool const verbose)
Size	protocols::swa::rna::make_cut_at_moving_suite (pose::Pose &pose, Size const &moving_suite)
Size	protocols::swa::rna::make_cut_at_moving_suite (core::kinematics::FoldTree &fold_tree, Size const &moving_suite)
void	protocols::swa::rna::apply_rotamer (pose::Pose &pose, utility::vector1< Torsion_Info > const &rotamer_list)
bool	protocols::swa::rna::check_for_messed_up_structure (core::pose::Pose const &pose, std::string const &tag)
BaseState	protocols::swa::rna::Get_residue_base_state (core::pose::Pose const &pose, Size const seq_num)
PuckerState	protocols::swa::rna::Get_residue_pucker_state (core::pose::Pose const &pose, Size const seq_num, bool const verbose)
bool	protocols::swa::rna::Is_same_ribose_pucker (core::pose::Pose const &current_pose, core::pose::Pose const &cluster_center_pose, Size const seq_num)
void	protocols::swa::rna::sleep (core::Size mseconds)
void	protocols::swa::rna::setup_simple_fold_tree (core::pose::Pose &pose)
void	protocols::swa::rna::get_atom_coordinates (utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > &xyz_list, core::Size const &seq_num, core::conformation::Residue const &rsd_at_origin, core::kinematics::Stub const &moving_res_base_stub)
void	protocols::swa::rna::import_pose_from_silent_file (core::pose::Pose &import_pose, std::string const &silent_file, std::string const &input_tag)
std::string	protocols::swa::rna::path_basename (std::string const full_path)
bool	protocols::swa::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::swa::rna::set_CCD_torsions_to_zero (core::pose::Pose &pose, Size const five_prime_res)
void	protocols::swa::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::swa::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::swa::rna::get_tag_from_pdb_filename (std::string const pdb_filename)
void	protocols::swa::rna::move_jump_atom_to_base (core::kinematics::FoldTree &fold_tree, std::string const &working_sequence)
void	protocols::swa::rna::print_JobParameters_info (StepWiseRNA_JobParametersOP const &JP, std::string const JP_name, bool const Is_simple_full_length_JP)
void	protocols::swa::rna::print_JobParameters_info (StepWiseRNA_JobParametersCOP const &const_JP, std::string const JP_name, bool const Is_simple_full_length_JP)
void	protocols::swa::rna::set_nucleotide_to_A_form (pose::Pose &pose, Size const seq_num)
void	protocols::swa::rna::print_atom_info (pose::Pose const &pose, Size const seq_num, std::string const pose_name)
void	protocols::swa::rna::print_individual_atom_info (core::conformation::Residue const &rsd, Size const atomno, std::string const rsd_name)
void	protocols::swa::rna::print_base_state (std::string const tag, BaseState const base_state)
void	protocols::swa::rna::print_ribose_pucker_state (std::string const tag, PuckerState const pucker_state)
void	protocols::swa::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 &o2star_pack_scorefxn_)
void	protocols::swa::rna::copy_all_o2star_torsions (core::pose::Pose &mod_pose, core::pose::Pose const &template_pose)
core::scoring::ScoreFunctionOP	protocols::swa::rna::rescale_scorefxn (core::scoring::ScoreFunctionOP const &starting_scorefxn, Real const scaling_factor)
void	protocols::swa::rna::show_scorefxn_weight_lines (core::scoring::ScoreFunctionOP const &scorefxn, std::string const title)

Detailed Description

Detailed:

Author

Rhiju Das

Detailed:

Author

Parin Sripakdeevong

Definition in file StepWiseRNA_Util.hh.

Typedef Documentation

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

Definition at line 45 of file StepWiseRNA_Util.hh.