protocols::swa::rna Namespace Reference

Classes
class	RNA_AnalyticLoopCloser
	The RNA de novo structure modeling protocol. More...
class	RNA_LoopCloseSampler
class	StepWiseRNA_AnalyticalLoopCloseSampler
class	StepWiseRNA_Base_Sugar_Rotamer
class	StepWiseRNA_BaseCentroidScreener
class	Jump_point
struct	pose_data_struct2
struct	Torsion_Info
struct	output_data_struct
class	InternalWorkingResidueParameter
class	SillyCountStruct
class	SlicedPoseJobParameters
class	Cluster_Member
class	StepWiseRNA_Clusterer
class	Combine_Tags_Info
class	Filterer_Count
class	StepWiseRNA_CombineLongLoopFilterer
struct	Anchor_ribose_stub
struct	Euler_angles
struct	Base_bin
struct	compare_base_bin
struct	compare_int_pair
struct	compare_test
class	StepWiseRNA_JobParameters
class	StepWiseRNA_JobParameters_Setup
class	StepWiseRNA_Minimizer
class	StepWiseRNA_PoseSetup
struct	Residue_info
class	StepWiseRNA_ResidueSampler
class	StepWiseRNA_RotamerGenerator
class	StepWiseRNA_RotamerGenerator_Wrapper
struct	Atom_Bin
class	VDW_RepScreeninfo
class	StepWiseRNA_VDW_Bin_Screener
class	FB_Pose_Data
class	FloatingBaseChainClosureJobParameter

Typedefs
typedef utility::pointer::owning_ptr < StepWiseRNA_Base_Sugar_Rotamer >	StepWiseRNA_Base_Sugar_RotamerOP
typedef utility::pointer::owning_ptr < StepWiseRNA_Base_Sugar_Rotamer const >	StepWiseRNA_Base_Sugar_RotamerCOP
typedef utility::pointer::owning_ptr < StepWiseRNA_BaseCentroidScreener >	StepWiseRNA_BaseCentroidScreenerOP
typedef utility::pointer::owning_ptr < StepWiseRNA_BaseCentroidScreener const >	StepWiseRNA_BaseCentroidScreenerCOP
typedef utility::pointer::owning_ptr < StepWiseRNA_CombineLongLoopFilterer >	StepWiseRNA_CombineLongLoopFiltererOP
typedef utility::pointer::owning_ptr < StepWiseRNA_CombineLongLoopFilterer const >	StepWiseRNA_CombineLongLoopFiltererpCOP
typedef utility::pointer::owning_ptr < StepWiseRNA_JobParameters >	StepWiseRNA_JobParametersOP
typedef utility::pointer::owning_ptr < StepWiseRNA_JobParameters const >	StepWiseRNA_JobParametersCOP
typedef utility::pointer::owning_ptr < StepWiseRNA_PoseSetup >	StepWiseRNA_PoseSetupOP
typedef utility::pointer::owning_ptr < StepWiseRNA_PoseSetup const >	StepWiseRNA_PoseSetupCOP
typedef utility::pointer::owning_ptr < StepWiseRNA_RotamerGenerator >	StepWiseRNA_RotamerGeneratorOP
typedef utility::pointer::owning_ptr < StepWiseRNA_RotamerGenerator const >	StepWiseRNA_RotamerGeneratorCOP
typedef utility::pointer::owning_ptr < StepWiseRNA_RotamerGenerator_Wrapper >	StepWiseRNA_RotamerGenerator_WrapperOP
typedef utility::pointer::owning_ptr < StepWiseRNA_RotamerGenerator_Wrapper const >	StepWiseRNA_RotamerGenerator_WrapperCOP
typedef utility::pointer::owning_ptr < StepWiseRNA_VDW_Bin_Screener >	StepWiseRNA_VDW_Bin_ScreenerOP
typedef utility::pointer::owning_ptr < StepWiseRNA_VDW_Bin_Screener const >	StepWiseRNA_VDW_Bin_ScreenerCOP

Enumerations
enum	PuckerState { ALL, NORTH, SOUTH }
enum	BaseState { BOTH, ANTI, SYN, NONE }

Functions
bool	sort_criteria2 (pose_data_struct2 pose_data_1, pose_data_struct2 pose_data_2)
bool	score_sort_citeria (Combine_Tags_Info tag_info_1, Combine_Tags_Info tag_info_2)
bool	Is_base_stack (core::kinematics::Stub const &moving_res_base, utility::vector1< core::kinematics::Stub > const &other_residues_base_list, core::Real const base_axis_CUTOFF, core::Real const base_planarity_CUTOFF)
bool	Is_base_pair (core::kinematics::Stub const &moving_res_base, utility::vector1< core::kinematics::Stub > const &other_residues_base_list, core::Real const base_axis_CUTOFF, core::Real const base_planarity_CUTOFF)
bool	Is_strong_base_stack (core::kinematics::Stub const &moving_res_base, utility::vector1< core::kinematics::Stub > const &other_residues_base_list)
bool	Is_medium_base_stack_and_medium_base_pair (core::kinematics::Stub const &moving_res_base, utility::vector1< core::kinematics::Stub > const &other_residues_base_list)
bool	Base_centroid_screening (core::kinematics::Stub const &moving_res_base, utility::vector1< core::kinematics::Stub > const &other_residues_base_list, Size const num_nucleotides, SillyCountStruct &count_data, bool const allow_base_pair_only_screen)
core::kinematics::Stub	Get_ribose_stub (conformation::Residue const &rsd, bool const Is_prepend, bool const verbose)
Base_bin	Get_euler_stub_bin (numeric::xyzVector< core::Real > const &centriod, Euler_angles const &euler_angles)
int	DOF_bin_value (std::map< Base_bin, int, compare_base_bin >::const_iterator const &base_bin_it, std::string const &DOF)
Real	DOF_bin_size (std::string const &DOF)
void	Analyze_base_bin_map (std::map< Base_bin, int, compare_base_bin > const &base_bin_map, std::string const &DOF_one, std::string const &DOF_two, std::string const foldername)
void	Analyze_base_bin_map (std::map< Base_bin, int, compare_base_bin > const &base_bin_map, std::string const foldername)
Euler_angles	Get_euler_angles (numeric::xyzMatrix< core::Real > const &coordinate_matrix)
void	convert_euler_to_coordinate_matrix (Euler_angles const &E, numeric::xyzMatrix< core::Real > &coordinate_matrix)
void	translate_then_rotate_pose (core::pose::Pose &pose, numeric::xyzVector< core::Real > const &vector, numeric::xyzMatrix< core::Real > const matrix, bool const verbose)
void	set_to_origin (pose::Pose &pose, Size const seq_num, bool verbose)
void	get_specific_atom_coordinate (std::string const &atom_name, numeric::xyzVector< core::Real > &atom_pos, core::conformation::Residue const &rsd_at_origin, core::kinematics::Stub const &moving_res_base_stub)
core::Real	get_max_centroid_to_atom_distance (utility::vector1< core::conformation::ResidueOP > const &rsd_at_origin_list, std::string const atom_name)
utility::vector1 < core::conformation::ResidueOP >	setup_residue_at_origin_list (pose::Pose const &pose, Size const &moving_res, bool const extra_anti_chi_rotamer, bool const extra_syn_chi_rotamer, std::string const pose_name)
bool	check_floating_base_chain_closable (core::Size const &reference_res, utility::vector1< pose_data_struct2 > pose_data_list, utility::vector1< core::conformation::ResidueOP > const &rsd_at_origin_list, core::kinematics::Stub const &moving_res_base_stub, bool const Is_prepend, core::Size const gap_size)
bool	check_floating_base_chain_closable (core::Size const &reference_res, core::pose::Pose const &pose, utility::vector1< core::conformation::ResidueOP > const &rsd_at_origin_list, core::kinematics::Stub const &moving_res_base_stub, bool const Is_prepend, Size const gap_size)
void	set_base_coordinate_frame (pose::Pose &pose, Size const &seq_num, core::conformation::Residue const &rsd_at_origin, core::kinematics::Stub const &moving_res_base_stub)
bool	possible_root (core::kinematics::FoldTree const &f, Size const &n)
bool	minimizer_sort_criteria (pose_data_struct2 pose_data_1, pose_data_struct2 pose_data_2)
core::io::silent::BinaryRNASilentStruct	get_binary_rna_silent_struct_safe (pose::Pose const &const_pose, std::string const &tag, std::string const &silent_file)
core::io::silent::BinaryRNASilentStruct	get_binary_rna_silent_struct_safe_wrapper (pose::Pose const &const_pose, std::string const &tag, std::string const &silent_file, bool const write_score_only)
void	Output_data (core::io::silent::SilentFileData &silent_file_data, std::string const &silent_file, std::string const &tag, bool const write_score_only, pose::Pose const &pose, core::pose::PoseCOP native_poseCOP, StepWiseRNA_JobParametersCOP job_parameters_)
void	Print_torsion_info (core::pose::Pose const &pose, core::Size const seq_num, core::Size const rna_torsion_number, std::string const type)
utility::vector1< Residue_info >	Convert_rebuild_residue_string_to_list (std::string const &rebuild_residue_string)
void	Output_residue_struct (Residue_info const &residue)
std::string	Get_one_letter_name (std::string const &three_letter_name)
std::string	Get_three_letter_name (std::string const &one_letter_name)
Size	get_max_seq_num_from_res_map (std::map< core::Size, core::Size > const &my_map)
void	output_res_map (std::map< core::Size, core::Size > const &my_map, Size const max_seq_num)
void	Output_residue_list (utility::vector1< Residue_info > residue_list)
utility::vector1< Residue_info >	Get_residue_list_from_fasta (std::string const full_fasta_sequence)
Residue_info	Get_residue_from_seq_num (Size const &seq_num, utility::vector1< Residue_info > const &residue_list)
bool	Contain_residue_at_seq_num (Size seq_num, utility::vector1< Residue_info > const &residue_list)
utility::vector1 < utility::vector1 < Residue_info > >	Create_strand_list (utility::vector1< Residue_info > const &residue_list)
utility::vector1< Residue_info >	Set_Difference (utility::vector1< Residue_info > const &residue_list_1, utility::vector1< Residue_info > const &residue_list_2)
utility::vector1< Residue_info >	Set_Union (utility::vector1< Residue_info > const &residue_list_1, utility::vector1< Residue_info > const &residue_list_2)
bool	residue_list_sort_citeria (Residue_info residue_info_1, Residue_info residue_info_2)
void	sort_residue_list (utility::vector1< Residue_info > &residue_list)
bool	sort_criteria (pose_data_struct2 pose_data_1, pose_data_struct2 pose_data_2)
bool	Is_O1P_atom (std::string const &atom_name)
bool	Is_O2P_atom (std::string const &atom_name)
bool	Is_P_atom (std::string const &atom_name)
bool	Is_O2star_atom (std::string const &atom_name)
bool	Is_O3star_atom (std::string const &atom_name)
bool	Is_O4star_atom (std::string const &atom_name)
bool	Is_O5star_atom (std::string const &atom_name)
bool	Is_C2star_atom (std::string const &atom_name)
bool	Is_C3star_atom (std::string const &atom_name)
bool	Is_C4star_atom (std::string const &atom_name)
bool	Is_C5star_atom (std::string const &atom_name)
bool	Is_1H5star_atom (std::string const &atom_name)
bool	Is_2H5star_atom (std::string const &atom_name)
bool	Is_H3star_atom (std::string const &atom_name)
bool	Is_H4star_atom (std::string const &atom_name)
bool	Is_three_prime_phosphate_atom (std::string const &atom_name)
bool	Is_five_prime_phosphate_atom (std::string const &atom_name)
bool	Is_phosphate_atom (std::string const &atom_name)
void	minimize_with_constraints (core::pose::Pose &pose, core::kinematics::MoveMap const &mm, core::scoring::ScoreFunctionOP const &scorefxn, core::optimization::MinimizerOptions const &options)
bool	assert_can_prepend (utility::vector1< core::Size > const &seq_num_list)
bool	assert_can_append (utility::vector1< core::Size > const &seq_num_list)
void	apply_protonated_H1_adenosine_variant_type (core::pose::Pose &pose, core::Size const &seq_num, bool const apply_check)
void	apply_virtual_rna_residue_variant_type (core::pose::Pose &pose, core::Size const &seq_num, bool const apply_check)
void	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	remove_virtual_rna_residue_variant_type (pose::Pose &pose, Size const &seq_num)
bool	has_virtual_rna_residue_variant_type (pose::Pose &pose, Size const &seq_num)
void	remove_all_variant_types (pose::Pose &pose)
utility::vector1< Size >	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 >	apply_full_to_sub_mapping (utility::vector1< Size > const &res_vector, StepWiseRNA_JobParametersCOP job_parameters)
utility::vector1< Size >	apply_sub_to_full_mapping (utility::vector1< Size > const &working_res_vector, StepWiseRNA_JobParametersCOP job_parameters)
void	ensure_valid_full_seq_num (Size const full_seq_num, StepWiseRNA_JobParametersCOP const &job_parameters)
bool	check_is_working_res (Size const full_seq_num, StepWiseRNA_JobParametersCOP const &job_parameters)
core::Size	check_validity_and_get_working_res (Size const full_seq_num, StepWiseRNA_JobParametersCOP const &job_parameters)
std::map< core::Size, core::Size >	create_full_to_input_res_map (utility::vector1< core::Size > const &input_res_vector)
core::Size	string_to_int (std::string const input_string)
core::Real	string_to_real (std::string const input_string)
utility::vector1< std::string >	Tokenize (std::string const str, std::string delimiters)
bool	Contain_seq_num (Size const &seq_num, utility::vector1< std::pair< core::Size, core::Size > > const &residue_pair_list)
bool	Contain_seq_num (Size const &seq_num, utility::vector1< core::Size > const &residue_list)
bool	Is_virtual_base (conformation::Residue const &rsd)
void	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	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	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	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 >	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	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)
void	output_pair_size (std::pair< Size, Size > const &pair_size)
void	output_pair_size_vector (utility::vector1< std::pair< Size, Size > > const &pair_size_vector, std::string const &output_string, core::Size const spacing)
bool	pair_sort_citeria (std::pair< Size, Size > pair_one, std::pair< Size, Size > pair_two)
void	Sort_pair_list (utility::vector1< std::pair< Size, Size > > pair_list)
bool	seq_num_sort_citeria (core::Size seq_num_1, core::Size seq_num_2)
void	sort_seq_num_list (utility::vector1< core::Size > &seq_num_list)
void	Output_seq_num_list (std::string const tag, utility::vector1< core::Size > const &seq_num_list, core::Size const spacing)
bool	Is_equivalent_vector (utility::vector1< core::Size > const &seq_num_list_1, utility::vector1< core::Size > const &seq_num_list_2)
void	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	Output_bool_list (std::string const tag, utility::vector1< Size > const &size_list, core::Size const spacing)
void	Output_bool_list (std::string const tag, utility::vector1< bool > const &bool_list, core::Size const spacing)
void	Output_size_list (std::string const tag, utility::vector1< Size > const &size_list, core::Size const spacing)
bool	Is_close_chain_break (pose::Pose const &pose)
void	Add_harmonic_chainbreak_constraint (pose::Pose &pose, Size const five_prime_res)
void	Output_title_text (std::string const title)
void	Output_fold_tree_info (kinematics::FoldTree const &fold_tree, std::string const pose_name)
void	Output_fold_tree_info (pose::Pose const &pose, std::string pose_name)
bool	file_exists (std::string const &file_name)
void	remove_file (std::string const &file_name)
void	output_rotamer (utility::vector1< Real > &rotamer)
void	Add_virtual_O2Star_hydrogen (core::pose::Pose &pose)
bool	Remove_virtual_O2Star_hydrogen (pose::Pose &pose)
Real	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	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	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	rmsd_over_residue_list (pose::Pose const &pose1, pose::Pose const &pose2, StepWiseRNA_JobParametersCOP job_parameters_, bool const ignore_virtual_atom)
void	Print_heavy_atoms (Size const &suite_num_1, Size const &suite_num_2, pose::Pose const &pose1, pose::Pose const &pose2)
Size	Get_num_side_chain_atom_from_res_name (chemical::AA const &res_aa, bool const verbose)
Real	atom_square_deviation (conformation::Residue const &rsd_1, conformation::Residue const &rsd_2, Size const &atomno_1, Size const &atomno_2, bool verbose)
void	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	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	phosphate_base_phosphate_rmsd (pose::Pose const &pose1, pose::Pose const &pose2, Size const &moving_res_num, bool const ignore_virtual_atom)
void	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)
void	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)
bool	Check_chain_closable (pose::Pose const &pose, Size const five_prime_chain_break_res, Size const gap_size)
bool	Check_chain_closable (numeric::xyzVector< core::Real > const &xyz_1, numeric::xyzVector< core::Real > const &xyz_2, core::Size const gap_size)
bool	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	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	Freeze_sugar_torsions (core::kinematics::MoveMap &mm, Size const total_residue)
void	Output_boolean (std::string const &tag, bool boolean)
void	Output_boolean (bool boolean)
void	Output_movemap (kinematics::MoveMap const &mm, core::pose::Pose const &pose)
utility::vector1< core::Size >	get_surrounding_O2star_hydrogen (pose::Pose const &pose, utility::vector1< core::Size > const &moving_res, bool verbose)
void	o2star_minimize (pose::Pose &pose, core::scoring::ScoreFunctionOP const &packer_scorefxn)
void	o2star_minimize (pose::Pose &pose, core::scoring::ScoreFunctionOP const &packer_scorefxn, utility::vector1< core::Size > const &O2star_pack_seq_num)
pack::task::PackerTaskOP	create_standard_o2star_pack_task (pose::Pose const &pose, utility::vector1< core::Size > const &O2star_pack_seq_num)
void	print_backbone_torsions (pose::Pose const &pose, Size const five_prime_chainbreak)
void	Correctly_position_cutpoint_phosphate_torsions (pose::Pose &current_pose, Size const five_prime_chainbreak, bool verbose)
void	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	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	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	setup_bulge_jump_point (pose::Pose &pose, Size const &moving_base, Size const &reference_base, bool const verbose)
Size	make_cut_at_moving_suite (core::kinematics::FoldTree &fold_tree, Size const &moving_suite)
Size	make_cut_at_moving_suite (pose::Pose &pose, Size const &moving_suite)
void	apply_rotamer (pose::Pose &pose, utility::vector1< Torsion_Info > const &rotamer_list)
bool	check_for_messed_up_structure (core::pose::Pose const &pose, std::string const &tag)
BaseState	Get_residue_base_state (core::pose::Pose const &pose, Size const seq_num)
PuckerState	Get_residue_pucker_state (core::pose::Pose const &pose, Size const seq_num, bool const verbose)
bool	Is_same_ribose_pucker (core::pose::Pose const &current_pose, core::pose::Pose const &cluster_center_pose, Size const seq_num)
void	sleep (core::Size mseconds)
void	setup_simple_fold_tree (core::pose::Pose &pose)
void	get_atom_coordinates (utility::vector1< std::pair< id::AtomID, numeric::xyzVector< core::Real > > > &xyz_list, Size const &seq_num, core::conformation::Residue const &rsd_at_origin, core::kinematics::Stub const &moving_res_base_stub)
void	import_pose_from_silent_file (core::pose::Pose &import_pose, std::string const &silent_file, std::string const &input_tag)
std::string	path_basename (std::string const full_path)
bool	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	set_CCD_torsions_to_zero (core::pose::Pose &pose, Size const five_prime_res)
void	get_default_allowed_bulge_res (utility::vector1< core::Size > &allow_bulge_res_list, core::pose::Pose const &pose, bool const verbose)
core::Size	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	get_tag_from_pdb_filename (std::string const pdb_filename)
void	move_jump_atom_to_base (core::kinematics::FoldTree &fold_tree, std::string const &working_sequence)
void	print_JobParameters_info (StepWiseRNA_JobParametersCOP const &const_JP, std::string const JP_name, bool const Is_simple_full_length_JP)
void	print_JobParameters_info (StepWiseRNA_JobParametersOP const &JP, std::string const JP_name, bool const Is_simple_full_length_JP)
void	set_nucleotide_to_A_form (pose::Pose &pose, Size const seq_num)
void	print_atom_info (pose::Pose const &pose, Size const seq_num, std::string const pose_name)
void	print_individual_atom_info (core::conformation::Residue const &rsd, Size const atomno, std::string const rsd_name)
void	print_base_state (std::string const tag, BaseState const base_state)
void	print_ribose_pucker_state (std::string const tag, PuckerState const pucker_state)
void	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	copy_all_o2star_torsions (core::pose::Pose &mod_pose, core::pose::Pose const &template_pose)
core::scoring::ScoreFunctionOP	rescale_scorefxn (core::scoring::ScoreFunctionOP const &starting_scorefxn, Real const scaling_factor)
void	show_scorefxn_weight_lines (core::scoring::ScoreFunctionOP const &scorefxn, std::string const title)
void	output_pair_size (std::pair< core::Size, core::Size > const &pair_size)
void	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	pair_sort_citeria (std::pair< core::Size, core::Size > pair_one, std::pair< core::Size, core::Size > pair_two)
void	Sort_pair_list (utility::vector1< std::pair< core::Size, core::Size > > pair_list)
void	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)
bool	fast_full_atom_VDW_repulsion_screen (core::pose::Pose const &pose, core::Size const res_1, core::Size const res_2, bool const Is_prepend)
bool	floating_base_full_atom_van_der_Waals_screening (core::pose::Pose &current_pose_screen, core::Real const &base_rep_score, core::scoring::ScoreFunctionOP const &atr_rep_screening_scorefxn, SillyCountStruct &count_data, bool const verbose)
bool	floating_base_chain_break_screening (core::pose::Pose &chain_break_screening_pose, core::scoring::ScoreFunctionOP const &chainbreak_scorefxn, SillyCountStruct &count_data, core::Size const &five_prime_res, std::string const &tag, bool const verbose)
utility::vector1< FB_Pose_Data >	floating_base_chain_closure_setup (utility::vector1< pose_data_struct2 > const &input_pose_data_list, FloatingBaseChainClosureJobParameter const &FB_job_params, core::scoring::ScoreFunctionOP const &atr_rep_screening_scorefxn, core::scoring::ScoreFunctionOP const &full_scorefxn, pose::Pose &viewer_pose, bool const do_minimize)
void	floating_base_chain_closure_sampling (utility::vector1< FB_Pose_Data > &pose_data_list, core::pose::Pose &viewer_pose, FloatingBaseChainClosureJobParameter const &FB_job_params, core::scoring::ScoreFunctionOP const &chainbreak_scorefxn, core::scoring::ScoreFunctionOP const &atr_rep_screening_scorefxn, StepWiseRNA_VDW_Bin_ScreenerOP const &VDW_bin_screener, bool const CCD_grid_index_screen)
utility::vector1 < pose_data_struct2 >	floating_base_chain_closure_post_process (utility::vector1< FB_Pose_Data > &pose_data_list, core::pose::Pose &viewer_pose, core::scoring::ScoreFunctionOP const &sampling_scorefxn, FloatingBaseChainClosureJobParameter const &FB_job_params, bool const rm_chain_break_jump_point)
void	minimize_all_sampled_floating_bases (core::pose::Pose &viewer_pose, utility::vector1< FloatingBaseChainClosureJobParameter > const &FB_JP_list, utility::vector1< pose_data_struct2 > &pose_data_list, core::scoring::ScoreFunctionOP const &sampling_scorefxn, StepWiseRNA_JobParametersCOP const &job_parameters, bool const virtual_ribose_is_from_prior_step)
bool	Is_ribose_virtual (core::pose::Pose const &pose, core::Size const ribose_res, core::Size const bulge_res)
void	copy_bulge_res_and_ribose_torsion (FloatingBaseChainClosureJobParameter const &FB_job_params, core::pose::Pose &pose, core::pose::Pose const &template_pose)
bool	sort_pose_data_by_score (pose_data_struct2 pose_data_1, pose_data_struct2 pose_data_2)
utility::vector1 < pose_data_struct2 >	sample_virtual_ribose_and_bulge_and_close_chain (pose::Pose &viewer_pose, FloatingBaseChainClosureJobParameter const &FB_job_params, std::string const name, core::scoring::ScoreFunctionOP const &scorefxn, core::scoring::ScoreFunctionOP const &sampling_scorefxn, core::scoring::ScoreFunctionOP const &atr_rep_screening_scorefxn, core::scoring::ScoreFunctionOP const &chainbreak_scorefxn, StepWiseRNA_JobParametersCOP &job_parameters, bool const virtual_ribose_is_from_prior_step)
void	enumerate_starting_pose_data_list (utility::vector1< pose_data_struct2 > &starting_pose_data_list, utility::vector1< FloatingBaseChainClosureJobParameter > const &FB_CC_JP_list, core::pose::Pose const &pose)
utility::vector1 < FloatingBaseChainClosureJobParameter >	setup_FB_CC_JP_list (pose::Pose const &pose, utility::vector1< std::string > const &sample_virtual_ribose_string_list, StepWiseRNA_JobParametersCOP &job_parameters)
void	sample_user_specified_virtual_riboses (pose::Pose &pose, utility::vector1< std::string > const &sample_virtual_ribose_string_list, StepWiseRNA_JobParametersCOP &job_parameters, core::scoring::ScoreFunctionOP const &scorefxn, std::string const silent_file_out, std::string const input_tag)

Typedef Documentation

typedef utility::pointer::owning_ptr< StepWiseRNA_Base_Sugar_Rotamer const > protocols::swa::rna::StepWiseRNA_Base_Sugar_RotamerCOP

Definition at line 25 of file StepWiseRNA_Base_Sugar_Rotamer.fwd.hh.

typedef utility::pointer::owning_ptr< StepWiseRNA_Base_Sugar_Rotamer > protocols::swa::rna::StepWiseRNA_Base_Sugar_RotamerOP

Definition at line 23 of file StepWiseRNA_Base_Sugar_Rotamer.fwd.hh.

typedef utility::pointer::owning_ptr< StepWiseRNA_BaseCentroidScreener const > protocols::swa::rna::StepWiseRNA_BaseCentroidScreenerCOP

Definition at line 25 of file StepWiseRNA_BaseCentroidScreener.fwd.hh.

typedef utility::pointer::owning_ptr< StepWiseRNA_BaseCentroidScreener > protocols::swa::rna::StepWiseRNA_BaseCentroidScreenerOP

Definition at line 23 of file StepWiseRNA_BaseCentroidScreener.fwd.hh.

typedef utility::pointer::owning_ptr< StepWiseRNA_CombineLongLoopFilterer > protocols::swa::rna::StepWiseRNA_CombineLongLoopFiltererOP

Definition at line 23 of file StepWiseRNA_CombineLongLoopFilterer.fwd.hh.

typedef utility::pointer::owning_ptr< StepWiseRNA_CombineLongLoopFilterer const > protocols::swa::rna::StepWiseRNA_CombineLongLoopFiltererpCOP

Definition at line 25 of file StepWiseRNA_CombineLongLoopFilterer.fwd.hh.

typedef utility::pointer::owning_ptr< StepWiseRNA_JobParameters const > protocols::swa::rna::StepWiseRNA_JobParametersCOP

Definition at line 25 of file StepWiseRNA_JobParameters.fwd.hh.

typedef utility::pointer::owning_ptr< StepWiseRNA_JobParameters > protocols::swa::rna::StepWiseRNA_JobParametersOP

Definition at line 23 of file StepWiseRNA_JobParameters.fwd.hh.

typedef utility::pointer::owning_ptr< StepWiseRNA_PoseSetup const > protocols::swa::rna::StepWiseRNA_PoseSetupCOP

Definition at line 25 of file StepWiseRNA_PoseSetup.fwd.hh.

typedef utility::pointer::owning_ptr< StepWiseRNA_PoseSetup > protocols::swa::rna::StepWiseRNA_PoseSetupOP

Definition at line 23 of file StepWiseRNA_PoseSetup.fwd.hh.

typedef utility::pointer::owning_ptr< StepWiseRNA_RotamerGenerator_Wrapper const > protocols::swa::rna::StepWiseRNA_RotamerGenerator_WrapperCOP

Definition at line 26 of file StepWiseRNA_RotamerGenerator_Wrapper.fwd.hh.

typedef utility::pointer::owning_ptr< StepWiseRNA_RotamerGenerator_Wrapper > protocols::swa::rna::StepWiseRNA_RotamerGenerator_WrapperOP

Definition at line 24 of file StepWiseRNA_RotamerGenerator_Wrapper.fwd.hh.

typedef utility::pointer::owning_ptr< StepWiseRNA_RotamerGenerator const > protocols::swa::rna::StepWiseRNA_RotamerGeneratorCOP

Definition at line 22 of file StepWiseRNA_RotamerGenerator.fwd.hh.

typedef utility::pointer::owning_ptr< StepWiseRNA_RotamerGenerator > protocols::swa::rna::StepWiseRNA_RotamerGeneratorOP

Definition at line 20 of file StepWiseRNA_RotamerGenerator.fwd.hh.

typedef utility::pointer::owning_ptr< StepWiseRNA_VDW_Bin_Screener const > protocols::swa::rna::StepWiseRNA_VDW_Bin_ScreenerCOP

Definition at line 25 of file StepWiseRNA_VDW_Bin_Screener.fwd.hh.

typedef utility::pointer::owning_ptr< StepWiseRNA_VDW_Bin_Screener > protocols::swa::rna::StepWiseRNA_VDW_Bin_ScreenerOP

Definition at line 23 of file StepWiseRNA_VDW_Bin_Screener.fwd.hh.

Enumeration Type Documentation

enum protocols::swa::rna::BaseState

Enumerator
BOTH
ANTI
SYN
NONE

Definition at line 50 of file StepWiseRNA_Classes.hh.

enum protocols::swa::rna::PuckerState

Enumerator
ALL
NORTH
SOUTH

Definition at line 49 of file StepWiseRNA_Classes.hh.

Function Documentation

void protocols::swa::rna::Add_harmonic_chainbreak_constraint	(	pose::Pose &	pose,
		Size const	five_prime_res
	)

Definition at line 946 of file StepWiseRNA_Util.cc.

References core::pose::Pose::constraint_set(), and core::pose::Pose::residue().

Referenced by floating_base_chain_closure_setup(), protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling(), and protocols::swa::rna::StepWiseRNA_ResidueSampler::standard_sampling().

void protocols::swa::rna::Add_virtual_O2Star_hydrogen

(

core::pose::Pose &

pose)

Definition at line 1120 of file StepWiseRNA_Util.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::create_VDW_rep_screen_pose(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::FARFAR_setup_using_user_input_VDW_pose(), protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::setup_using_user_input_VDW_pose(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::setup_using_working_pose(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::standard_sampling(), and protocols::swa::rna::StepWiseRNA_ResidueSampler::standard_sampling().

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
	)

Definition at line 731 of file StepWiseRNA_Util.cc.

References check_for_messed_up_structure(), create_alignment_id_map(), protocols::pack_daemon::error_message, Is_virtual_base(), Output_boolean(), core::pose::Pose::residue(), and core::scoring::superimpose_pose().

Referenced by protocols::swa::rna::StepWiseRNA_Clusterer::align_to_quick_alignment_pose(), protocols::swa::rna::StepWiseRNA_Clusterer::create_large_cluster_centers_member_list(), protocols::swa::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file(), protocols::swa::rna::StepWiseRNA_Clusterer::Is_new_cluster_center_with_job_parameters(), Output_data(), protocols::swa::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file(), protocols::swa::rna::StepWiseRNA_Clusterer::setup_fail_triangle_inequailty_list(), protocols::swa::rna::StepWiseRNA_PoseSetup::setup_native_pose(), and protocols::swa::rna::StepWiseRNA_ResidueSampler::standard_sampling().

void protocols::swa::rna::Analyze_base_bin_map	(	std::map< Base_bin, int, compare_base_bin > const &	base_bin_map,
		std::string const &	DOF_one,
		std::string const &	DOF_two,
		std::string const	foldername
	)

Definition at line 423 of file StepWiseRNA_FloatingBase_Sampler_Util.cc.

References DOF_bin_size(), DOF_bin_value(), protocols::abinitio::filename(), and core::sequence::left.

Referenced by Analyze_base_bin_map(), and protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling().

void protocols::swa::rna::Analyze_base_bin_map	(	std::map< Base_bin, int, compare_base_bin > const &	base_bin_map,
		std::string const	foldername
	)

Definition at line 510 of file StepWiseRNA_FloatingBase_Sampler_Util.cc.

References Analyze_base_bin_map(), centroid_bin_size, euler_angle_bin_size, and euler_z_bin_size.

utility::vector1< core::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
	)

Definition at line 355 of file StepWiseRNA_Util.cc.

Referenced by apply_full_to_sub_mapping(), protocols::swa::rna::StepWiseRNA_Clusterer::create_silent_file_and_tag_list(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::get_user_input_alignment_res_list(), protocols::swa::rna::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_fixed_res(), protocols::swa::rna::StepWiseRNA_JobParameters::set_force_north_ribose_list(), protocols::swa::rna::StepWiseRNA_JobParameters::set_force_south_ribose_list(), protocols::swa::rna::StepWiseRNA_JobParameters::set_force_syn_chi_res_list(), protocols::swa::rna::StepWiseRNA_JobParameters::set_global_sample_res_list(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_native_alignment_res(), protocols::swa::rna::StepWiseRNA_JobParameters::set_protonated_H1_adenosine_list(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_terminal_res(), protocols::swa::rna::SlicedPoseJobParameters::setup(), protocols::swa::rna::StepWiseRNA_PoseSetup::setup_native_pose(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::setup_using_user_input_VDW_pose(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::StepWiseRNA_AnalyticalLoopCloseSampler(), and protocols::swa::rna::StepWiseRNA_ResidueSampler::StepWiseRNA_ResidueSampler().

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

Definition at line 385 of file StepWiseRNA_Util.cc.

References apply_full_to_sub_mapping().

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

Definition at line 165 of file StepWiseRNA_Util.cc.

References core::conformation::Residue::aa(), core::pose::add_variant_type_to_pose_residue(), core::conformation::Residue::has_variant_type(), core::chemical::na_rad, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by protocols::swa::rna::StepWiseRNA_PoseSetup::add_protonated_H1_adenosine_variants(), and protocols::swa::rna::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs().

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

Definition at line 2557 of file StepWiseRNA_Util.cc.

References core::pose::Pose::set_torsion().

Referenced by floating_base_chain_closure_sampling(), and protocols::swa::rna::StepWiseRNA_ResidueSampler::standard_sampling().

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

Definition at line 398 of file StepWiseRNA_Util.cc.

Referenced by protocols::swa::rna::StepWiseRNA_PoseSetup::apply_bulge_variants(), protocols::swa::rna::StepWiseRNA_PoseSetup::apply_virtual_res_variant(), and protocols::swa::rna::StepWiseRNA_JobParameters_Setup::get_user_input_alignment_res_list().

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

Definition at line 199 of file StepWiseRNA_Util.cc.

Referenced by protocols::swa::rna::StepWiseRNA_ResidueSampler::apply_bulge_variant(), protocols::swa::rna::StepWiseRNA_PoseSetup::apply_virtual_res_variant(), floating_base_chain_closure_post_process(), protocols::swa::rna::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs(), protocols::swa::rna::StepWiseRNA_PoseSetup::setup_native_pose(), and virtualize_bulges().

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
	)

Definition at line 208 of file StepWiseRNA_Util.cc.

References core::pose::add_variant_type_to_pose_residue(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

bool protocols::swa::rna::assert_can_append

(

utility::vector1< core::Size > const &

seq_num_list)

Definition at line 155 of file StepWiseRNA_Util.cc.

Referenced by protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_partition_definition(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_Prepend_Internal(), and protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::StepWiseRNA_RotamerGenerator_Wrapper().

bool protocols::swa::rna::assert_can_prepend

(

utility::vector1< core::Size > const &

seq_num_list)

Definition at line 146 of file StepWiseRNA_Util.cc.

Referenced by protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_partition_definition(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_Prepend_Internal(), and protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::StepWiseRNA_RotamerGenerator_Wrapper().

core::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
	)

Definition at line 1404 of file StepWiseRNA_Util.cc.

References core::chemical::ResidueType::atom_name(), core::conformation::Residue::seqpos(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by base_atoms_square_deviation(), phosphate_base_phosphate_square_deviation(), phosphate_square_deviation(), and suite_square_deviation().

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
	)

Definition at line 1440 of file StepWiseRNA_Util.cc.

References core::conformation::Residue::aa(), core::chemical::ResidueType::atom_name(), atom_square_deviation(), core::conformation::Residue::atom_type(), core::conformation::Residue::first_sidechain_atom(), Get_num_side_chain_atom_from_res_name(), core::chemical::AtomType::name(), core::chemical::name_from_aa(), core::pose::Pose::residue(), and core::conformation::Residue::type().

Referenced by protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::align_VDW_rep_screen_pose().

bool protocols::swa::rna::Base_centroid_screening	(	core::kinematics::Stub const &	moving_res_base,
		utility::vector1< core::kinematics::Stub > const &	other_residues_base_list,
		Size const	num_nucleotides,
		SillyCountStruct &	count_data,
		bool const	allow_base_pair_only_screen
	)

Definition at line 250 of file StepWiseRNA_FloatingBase_Sampler_Util.cc.

References protocols::swa::rna::SillyCountStruct::base_pairing_count, protocols::swa::rna::SillyCountStruct::base_stack_count, Is_base_pair(), Is_base_stack(), Is_medium_base_stack_and_medium_base_pair(), Is_strong_base_stack(), protocols::swa::rna::SillyCountStruct::pass_base_centroid_screen, and protocols::swa::rna::SillyCountStruct::strict_base_pairing_count.

Referenced by protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling().

bool protocols::swa::rna::Check_chain_closable	(	pose::Pose const &	pose,
		Size const	five_prime_chain_break_res,
		Size const	gap_size
	)

Definition at line 1698 of file StepWiseRNA_Util.cc.

References core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by check_floating_base_chain_closable(), protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling(), protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::pass_all_filters(), protocols::swa::rna::StepWiseRNA_Minimizer::pass_all_pose_screens(), and protocols::swa::rna::StepWiseRNA_ResidueSampler::standard_sampling().

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
	)

Definition at line 1711 of file StepWiseRNA_Util.cc.

References C5I_C5I_PLUS_ONE_MAX_DIST, and O3I_C5IPLUS2_MAX_DIST.

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
	)

Definition at line 1760 of file StepWiseRNA_Util.cc.

References get_C4_C3_distance_range(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by floating_base_chain_closure_sampling(), protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling(), and protocols::swa::rna::StepWiseRNA_ResidueSampler::standard_sampling().

bool protocols::swa::rna::check_floating_base_chain_closable	(	core::Size const &	reference_res,
		utility::vector1< pose_data_struct2 >	pose_data_list,
		utility::vector1< core::conformation::ResidueOP > const &	rsd_at_origin_list,
		core::kinematics::Stub const &	moving_res_base_stub,
		bool const	Is_prepend,
		core::Size const	gap_size
	)

Definition at line 791 of file StepWiseRNA_FloatingBase_Sampler_Util.cc.

References Check_chain_closable(), get_specific_atom_coordinate(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling().

bool protocols::swa::rna::check_floating_base_chain_closable	(	core::Size const &	reference_res,
		core::pose::Pose const &	pose,
		utility::vector1< core::conformation::ResidueOP > const &	rsd_at_origin_list,
		core::kinematics::Stub const &	moving_res_base_stub,
		bool const	Is_prepend,
		Size const	gap_size
	)

Definition at line 830 of file StepWiseRNA_FloatingBase_Sampler_Util.cc.

References Check_chain_closable(), get_specific_atom_coordinate(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

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

Definition at line 2575 of file StepWiseRNA_Util.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::scoring::dna::DELTA, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by align_poses(), protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::convert_silent_file_to_pose_data_list(), protocols::swa::rna::StepWiseRNA_Clusterer::create_large_cluster_centers_member_list(), protocols::swa::rna::StepWiseRNA_Clusterer::create_silent_file_and_tag_list(), protocols::swa::rna::StepWiseRNA_Clusterer::do_some_clustering(), protocols::swa::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file(), get_binary_rna_silent_struct_safe(), import_pose_from_silent_file(), protocols::swa::rna::StepWiseRNA_Clusterer::initialize_max_memory_pose_num(), protocols::swa::rna::StepWiseRNA_Clusterer::initialize_quick_alignment_pose(), protocols::swa::rna::StepWiseRNA_Clusterer::initialize_VDW_rep_screener(), protocols::swa::rna::StepWiseRNA_Minimizer::pass_all_pose_screens(), and protocols::swa::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file().

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

Definition at line 432 of file StepWiseRNA_Util.cc.

References ensure_valid_full_seq_num().

Referenced by check_validity_and_get_working_res(), and setup_FB_CC_JP_list().

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

Definition at line 445 of file StepWiseRNA_Util.cc.

References check_is_working_res().

Referenced by setup_FB_CC_JP_list().

bool protocols::swa::rna::Contain_residue_at_seq_num	(	Size	seq_num,
		utility::vector1< Residue_info > const &	residue_list
	)

Definition at line 249 of file StepWiseRNA_ResidueInfo.cc.

Referenced by Set_Difference(), and Set_Union().

bool protocols::swa::rna::Contain_seq_num	(	Size const &	seq_num,
		utility::vector1< std::pair< core::Size, core::Size > > const &	residue_pair_list
	)

Definition at line 568 of file StepWiseRNA_Util.cc.

Referenced by protocols::swa::rna::StepWiseRNA_PoseSetup::add_protonated_H1_adenosine_variants(), protocols::swa::rna::StepWiseRNA_Minimizer::apply(), protocols::swa::rna::StepWiseRNA_PoseSetup::apply_bulge_variants(), protocols::swa::rna::StepWiseRNA_PoseSetup::apply_virtual_res_variant(), protocols::swa::rna::StepWiseRNA_PoseSetup::correctly_copy_HO2star_positions(), protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::figure_out_appended_and_prepended_res_list(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_Is_residue_prepend(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_jump_partners(), protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::get_matching_res_in_VDW_rep_screen_pose(), protocols::swa::rna::StepWiseRNA_PoseSetup::get_nearest_dist_to_O2star(), protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::Get_residue_pucker_state_internal(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::get_user_input_alignment_res_list(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::initialize_o2star_packer_task(), protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::initialize_rotamer_generator_list(), protocols::swa::rna::StepWiseRNA_RotamerGenerator::initialize_sample_base_states(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::input_struct_definition(), protocols::swa::rna::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs(), protocols::swa::rna::FloatingBaseChainClosureJobParameter::set_base_and_pucker_state(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_fixed_res(), protocols::swa::rna::StepWiseRNA_JobParameters::set_force_north_ribose_list(), protocols::swa::rna::StepWiseRNA_JobParameters::set_force_south_ribose_list(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_jump_point_pair_list(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::setup_additional_cutpoint_closed(), protocols::swa::rna::StepWiseRNA_PoseSetup::setup_native_pose(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::setup_using_user_input_VDW_pose(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::update_VDW_screen_bin(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::VDW_rep_screen_with_act_pose(), and protocols::swa::rna::StepWiseRNA_PoseSetup::verify_protonated_H1_adenosine_variants().

bool protocols::swa::rna::Contain_seq_num	(	Size const &	seq_num,
		utility::vector1< core::Size > const &	residue_list
	)

Definition at line 578 of file StepWiseRNA_Util.cc.

void protocols::swa::rna::convert_euler_to_coordinate_matrix	(	Euler_angles const &	E,
		numeric::xyzMatrix< core::Real > &	coordinate_matrix
	)

Definition at line 573 of file StepWiseRNA_FloatingBase_Sampler_Util.cc.

References protocols::swa::rna::Euler_angles::alpha, protocols::swa::rna::Euler_angles::beta, and protocols::swa::rna::Euler_angles::gamma.

Referenced by protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling(), and get_binary_rna_silent_struct_safe().

utility::vector1< Residue_info > protocols::swa::rna::Convert_rebuild_residue_string_to_list

(

std::string const &

rebuild_residue_string)

Definition at line 89 of file StepWiseRNA_ResidueInfo.cc.

References Get_three_letter_name(), protocols::swa::rna::Residue_info::name, protocols::swa::rna::Residue_info::seq_num, core::scoring::rna::chemical_shift::string_to_int(), and protocols::Tokenize().

void protocols::swa::rna::copy_all_o2star_torsions	(	core::pose::Pose &	mod_pose,
		core::pose::Pose const &	template_pose
	)

Definition at line 3568 of file StepWiseRNA_Util.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::id::CHI, core::pose::Pose::residue(), core::pose::Pose::set_torsion(), core::pose::Pose::torsion(), and core::pose::Pose::total_residue().

Referenced by protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling(), protocols::swa::rna::StepWiseRNA_ResidueSampler::sample_o2star_hydrogen(), and protocols::swa::rna::StepWiseRNA_ResidueSampler::standard_sampling().

void protocols::swa::rna::copy_bulge_res_and_ribose_torsion	(	FloatingBaseChainClosureJobParameter const &	FB_job_params,
		core::pose::Pose &	pose,
		core::pose::Pose const &	template_pose
	)

Definition at line 953 of file StepWiseRNA_VirtualRiboseSampler.cc.

References protocols::swa::rna::FloatingBaseChainClosureJobParameter::bulge_res, core::pose::copy_dofs_match_atom_names(), protocols::swa::rna::FloatingBaseChainClosureJobParameter::moving_res, protocols::swa::rna::FloatingBaseChainClosureJobParameter::reference_res, and core::pose::remove_variant_type_from_pose_residue().

Referenced by enumerate_starting_pose_data_list(), protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling(), and protocols::swa::rna::StepWiseRNA_ResidueSampler::standard_sampling_WRAPPER().

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
	)

Definition at line 2372 of file StepWiseRNA_Util.cc.

References core::id::BB, core::id::CHI, core::conformation::Residue::chi(), core::pose::Pose::fold_tree(), core::conformation::Residue::mainchain_torsion(), core::scoring::rna::NUM_RNA_MAINCHAIN_TORSIONS(), Output_fold_tree_info(), core::pose::Pose::residue(), core::id::TorsionID::rsd(), core::pose::Pose::set_torsion(), core::id::TorsionID::torsion(), core::pose::Pose::total_residue(), and core::id::TorsionID::type().

void protocols::swa::rna::Correctly_position_cutpoint_phosphate_torsions	(	pose::Pose &	current_pose,
		Size const	five_prime_chainbreak,
		bool	verbose
	)

Definition at line 2289 of file StepWiseRNA_Util.cc.

References core::chemical::aa_from_name(), core::id::BB, core::conformation::ResidueFactory::create_residue(), core::pose::Pose::delete_polymer_residue(), core::chemical::ChemicalManager::get_instance(), Output_title_text(), core::pose::Pose::prepend_polymer_residue_before_seqpos(), print_backbone_torsions(), core::chemical::RNA, and core::pose::Pose::set_torsion().

Referenced by protocols::swa::rna::StepWiseRNA_PoseSetup::apply_cutpoint_variants(), protocols::swa::StepWisePoseSetup::apply_cutpoint_variants(), setup_chain_break_jump_point(), and protocols::rna::RNA_StructureParameters::setup_chainbreak_variants().

core::id::AtomID_Map< core::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
	)

Definition at line 702 of file StepWiseRNA_Util.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::id::BOGUS_ATOM_ID, core::scoring::rna::chemical_shift::Contain_seq_num(), core::pose::initialize_atomid_map(), core::pose::Pose::residue(), core::pose::Pose::sequence(), setup_suite_atom_id_map(), and core::pose::Pose::total_residue().

Referenced by align_poses(), and protocols::swa::create_alignment_id_map().

std::map< core::Size, core::Size > protocols::swa::rna::create_full_to_input_res_map

(

utility::vector1< core::Size > const &

input_res_vector)

Definition at line 470 of file StepWiseRNA_Util.cc.

Referenced by protocols::swa::rna::StepWiseRNA_PoseSetup::correctly_copy_HO2star_positions(), and protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::StepWiseRNA_CombineLongLoopFilterer().

core::pack::task::PackerTaskOP protocols::swa::rna::create_standard_o2star_pack_task	(	pose::Pose const &	pose,
		utility::vector1< core::Size > const &	O2star_pack_seq_num
	)

Definition at line 2205 of file StepWiseRNA_Util.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::scoring::rna::chemical_shift::Contain_seq_num(), core::pack::task::TaskFactory::create_packer_task(), core::conformation::Residue::is_RNA(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by protocols::swa::rna::StepWiseRNA_ResidueSampler::initialize_o2star_packer_task(), and o2star_minimize().

utility::vector1< utility::vector1< Residue_info > > protocols::swa::rna::Create_strand_list

(

utility::vector1< Residue_info > const &

residue_list)

Definition at line 260 of file StepWiseRNA_ResidueInfo.cc.

References sort_residue_list().

core::Real protocols::swa::rna::DOF_bin_size

(

std::string const &

DOF)

Definition at line 406 of file StepWiseRNA_FloatingBase_Sampler_Util.cc.

References centroid_bin_size, euler_angle_bin_size, and euler_z_bin_size.

Referenced by Analyze_base_bin_map().

int protocols::swa::rna::DOF_bin_value	(	std::map< Base_bin, int, compare_base_bin >::const_iterator const &	base_bin_it,
		std::string const &	DOF
	)

Definition at line 383 of file StepWiseRNA_FloatingBase_Sampler_Util.cc.

Referenced by Analyze_base_bin_map().

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

Definition at line 418 of file StepWiseRNA_Util.cc.

Referenced by check_is_working_res().

void protocols::swa::rna::enumerate_starting_pose_data_list	(	utility::vector1< pose_data_struct2 > &	starting_pose_data_list,
		utility::vector1< FloatingBaseChainClosureJobParameter > const &	FB_CC_JP_list,
		core::pose::Pose const &	pose
	)

Definition at line 1139 of file StepWiseRNA_VirtualRiboseSampler.cc.

References copy_bulge_res_and_ribose_torsion(), protocols::swa::rna::FloatingBaseChainClosureJobParameter::PDL, protocols::swa::rna::pose_data_struct2::pose_OP, protocols::swa::rna::pose_data_struct2::score, and protocols::swa::rna::pose_data_struct2::tag.

Referenced by sample_user_specified_virtual_riboses().

bool protocols::swa::rna::fast_full_atom_VDW_repulsion_screen	(	core::pose::Pose const &	pose,
		core::Size const	res_1,
		core::Size const	res_2,
		bool const	Is_prepend
	)

Definition at line 92 of file StepWiseRNA_VirtualRiboseSampler.cc.

References core::conformation::Residue::atom_type(), core::chemical::AtomType::lj_radius(), core::chemical::AtomType::name(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by floating_base_chain_closure_sampling().

bool protocols::swa::rna::file_exists

(

std::string const &

file_name)

Definition at line 1054 of file StepWiseRNA_Util.cc.

Referenced by core::chemical::add_atom_type_set_parameters_from_command_line(), protocols::canonical_sampling::MetropolisHastingsMover::add_shear_mover(), protocols::canonical_sampling::MetropolisHastingsMover::add_small_mover(), protocols::protein_interface_design::movers::HotspotHasherMover::apply(), protocols::canonical_sampling::CanonicalSamplingMover::apply(), protocols::flxbb::LayerDesignOperation::apply(), protocols::jobdist::AtomTreeDiffJobDistributor::AtomTreeDiffJobDistributor(), protocols::dna::checkpoint_cleanup(), protocols::jd2::BOINCJobDistributor::checkpoint_clear(), protocols::jobdist::BaseJobDistributor::checkpoint_clear(), protocols::jd2::BOINCJobDistributor::checkpoint_read(), protocols::jobdist::BaseJobDistributor::checkpoint_read(), protocols::constraints_additional::ConstraintEvaluator::ConstraintEvaluator(), protocols::simple_filters::EvaluatedTrialMover::dump_file(), protocols::jd2::AtomTreeDiffJobOutputter::dump_pose(), protocols::jobdist::PlainPdbJobDistributor::dump_pose_and_map(), protocols::enzdes::EnzdesJobOutputter::EnzdesJobOutputter(), protocols::simple_filters::ExternalEvaluator::ExternalEvaluator(), protocols::jd2::archive::ArchiveManager::finalize_batch(), protocols::abinitio::IterativeBase::gen_noe_assignments(), protocols::comparative_modeling::AlignmentClustering::generateRankedAlignments(), get_binary_rna_silent_struct_safe(), protocols::jd2::FileSystemJobDistributor::get_new_job_id(), protocols::motifs::get_targetconformers_user(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::import_exp_chemical_shift_data(), protocols::MakeRotLib::init_rotamers_centroids(), core::scoring::rna::RNA_TorsionPotential::initialize_potential_from_file(), protocols::coarse_rna::CoarseRNA_DeNovoProtocol::initialize_tag_is_done(), protocols::rna::RNA_DeNovoProtocol::initialize_tag_is_done(), protocols::jobdist::PlainPdbJobDistributor::is_finished(), protocols::jd2::PDBJobOutputter::job_has_completed(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::load_lib(), protocols::jobdist::load_s_and_l(), protocols::dna::make_subdirs(), protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::max_level_index(), protocols::motifs::MotifLibrary::MotifLibrary(), protocols::swa::rna::StepWiseRNA_Minimizer::output_empty_minimizer_silent_file(), protocols::jobdist::PlainRawJobDistributor::PlainRawJobDistributor(), protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::pool_exists(), protocols::comparative_modeling::AlignmentClustering::poses_from_cmd_line(), protocols::comparative_modeling::poses_from_cmd_line(), protocols::constraints_additional::ConstraintEvaluator::prepare_pose(), core::import_pose::pose_stream::SilentFilePoseInputStream::read_all_files_(), protocols::frag_picker::nonlocal::NonlocalFrags::read_checkpoint_file(), core::scoring::UnfoldedStatePotential::read_database_file(), protocols::constraints_additional::SequenceCoupling1BDConstraint::read_def(), protocols::constraints_additional::SequenceCouplingConstraint::read_def(), core::scoring::constraints::SequenceProfileConstraint::read_def(), protocols::jd2::ScoreOnlyJobOutputter::read_done_jobs(), protocols::jd2::SilentFileJobOutputter::read_done_jobs(), protocols::jd2::archive::ArchiveManager::read_existing_batches(), core::chemical::read_topology_file(), protocols::abinitio::IterativeBase::reassign_noesy_data(), protocols::checkpoint::CheckPointer::recover_checkpoint(), protocols::enzdes::EnzdesFlexBBProtocol::recover_loops_from_file(), remove_file(), protocols::genetic_algorithm::GeneticAlgorithm::rename_checkpoint_files(), protocols::jd2::archive::ArchiveBase::restore_from_file(), protocols::abinitio::HedgeArchive::restore_status(), protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::RestrictConservedLowDdgOperation(), protocols::jd2::MpiFileBuffer::run(), protocols::motifs::LigandMotifSearch::run(), protocols::abinitio::HedgeArchive::save_decoys(), protocols::jd2::archive::ArchiveBase::save_to_file(), core::sequence::SequenceFactory::seq_from_file(), protocols::toolbox::task_operations::SeqprofConsensusOperation::SeqprofConsensusOperation(), protocols::abinitio::IterativeBase::setup_autoNOE(), protocols::jd2::archive::ArchiveManager::start_new_batch(), protocols::jobdist::PlainSilentFileJobDistributor::startup(), protocols::jobdist::universal_main(), protocols::qsar::scoring_grid::GridManager::update_grids(), core::io::raw_data::RawFileData::write_all(), core::conformation::symmetry::SymmetryInfo::write_silent_struct(), core::io::raw_data::DecoyFileData::write_struct(), core::io::raw_data::ScoreFileData::write_struct(), and protocols::jd2::WriteFileSFB::WriteFileSFB().

bool protocols::swa::rna::floating_base_chain_break_screening	(	core::pose::Pose &	chain_break_screening_pose,
		core::scoring::ScoreFunctionOP const &	chainbreak_scorefxn,
		SillyCountStruct &	count_data,
		core::Size const &	five_prime_res,
		std::string const &	tag,
		bool const	verbose
	)

Definition at line 172 of file StepWiseRNA_VirtualRiboseSampler.cc.

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, protocols::swa::rna::SillyCountStruct::chain_break_screening_count, protocols::swa::rna::SillyCountStruct::chain_closable_count, core::pose::Pose::energies(), protocols::swa::rna::SillyCountStruct::good_angle_count, protocols::swa::rna::SillyCountStruct::good_distance_count, protocols::swa::rna::SillyCountStruct::in_range_CCD_torsion, set_CCD_torsions_to_zero(), protocols::swa::rna::SillyCountStruct::tot_rotamer_count, and core::scoring::Energies::total_energies().

Referenced by floating_base_chain_closure_sampling().

utility::vector1< pose_data_struct2 > protocols::swa::rna::floating_base_chain_closure_post_process	(	utility::vector1< FB_Pose_Data > &	pose_data_list,
		core::pose::Pose &	viewer_pose,
		core::scoring::ScoreFunctionOP const &	sampling_scorefxn,
		FloatingBaseChainClosureJobParameter const &	FB_job_params,
		bool const	rm_chain_break_jump_point
	)

Definition at line 702 of file StepWiseRNA_VirtualRiboseSampler.cc.

References core::scoring::angle_constraint, apply_virtual_rna_residue_variant_type(), core::scoring::atom_pair_constraint, core::id::BB, protocols::swa::rna::FloatingBaseChainClosureJobParameter::bulge_res, core::id::CHI, core::pose::Pose::constraint_set(), core::scoring::fa_rep, protocols::swa::rna::FloatingBaseChainClosureJobParameter::five_prime_chain_break, core::scoring::linear_chainbreak, core::optimization::MinimizerOptions::nblist_auto_update(), Output_title_text(), protocols::swa::rna::pose_data_struct2::pose_OP, remove_chain_break_jump_point(), core::pose::remove_variant_type_from_pose_residue(), core::scoring::rna_sugar_close, core::kinematics::MoveMap::set_bb(), and core::scoring::ScoreFunction::set_weight().

Referenced by sample_virtual_ribose_and_bulge_and_close_chain().

void protocols::swa::rna::floating_base_chain_closure_sampling	(	utility::vector1< FB_Pose_Data > &	pose_data_list,
		core::pose::Pose &	viewer_pose,
		FloatingBaseChainClosureJobParameter const &	FB_job_params,
		core::scoring::ScoreFunctionOP const &	chainbreak_scorefxn,
		core::scoring::ScoreFunctionOP const &	atr_rep_screening_scorefxn,
		StepWiseRNA_VDW_Bin_ScreenerOP const &	VDW_bin_screener,
		bool const	CCD_grid_index_screen
	)

Definition at line 484 of file StepWiseRNA_VirtualRiboseSampler.cc.

References apply_rotamer(), protocols::swa::rna::FB_Pose_Data::base_rep_score, core::id::BB, protocols::swa::rna::FloatingBaseChainClosureJobParameter::bulge_res, protocols::swa::rna::FloatingBaseChainClosureJobParameter::bulge_res_base_state, protocols::swa::rna::FloatingBaseChainClosureJobParameter::bulge_res_pucker_state, protocols::swa::rna::FloatingBaseChainClosureJobParameter::bulge_suite, Check_chain_closable_floating_base(), core::id::CHI, fast_full_atom_VDW_repulsion_screen(), protocols::swa::rna::FloatingBaseChainClosureJobParameter::five_prime_chain_break, floating_base_chain_break_screening(), floating_base_full_atom_van_der_Waals_screening(), protocols::swa::rna::Torsion_Info::id, protocols::swa::rna::FB_Pose_Data::Is_chain_close, protocols::swa::rna::FloatingBaseChainClosureJobParameter::Is_prepend, protocols::swa::rna::FloatingBaseChainClosureJobParameter::moving_res, Output_title_text(), protocols::swa::rna::FB_Pose_Data::pose_OP, core::pose::Pose::residue(), protocols::swa::rna::FB_Pose_Data::tag, protocols::swa::rna::Torsion_Info::value, and core::conformation::Residue::xyz().

Referenced by sample_virtual_ribose_and_bulge_and_close_chain().

utility::vector1< FB_Pose_Data > protocols::swa::rna::floating_base_chain_closure_setup	(	utility::vector1< pose_data_struct2 > const &	input_pose_data_list,
		FloatingBaseChainClosureJobParameter const &	FB_job_params,
		core::scoring::ScoreFunctionOP const &	atr_rep_screening_scorefxn,
		core::scoring::ScoreFunctionOP const &	full_scorefxn,
		pose::Pose &	viewer_pose,
		bool const	do_minimize
	)

Definition at line 221 of file StepWiseRNA_VirtualRiboseSampler.cc.

References Add_harmonic_chainbreak_constraint(), core::pose::add_variant_type_to_pose_residue(), core::scoring::angle_constraint, core::scoring::atom_pair_constraint, protocols::swa::rna::FB_Pose_Data::base_rep_score, protocols::swa::rna::FB_Pose_Data::base_tag, core::id::BB, protocols::swa::rna::FloatingBaseChainClosureJobParameter::bulge_res, core::scoring::ch_bond, core::id::CHI, core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::kinematics::FoldTree::cutpoint(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::energies(), core::scoring::fa_rep, protocols::swa::rna::FloatingBaseChainClosureJobParameter::five_prime_chain_break, core::pose::Pose::fold_tree(), protocols::swa::rna::FB_Pose_Data::Is_chain_close, protocols::swa::rna::FloatingBaseChainClosureJobParameter::Is_prepend, core::scoring::linear_chainbreak, core::optimization::MinimizerOptions::min_type(), core::optimization::MinimizerOptions::minimize_tolerance(), minimize_with_constraints(), protocols::swa::rna::FloatingBaseChainClosureJobParameter::moving_res, protocols::swa::rna::FloatingBaseChainClosureJobParameter::moving_res_base_state, protocols::swa::rna::FloatingBaseChainClosureJobParameter::moving_res_pucker_state, core::optimization::MinimizerOptions::nblist_auto_update(), core::kinematics::FoldTree::num_jump(), O3I_C5IPLUS2_MAX_DIST, Output_title_text(), protocols::swa::rna::FB_Pose_Data::pose_OP, protocols::swa::rna::pose_data_struct2::pose_OP, protocols::swa::rna::FloatingBaseChainClosureJobParameter::reference_res, core::pose::remove_variant_type_from_pose_residue(), remove_virtual_rna_residue_variant_type(), rescale_scorefxn(), core::pose::Pose::residue(), core::optimization::AtomTreeMinimizer::run(), protocols::swa::rna::FB_Pose_Data::score, core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), core::pose::Pose::set_torsion(), setup_chain_break_jump_point(), protocols::swa::rna::FB_Pose_Data::starting_cst_set_OP, protocols::swa::rna::FB_Pose_Data::starting_fold_tree, protocols::swa::rna::FB_Pose_Data::tag, protocols::swa::rna::pose_data_struct2::tag, core::scoring::Energies::total_energies(), core::kinematics::FoldTree::upstream_jump_residue(), and core::conformation::Residue::xyz().

Referenced by sample_virtual_ribose_and_bulge_and_close_chain().

bool protocols::swa::rna::floating_base_full_atom_van_der_Waals_screening	(	core::pose::Pose &	current_pose_screen,
		core::Real const &	base_rep_score,
		core::scoring::ScoreFunctionOP const &	atr_rep_screening_scorefxn,
		SillyCountStruct &	count_data,
		bool const	verbose
	)

Definition at line 131 of file StepWiseRNA_VirtualRiboseSampler.cc.

References core::pose::Pose::energies(), core::scoring::fa_rep, protocols::swa::rna::SillyCountStruct::fast_full_atom_VDW_replusion_screen, protocols::swa::rna::SillyCountStruct::good_bin_rep_count, protocols::swa::rna::SillyCountStruct::good_rep_rotamer_count, protocols::swa::rna::SillyCountStruct::tot_rotamer_count, and core::scoring::Energies::total_energies().

Referenced by floating_base_chain_closure_sampling().

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

Definition at line 1908 of file StepWiseRNA_Util.cc.

References core::id::BB, core::id::CHI, and core::kinematics::MoveMap::set().

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
	)

Definition at line 1165 of file StepWiseRNA_Util.cc.

References core::scoring::rna::chemical_shift::Contain_seq_num(), core::conformation::Residue::has_variant_type(), Output_boolean(), Output_seq_num_list(), Output_title_text(), phosphate_square_deviation(), core::pose::Pose::residue(), core::pose::Pose::sequence(), suite_square_deviation(), and core::pose::Pose::total_residue().

Referenced by protocols::swa::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file(), protocols::swa::rna::StepWiseRNA_Clusterer::Is_new_cluster_center_with_job_parameters(), and protocols::swa::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file().

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::get_atom_coordinates	(	utility::vector1< std::pair< id::AtomID, numeric::xyzVector< core::Real > > > &	xyz_list,
		Size const &	seq_num,
		core::conformation::Residue const &	rsd_at_origin,
		core::kinematics::Stub const &	moving_res_base_stub
	)

Definition at line 2718 of file StepWiseRNA_Util.cc.

References core::io::serialization::at(), core::kinematics::Stub::M, core::conformation::Residue::natoms(), core::kinematics::Stub::v, and core::conformation::Residue::xyz().

Referenced by set_base_coordinate_frame(), and protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::VDW_rep_screen().

core::io::silent::BinaryRNASilentStruct protocols::swa::rna::get_binary_rna_silent_struct_safe	(	pose::Pose const &	const_pose,
		std::string const &	tag,
		std::string const &	silent_file
	)

Definition at line 91 of file StepWiseRNA_OutputData.cc.

References protocols::swa::rna::Euler_angles::alpha, core::io::serialization::at(), core::io::silent::SilentFileData::begin(), protocols::swa::rna::Euler_angles::beta, check_for_messed_up_structure(), convert_euler_to_coordinate_matrix(), core::sequence::end, core::io::silent::SilentFileData::end(), file_exists(), protocols::swa::rna::Euler_angles::gamma, core::chemical::ChemicalManager::get_instance(), core::io::silent::SilentFileData::read_file(), remove_file(), core::pose::Pose::residue(), core::chemical::RNA, core::pose::Pose::set_xyz(), core::pose::Pose::total_residue(), core::pose::Pose::xyz(), and protocols::swa::rna::Euler_angles::z.

Referenced by get_binary_rna_silent_struct_safe_wrapper().

core::io::silent::BinaryRNASilentStruct protocols::swa::rna::get_binary_rna_silent_struct_safe_wrapper	(	pose::Pose const &	const_pose,
		std::string const &	tag,
		std::string const &	silent_file,
		bool const	write_score_only
	)

Definition at line 246 of file StepWiseRNA_OutputData.cc.

References get_binary_rna_silent_struct_safe().

Referenced by Output_data().

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
	)

Definition at line 1800 of file StepWiseRNA_Util.cc.

References core::conformation::Residue::xyz().

Referenced by Check_chain_closable_floating_base().

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
	)

Definition at line 2874 of file StepWiseRNA_Util.cc.

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by virtualize_bulges().

Euler_angles protocols::swa::rna::Get_euler_angles

(

numeric::xyzMatrix< core::Real > const &

coordinate_matrix)

Definition at line 544 of file StepWiseRNA_FloatingBase_Sampler_Util.cc.

References protocols::swa::rna::Euler_angles::alpha, protocols::swa::rna::Euler_angles::gamma, and protocols::swa::rna::Euler_angles::z.

Base_bin protocols::swa::rna::Get_euler_stub_bin	(	numeric::xyzVector< core::Real > const &	centriod,
		Euler_angles const &	euler_angles
	)

Definition at line 356 of file StepWiseRNA_FloatingBase_Sampler_Util.cc.

References protocols::swa::rna::Euler_angles::alpha, centroid_bin_size, protocols::swa::rna::Base_bin::centroid_x, protocols::swa::rna::Base_bin::centroid_y, protocols::swa::rna::Base_bin::centroid_z, protocols::swa::rna::Base_bin::euler_alpha, euler_angle_bin_size, protocols::swa::rna::Base_bin::euler_gamma, protocols::swa::rna::Base_bin::euler_z, euler_z_bin_size, protocols::swa::rna::Euler_angles::gamma, and protocols::swa::rna::Euler_angles::z.

core::Real protocols::swa::rna::get_max_centroid_to_atom_distance	(	utility::vector1< core::conformation::ResidueOP > const &	rsd_at_origin_list,
		std::string const	atom_name
	)

Definition at line 706 of file StepWiseRNA_FloatingBase_Sampler_Util.cc.

References core::kinematics::distance(), core::scoring::rna::get_rna_base_centroid(), core::chemical::name_from_aa(), and core::conformation::Residue::xyz().

Referenced by protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling().

core::Size protocols::swa::rna::get_max_seq_num_from_res_map

(

std::map< core::Size, core::Size > const &

my_map)

Definition at line 152 of file StepWiseRNA_ResidueInfo.cc.

core::Size protocols::swa::rna::Get_num_side_chain_atom_from_res_name	(	chemical::AA const &	res_aa,
		bool const	verbose
	)

Definition at line 1377 of file StepWiseRNA_Util.cc.

References core::chemical::name_from_aa().

Referenced by base_atoms_square_deviation(), phosphate_base_phosphate_square_deviation(), and suite_square_deviation().

std::string protocols::swa::rna::Get_one_letter_name

(

std::string const &

three_letter_name)

Definition at line 129 of file StepWiseRNA_ResidueInfo.cc.

Referenced by Output_residue_struct().

BaseState protocols::swa::rna::Get_residue_base_state	(	core::pose::Pose const &	pose,
		Size const	seq_num
	)

Definition at line 2605 of file StepWiseRNA_Util.cc.

References ANTI, core::id::CHI, core::scoring::rna::NUM_RNA_MAINCHAIN_TORSIONS(), core::pose::Pose::residue(), and SYN.

Referenced by protocols::swa::rna::StepWiseRNA_Clusterer::create_silent_file_and_tag_list().

Residue_info protocols::swa::rna::Get_residue_from_seq_num	(	Size const &	seq_num,
		utility::vector1< Residue_info > const &	residue_list
	)

Definition at line 236 of file StepWiseRNA_ResidueInfo.cc.

utility::vector1< Residue_info > protocols::swa::rna::Get_residue_list_from_fasta

(

std::string const

full_fasta_sequence)

Definition at line 215 of file StepWiseRNA_ResidueInfo.cc.

References protocols::swa::rna::Residue_info::name, and protocols::swa::rna::Residue_info::seq_num.

PuckerState protocols::swa::rna::Get_residue_pucker_state	(	core::pose::Pose const &	pose,
		Size const	seq_num,
		bool const	verbose
	)

Definition at line 2626 of file StepWiseRNA_Util.cc.

References core::scoring::dna::DELTA, core::conformation::Residue::has_variant_type(), NORTH, core::pose::Pose::residue(), and SOUTH.

Referenced by protocols::swa::rna::RNA_LoopCloseSampler::apply(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::cluster_pose_data_list(), protocols::swa::rna::StepWiseRNA_ResidueSampler::cluster_pose_data_list(), protocols::swa::rna::StepWiseRNA_Clusterer::create_silent_file_and_tag_list(), protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::Get_residue_pucker_state_internal(), protocols::swa::rna::StepWiseRNA_Clusterer::Is_old_individual_suite_cluster(), Is_same_ribose_pucker(), and protocols::swa::rna::RNA_LoopCloseSampler::torsion_angles_within_cutoffs().

core::kinematics::Stub protocols::swa::rna::Get_ribose_stub	(	conformation::Residue const &	rsd,
		bool const	Is_prepend,
		bool const	verbose
	)

Definition at line 311 of file StepWiseRNA_FloatingBase_Sampler_Util.cc.

References core::conformation::Residue::is_RNA(), Output_boolean(), and core::conformation::Residue::xyz().

Referenced by protocols::swa::rna::StepWiseRNA_ResidueSampler::get_reference_stub().

void protocols::swa::rna::get_specific_atom_coordinate	(	std::string const &	atom_name,
		numeric::xyzVector< core::Real > &	atom_pos,
		core::conformation::Residue const &	rsd_at_origin,
		core::kinematics::Stub const &	moving_res_base_stub
	)

Definition at line 689 of file StepWiseRNA_FloatingBase_Sampler_Util.cc.

References core::kinematics::Stub::M, core::kinematics::Stub::v, and core::conformation::Residue::xyz().

Referenced by check_floating_base_chain_closable().

utility::vector1< core::Size > protocols::swa::rna::get_surrounding_O2star_hydrogen	(	pose::Pose const &	pose,
		utility::vector1< core::Size > const &	moving_res,
		bool	verbose
	)

Definition at line 2014 of file StepWiseRNA_Util.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::io::serialization::at(), core::conformation::Residue::atom_index(), core::chemical::ResidueType::atom_name(), core::conformation::Residue::atom_type(), core::scoring::rna::chemical_shift::Contain_seq_num(), core::conformation::Residue::first_sidechain_atom(), core::chemical::AtomType::name(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by protocols::swa::rna::StepWiseRNA_Minimizer::apply(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::initialize_o2star_packer_task(), and protocols::swa::rna::StepWiseRNA_ResidueSampler::initialize_o2star_packer_task().

std::string protocols::swa::rna::get_tag_from_pdb_filename

(

std::string const

pdb_filename)

Definition at line 3060 of file StepWiseRNA_Util.cc.

std::string protocols::swa::rna::Get_three_letter_name

(

std::string const &

one_letter_name)

Definition at line 139 of file StepWiseRNA_ResidueInfo.cc.

Referenced by Convert_rebuild_residue_string_to_list().

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

Definition at line 286 of file StepWiseRNA_Util.cc.

References core::conformation::Residue::has_variant_type(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by protocols::swa::rna::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs().

void protocols::swa::rna::import_pose_from_silent_file	(	core::pose::Pose &	import_pose,
		std::string const &	silent_file,
		std::string const &	input_tag
	)

Definition at line 2742 of file StepWiseRNA_Util.cc.

References check_for_messed_up_structure(), core::sequence::end, core::chemical::ChemicalManager::get_instance(), core::io::silent::SilentFileData::read_file(), and core::chemical::RNA.

Referenced by protocols::swa::rna::StepWiseRNA_JobParameters_Setup::get_previously_closed_cutpoint_from_imported_silent_file(), and protocols::swa::rna::StepWiseRNA_PoseSetup::Import_pose().

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_
	)

Definition at line 3488 of file StepWiseRNA_Util.cc.

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::chainbreak, core::scoring::fa_atr, core::scoring::fa_rep, core::scoring::fa_sol, core::scoring::hbond_lr_bb_sc, core::scoring::hbond_sc, core::scoring::hbond_sr_bb_sc, core::scoring::linear_chainbreak, and core::scoring::lk_nonpolar.

Referenced by protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::initialize_scorefunctions(), protocols::swa::rna::StepWiseRNA_ResidueSampler::initialize_scorefunctions(), and sample_user_specified_virtual_riboses().

bool protocols::swa::rna::Is_1H5star_atom

(

std::string const &

atom_name)

Definition at line 111 of file StepWiseRNA_Util.cc.

bool protocols::swa::rna::Is_2H5star_atom

(

std::string const &

atom_name)

Definition at line 113 of file StepWiseRNA_Util.cc.

bool protocols::swa::rna::Is_base_pair	(	core::kinematics::Stub const &	moving_res_base,
		utility::vector1< core::kinematics::Stub > const &	other_residues_base_list,
		core::Real const	base_axis_CUTOFF,
		core::Real const	base_planarity_CUTOFF
	)

Definition at line 143 of file StepWiseRNA_FloatingBase_Sampler_Util.cc.

References core::kinematics::Stub::M, and core::kinematics::Stub::v.

Referenced by Base_centroid_screening(), and Is_medium_base_stack_and_medium_base_pair().

bool protocols::swa::rna::Is_base_stack	(	core::kinematics::Stub const &	moving_res_base,
		utility::vector1< core::kinematics::Stub > const &	other_residues_base_list,
		core::Real const	base_axis_CUTOFF,
		core::Real const	base_planarity_CUTOFF
	)

Definition at line 84 of file StepWiseRNA_FloatingBase_Sampler_Util.cc.

References core::kinematics::Stub::M, and core::kinematics::Stub::v.

Referenced by Base_centroid_screening(), Is_medium_base_stack_and_medium_base_pair(), and Is_strong_base_stack().

bool protocols::swa::rna::Is_C2star_atom

(

std::string const &

atom_name)

Definition at line 103 of file StepWiseRNA_Util.cc.

bool protocols::swa::rna::Is_C3star_atom

(

std::string const &

atom_name)

Definition at line 105 of file StepWiseRNA_Util.cc.

bool protocols::swa::rna::Is_C4star_atom

(

std::string const &

atom_name)

Definition at line 107 of file StepWiseRNA_Util.cc.

bool protocols::swa::rna::Is_C5star_atom

(

std::string const &

atom_name)

Definition at line 109 of file StepWiseRNA_Util.cc.

bool protocols::swa::rna::Is_close_chain_break

(

pose::Pose const &

pose)

Definition at line 911 of file StepWiseRNA_Util.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Residue::has_variant_type(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

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
	)

Definition at line 831 of file StepWiseRNA_Util.cc.

References sort_seq_num_list().

bool protocols::swa::rna::Is_five_prime_phosphate_atom

(

std::string const &

atom_name)

Definition at line 121 of file StepWiseRNA_Util.cc.

References Is_O1P_atom(), Is_O2P_atom(), Is_O5star_atom(), and Is_P_atom().

Referenced by Is_phosphate_atom().

bool protocols::swa::rna::Is_H3star_atom

(

std::string const &

atom_name)

Definition at line 115 of file StepWiseRNA_Util.cc.

bool protocols::swa::rna::Is_H4star_atom

(

std::string const &

atom_name)

Definition at line 117 of file StepWiseRNA_Util.cc.

bool protocols::swa::rna::Is_medium_base_stack_and_medium_base_pair	(	core::kinematics::Stub const &	moving_res_base,
		utility::vector1< core::kinematics::Stub > const &	other_residues_base_list
	)

Definition at line 232 of file StepWiseRNA_FloatingBase_Sampler_Util.cc.

References Is_base_pair(), and Is_base_stack().

Referenced by Base_centroid_screening().

bool protocols::swa::rna::Is_O1P_atom

(

std::string const &

atom_name)

Definition at line 89 of file StepWiseRNA_Util.cc.

Referenced by Is_five_prime_phosphate_atom().

bool protocols::swa::rna::Is_O2P_atom

(

std::string const &

atom_name)

Definition at line 91 of file StepWiseRNA_Util.cc.

Referenced by Is_five_prime_phosphate_atom().

bool protocols::swa::rna::Is_O2star_atom

(

std::string const &

atom_name)

Definition at line 95 of file StepWiseRNA_Util.cc.

bool protocols::swa::rna::Is_O3star_atom

(

std::string const &

atom_name)

Definition at line 97 of file StepWiseRNA_Util.cc.

Referenced by Is_three_prime_phosphate_atom().

bool protocols::swa::rna::Is_O4star_atom

(

std::string const &

atom_name)

Definition at line 99 of file StepWiseRNA_Util.cc.

bool protocols::swa::rna::Is_O5star_atom

(

std::string const &

atom_name)

Definition at line 101 of file StepWiseRNA_Util.cc.

Referenced by Is_five_prime_phosphate_atom().

bool protocols::swa::rna::Is_P_atom

(

std::string const &

atom_name)

Definition at line 93 of file StepWiseRNA_Util.cc.

Referenced by Is_five_prime_phosphate_atom().

bool protocols::swa::rna::Is_phosphate_atom

(

std::string const &

atom_name)

Definition at line 123 of file StepWiseRNA_Util.cc.

References Is_five_prime_phosphate_atom(), and Is_three_prime_phosphate_atom().

Referenced by core::chemical::rna::RNA_ResidueType::update_derived_rna_data().

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
	)

Definition at line 2793 of file StepWiseRNA_Util.cc.

References core::pose::Pose::residue().

Referenced by protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::previously_builded_res_VDW_filter(), protocols::swa::rna::StepWiseRNA_ResidueSampler::standard_sampling(), and protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::VDW_rep_screen_with_act_pose().

bool protocols::swa::rna::Is_ribose_virtual	(	core::pose::Pose const &	pose,
		core::Size const	ribose_res,
		core::Size const	bulge_res
	)

Definition at line 917 of file StepWiseRNA_VirtualRiboseSampler.cc.

References core::conformation::Residue::has_variant_type(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by protocols::swa::rna::StepWiseRNA_ResidueSampler::Is_current_sugar_virtual(), protocols::swa::rna::StepWiseRNA_ResidueSampler::Is_five_prime_chain_break_sugar_virtual(), protocols::swa::rna::StepWiseRNA_ResidueSampler::Is_previous_sugar_virtual(), and protocols::swa::rna::StepWiseRNA_ResidueSampler::Is_three_prime_chain_break_sugar_virtual().

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
	)

Definition at line 2681 of file StepWiseRNA_Util.cc.

References Get_residue_pucker_state().

Referenced by protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::cluster_pose_data_list(), protocols::swa::rna::StepWiseRNA_ResidueSampler::cluster_pose_data_list(), and protocols::swa::rna::StepWiseRNA_Clusterer::Is_old_individual_suite_cluster().

bool protocols::swa::rna::Is_strong_base_stack	(	core::kinematics::Stub const &	moving_res_base,
		utility::vector1< core::kinematics::Stub > const &	other_residues_base_list
	)

Definition at line 220 of file StepWiseRNA_FloatingBase_Sampler_Util.cc.

References Is_base_stack().

Referenced by Base_centroid_screening().

bool protocols::swa::rna::Is_three_prime_phosphate_atom

(

std::string const &

atom_name)

Definition at line 119 of file StepWiseRNA_Util.cc.

References Is_O3star_atom().

Referenced by Is_phosphate_atom().

bool protocols::swa::rna::Is_virtual_base

(

conformation::Residue const &

rsd)

Definition at line 590 of file StepWiseRNA_Util.cc.

References core::conformation::Residue::aa(), core::conformation::Residue::atom_type(), core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::has_variant_type(), core::chemical::AtomType::name(), core::chemical::name_from_aa(), core::conformation::Residue::nheavyatoms(), and Output_boolean().

Referenced by align_poses(), and protocols::swa::rna::StepWiseRNA_ResidueSampler::apply_bulge_variant().

core::Size protocols::swa::rna::make_cut_at_moving_suite	(	core::kinematics::FoldTree &	fold_tree,
		Size const &	moving_suite
	)

Definition at line 2522 of file StepWiseRNA_Util.cc.

References core::kinematics::FoldTree::downstream_jump_residue(), core::kinematics::FoldTree::new_jump(), core::kinematics::FoldTree::num_jump(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_partition_definition(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::get_base_atr_rep_score(), protocols::swa::rna::StepWiseRNA_ResidueSampler::get_base_atr_rep_score(), protocols::swa::rna::RNA_LoopCloseSampler::initialize_fa_rep(), and make_cut_at_moving_suite().

core::Size protocols::swa::rna::make_cut_at_moving_suite	(	pose::Pose &	pose,
		Size const &	moving_suite
	)

Definition at line 2541 of file StepWiseRNA_Util.cc.

References core::pose::Pose::fold_tree(), and make_cut_at_moving_suite().

void protocols::swa::rna::minimize_all_sampled_floating_bases	(	core::pose::Pose &	viewer_pose,
		utility::vector1< FloatingBaseChainClosureJobParameter > const &	FB_JP_list,
		utility::vector1< pose_data_struct2 > &	pose_data_list,
		core::scoring::ScoreFunctionOP const &	sampling_scorefxn,
		StepWiseRNA_JobParametersCOP const &	job_parameters,
		bool const	virtual_ribose_is_from_prior_step
	)

Definition at line 808 of file StepWiseRNA_VirtualRiboseSampler.cc.

References core::pose::add_variant_type_to_pose_residue(), core::id::BB, protocols::swa::rna::FloatingBaseChainClosureJobParameter::bulge_res, core::id::CHI, core::scoring::rna::chemical_shift::Contain_seq_num(), core::conformation::Residue::has_variant_type(), core::optimization::MinimizerOptions::nblist_auto_update(), Output_title_text(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), and core::kinematics::MoveMap::set_bb().

Referenced by sample_user_specified_virtual_riboses(), and protocols::swa::rna::StepWiseRNA_ResidueSampler::standard_sampling_WRAPPER().

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
	)

Definition at line 127 of file StepWiseRNA_Util.cc.

References core::scoring::constraints::add_coordinate_constraints(), and core::pose::Pose::constraint_set().

Referenced by floating_base_chain_closure_setup().

bool protocols::swa::rna::minimizer_sort_criteria	(	pose_data_struct2	pose_data_1,
		pose_data_struct2	pose_data_2
	)

Definition at line 130 of file StepWiseRNA_Minimizer.cc.

References protocols::swa::rna::pose_data_struct2::score.

Referenced by protocols::swa::rna::StepWiseRNA_Minimizer::apply().

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

Definition at line 3083 of file StepWiseRNA_Util.cc.

References core::kinematics::FoldTree::downstream_jump_residue(), core::kinematics::FoldTree::num_cutpoint(), core::kinematics::FoldTree::set_jump_atoms(), and core::kinematics::FoldTree::upstream_jump_residue().

void protocols::swa::rna::o2star_minimize	(	pose::Pose &	pose,
		core::scoring::ScoreFunctionOP const &	packer_scorefxn
	)

Definition at line 2176 of file StepWiseRNA_Util.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by protocols::swa::rna::StepWiseRNA_Minimizer::apply(), and protocols::swa::RigidBodySampler::search_translations().

void protocols::swa::rna::o2star_minimize	(	pose::Pose &	pose,
		core::scoring::ScoreFunctionOP const &	packer_scorefxn,
		utility::vector1< core::Size > const &	O2star_pack_seq_num
	)

Definition at line 2191 of file StepWiseRNA_Util.cc.

References create_standard_o2star_pack_task(), Output_seq_num_list(), and core::pack::rotamer_trials().

void protocols::swa::rna::Output_bool_list	(	std::string const	tag,
		utility::vector1< Size > const &	size_list,
		core::Size const	spacing
	)

Definition at line 872 of file StepWiseRNA_Util.cc.

Referenced by protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_Is_residue_prepend(), print_JobParameters_info(), and protocols::swa::rna::StepWiseRNA_JobParameters_Setup::setup_additional_cutpoint_closed().

void protocols::swa::rna::Output_bool_list	(	std::string const	tag,
		utility::vector1< bool > const &	bool_list,
		core::Size const	spacing
	)

Definition at line 882 of file StepWiseRNA_Util.cc.

References Output_boolean().

void protocols::swa::rna::Output_boolean	(	std::string const &	tag,
		bool	boolean
	)

Definition at line 1925 of file StepWiseRNA_Util.cc.

References protocols::comparative_modeling::features::A.

Referenced by align_poses(), protocols::rna::RNA_Minimizer::apply(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::apply(), protocols::swa::rna::StepWiseRNA_Minimizer::apply(), protocols::swa::rna::StepWiseRNA_ResidueSampler::apply(), protocols::swa::rna::StepWiseRNA_PoseSetup::apply_virtual_res_variant(), protocols::swa::rna::StepWiseRNA_Clusterer::cluster(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::cluster_pose_data_list(), protocols::swa::rna::StepWiseRNA_ResidueSampler::cluster_pose_data_list(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::create_VDW_screen_bin(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_jump_partners(), protocols::swa::rna::StepWiseRNA_Minimizer::Figure_out_moving_residues(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_partition_definition(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_Prepend_Internal(), protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::filter(), protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling(), full_length_rmsd_over_residue_list(), protocols::swa::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::get_matching_res_in_VDW_rep_screen_pose(), Get_ribose_stub(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::get_user_input_alignment_res_list(), protocols::swa::rna::StepWiseRNA_Clusterer::initialize_max_memory_pose_num(), protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::initialize_rotamer_generator_list(), protocols::swa::rna::StepWiseRNA_RotamerGenerator::initialize_rotamers(), protocols::swa::rna::StepWiseRNA_Clusterer::Is_new_cluster_center_with_job_parameters(), protocols::swa::rna::StepWiseRNA_Clusterer::Is_old_individual_suite_cluster(), Is_virtual_base(), Output_bool_list(), protocols::swa::Output_movemap(), Output_movemap(), print_JobParameters_info(), protocols::swa::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file(), rmsd_over_residue_list(), protocols::swa::rna::FloatingBaseChainClosureJobParameter::set_base_and_pucker_state(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_fixed_res(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_jump_point_pair_list(), setup_FB_CC_JP_list(), setup_residue_at_origin_list(), protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::setup_rotamer_generator(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::standard_sampling(), protocols::swa::rna::StepWiseRNA_ResidueSampler::standard_sampling(), and virtualize_bulges().

void protocols::swa::rna::Output_boolean

(

bool

boolean)

Definition at line 1940 of file StepWiseRNA_Util.cc.

References protocols::comparative_modeling::features::A.

void protocols::swa::rna::Output_data	(	core::io::silent::SilentFileData &	silent_file_data,
		std::string const &	silent_file,
		std::string const &	tag,
		bool const	write_score_only,
		pose::Pose const &	pose,
		core::pose::PoseCOP	native_poseCOP,
		StepWiseRNA_JobParametersCOP	job_parameters_
	)

Definition at line 273 of file StepWiseRNA_OutputData.cc.

References align_poses(), get_binary_rna_silent_struct_safe_wrapper(), phosphate_base_phosphate_rmsd(), remove_all_variant_types(), core::scoring::rms_at_corresponding_heavy_atoms(), rmsd_over_residue_list(), suite_rmsd(), and core::io::silent::SilentFileData::write_silent_struct().

Referenced by protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::output_pose_data_list(), protocols::swa::rna::StepWiseRNA_ResidueSampler::output_pose_data_list(), protocols::swa::rna::StepWiseRNA_Minimizer::output_pose_data_wrapper(), sample_user_specified_virtual_riboses(), sample_virtual_ribose_and_bulge_and_close_chain(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::standard_sampling(), protocols::swa::rna::StepWiseRNA_ResidueSampler::standard_sampling(), and protocols::swa::rna::StepWiseRNA_ResidueSampler::standard_sampling_WRAPPER().

void protocols::swa::rna::Output_fold_tree_info	(	kinematics::FoldTree const &	fold_tree,
		std::string const	pose_name
	)

Definition at line 1034 of file StepWiseRNA_Util.cc.

References core::kinematics::FoldTree::cutpoint(), core::kinematics::FoldTree::downstream_atom(), core::kinematics::FoldTree::jump_point(), core::kinematics::FoldTree::num_cutpoint(), and core::kinematics::FoldTree::upstream_atom().

Referenced by copy_torsions_FROM_TO(), Output_fold_tree_info(), print_JobParameters_info(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::reroot_fold_tree(), setup_bulge_jump_point(), and protocols::swa::rna::StepWiseRNA_JobParameters_Setup::setup_fold_tree().

void protocols::swa::rna::Output_fold_tree_info	(	pose::Pose const &	pose,
		std::string	pose_name
	)

Definition at line 1046 of file StepWiseRNA_Util.cc.

References core::pose::Pose::fold_tree(), and Output_fold_tree_info().

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
	)

Definition at line 849 of file StepWiseRNA_Util.cc.

Referenced by print_JobParameters_info(), protocols::swa::rna::SlicedPoseJobParameters::setup(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::StepWiseRNA_AnalyticalLoopCloseSampler(), and protocols::swa::rna::StepWiseRNA_ResidueSampler::StepWiseRNA_ResidueSampler().

void protocols::swa::rna::Output_movemap	(	kinematics::MoveMap const &	mm,
		core::pose::Pose const &	pose
	)

Definition at line 1954 of file StepWiseRNA_Util.cc.

References protocols::comparative_modeling::features::A, core::id::BB, core::id::CHI, core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::kinematics::MoveMap::get(), core::kinematics::MoveMap::get_jump(), core::kinematics::MoveMap::jump_id_begin(), core::kinematics::MoveMap::jump_id_end(), core::kinematics::FoldTree::num_jump(), Output_boolean(), core::pose::Pose::total_residue(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by protocols::swa::rna::StepWiseRNA_Minimizer::apply().

void protocols::swa::rna::output_pair_size

(

std::pair< core::Size, core::Size > const &

pair_size)

void protocols::swa::rna::output_pair_size

(

std::pair< Size, Size > const &

pair_size)

Definition at line 770 of file StepWiseRNA_Util.cc.

Referenced by output_pair_size_vector(), and protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_jump_point_pair_list().

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
	)

void protocols::swa::rna::output_pair_size_vector	(	utility::vector1< std::pair< Size, Size > > const &	pair_size_vector,
		std::string const &	output_string,
		core::Size const	spacing
	)

Definition at line 775 of file StepWiseRNA_Util.cc.

References core::sequence::left, and output_pair_size().

Referenced by protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_jump_point_pair_list(), and protocols::swa::rna::SlicedPoseJobParameters::setup().

void protocols::swa::rna::output_res_map	(	std::map< core::Size, core::Size > const &	my_map,
		Size const	max_seq_num
	)

Definition at line 163 of file StepWiseRNA_ResidueInfo.cc.

References protocols::comparative_modeling::features::A.

void protocols::swa::rna::Output_residue_list

(

utility::vector1< Residue_info >

residue_list)

Definition at line 190 of file StepWiseRNA_ResidueInfo.cc.

References protocols::comparative_modeling::features::A, Output_residue_struct(), protocols::swa::rna::Residue_info::seq_num, and sort_residue_list().

void protocols::swa::rna::Output_residue_struct

(

Residue_info const &

residue)

Definition at line 117 of file StepWiseRNA_ResidueInfo.cc.

References protocols::comparative_modeling::features::A, Get_one_letter_name(), protocols::swa::rna::Residue_info::name, and protocols::swa::rna::Residue_info::seq_num.

Referenced by Output_residue_list().

void protocols::swa::rna::output_rotamer

(

utility::vector1< Real > &

rotamer)

Definition at line 1095 of file StepWiseRNA_Util.cc.

void protocols::swa::rna::Output_seq_num_list	(	std::string const	tag,
		utility::vector1< core::Size > const &	seq_num_list,
		core::Size const	spacing
	)

Definition at line 805 of file StepWiseRNA_Util.cc.

References protocols::comparative_modeling::features::A, and sort_seq_num_list().

Referenced by protocols::swa::rna::StepWiseRNA_PoseSetup::add_terminal_res_repulsion(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::apply(), protocols::swa::rna::StepWiseRNA_Minimizer::apply(), protocols::swa::rna::StepWiseRNA_ResidueSampler::apply(), protocols::swa::rna::StepWiseRNA_PoseSetup::correctly_copy_HO2star_positions(), protocols::swa::rna::StepWiseRNA_Clusterer::create_silent_file_and_tag_list(), protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::figure_out_appended_and_prepended_res_list(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_best_working_alignment(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_Is_prepend_map(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_partition_definition(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_Prepend_Internal(), full_length_rmsd_over_residue_list(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::get_matching_res_in_VDW_rep_screen_pose(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::get_previously_closed_cutpoint_from_imported_silent_file(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::get_user_input_alignment_res_list(), protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::Initialize_base_stub_list(), protocols::swa::rna::StepWiseRNA_Clusterer::initialize_quick_alignment_pose(), protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::initialize_rotamer_generator_list(), o2star_minimize(), print_JobParameters_info(), protocols::swa::rna::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs(), rmsd_over_residue_list(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_fixed_res(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_native_alignment_res(), protocols::swa::rna::SlicedPoseJobParameters::setup(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::setup_additional_cutpoint_closed(), protocols::swa::rna::StepWiseRNA_PoseSetup::setup_native_pose(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::setup_using_user_input_VDW_pose(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::StepWiseRNA_AnalyticalLoopCloseSampler(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::StepWiseRNA_JobParameters_Setup(), protocols::swa::rna::StepWiseRNA_ResidueSampler::StepWiseRNA_ResidueSampler(), protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::StepWiseRNA_RotamerGenerator_Wrapper(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::update_VDW_screen_bin(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::VDW_rep_screen_with_act_pose(), and virtualize_bulges().

void protocols::swa::rna::Output_size_list	(	std::string const	tag,
		utility::vector1< Size > const &	size_list,
		core::Size const	spacing
	)

Definition at line 896 of file StepWiseRNA_Util.cc.

Referenced by protocols::swa::rna::StepWiseRNA_JobParameters_Setup::setup_additional_cutpoint_closed().

void protocols::swa::rna::Output_title_text

(

std::string const

title)

Definition at line 1010 of file StepWiseRNA_Util.cc.

Referenced by protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::align_all_pose(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::align_VDW_rep_screen_pose(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::apply(), protocols::swa::rna::StepWiseRNA_PoseSetup::apply(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::apply(), protocols::swa::rna::StepWiseRNA_Minimizer::apply(), protocols::swa::rna::StepWiseRNA_ResidueSampler::apply(), protocols::swa::rna::StepWiseRNA_Clusterer::cluster(), protocols::swa::rna::StepWiseRNA_PoseSetup::correctly_copy_HO2star_positions(), Correctly_position_cutpoint_phosphate_torsions(), protocols::swa::rna::StepWiseRNA_Clusterer::create_large_cluster_centers_member_list(), protocols::swa::rna::StepWiseRNA_Clusterer::create_silent_file_and_tag_list(), protocols::swa::rna::StepWiseRNA_Clusterer::create_tags_map(), protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::do_some_filtering(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::FARFAR_setup_using_user_input_VDW_pose(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_best_working_alignment(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_chain_boundaries(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_Is_prepend_map(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_jump_partners(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_Prepend_Internal(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_working_sequence_and_mapping(), protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::filter(), floating_base_chain_closure_post_process(), floating_base_chain_closure_sampling(), floating_base_chain_closure_setup(), protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling(), full_length_rmsd_over_residue_list(), protocols::swa::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::get_matching_res_in_VDW_rep_screen_pose(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::get_user_input_alignment_res_list(), protocols::swa::rna::StepWiseRNA_RotamerGenerator::initialize_rotamer_generator(), protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::initialize_rotamer_generator_list(), minimize_all_sampled_floating_bases(), print_JobParameters_info(), protocols::swa::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::reroot_fold_tree(), rmsd_over_residue_list(), sample_user_specified_virtual_riboses(), sample_virtual_ribose_and_bulge_and_close_chain(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_fixed_res(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_native_alignment_res(), protocols::swa::rna::SlicedPoseJobParameters::setup(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::setup_additional_cutpoint_closed(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::setup_fold_tree(), protocols::swa::rna::StepWiseRNA_PoseSetup::setup_native_pose(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::setup_using_user_input_VDW_pose(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::setup_using_working_pose(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::standard_sampling(), protocols::swa::rna::StepWiseRNA_ResidueSampler::standard_sampling(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::StepWiseRNA_JobParameters_Setup(), and protocols::swa::rna::StepWiseRNA_Clusterer::two_stage_clustering().

bool protocols::swa::rna::pair_sort_citeria	(	std::pair< core::Size, core::Size >	pair_one,
		std::pair< core::Size, core::Size >	pair_two
	)

bool protocols::swa::rna::pair_sort_citeria	(	std::pair< Size, Size >	pair_one,
		std::pair< Size, Size >	pair_two
	)

Definition at line 785 of file StepWiseRNA_Util.cc.

Referenced by Sort_pair_list().

std::string protocols::swa::rna::path_basename

(

std::string const

full_path)

Definition at line 2774 of file StepWiseRNA_Util.cc.

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
	)

Definition at line 1515 of file StepWiseRNA_Util.cc.

References phosphate_base_phosphate_square_deviation().

Referenced by protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::cluster_pose_data_list(), protocols::swa::rna::StepWiseRNA_ResidueSampler::cluster_pose_data_list(), protocols::swa::rna::StepWiseRNA_Clusterer::Is_old_individual_suite_cluster(), and Output_data().

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
	)

Definition at line 1533 of file StepWiseRNA_Util.cc.

References core::conformation::Residue::aa(), atom_square_deviation(), core::conformation::Residue::atom_type(), core::conformation::Residue::first_sidechain_atom(), Get_num_side_chain_atom_from_res_name(), core::chemical::AtomType::name(), core::chemical::name_from_aa(), and core::pose::Pose::residue().

Referenced by phosphate_base_phosphate_rmsd().

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
	)

Definition at line 1484 of file StepWiseRNA_Util.cc.

References core::conformation::Residue::aa(), atom_square_deviation(), core::conformation::Residue::atom_type(), core::chemical::AtomType::name(), core::chemical::name_from_aa(), and core::pose::Pose::residue().

Referenced by full_length_rmsd_over_residue_list().

bool protocols::swa::rna::possible_root	(	core::kinematics::FoldTree const &	f,
		Size const &	n
	)

Definition at line 1093 of file StepWiseRNA_JobParameters_Setup.cc.

References core::kinematics::FoldTree::is_cutpoint(), and core::kinematics::FoldTree::nres().

Referenced by protocols::swa::rna::StepWiseRNA_JobParameters_Setup::reroot_fold_tree(), and protocols::swa::rna::StepWiseRNA_JobParameters_Setup::reroot_fold_tree_simple().

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

Definition at line 3418 of file StepWiseRNA_Util.cc.

References core::io::serialization::at(), core::chemical::ResidueType::atom_name(), core::conformation::Residue::atom_type(), core::chemical::AtomType::element(), core::chemical::AtomType::name(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), and core::conformation::Residue::type().

Referenced by protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling().

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

Definition at line 2262 of file StepWiseRNA_Util.cc.

References core::conformation::Residue::mainchain_torsion(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by protocols::swa::rna::StepWiseRNA_PoseSetup::apply_cutpoint_variants(), and Correctly_position_cutpoint_phosphate_torsions().

void protocols::swa::rna::print_base_state	(	std::string const	tag,
		BaseState const	base_state
	)

Definition at line 3444 of file StepWiseRNA_Util.cc.

References ANTI, BOTH, core::sequence::left, protocols::jd2::JobInputterInputSource::NONE, and SYN.

Referenced by protocols::swa::rna::StepWiseRNA_RotamerGenerator::initialize_rotamers(), and protocols::swa::rna::FloatingBaseChainClosureJobParameter::set_base_and_pucker_state().

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
	)

Definition at line 1356 of file StepWiseRNA_Util.cc.

References core::conformation::Residue::atom_name(), core::conformation::Residue::nheavyatoms(), core::pose::num_atoms(), and core::pose::Pose::residue().

Referenced by suite_square_deviation().

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

Definition at line 3433 of file StepWiseRNA_Util.cc.

References core::chemical::ResidueType::atom_name(), core::conformation::Residue::atom_type(), core::chemical::AtomType::element(), core::chemical::AtomType::name(), and core::conformation::Residue::type().

void protocols::swa::rna::print_JobParameters_info	(	StepWiseRNA_JobParametersCOP const &	const_JP,
		std::string const	JP_name,
		bool const	Is_simple_full_length_JP
	)

Definition at line 3127 of file StepWiseRNA_Util.cc.

Referenced by protocols::swa::rna::StepWiseRNA_PoseSetup::verify_protonated_H1_adenosine_variants().

void protocols::swa::rna::print_JobParameters_info	(	StepWiseRNA_JobParametersOP const &	JP,
		std::string const	JP_name,
		bool const	Is_simple_full_length_JP
	)

Definition at line 3139 of file StepWiseRNA_Util.cc.

References Output_bool_list(), Output_boolean(), Output_fold_tree_info(), Output_is_prepend_map(), Output_seq_num_list(), and Output_title_text().

void protocols::swa::rna::print_ribose_pucker_state	(	std::string const	tag,
		PuckerState const	pucker_state
	)

Definition at line 3467 of file StepWiseRNA_Util.cc.

References protocols::sic_dock::ALL, core::sequence::left, NORTH, and SOUTH.

Referenced by protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::cluster_pose_data_list(), protocols::swa::rna::StepWiseRNA_ResidueSampler::cluster_pose_data_list(), protocols::swa::rna::StepWiseRNA_RotamerGenerator::initialize_rotamers(), protocols::swa::rna::StepWiseRNA_Clusterer::Is_old_individual_suite_cluster(), and protocols::swa::rna::FloatingBaseChainClosureJobParameter::set_base_and_pucker_state().

void protocols::swa::rna::Print_torsion_info	(	core::pose::Pose const &	pose,
		core::Size const	seq_num,
		core::Size const	rna_torsion_number,
		std::string const	type
	)

Definition at line 46 of file StepWiseRNA_ResidueInfo.cc.

References core::chemical::ResidueType::atom_name(), core::id::BB, core::id::CHI, core::conformation::Residue::chi(), core::pose::Pose::conformation(), core::conformation::Conformation::get_torsion_angle_atom_ids(), core::conformation::Residue::mainchain_torsion(), core::pose::Pose::residue(), and core::conformation::Residue::type().

void protocols::swa::rna::remove_all_variant_types

(

pose::Pose &

pose)

Definition at line 308 of file StepWiseRNA_Util.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::chemical::ResidueType::has_variant_type(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::conformation::Residue::type(), and core::chemical::ResidueType::variant_types().

Referenced by Output_data(), and protocols::swa::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file().

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
	)

Definition at line 2450 of file StepWiseRNA_Util.cc.

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), and core::pose::remove_variant_type_from_pose_residue().

Referenced by floating_base_chain_closure_post_process().

void protocols::swa::rna::remove_file

(

std::string const &

file_name)

Definition at line 1070 of file StepWiseRNA_Util.cc.

References protocols::pack_daemon::error_message, and file_exists().

Referenced by get_binary_rna_silent_struct_safe().

bool protocols::swa::rna::Remove_virtual_O2Star_hydrogen

(

pose::Pose &

pose)

Definition at line 1130 of file StepWiseRNA_Util.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::chemical::ResidueType::has_variant_type(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by protocols::swa::rna::StepWiseRNA_Minimizer::apply().

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

Definition at line 267 of file StepWiseRNA_Util.cc.

References core::pose::remove_variant_type_from_pose_residue(), and core::pose::Pose::total_residue().

Referenced by protocols::swa::rna::StepWiseRNA_ResidueSampler::apply(), floating_base_chain_closure_setup(), and protocols::swa::rna::StepWiseRNA_ResidueSampler::standard_sampling().

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

According to Kyle B., DFPMIN should be start enough to determine what is the ideal step size. However, the exception is the first minimizing step which could lead to "blow up" error! To prevent can create new scorefxn with scaling_factor=0.1 and minimize with this new score function Sept 20, 2011. Parin S.

Definition at line 3602 of file StepWiseRNA_Util.cc.

References core::scoring::n_score_types, and show_scorefxn_weight_lines().

Referenced by floating_base_chain_closure_setup().

bool protocols::swa::rna::residue_list_sort_citeria	(	Residue_info	residue_info_1,
		Residue_info	residue_info_2
	)

Definition at line 323 of file StepWiseRNA_ResidueInfo.cc.

References protocols::swa::rna::Residue_info::seq_num.

Referenced by sort_residue_list().

core::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
	)

Definition at line 1291 of file StepWiseRNA_Util.cc.

References core::conformation::Residue::has_variant_type(), Output_boolean(), Output_seq_num_list(), Output_title_text(), core::pose::Pose::residue(), and suite_square_deviation().

Referenced by protocols::swa::rna::StepWiseRNA_Clusterer::create_large_cluster_centers_member_list(), protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling(), protocols::swa::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file(), protocols::swa::rna::StepWiseRNA_Clusterer::Is_new_cluster_center_with_job_parameters(), Output_data(), protocols::swa::rna::StepWiseRNA_Minimizer::pass_all_pose_screens(), protocols::swa::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file(), rmsd_over_residue_list(), protocols::swa::rna::StepWiseRNA_Clusterer::setup_fail_triangle_inequailty_list(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::standard_sampling(), and protocols::swa::rna::StepWiseRNA_ResidueSampler::standard_sampling().

core::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
	)

Definition at line 1344 of file StepWiseRNA_Util.cc.

References rmsd_over_residue_list().

void protocols::swa::rna::sample_user_specified_virtual_riboses	(	pose::Pose &	pose,
		utility::vector1< std::string > const &	sample_virtual_ribose_string_list,
		StepWiseRNA_JobParametersCOP &	job_parameters,
		core::scoring::ScoreFunctionOP const &	scorefxn,
		std::string const	silent_file_out,
		std::string const	input_tag
	)

Definition at line 1276 of file StepWiseRNA_VirtualRiboseSampler.cc.

References core::pose::Pose::conformation(), enumerate_starting_pose_data_list(), initialize_common_scorefxns(), minimize_all_sampled_floating_bases(), Output_data(), Output_title_text(), protocols::swa::rna::FloatingBaseChainClosureJobParameter::PDL, sample_virtual_ribose_and_bulge_and_close_chain(), protocols::swa::rna::FloatingBaseChainClosureJobParameter::set_base_and_pucker_state(), core::pose::Pose::set_new_conformation(), setup_FB_CC_JP_list(), and sort_pose_data_by_score().

utility::vector1< pose_data_struct2 > protocols::swa::rna::sample_virtual_ribose_and_bulge_and_close_chain	(	pose::Pose &	viewer_pose,
		FloatingBaseChainClosureJobParameter const &	FB_job_params,
		std::string const	name,
		core::scoring::ScoreFunctionOP const &	scorefxn,
		core::scoring::ScoreFunctionOP const &	sampling_scorefxn,
		core::scoring::ScoreFunctionOP const &	atr_rep_screening_scorefxn,
		core::scoring::ScoreFunctionOP const &	chainbreak_scorefxn,
		StepWiseRNA_JobParametersCOP &	job_parameters,
		bool const	virtual_ribose_is_from_prior_step
	)

Definition at line 995 of file StepWiseRNA_VirtualRiboseSampler.cc.

References core::pose::add_variant_type_to_pose_residue(), protocols::swa::rna::FloatingBaseChainClosureJobParameter::bulge_res, protocols::swa::rna::FloatingBaseChainClosureJobParameter::check_compatibility(), core::scoring::rna::chemical_shift::Contain_seq_num(), floating_base_chain_closure_post_process(), floating_base_chain_closure_sampling(), floating_base_chain_closure_setup(), core::scoring::rna::get_rna_base_centroid(), core::scoring::rna::get_rna_base_coordinate_system(), protocols::swa::rna::FloatingBaseChainClosureJobParameter::Is_prepend, protocols::swa::rna::FloatingBaseChainClosureJobParameter::moving_res, Output_data(), Output_title_text(), protocols::swa::rna::pose_data_struct2::pose_OP, protocols::swa::rna::FloatingBaseChainClosureJobParameter::reference_res, core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::total_residue(), and core::kinematics::Stub::v.

Referenced by protocols::swa::rna::StepWiseRNA_ResidueSampler::previous_floating_base_chain_closure(), and sample_user_specified_virtual_riboses().

bool protocols::swa::rna::score_sort_citeria	(	Combine_Tags_Info	tag_info_1,
		Combine_Tags_Info	tag_info_2
	)

Definition at line 870 of file StepWiseRNA_CombineLongLoopFilterer.cc.

References protocols::swa::rna::Combine_Tags_Info::combine_score.

Referenced by protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::sort_Combine_Tags_Info().

bool protocols::swa::rna::seq_num_sort_citeria	(	core::Size	seq_num_1,
		core::Size	seq_num_2
	)

Definition at line 796 of file StepWiseRNA_Util.cc.

Referenced by sort_seq_num_list().

void protocols::swa::rna::set_base_coordinate_frame	(	pose::Pose &	pose,
		Size const &	seq_num,
		core::conformation::Residue const &	rsd_at_origin,
		core::kinematics::Stub const &	moving_res_base_stub
	)

Definition at line 862 of file StepWiseRNA_FloatingBase_Sampler_Util.cc.

References get_atom_coordinates(), and core::pose::Pose::set_xyz().

Referenced by protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling().

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

Definition at line 2850 of file StepWiseRNA_Util.cc.

References core::id::BB, and core::pose::Pose::set_torsion().

Referenced by protocols::swa::rna::StepWiseRNA_ResidueSampler::Chain_break_screening_general(), and floating_base_chain_break_screening().

utility::vector1< Residue_info > protocols::swa::rna::Set_Difference	(	utility::vector1< Residue_info > const &	residue_list_1,
		utility::vector1< Residue_info > const &	residue_list_2
	)

Definition at line 294 of file StepWiseRNA_ResidueInfo.cc.

References Contain_residue_at_seq_num().

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

Definition at line 3398 of file StepWiseRNA_Util.cc.

References core::id::BB, core::id::CHI, and core::pose::Pose::set_torsion().

void protocols::swa::rna::set_to_origin	(	pose::Pose &	pose,
		Size const	seq_num,
		bool	verbose
	)

Definition at line 654 of file StepWiseRNA_FloatingBase_Sampler_Util.cc.

References core::io::serialization::at(), core::scoring::rna::get_rna_base_centroid(), core::scoring::rna::get_rna_base_coordinate_system(), core::pose::Pose::residue(), core::pose::Pose::set_xyz(), and core::pose::Pose::xyz().

Referenced by setup_residue_at_origin_list().

utility::vector1< Residue_info > protocols::swa::rna::Set_Union	(	utility::vector1< Residue_info > const &	residue_list_1,
		utility::vector1< Residue_info > const &	residue_list_2
	)

Definition at line 308 of file StepWiseRNA_ResidueInfo.cc.

References Contain_residue_at_seq_num().

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

Definition at line 2465 of file StepWiseRNA_Util.cc.

References core::pose::Pose::fold_tree(), Output_fold_tree_info(), and core::pose::Pose::residue().

Referenced by setup_chain_break_jump_point().

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
	)

Definition at line 2435 of file StepWiseRNA_Util.cc.

References core::pose::add_variant_type_to_pose_residue(), Correctly_position_cutpoint_phosphate_torsions(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, and setup_bulge_jump_point().

Referenced by floating_base_chain_closure_setup(), and protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling().

utility::vector1< FloatingBaseChainClosureJobParameter > protocols::swa::rna::setup_FB_CC_JP_list	(	pose::Pose const &	pose,
		utility::vector1< std::string > const &	sample_virtual_ribose_string_list,
		StepWiseRNA_JobParametersCOP &	job_parameters
	)

Definition at line 1190 of file StepWiseRNA_VirtualRiboseSampler.cc.

References check_is_working_res(), check_validity_and_get_working_res(), core::conformation::Residue::has_variant_type(), Output_boolean(), core::pose::Pose::residue(), core::scoring::rna::chemical_shift::string_to_int(), protocols::Tokenize(), and core::pose::Pose::total_residue().

Referenced by sample_user_specified_virtual_riboses().

utility::vector1< core::conformation::ResidueOP > protocols::swa::rna::setup_residue_at_origin_list	(	pose::Pose const &	pose,
		Size const &	moving_res,
		bool const	extra_anti_chi_rotamer,
		bool const	extra_syn_chi_rotamer,
		std::string const	pose_name
	)

Definition at line 733 of file StepWiseRNA_FloatingBase_Sampler_Util.cc.

References protocols::sic_dock::ALL, ANTI, core::id::BB, BOTH, core::id::CHI, core::conformation::Residue::clone(), core::scoring::rna::is_purine(), Output_boolean(), core::pose::Pose::residue(), set_to_origin(), and core::pose::Pose::set_torsion().

Referenced by protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling().

void protocols::swa::rna::setup_simple_fold_tree

(

core::pose::Pose &

pose)

Definition at line 2701 of file StepWiseRNA_Util.cc.

References core::pose::Pose::fold_tree(), protocols::antibody::simple_fold_tree(), core::kinematics::FoldTree::simple_tree(), and core::pose::Pose::total_residue().

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
	)

Definition at line 623 of file StepWiseRNA_Util.cc.

References core::conformation::Residue::seqpos().

Referenced by protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::align_all_pose(), protocols::swa::create_alignment_id_map(), create_alignment_id_map(), and setup_suite_atom_id_map().

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
	)

Definition at line 633 of file StepWiseRNA_Util.cc.

References core::conformation::Residue::aa(), core::conformation::Residue::atom_index(), core::chemical::ResidueType::atom_name(), core::conformation::Residue::atom_type(), core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::has(), core::chemical::AtomType::name(), core::chemical::name_from_aa(), core::conformation::Residue::nheavyatoms(), core::id::AtomID_Map< T >::set(), and core::conformation::Residue::type().

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
	)

Definition at line 678 of file StepWiseRNA_Util.cc.

References core::pose::Pose::residue(), and setup_suite_atom_id_map().

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
	)

Parameters

pose_2

/Dec 23, 2011.

Definition at line 691 of file StepWiseRNA_Util.cc.

References core::pose::Pose::residue(), and setup_suite_atom_id_map().

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

Definition at line 3637 of file StepWiseRNA_Util.cc.

References core::scoring::n_score_types.

Referenced by rescale_scorefxn().

void protocols::swa::rna::sleep

(

core::Size

mseconds)

Definition at line 2691 of file StepWiseRNA_Util.cc.

Referenced by protocols::optimize_weights::attach_debugger(), protocols::pmut_scan::PointMutScanDriver::divide_up_mutations(), protocols::match::downstream::ScoringSecMatchRPE::evaluate_residues(), protocols::jd2::archive::ArchiveManager::go(), protocols::jd2::archive::ArchiveManager::idle(), protocols::jd2::archive::ArchiveManager::jobs_completed(), protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::load_pool(), protocols::wum2::WorkUnit_Wait::run(), protocols::wum::WorkUnit_Wait::run(), and protocols::jd2::WriteFileSFB::WriteFileSFB().

bool protocols::swa::rna::sort_criteria	(	pose_data_struct2	pose_data_1,
		pose_data_struct2	pose_data_2
	)

Definition at line 190 of file StepWiseRNA_ResidueSampler.cc.

References protocols::swa::rna::pose_data_struct2::score.

Referenced by protocols::swa::rna::StepWiseRNA_ResidueSampler::apply(), protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling(), protocols::swa::rna::StepWiseRNA_ResidueSampler::Pose_selection_by_full_score(), and protocols::swa::rna::StepWiseRNA_ResidueSampler::standard_sampling().

bool protocols::swa::rna::sort_criteria2	(	pose_data_struct2	pose_data_1,
		pose_data_struct2	pose_data_2
	)

Definition at line 148 of file StepWiseRNA_AnalyticalLoopCloseSampler.cc.

References protocols::swa::rna::pose_data_struct2::score.

Referenced by protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::Pose_selection_by_full_score(), and protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::standard_sampling().

void protocols::swa::rna::Sort_pair_list

(

utility::vector1< std::pair< core::Size, core::Size > >

pair_list)

void protocols::swa::rna::Sort_pair_list

(

utility::vector1< std::pair< Size, Size > >

pair_list)

Definition at line 790 of file StepWiseRNA_Util.cc.

References pair_sort_citeria().

Referenced by protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_jump_point_pair_list().

bool protocols::swa::rna::sort_pose_data_by_score	(	pose_data_struct2	pose_data_1,
		pose_data_struct2	pose_data_2
	)

Definition at line 975 of file StepWiseRNA_VirtualRiboseSampler.cc.

References protocols::swa::rna::pose_data_struct2::score.

Referenced by sample_user_specified_virtual_riboses().

void protocols::swa::rna::sort_residue_list

(

utility::vector1< Residue_info > &

residue_list)

Definition at line 329 of file StepWiseRNA_ResidueInfo.cc.

References residue_list_sort_citeria().

Referenced by Create_strand_list(), and Output_residue_list().

void protocols::swa::rna::sort_seq_num_list

(

utility::vector1< core::Size > &

seq_num_list)

Definition at line 801 of file StepWiseRNA_Util.cc.

References seq_num_sort_citeria().

Referenced by Is_equivalent_vector(), Output_seq_num_list(), and protocols::swa::rna::StepWiseRNA_JobParameters::set_rmsd_res_list().

core::Size protocols::swa::rna::string_to_int

(

std::string const

input_string)

Definition at line 495 of file StepWiseRNA_Util.cc.

Referenced by protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::FARFAR_setup_using_user_input_VDW_pose(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::get_matching_res_in_VDW_rep_screen_pose(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::get_user_input_alignment_res_list(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_jump_point_pair_list(), and protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::setup_using_user_input_VDW_pose().

core::Real protocols::swa::rna::string_to_real

(

std::string const

input_string)

Definition at line 526 of file StepWiseRNA_Util.cc.

core::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
	)

Definition at line 1144 of file StepWiseRNA_Util.cc.

References suite_square_deviation().

Referenced by protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::cluster_pose_data_list(), protocols::swa::rna::StepWiseRNA_ResidueSampler::cluster_pose_data_list(), protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling(), protocols::swa::rna::StepWiseRNA_Clusterer::Is_old_individual_suite_cluster(), Output_data(), protocols::swa::rna::StepWiseRNA_Minimizer::pass_all_pose_screens(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::standard_sampling(), and protocols::swa::rna::StepWiseRNA_ResidueSampler::standard_sampling().

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
	)

Definition at line 1603 of file StepWiseRNA_Util.cc.

References core::conformation::Residue::aa(), core::conformation::Residue::atom_name(), atom_square_deviation(), core::conformation::Residue::atom_type(), core::conformation::Residue::first_sidechain_atom(), Get_num_side_chain_atom_from_res_name(), core::chemical::AtomType::name(), core::chemical::name_from_aa(), core::conformation::Residue::nheavyatoms(), Print_heavy_atoms(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by full_length_rmsd_over_residue_list(), rmsd_over_residue_list(), and suite_rmsd().

utility::vector1< std::string > protocols::swa::rna::Tokenize	(	std::string const	str,
		std::string	delimiters
	)

Definition at line 546 of file StepWiseRNA_Util.cc.

Referenced by protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::FARFAR_setup_using_user_input_VDW_pose(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::get_matching_res_in_VDW_rep_screen_pose(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::get_user_input_alignment_res_list(), protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::Is_sibling_ribose_rotamer_pose(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_jump_point_pair_list(), and protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::setup_using_user_input_VDW_pose().

void protocols::swa::rna::translate_then_rotate_pose	(	core::pose::Pose &	pose,
		numeric::xyzVector< core::Real > const &	vector,
		numeric::xyzMatrix< core::Real > const	matrix,
		bool const	verbose
	)

Definition at line 626 of file StepWiseRNA_FloatingBase_Sampler_Util.cc.

References core::io::serialization::at(), core::pose::Pose::residue(), core::pose::Pose::set_xyz(), core::pose::Pose::total_residue(), and core::pose::Pose::xyz().

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
	)

Definition at line 2924 of file StepWiseRNA_Util.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, apply_virtual_rna_residue_variant_type(), core::scoring::rna::chemical_shift::Contain_seq_num(), get_default_allowed_bulge_res(), core::conformation::Residue::has_variant_type(), Output_boolean(), Output_seq_num_list(), core::pose::Pose::residue(), core::scoring::rna_bulge, and core::pose::Pose::total_residue().

Referenced by protocols::rna::RNA_DeNovoProtocol::apply().