protocols::stepwise::sampling::rna Namespace Reference

Namespaces
	bulge
	checker
	connection
	helix
	legacy
	o2prime
	phosphate
	rigid_body
	sugar

Classes
class	Cluster_Member
class	Combine_Tags_Info
class	Filterer_Count
class	InternalWorkingResidueParameter
class	Jump_point
struct	output_data_struct
struct	Residue_info
class	SlicedPoseJobParameters
class	StepWiseRNA_Clusterer
class	StepWiseRNA_CombineLongLoopFilterer
class	StepWiseRNA_CountStruct
class	StepWiseRNA_JobParameters
class	StepWiseRNA_Minimizer
class	StepWiseRNA_Modeler
class	StepWiseRNA_ModelerOptions
class	StepWiseRNA_PoseSelection
class	StepWiseRNA_ResidueSampler
struct	Torsion_Info

Typedefs
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_JobParametersUtil >	StepWiseRNA_JobParametersUtilOP
typedef utility::pointer::owning_ptr < StepWiseRNA_JobParametersUtil const >	StepWiseRNA_JobParametersUtilCOP
typedef utility::pointer::owning_ptr < StepWiseRNA_Minimizer >	StepWiseRNA_MinimizerOP
typedef utility::pointer::owning_ptr < StepWiseRNA_Minimizer const >	StepWiseRNA_MinimizerCOP
typedef utility::pointer::owning_ptr < StepWiseRNA_Modeler >	StepWiseRNA_ModelerOP
typedef utility::pointer::owning_ptr < StepWiseRNA_Modeler const >	StepWiseRNA_ModelerCOP
typedef utility::pointer::owning_ptr < StepWiseRNA_ModelerOptions >	StepWiseRNA_ModelerOptionsOP
typedef utility::pointer::owning_ptr < StepWiseRNA_ModelerOptions const >	StepWiseRNA_ModelerOptionsCOP
typedef utility::pointer::owning_ptr < StepWiseRNA_PoseSelection >	StepWiseRNA_PoseSelectionOP
typedef utility::pointer::owning_ptr < StepWiseRNA_PoseSelection const >	StepWiseRNA_PoseSelectionCOP

Functions
bool	score_sort_criterion (Combine_Tags_Info tag_info_1, Combine_Tags_Info tag_info_2)
StepWiseRNA_JobParametersOP	setup_job_parameters_for_swa (Size const rebuild_res, pose::Pose const &pose, pose::PoseCOP native_pose, utility::vector1< Size > const &calc_rms_res, utility::vector1< Size > const &terminal_res, utility::vector1< Size > const &syn_chi_res_list, utility::vector1< Size > const &extra_minimize_res, utility::vector1< Size > &working_fixed_res, utility::vector1< Size > &working_minimize_res, toolbox::AllowInsertOP &allow_insert, kinematics::MoveMapOP &minimize_move_map)
void	figure_out_root_partition_res (pose::Pose const &pose, StepWiseRNA_JobParametersCOP job_parameters, utility::vector1< Size > &root_partition_res, utility::vector1< Size > &moving_partition_res)
StepWiseRNA_JobParametersOP	setup_job_parameters_explicit (Size const rebuild_res, pose::Pose const &pose, pose::PoseCOP native_pose, utility::vector1< Size > const &calc_rms_res, utility::vector1< Size > const &terminal_res, utility::vector1< Size > const &syn_chi_res_list, utility::vector1< Size > &working_fixed_res_guess, utility::vector1< Size > &suites_that_must_be_minimized)
StepWiseRNA_JobParametersOP	setup_job_parameters_legacy (Size const rebuild_res, pose::Pose const &pose, pose::PoseCOP native_pose, utility::vector1< Size > const &calc_rms_res, utility::vector1< Size > const &terminal_res, utility::vector1< Size > const &syn_chi_res_list, utility::vector1< Size > &working_fixed_res_guess, utility::vector1< Size > &suites_that_must_be_minimized)
bool	figure_out_rebuild_bulge_mode (pose::Pose const &pose, Size const rebuild_res)
bool	figure_out_sample_both_sugar_base_rotamer (pose::Pose const &pose, bool const floating_base, Size const rebuild_suite)
core::io::silent::BinarySilentStruct	get_binary_rna_silent_struct_safe (pose::Pose const &const_pose, std::string const &tag, std::string const &silent_file)
core::io::silent::BinarySilentStruct	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 (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	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_copy_dofs (utility::vector1< Residue_info > copy_dofs)
utility::vector1< Residue_info >	get_copy_dofs_from_fasta (std::string const full_fasta_sequence)
Residue_info	get_residue_from_seq_num (Size const &seq_num, utility::vector1< Residue_info > const &copy_dofs)
bool	contain_residue_at_seq_num (Size seq_num, utility::vector1< Residue_info > const &copy_dofs)
utility::vector1 < utility::vector1 < Residue_info > >	create_strand_list (utility::vector1< Residue_info > const &copy_dofs)
utility::vector1< Residue_info >	set_difference (utility::vector1< Residue_info > const &copy_dofs_1, utility::vector1< Residue_info > const &copy_dofs_2)
utility::vector1< Residue_info >	set_union (utility::vector1< Residue_info > const &copy_dofs_1, utility::vector1< Residue_info > const &copy_dofs_2)
bool	copy_dofs_sort_criterion (Residue_info residue_info_1, Residue_info residue_info_2)
void	sort_copy_dofs (utility::vector1< Residue_info > &copy_dofs)
bool	is_OP2_atom (std::string const &atom_name)
bool	is_OP1_atom (std::string const &atom_name)
bool	is_P_atom (std::string const &atom_name)
bool	is_O2prime_atom (std::string const &atom_name)
bool	is_O3prime_atom (std::string const &atom_name)
bool	is_O4prime_atom (std::string const &atom_name)
bool	is_O5prime_atom (std::string const &atom_name)
bool	is_C2prime_atom (std::string const &atom_name)
bool	is_C3prime_atom (std::string const &atom_name)
bool	is_C4prime_atom (std::string const &atom_name)
bool	is_C5prime_atom (std::string const &atom_name)
bool	is_1H5prime_atom (std::string const &atom_name)
bool	is_2H5prime_atom (std::string const &atom_name)
bool	is_H3prime_atom (std::string const &atom_name)
bool	is_H4prime_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	check_can_prepend (utility::vector1< core::Size > const &seq_num_list)
bool	check_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	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, std::ostream &outstream)
void	output_pair_size (utility::vector1< std::pair< Size, Size > > const &pair_size_vector, std::string const &output_string, std::ostream &outstream, core::Size const spacing)
bool	pair_sort_criterion (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_criterion (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, std::ostream &outstream, 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, std::ostream &outstream, core::Size const tag_spacing)
void	output_bool_list (std::string const tag, utility::vector1< Size > const &size_list, std::ostream &outstream, core::Size const spacing)
void	output_bool_list (std::string const tag, utility::vector1< bool > const &bool_list, std::ostream &outstream, core::Size const spacing)
void	output_size_list (std::string const tag, utility::vector1< Size > const &size_list, std::ostream &outstream, core::Size const spacing)
void	output_title_text (std::string const title, std::ostream &outstream)
void	output_fold_tree_info (kinematics::FoldTree const &fold_tree, std::string const pose_name, std::ostream &outstream)
void	output_fold_tree_info (pose::Pose const &pose, std::string pose_name, std::ostream &outstream)
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_O2Prime_hydrogen (core::pose::Pose &pose)
bool	remove_virtual_O2Prime_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)
void	Freeze_sugar_torsions (core::kinematics::MoveMap &mm, Size const total_residue)
void	output_boolean (std::string const &tag, bool boolean, std::ostream &outstream)
void	output_boolean (bool boolean, std::ostream &outstream)
void	output_movemap (kinematics::MoveMap const &mm, core::pose::Pose const &pose, std::ostream &outstream)
utility::vector1< core::Size >	get_surrounding_O2prime_hydrogen (pose::Pose const &pose, utility::vector1< core::Size > const &moving_res, bool verbose)
void	o2prime_trials (pose::Pose &pose, core::scoring::ScoreFunctionOP const &packer_scorefxn)
void	o2prime_trials (pose::Pose &pose, core::scoring::ScoreFunctionOP const &packer_scorefxn, utility::vector1< core::Size > const &O2prime_pack_seq_num)
pack::task::PackerTaskOP	create_standard_o2prime_pack_task (pose::Pose const &pose, utility::vector1< core::Size > const &O2prime_pack_seq_num)
void	print_backbone_torsions (pose::Pose const &pose, Size const five_prime_chainbreak)
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 moving_res, core::Size const reference_res)
void	setup_chain_break_variants (core::pose::Pose &pose, Size const cutpoint)
void	remove_chain_break_variants (core::pose::Pose &pose, Size const &cutpoint)
void	remove_chain_break_jump_point (core::pose::Pose &pose, core::Size const moving_res, core::Size const reference_res)
core::Size	setup_bulge_jump_point (pose::Pose &pose, Size const &moving_base, Size const &reference_base, bool const verbose)
utility::vector1< bool >	get_partition_definition_floating_base (pose::Pose const &pose, Size const &moving_res)
Size	get_anchor_res (Size const rebuild_res, pose::Pose const &pose)
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)
core::Size	get_residue_base_state (core::pose::Pose const &pose, Size const seq_num)
core::Size	get_residue_pucker_state (core::pose::Pose const &pose, Size const seq_num, bool const verbose)
bool	is_same_sugar_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	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, std::ostream &outstream, bool const is_simple_full_length_JP)
void	print_JobParameters_info (StepWiseRNA_JobParametersOP const &JP, std::string const JP_name, std::ostream &outstream, 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, core::Size const base_state, std::ostream &outstream)
void	print_sugar_pucker_state (std::string const tag, core::Size const pucker_state, std::ostream &outstream)
scoring::ScoreFunctionOP	get_sampling_scorefxn (scoring::ScoreFunctionCOP scorefxn)
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 &o2prime_pack_scorefxn_)
void	copy_all_o2prime_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	figure_out_stepwise_rna_movemap (core::kinematics::MoveMap &mm, core::pose::Pose const &pose, utility::vector1< Size > const &minimize_res)
void	figure_out_stepwise_rna_movemap (core::kinematics::MoveMap &mm, core::pose::Pose const &pose, toolbox::AllowInsertOP const &allow_insert)
void	update_allow_insert_with_extra_minimize_res (pose::Pose const &pose, toolbox::AllowInsertOP &allow_insert, utility::vector1< core::Size > const &extra_minimize_res)
void	choose_random_if_unspecified_nucleotide (char &newrestype)
bool	mutate_res_if_allowed (pose::Pose &pose, Size const mutate_res, Real const mutation_frequency)
std::string	create_tag (std::string const &prestring, Size const i)
std::string	create_torsion_value_string (core::Real const &torsion_value)
std::string	create_rotamer_string (core::pose::Pose const &pose, Size const moving_res, bool const is_prepend)
std::string	create_rotamer_string (core::pose::Pose const &pose, Size const moving_res, Size const reference_res)
void	add_fade_chain_break_constraint_across_gap (pose::Pose &pose, Size const five_prime_res, Size const three_prime_res, Size const gap_size)
void	add_harmonic_chain_break_constraint (pose::Pose &pose, Size const five_prime_res)
void	get_possible_O3prime_C5prime_distance_range (Size const gap_size_, Distance &min_dist, Distance &max_dist)

Variables
StepWiseRNA_CountStruct	local_count_data

Typedef Documentation

typedef utility::pointer::owning_ptr< StepWiseRNA_CombineLongLoopFilterer > protocols::stepwise::sampling::rna::StepWiseRNA_CombineLongLoopFiltererOP

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

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

typedef utility::pointer::owning_ptr< StepWiseRNA_JobParameters > protocols::stepwise::sampling::rna::StepWiseRNA_JobParametersOP

typedef utility::pointer::owning_ptr< StepWiseRNA_JobParametersUtil const > protocols::stepwise::sampling::rna::StepWiseRNA_JobParametersUtilCOP

typedef utility::pointer::owning_ptr< StepWiseRNA_JobParametersUtil > protocols::stepwise::sampling::rna::StepWiseRNA_JobParametersUtilOP

typedef utility::pointer::owning_ptr< StepWiseRNA_Minimizer const > protocols::stepwise::sampling::rna::StepWiseRNA_MinimizerCOP

typedef utility::pointer::owning_ptr< StepWiseRNA_Minimizer > protocols::stepwise::sampling::rna::StepWiseRNA_MinimizerOP

typedef utility::pointer::owning_ptr< StepWiseRNA_Modeler const > protocols::stepwise::sampling::rna::StepWiseRNA_ModelerCOP

typedef utility::pointer::owning_ptr< StepWiseRNA_Modeler > protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOP

typedef utility::pointer::owning_ptr< StepWiseRNA_ModelerOptions const > protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsCOP

typedef utility::pointer::owning_ptr< StepWiseRNA_ModelerOptions > protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsOP

typedef utility::pointer::owning_ptr< StepWiseRNA_PoseSelection const > protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelectionCOP

typedef utility::pointer::owning_ptr< StepWiseRNA_PoseSelection > protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelectionOP

Function Documentation

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

References core::pose::Pose::constraint_set(), GAP_SIZE_DUMMY, get_possible_O3prime_C5prime_distance_range(), core::pose::Pose::residue(), and runtime_assert.

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::setup_sugar_conformations().

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

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

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::bulge_chain_closure_legacy(), protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::initialize_poses_and_checkers(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::reinstantiate_backbone_and_add_constraint_at_moving_res(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler::reinstantiate_backbone_and_add_constraint_at_moving_res(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::reinstantiate_backbone_and_add_constraint_at_moving_res(), protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler::reinstantiate_backbone_and_add_constraint_at_moving_res(), and protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::setup_sugar_conformations().

void protocols::stepwise::sampling::rna::add_virtual_O2Prime_hydrogen

(

core::pose::Pose &

pose

)

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

Referenced by protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::create_VDW_rep_screen_pose(), protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::FARFAR_setup_using_user_input_VDW_pose(), protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::initialize_poses_and_checkers(), protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler::initialize_poses_and_checkers(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_poses_and_stubs_and_checkers(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler::initialize_poses_and_stubs_and_checkers(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::initialize_poses_and_stubs_and_checkers(), protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::setup_using_user_input_VDW_pose(), and protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::setup_using_working_pose().

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

References check_for_messed_up_structure(), create_alignment_id_map(), protocols::pack_daemon::error_message, is_virtual_base(), output_boolean(), core::pose::Pose::residue(), core::scoring::superimpose_pose(), core::chemical::rna::TR, and utility_exit_with_message.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::align_to_quick_alignment_pose(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::create_large_cluster_centers_member_list(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::is_new_cluster_center_with_job_parameters(), output_data(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::setup_fail_triangle_inequailty_list(), and protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::setup_native_pose().

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

References runtime_assert.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::create_silent_file_and_tag_list(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::get_user_input_alignment_res_list(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::set_fixed_res(), protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_force_north_sugar_list(), protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_force_south_sugar_list(), protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_force_syn_chi_res_list(), protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_global_sample_res_list(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::set_native_alignment_res(), protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_protonated_H1_adenosine_list(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::set_terminal_res(), protocols::stepwise::sampling::rna::SlicedPoseJobParameters::setup(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::setup_native_pose(), and protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::setup_using_user_input_VDW_pose().

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

References full_to_sub().

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

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(), core::pose::Pose::total_residue(), core::chemical::rna::TR, utility_exit_with_message, and verbose.

Referenced by protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::add_protonated_H1_adenosine_variants(), and protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::do_checks_and_apply_protonated_H1_adenosine_variant().

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

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

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

References runtime_assert, and sub_to_full().

Referenced by protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::apply_bulge_variants(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::apply_virtual_res_variant(), and protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::get_user_input_alignment_res_list().

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

References apply_virtual_rna_residue_variant_type().

Referenced by protocols::stepwise::sampling::rna::bulge::BulgeApplyMover::apply(), protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::apply_bulge_variant(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::apply_virtual_res_variant(), protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::do_the_sampling(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::do_the_sampling(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::restore_pose_variants_after_chain_closure(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::setup_native_pose(), and protocols::stepwise::sampling::rna::legacy::setup_simple_full_length_rna_job_parameters().

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

References core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::annotated_sequence(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::chemical::ResidueType::has_variant_type(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), protocols::stepwise::is_cutpoint_closed(), is_cutpoint_open(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), runtime_assert, core::pose::Pose::total_residue(), core::chemical::rna::TR, and utility_exit_with_message.

Referenced by apply_virtual_rna_residue_variant_type(), and virtualize_bulges().

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

References core::chemical::ResidueType::atom_name(), core::conformation::Residue::seqpos(), core::chemical::rna::TR, core::conformation::Residue::type(), utility_exit_with_message, 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::stepwise::sampling::rna::base_atoms_square_deviation	(	pose::Pose const &	pose1,
		pose::Pose const &	pose2,
		Size const &	moving_res_1,
		Size const &	moving_res_2,
		Size &	atom_count,
		Real &	sum_sd,
		bool	verbose,
		bool const	ignore_virtual_atom
	)

References core::conformation::Residue::aa(), core::chemical::ResidueType::atom_name(), atom_square_deviation(), core::conformation::Residue::first_sidechain_atom(), get_num_side_chain_atom_from_res_name(), core::conformation::Residue::is_virtual(), core::chemical::name_from_aa(), core::pose::Pose::residue(), core::chemical::rna::TR, core::conformation::Residue::type(), and utility_exit_with_message.

Referenced by protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::align_VDW_rep_screen_pose().

bool protocols::stepwise::sampling::rna::check_can_append

(

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

seq_num_list

)

Referenced by protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::figure_out_partition_definition(), and protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::figure_out_prepend_internal().

bool protocols::stepwise::sampling::rna::check_can_prepend

(

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

seq_num_list

)

Referenced by protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::figure_out_partition_definition(), and protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::figure_out_prepend_internal().

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

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::chemical::rna::DELTA, core::conformation::Residue::is_RNA(), numeric::principal_angle_degrees(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::chemical::rna::TR.

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

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

References ensure_valid_full_seq_num().

Referenced by check_validity_and_get_working_res(), and protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList::setup_sugar_modeling_list().

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

References check_is_working_res(), full_to_sub(), and utility_exit_with_message.

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList::setup_sugar_modeling_list().

void protocols::stepwise::sampling::rna::choose_random_if_unspecified_nucleotide

(

char &

newrestype

)

References numeric::random::RandomGenerator::random_range(), RG, and core::chemical::rna::TR.

Referenced by protocols::stepwise::monte_carlo::rna::AddMover::append_residue(), protocols::stepwise::monte_carlo::rna::FromScratchMover::apply(), mutate_res_if_allowed(), and protocols::stepwise::monte_carlo::rna::AddMover::prepend_residue().

bool protocols::stepwise::sampling::rna::contain_residue_at_seq_num	(	Size	seq_num,
		utility::vector1< Residue_info > const &	copy_dofs
	)

References j.

Referenced by set_difference(), and set_union().

utility::vector1< Residue_info > protocols::stepwise::sampling::rna::Convert_rebuild_residue_string_to_list

(

std::string const &

rebuild_residue_string

)

References get_three_letter_name(), length, protocols::stepwise::sampling::rna::Residue_info::name, protocols::stepwise::sampling::rna::Residue_info::seq_num, string_to_int(), and tokenize().

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

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(), core::pose::Pose::total_residue(), and utility_exit_with_message.

Referenced by protocols::stepwise::sampling::rna::o2prime::O2PrimePacker::apply(), protocols::stepwise::sampling::rna::o2prime::O2PrimePacker::copy_all_o2prime_torsions(), and protocols::stepwise::sampling::rna::o2prime::O2PrimePacker::sample_o2prime_hydrogen().

bool protocols::stepwise::sampling::rna::copy_dofs_sort_criterion	(	Residue_info	residue_info_1,
		Residue_info	residue_info_2
	)

References protocols::stepwise::sampling::rna::Residue_info::seq_num.

Referenced by sort_copy_dofs().

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

References core::id::BB, core::id::CHI, core::conformation::Residue::chi(), core::pose::Pose::fold_tree(), core::conformation::Residue::mainchain_torsion(), core::chemical::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(), core::chemical::rna::TR, core::id::TorsionID::type(), and utility_exit_with_message.

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

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::id::BOGUS_ATOM_ID, chemical, utility::vector1< T, class >::has_value(), core::pose::initialize_atomid_map(), core::pose::Pose::residue(), core::pose::Pose::sequence(), setup_suite_atom_id_map(), core::pose::Pose::total_residue(), core::chemical::rna::TR, and utility_exit_with_message.

Referenced by align_poses().

std::map< Size, Size > protocols::stepwise::sampling::rna::create_full_to_input_res_map

(

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

input_res_vector

)

Referenced by protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::correctly_copy_HO2prime_positions(), and protocols::stepwise::sampling::rna::StepWiseRNA_CombineLongLoopFilterer::StepWiseRNA_CombineLongLoopFilterer().

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

References create_rotamer_string().

Referenced by protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::apply(), and protocols::stepwise::screener::TagDefinition::check_screen().

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

References core::conformation::Residue::chi(), create_torsion_value_string(), core::conformation::Residue::mainchain_torsion(), core::pose::Pose::residue(), and runtime_assert.

Referenced by create_rotamer_string().

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

References core::pack::task::TaskFactory::create_packer_task(), utility::vector1< T, class >::has_value(), core::conformation::Residue::is_RNA(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by protocols::stepwise::sampling::rna::o2prime::O2PrimePacker::initialize_o2prime_packer_task(), and o2prime_trials().

utility::vector1< utility::vector1< Residue_info > > protocols::stepwise::sampling::rna::create_strand_list

(

utility::vector1< Residue_info > const &

copy_dofs

)

References j, and sort_copy_dofs().

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

References tag.

Referenced by protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::apply(), and protocols::stepwise::screener::TagDefinition::check_screen().

std::string protocols::stepwise::sampling::rna::create_torsion_value_string

(

core::Real const &

torsion_value

)

References numeric::principal_angle_degrees().

Referenced by create_rotamer_string().

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

References runtime_assert.

Referenced by check_is_working_res().

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

References core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), protocols::stepwise::is_cutpoint_closed(), core::kinematics::FoldTree::jump_nr(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by setup_job_parameters_explicit(), and setup_job_parameters_legacy().

void protocols::stepwise::sampling::rna::figure_out_root_partition_res	(	pose::Pose const &	pose,
		StepWiseRNA_JobParametersCOP	job_parameters,
		utility::vector1< Size > &	root_partition_res,
		utility::vector1< Size > &	moving_partition_res
	)

References utility::vector1< T, class >::has_value(), runtime_assert, and core::pose::Pose::total_residue().

bool protocols::stepwise::sampling::rna::figure_out_sample_both_sugar_base_rotamer	(	pose::Pose const &	pose,
		bool const	floating_base,
		Size const	rebuild_suite
	)

References core::conformation::Residue::has_variant_type(), core::pose::Pose::residue(), protocols::rotamer_sampler::rna::sampling_sugar_at_five_prime(), protocols::rotamer_sampler::rna::sampling_sugar_at_three_prime(), and TR.

Referenced by setup_job_parameters_explicit(), and setup_job_parameters_legacy().

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

References figure_out_stepwise_rna_movemap(), utility::vector1< T, class >::has_value(), core::chemical::ResidueType::has_variant_type(), core::chemical::ResidueType::is_RNA(), nres, core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and core::chemical::VIRTUAL_PHOSPHATE.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::figure_out_moving_residues(), and setup_job_parameters_for_swa().

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

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::id::BB, core::id::CHI, core::pose::Pose::conformation(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::kinematics::MoveMap::get(), utility::pointer::owning_ptr< T >::get(), core::conformation::Conformation::get_torsion_angle_atom_ids(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_RNA(), utility::tools::make_vector1(), core::conformation::Residue::nchi(), nres, core::kinematics::FoldTree::num_jump(), core::chemical::rna::NUM_RNA_MAINCHAIN_TORSIONS(), output_boolean(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), runtime_assert, core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), core::pose::Pose::total_residue(), core::chemical::rna::TR, and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by figure_out_stepwise_rna_movemap().

bool protocols::stepwise::sampling::rna::file_exists

(

std::string const &

file_name

)

References file_exists().

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

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

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

References utility::vector1< T, class >::has_value(), core::conformation::Residue::has_variant_type(), output_boolean(), output_seq_num_list(), output_title_text(), phosphate_square_deviation(), core::pose::Pose::residue(), rmsd, runtime_assert, core::pose::Pose::sequence(), suite_square_deviation(), core::pose::Pose::total_residue(), core::chemical::rna::TR, and utility_exit_with_message.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::is_new_cluster_center_with_job_parameters(), and protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file().

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

References core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), jump_nr, protocols::stepwise::look_for_unique_jump_to_moving_res(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by protocols::stepwise::monte_carlo::SWA_MoveSelector::get_intramolecular_split_move_elements(), and setup_job_parameters_legacy().

core::io::silent::BinarySilentStruct protocols::stepwise::sampling::rna::get_binary_rna_silent_struct_safe	(	pose::Pose const &	const_pose,
		std::string const &	tag,
		std::string const &	silent_file
	)

References at(), core::io::silent::SilentFileData::begin(), centroid, check_for_messed_up_structure(), protocols::rotamer_sampler::rigid_body::EulerAngles::convert_to_rotation_matrix(), end, core::io::silent::SilentFileData::end(), file_exists(), core::chemical::ChemicalManager::get_instance(), RADS_PER_DEG, core::io::silent::SilentFileData::read_file(), remove_file(), core::pose::Pose::residue(), residue_type_set, core::chemical::RNA, rotation_matrix(), protocols::rotamer_sampler::rigid_body::EulerAngles::set_alpha(), protocols::rotamer_sampler::rigid_body::EulerAngles::set_gamma(), core::pose::Pose::set_xyz(), protocols::rotamer_sampler::rigid_body::EulerAngles::set_z(), core::pose::Pose::total_residue(), TR, utility_exit_with_message, and core::pose::Pose::xyz().

Referenced by get_binary_rna_silent_struct_safe_wrapper().

core::io::silent::BinarySilentStruct protocols::stepwise::sampling::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
	)

References get_binary_rna_silent_struct_safe(), and s.

Referenced by output_data().

utility::vector1< Residue_info > protocols::stepwise::sampling::rna::get_copy_dofs_from_fasta

(

std::string const

full_fasta_sequence

)

References protocols::stepwise::sampling::rna::Residue_info::name, residue, and protocols::stepwise::sampling::rna::Residue_info::seq_num.

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

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(), core::pose::Pose::total_residue(), core::chemical::rna::TR, and utility_exit_with_message.

Referenced by virtualize_bulges().

core::Size protocols::stepwise::sampling::rna::get_max_seq_num_from_res_map

(

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

my_map

)

References TR.

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

References exit, core::chemical::name_from_aa(), and core::chemical::rna::TR.

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

std::string protocols::stepwise::sampling::rna::get_one_letter_name

(

std::string const &

three_letter_name

)

References exit, and TR.

Referenced by output_residue_struct().

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

References core::pose::Pose::fold_tree(), protocols::stepwise::get_partition_definition_by_jump(), jump_nr, and protocols::stepwise::look_for_unique_jump_to_moving_res().

Referenced by setup_job_parameters_explicit(), and setup_job_parameters_legacy().

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

References C5I_C5I_PLUS_ONE_MAX_DIST, O3I_C5I_MAX_DIST, O3I_C5I_MIN_DIST, and O3I_C5I_PLUS_TWO_MAX_DIST.

Referenced by add_fade_chain_break_constraint_across_gap(), and protocols::stepwise::sampling::rna::checker::ChainClosableGeometryChecker::initialize_distance_range().

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

References core::chemical::rna::ANTI, core::chemical::rna::CHI, core::chemical::rna::NUM_RNA_MAINCHAIN_TORSIONS(), numeric::principal_angle_degrees(), core::pose::Pose::residue(), and core::chemical::rna::SYN.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::create_silent_file_and_tag_list().

Residue_info protocols::stepwise::sampling::rna::get_residue_from_seq_num	(	Size const &	seq_num,
		utility::vector1< Residue_info > const &	copy_dofs
	)

References exit, and TR.

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

References core::chemical::rna::DELTA, core::conformation::Residue::has_variant_type(), core::chemical::rna::NORTH, numeric::principal_angle_degrees(), core::pose::Pose::residue(), core::chemical::rna::SOUTH, core::chemical::rna::TR, and utility_exit_with_message.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::cluster_pose_list(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::create_silent_file_and_tag_list(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::is_old_individual_suite_cluster(), and is_same_sugar_pucker().

scoring::ScoreFunctionOP protocols::stepwise::sampling::rna::get_sampling_scorefxn

(

scoring::ScoreFunctionCOP

scorefxn

)

References angle_constraint, atom_pair_constraint, chainbreak, fa_rep, and linear_chainbreak.

Referenced by initialize_common_scorefxns(), protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::initialize_sampling_scorefxn(), protocols::stepwise::sampling::rna::sugar::minimize_all_sampled_floating_bases(), and protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::restore_pose_variants_after_chain_closure().

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

References core::conformation::Residue::aa(), core::chemical::aa_vrt, at(), core::conformation::Residue::atom_index(), core::chemical::ResidueType::atom_name(), core::conformation::Residue::first_sidechain_atom(), core::chemical::ResidueType::has_variant_type(), core::chemical::ResidueType::is_RNA(), core::conformation::Residue::is_RNA(), core::conformation::Residue::is_virtual(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), core::chemical::rna::TR, core::conformation::Residue::type(), utility_exit_with_message, and core::conformation::Residue::xyz().

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::apply(), and protocols::stepwise::sampling::rna::o2prime::O2PrimePacker::initialize_o2prime_packer_task().

std::string protocols::stepwise::sampling::rna::get_tag_from_pdb_filename

(

std::string const

pdb_filename

)

References tag.

std::string protocols::stepwise::sampling::rna::get_three_letter_name

(

std::string const &

one_letter_name

)

References exit, and TR.

Referenced by Convert_rebuild_residue_string_to_list().

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

References core::conformation::Residue::has_variant_type(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::chemical::rna::TR, and utility_exit_with_message.

Referenced by protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs().

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

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

Referenced by protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::get_previously_closed_cutpoint_from_imported_silent_file(), and protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::Import_pose().

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

References angle_constraint, atom_pair_constraint, fa_atr, fa_rep, fa_sol, get_sampling_scorefxn(), hbond_lr_bb_sc, hbond_sc, hbond_sr_bb_sc, and lk_nonpolar.

bool protocols::stepwise::sampling::rna::is_1H5prime_atom

(

std::string const &

atom_name

)

bool protocols::stepwise::sampling::rna::is_2H5prime_atom

(

std::string const &

atom_name

)

bool protocols::stepwise::sampling::rna::is_C2prime_atom

(

std::string const &

atom_name

)

bool protocols::stepwise::sampling::rna::is_C3prime_atom

(

std::string const &

atom_name

)

bool protocols::stepwise::sampling::rna::is_C4prime_atom

(

std::string const &

atom_name

)

bool protocols::stepwise::sampling::rna::is_C5prime_atom

(

std::string const &

atom_name

)

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

References sort_seq_num_list().

bool protocols::stepwise::sampling::rna::is_five_prime_phosphate_atom

(

std::string const &

atom_name

)

References is_O5prime_atom(), is_OP1_atom(), is_OP2_atom(), and is_P_atom().

Referenced by is_phosphate_atom().

bool protocols::stepwise::sampling::rna::is_H3prime_atom

(

std::string const &

atom_name

)

bool protocols::stepwise::sampling::rna::is_H4prime_atom

(

std::string const &

atom_name

)

bool protocols::stepwise::sampling::rna::is_O2prime_atom

(

std::string const &

atom_name

)

bool protocols::stepwise::sampling::rna::is_O3prime_atom

(

std::string const &

atom_name

)

Referenced by is_three_prime_phosphate_atom().

bool protocols::stepwise::sampling::rna::is_O4prime_atom

(

std::string const &

atom_name

)

bool protocols::stepwise::sampling::rna::is_O5prime_atom

(

std::string const &

atom_name

)

Referenced by is_five_prime_phosphate_atom().

bool protocols::stepwise::sampling::rna::is_OP1_atom

(

std::string const &

atom_name

)

Referenced by is_five_prime_phosphate_atom().

bool protocols::stepwise::sampling::rna::is_OP2_atom

(

std::string const &

atom_name

)

Referenced by is_five_prime_phosphate_atom().

bool protocols::stepwise::sampling::rna::is_P_atom

(

std::string const &

atom_name

)

Referenced by is_five_prime_phosphate_atom().

bool protocols::stepwise::sampling::rna::is_phosphate_atom

(

std::string const &

atom_name

)

References is_five_prime_phosphate_atom(), and is_three_prime_phosphate_atom().

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

References length, core::pose::Pose::residue(), core::chemical::rna::TR, and utility_exit_with_message.

Referenced by protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::apply(), protocols::stepwise::screener::ResidueContactScreener::check_screen(), protocols::stepwise::sampling::rna::StepWiseRNA_CombineLongLoopFilterer::previously_builded_res_VDW_filter(), and protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen_with_act_pose().

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

References get_residue_pucker_state().

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::cluster_pose_list(), and protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::is_old_individual_suite_cluster().

bool protocols::stepwise::sampling::rna::is_three_prime_phosphate_atom

(

std::string const &

atom_name

)

References is_O3prime_atom().

Referenced by is_phosphate_atom().

bool protocols::stepwise::sampling::rna::is_virtual_base

(

conformation::Residue const &

rsd

)

References core::conformation::Residue::aa(), core::conformation::Residue::atom_type(), chemical, core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_RNA(), core::conformation::Residue::is_virtual(), core::chemical::AtomType::name(), core::chemical::name_from_aa(), core::conformation::Residue::nheavyatoms(), output_boolean(), runtime_assert, core::conformation::Residue::seqpos(), core::chemical::rna::TR, and utility_exit_with_message.

Referenced by align_poses(), protocols::stepwise::sampling::rna::bulge::BulgeApplyMover::apply(), protocols::stepwise::sampling::rna::bulge::BulgeUnApplyMover::apply(), protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::apply_bulge_variant(), and protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::bulge_variant_decision().

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

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

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::minimize_sugar().

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

References core::kinematics::FoldTree::downstream_jump_residue(), core::kinematics::FoldTree::num_cutpoint(), core::kinematics::FoldTree::set_jump_atoms(), core::chemical::rna::TR, core::kinematics::FoldTree::upstream_jump_residue(), and utility_exit_with_message.

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

References choose_random_if_unspecified_nucleotide(), const_full_model_info(), get_res_list_from_full_model_info(), core::pose::rna::mutate_position(), RG, core::pose::Pose::sequence(), sub_to_full(), and numeric::random::RandomGenerator::uniform().

Referenced by protocols::stepwise::monte_carlo::rna::ResampleMover::apply().

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

References core::conformation::Residue::aa(), core::chemical::aa_vrt, o2prime_trials(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::apply(), and protocols::stepwise::sampling::legacy::RigidBodySampler::search_translations().

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

References create_standard_o2prime_pack_task(), output_seq_num_list(), core::pack::rotamer_trials(), and core::chemical::rna::TR.

Referenced by o2prime_trials().

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

References output_bool_list().

Referenced by protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::figure_out_is_residue_prepend(), and protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::setup_additional_cutpoint_closed().

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

References output_boolean().

Referenced by output_bool_list(), and print_JobParameters_info().

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

Referenced by protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::apply_virtual_res_variant(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::cluster(), protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::cluster_pose_list(), protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::create_VDW_screen_bin(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::figure_out_jump_partners(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::figure_out_partition_definition(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::figure_out_prepend_internal(), protocols::stepwise::sampling::rna::StepWiseRNA_CombineLongLoopFilterer::filter(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file(), protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::stepwise::sampling::rna::rigid_body::get_sugar_stub(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::get_user_input_alignment_res_list(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::initialize_max_memory_pose_num(), protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::initialize_parameters(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::is_new_cluster_center_with_job_parameters(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::is_old_individual_suite_cluster(), protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::output_options(), protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::output_parameters(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file(), protocols::stepwise::sampling::rna::sugar::SugarModeling::set_base_and_pucker_state(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::set_fixed_res(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::set_jump_point_pair_list(), and protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList::setup_sugar_modeling_list().

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

Referenced by align_poses(), figure_out_stepwise_rna_movemap(), full_length_rmsd_over_residue_list(), is_virtual_base(), output_bool_list(), output_movemap(), print_JobParameters_info(), rmsd_over_residue_list(), and virtualize_bulges().

void protocols::stepwise::sampling::rna::output_copy_dofs

(

utility::vector1< Residue_info >

copy_dofs

)

References output_residue_struct(), residue, protocols::stepwise::sampling::rna::Residue_info::seq_num, sort_copy_dofs(), and TR.

void protocols::stepwise::sampling::rna::output_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_
	)

References output_data().

Referenced by protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::apply(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::apply(), protocols::stepwise::screener::PoseSelectionScreener::check_screen(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList::output_pose_data_list(), protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::output_pose_list(), protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::output_pose_wrapper(), and protocols::features::serialize_residue_xyz_coords().

void protocols::stepwise::sampling::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_
	)

References align_poses(), calc_rms_res, full_to_sub(), get_binary_rna_silent_struct_safe_wrapper(), output_extra_RMSDs, phosphate_base_phosphate_rmsd(), rms_at_corresponding_heavy_atoms(), rmsd_over_residue_list(), s, suite_rmsd(), and core::io::silent::SilentFileData::write_silent_struct().

Referenced by output_data().

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

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 protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::reroot_fold_tree(), and protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::setup_fold_tree().

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

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

Referenced by copy_torsions_FROM_TO(), print_JobParameters_info(), and setup_bulge_jump_point().

void protocols::stepwise::sampling::rna::output_is_prepend_map	(	std::string const	tag,
		std::map< core::Size, bool > const &	my_map,
		core::Size const	max_seq_num,
		std::ostream &	outstream,
		core::Size const	tag_spacing
	)

Referenced by print_JobParameters_info(), and protocols::stepwise::sampling::rna::SlicedPoseJobParameters::setup().

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

References 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(), protocols::abinitio::abscript::I, 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::stepwise::sampling::rna::StepWiseRNA_Minimizer::apply().

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

Referenced by protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::set_jump_point_pair_list(), and protocols::stepwise::sampling::rna::SlicedPoseJobParameters::setup().

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

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

References TR.

void protocols::stepwise::sampling::rna::output_residue_struct

(

Residue_info const &

residue

)

References get_one_letter_name(), protocols::stepwise::sampling::rna::Residue_info::name, protocols::stepwise::sampling::rna::Residue_info::seq_num, and TR.

Referenced by output_copy_dofs().

void protocols::stepwise::sampling::rna::output_rotamer

(

utility::vector1< Real > &

rotamer

)

References core::chemical::rna::TR.

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

References protocols::abinitio::abscript::I, and sort_seq_num_list().

Referenced by protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::add_terminal_res_repulsion(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::correctly_copy_HO2prime_positions(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::create_silent_file_and_tag_list(), protocols::stepwise::sampling::rna::StepWiseRNA_CombineLongLoopFilterer::figure_out_appended_and_prepended_res_list(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::figure_out_best_working_alignment(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::figure_out_is_prepend_map(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::figure_out_partition_definition(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::figure_out_prepend_internal(), full_length_rmsd_over_residue_list(), protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::get_previously_closed_cutpoint_from_imported_silent_file(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::get_user_input_alignment_res_list(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::initialize_quick_alignment_pose(), o2prime_trials(), protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::output_options(), protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::output_parameters(), print_JobParameters_info(), rmsd_over_residue_list(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::set_fixed_res(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::set_native_alignment_res(), protocols::stepwise::sampling::rna::SlicedPoseJobParameters::setup(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::setup_additional_cutpoint_closed(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::setup_native_pose(), protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::setup_using_user_input_VDW_pose(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::StepWiseRNA_JobParametersSetup(), protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::update_VDW_screen_bin(), protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen_with_act_pose(), and virtualize_bulges().

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

References protocols::abinitio::abscript::I.

Referenced by protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::setup_additional_cutpoint_closed().

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

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_CombineLongLoopFilterer::align_all_pose(), protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::align_VDW_rep_screen_pose(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList::apply(), protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler::apply(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::apply(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::apply(), protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::apply(), protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::apply(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::apply(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::apply(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler::apply(), protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler::apply(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::apply(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::bulge_chain_closure_legacy(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::bulge_chain_minimize_legacy(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::cluster(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::correctly_copy_HO2prime_positions(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::create_large_cluster_centers_member_list(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::create_silent_file_and_tag_list(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::create_tags_map(), protocols::stepwise::sampling::rna::StepWiseRNA_CombineLongLoopFilterer::do_some_filtering(), protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::do_the_sampling(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::do_the_sampling(), protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::FARFAR_setup_using_user_input_VDW_pose(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::figure_out_best_working_alignment(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::figure_out_chain_boundaries(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::figure_out_is_prepend_map(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::figure_out_is_residue_prepend(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::figure_out_jump_partners(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::figure_out_prepend_internal(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::figure_out_working_sequence_and_mapping(), protocols::stepwise::sampling::rna::StepWiseRNA_CombineLongLoopFilterer::filter(), full_length_rmsd_over_residue_list(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file(), protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::stepwise::sampling::rna::legacy::get_silent_file_tags(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::get_user_input_alignment_res_list(), protocols::stepwise::sampling::rna::sugar::minimize_all_sampled_floating_bases(), print_JobParameters_info(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::reroot_fold_tree(), rmsd_over_residue_list(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::set_fixed_res(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::set_native_alignment_res(), protocols::stepwise::sampling::rna::SlicedPoseJobParameters::setup(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::setup_additional_cutpoint_closed(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::setup_fold_tree(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::setup_native_pose(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::setup_sugar_conformations(), protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::setup_using_user_input_VDW_pose(), protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::setup_using_working_pose(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::StepWiseRNA_JobParametersSetup(), and protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::two_stage_clustering().

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

Referenced by sort_pair_list().

std::string protocols::stepwise::sampling::rna::path_basename

(

std::string const

full_path

)

References basename.

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

References phosphate_base_phosphate_square_deviation(), and rmsd.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::cluster_pose_list(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::is_old_individual_suite_cluster(), and output_data().

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

References core::conformation::Residue::aa(), atom_square_deviation(), core::conformation::Residue::first_sidechain_atom(), get_num_side_chain_atom_from_res_name(), core::conformation::Residue::is_virtual(), core::chemical::name_from_aa(), core::pose::Pose::residue(), core::chemical::rna::TR, and utility_exit_with_message.

Referenced by phosphate_base_phosphate_rmsd().

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

References core::conformation::Residue::aa(), atom_square_deviation(), core::conformation::Residue::is_virtual(), core::chemical::name_from_aa(), core::pose::Pose::residue(), core::chemical::rna::TR, and utility_exit_with_message.

Referenced by full_length_rmsd_over_residue_list().

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

References 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(), core::chemical::rna::TR, and core::conformation::Residue::type().

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

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

Referenced by protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::apply_cutpoint_variants().

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

References core::chemical::rna::ANTI, core::chemical::rna::ANY_CHI, core::chemical::rna::NO_CHI, core::chemical::rna::SYN, and utility_exit_with_message.

Referenced by protocols::stepwise::sampling::rna::sugar::SugarModeling::set_base_and_pucker_state().

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

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

Referenced by suite_square_deviation().

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

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

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

References print_JobParameters_info().

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::do_residue_sampling(), protocols::stepwise::sampling::rna::legacy::setup_simple_full_length_rna_job_parameters(), and protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::verify_protonated_H1_adenosine_variants().

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

References output_bool_list(), output_boolean(), output_extra_RMSDs, output_fold_tree_info(), output_is_prepend_map(), output_seq_num_list(), and output_title_text().

Referenced by print_JobParameters_info().

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

References core::chemical::rna::ANY_PUCKER, core::chemical::rna::NO_PUCKER, core::chemical::rna::NORTH, core::chemical::rna::SOUTH, and utility_exit_with_message.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::cluster_pose_list(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::is_old_individual_suite_cluster(), and protocols::stepwise::sampling::rna::sugar::SugarModeling::set_base_and_pucker_state().

void protocols::stepwise::sampling::rna::print_torsion_info	(	core::pose::Pose const &	pose,
		core::Size const	seq_num,
		core::Size const	rna_torsion_number,
		std::string const	type
	)

References core::id::BB, core::id::CHI, core::conformation::Residue::chi(), core::pose::Pose::conformation(), exit, core::conformation::Conformation::get_torsion_angle_atom_ids(), core::conformation::Residue::mainchain_torsion(), core::pose::Pose::residue(), and TR.

void protocols::stepwise::sampling::rna::remove_all_variant_types

(

pose::Pose &

pose

)

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(), runtime_assert, core::pose::Pose::total_residue(), core::conformation::Residue::type(), and core::chemical::ResidueType::variant_types().

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file().

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

References core::kinematics::FoldTree::delete_jump_and_intervening_cutpoint(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::jump_nr(), and runtime_assert.

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

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, protocols::stepwise::is_cutpoint_closed(), core::pose::remove_variant_type_from_pose_residue(), and runtime_assert.

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::restore_pose_variants_after_chain_closure().

void protocols::stepwise::sampling::rna::remove_file

(

std::string const &

file_name

)

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

Referenced by get_binary_rna_silent_struct_safe().

bool protocols::stepwise::sampling::rna::remove_virtual_O2Prime_hydrogen

(

pose::Pose &

pose

)

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::chemical::ResidueType::has_variant_type(), core::conformation::Residue::is_RNA(), 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::stepwise::sampling::rna::StepWiseRNA_Minimizer::apply(), protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler::initialize_poses_and_checkers(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_poses_and_stubs_and_checkers(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler::initialize_poses_and_stubs_and_checkers(), and protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::initialize_poses_and_stubs_and_checkers().

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

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

Referenced by protocols::stepwise::sampling::rna::bulge::BulgeUnApplyMover::apply(), protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::apply(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::initialize_pose_variants_for_chain_closure(), and protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::instantiate_residue_if_rebuilding_bulge().

scoring::ScoreFunctionOP protocols::stepwise::sampling::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.

References core::scoring::ScoreFunction::clone(), n_score_types, show_scorefxn_weight_lines(), and core::chemical::rna::TR.

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::get_sugar_setup_scorefxns().

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

References core::conformation::Residue::has_variant_type(), output_boolean(), output_seq_num_list(), output_title_text(), core::pose::Pose::residue(), rmsd, suite_square_deviation(), and core::chemical::rna::TR.

Referenced by protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::apply(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::apply(), protocols::stepwise::screener::NativeRMSD_Screener::check_screen(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::create_large_cluster_centers_member_list(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::is_new_cluster_center_with_job_parameters(), output_data(), protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::pass_all_pose_screens(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file(), and protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::setup_fail_triangle_inequailty_list().

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

References calc_rms_res, and full_to_sub().

bool protocols::stepwise::sampling::rna::score_sort_criterion	(	Combine_Tags_Info	tag_info_1,
		Combine_Tags_Info	tag_info_2
	)

References protocols::stepwise::sampling::rna::Combine_Tags_Info::combine_score.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_CombineLongLoopFilterer::sort_Combine_Tags_Info().

bool protocols::stepwise::sampling::rna::seq_num_sort_criterion	(	core::Size	seq_num_1,
		core::Size	seq_num_2
	)

Referenced by sort_seq_num_list().

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

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

Referenced by protocols::stepwise::sampling::rna::checker::ChainClosureChecker::chain_break_screening_general().

utility::vector1< Residue_info > protocols::stepwise::sampling::rna::set_difference	(	utility::vector1< Residue_info > const &	copy_dofs_1,
		utility::vector1< Residue_info > const &	copy_dofs_2
	)

References contain_residue_at_seq_num().

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

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

utility::vector1< Residue_info > protocols::stepwise::sampling::rna::set_union	(	utility::vector1< Residue_info > const &	copy_dofs_1,
		utility::vector1< Residue_info > const &	copy_dofs_2
	)

References contain_residue_at_seq_num().

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

References fold_tree, core::pose::Pose::fold_tree(), j, output_fold_tree_info(), core::pose::Pose::residue(), runtime_assert, and core::chemical::rna::TR.

Referenced by setup_chain_break_jump_point().

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

References setup_bulge_jump_point().

Referenced by protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::additional_setup_for_floating_base(), and protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::update_fold_tree_at_virtual_sugars().

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

References core::pose::add_variant_type_to_pose_residue(), core::pose::rna::correctly_position_cutpoint_phosphate_torsions(), core::chemical::CUTPOINT_LOWER, and core::chemical::CUTPOINT_UPPER.

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::initialize_pose_variants_for_chain_closure(), and protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::setup_sugar_conformations().

StepWiseRNA_JobParametersOP protocols::stepwise::sampling::rna::setup_job_parameters_explicit	(	Size const	rebuild_res,
		pose::Pose const &	pose,
		pose::PoseCOP	native_pose,
		utility::vector1< Size > const &	calc_rms_res,
		utility::vector1< Size > const &	terminal_res,
		utility::vector1< Size > const &	syn_chi_res_list,
		utility::vector1< Size > &	working_fixed_res_guess,
		utility::vector1< Size > &	suites_that_must_be_minimized
	)

References chemical, const_full_model_info(), cutpoint_closed, cutpoint_open, protocols::stepwise::figure_out_moving_chain_breaks(), figure_out_rebuild_bulge_mode(), figure_out_sample_both_sugar_base_rotamer(), floating_base, floating_base_anchor_res, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_parent_residue(), protocols::stepwise::get_partition_definition(), get_partition_definition_floating_base(), utility::vector1< T, class >::has_value(), input_res1, input_res2, core::kinematics::FoldTree::is_cutpoint(), make_tag_with_dashes(), make_vector1(), nres, runtime_assert, protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_output_extra_RMSDs(), core::pose::Pose::total_residue(), and TR.

Referenced by setup_job_parameters_for_swa().

StepWiseRNA_JobParametersOP protocols::stepwise::sampling::rna::setup_job_parameters_for_swa	(	Size const	rebuild_res,
		pose::Pose const &	pose,
		pose::PoseCOP	native_pose,
		utility::vector1< Size > const &	calc_rms_res,
		utility::vector1< Size > const &	terminal_res,
		utility::vector1< Size > const &	syn_chi_res_list,
		utility::vector1< Size > const &	extra_minimize_res,
		utility::vector1< Size > &	working_fixed_res,
		utility::vector1< Size > &	working_minimize_res,
		toolbox::AllowInsertOP &	allow_insert,
		kinematics::MoveMapOP &	minimize_move_map
	)

References core::id::BB, const_full_model_info(), figure_out_stepwise_rna_movemap(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_jump_that_builds_residue(), utility::vector1< T, class >::has_value(), nres, runtime_assert, core::pose::Pose::sequence(), setup_job_parameters_explicit(), core::pose::Pose::total_residue(), TR, and update_allow_insert_with_extra_minimize_res().

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::setup_job_parameters_for_stepwise_with_full_model_info().

StepWiseRNA_JobParametersOP protocols::stepwise::sampling::rna::setup_job_parameters_legacy	(	Size const	rebuild_res,
		pose::Pose const &	pose,
		pose::PoseCOP	native_pose,
		utility::vector1< Size > const &	calc_rms_res,
		utility::vector1< Size > const &	terminal_res,
		utility::vector1< Size > const &	syn_chi_res_list,
		utility::vector1< Size > &	working_fixed_res_guess,
		utility::vector1< Size > &	suites_that_must_be_minimized
	)

References alignment_res, protocols::stepwise::check_jump_to_next_residue_in_chain(), protocols::stepwise::check_jump_to_previous_residue_in_chain(), chemical, const_full_model_info(), cutpoint_closed, CUTPOINT_LOWER, cutpoint_open, CUTPOINT_UPPER, figure_out_chains_from_full_model_info_const(), figure_out_rebuild_bulge_mode(), figure_out_sample_both_sugar_base_rotamer(), floating_base, floating_base_anchor_res, core::pose::Pose::fold_tree(), get_anchor_res(), protocols::stepwise::get_partition_definition(), get_partition_definition_floating_base(), core::chemical::ResidueType::has_variant_type(), input_res1, input_res2, core::kinematics::FoldTree::is_cutpoint(), make_tag_with_dashes(), make_vector1(), nres, core::pose::Pose::residue_type(), runtime_assert, protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::set_fixed_res(), core::pose::Pose::total_residue(), TR, and utility_exit_with_message.

void protocols::stepwise::sampling::rna::setup_simple_fold_tree

(

core::pose::Pose &

pose

)

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

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

References core::conformation::Residue::seqpos(), and setup_suite_atom_id_map().

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_CombineLongLoopFilterer::align_all_pose(), and protocols::stepwise::create_alignment_id_map().

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

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

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

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

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

Parameters

pose_2

/Dec 23, 2011.

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

Referenced by create_alignment_id_map(), and setup_suite_atom_id_map().

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

References LJ, n_score_types, core::chemical::rna::TR, and weight.

Referenced by rescale_scorefxn().

void protocols::stepwise::sampling::rna::sleep

(

core::Size

mseconds

)

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().

void protocols::stepwise::sampling::rna::sort_copy_dofs

(

utility::vector1< Residue_info > &

copy_dofs

)

References copy_dofs_sort_criterion().

Referenced by create_strand_list(), and output_copy_dofs().

void protocols::stepwise::sampling::rna::sort_pair_list

(

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

pair_list

)

References pair_sort_criterion().

Referenced by protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::set_jump_point_pair_list().

void protocols::stepwise::sampling::rna::sort_seq_num_list

(

utility::vector1< core::Size > &

seq_num_list

)

References seq_num_sort_criterion().

Referenced by is_equivalent_vector(), output_seq_num_list(), and protocols::stepwise::sampling::rna::StepWiseRNA_JobParameters::set_calc_rms_res().

Size protocols::stepwise::sampling::rna::string_to_int

(

std::string const

input_string

)

References ss, string_to_int(), and utility_exit_with_message.

Referenced by protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::FARFAR_setup_using_user_input_VDW_pose(), protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::get_user_input_alignment_res_list(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::set_jump_point_pair_list(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList::setup_sugar_modeling_list(), and protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::setup_using_user_input_VDW_pose().

Real protocols::stepwise::sampling::rna::string_to_real

(

std::string const

input_string

)

References ss, string_to_real(), and utility_exit_with_message.

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

References rmsd, and suite_square_deviation().

Referenced by protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::apply(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::apply(), protocols::stepwise::screener::NativeRMSD_Screener::check_screen(), protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection::cluster_pose_list(), protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer::is_old_individual_suite_cluster(), output_data(), and protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::pass_all_pose_screens().

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

References core::conformation::Residue::aa(), core::conformation::Residue::atom_name(), atom_square_deviation(), core::conformation::Residue::first_sidechain_atom(), get_num_side_chain_atom_from_res_name(), core::conformation::Residue::is_virtual(), core::chemical::name_from_aa(), core::conformation::Residue::nheavyatoms(), print_heavy_atoms(), core::pose::Pose::residue(), core::chemical::rna::TR, utility_exit_with_message, 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::stepwise::sampling::rna::tokenize	(	std::string const	str,
		std::string	delimiters
	)

Referenced by Convert_rebuild_residue_string_to_list(), protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::FARFAR_setup_using_user_input_VDW_pose(), protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::stepwise::sampling::rna::legacy::get_silent_file_tags(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::get_user_input_alignment_res_list(), protocols::stepwise::sampling::rna::StepWiseRNA_CombineLongLoopFilterer::is_sibling_sugar_rotamer_pose(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup::set_jump_point_pair_list(), protocols::stepwise::sampling::rna::legacy::setup_simple_full_length_rna_job_parameters(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList::setup_sugar_modeling_list(), and protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::setup_using_user_input_VDW_pose().

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

References core::pose::full_model_info::const_full_model_info(), core::pose::Pose::fold_tree(), utility::vector1< T, class >::has_value(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_RNA(), core::conformation::Residue::is_virtual(), j, named_atom_id_to_atom_id(), core::conformation::Residue::natoms(), core::pose::full_model_info::FullModelInfo::res_list(), core::pose::Pose::residue(), runtime_assert, and core::pose::Pose::total_residue().

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::figure_out_moving_residues(), and setup_job_parameters_for_swa().

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

References core::conformation::Residue::aa(), core::chemical::aa_vrt, apply_virtual_rna_residue_variant_type(), get_default_allowed_bulge_res(), core::conformation::Residue::has_variant_type(), output_boolean(), output_seq_num_list(), core::pose::Pose::residue(), rna_bulge, core::pose::Pose::total_residue(), core::chemical::rna::TR, and utility_exit_with_message.

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

Variable Documentation

StepWiseRNA_CountStruct protocols::stepwise::sampling::rna::local_count_data