Namespaces
	bulge

	checker

	helix

	o2prime

	phosphate

	rigid_body

	sugar

Classes
class	Combine_Tags_Info

class	Filterer_Count

class	InternalWorkingResidueParameter

class	Jump_point

struct	output_data_struct

struct	Residue_info

class	StepWiseRNA_CombineLongLoopFilterer

class	StepWiseRNA_CountStruct

struct	Torsion_Info

Typedefs
typedef utility::pointer::owning_ptr < StepWiseRNA_CombineLongLoopFilterer >	StepWiseRNA_CombineLongLoopFiltererOP

typedef utility::pointer::owning_ptr < StepWiseRNA_CombineLongLoopFilterer const >	StepWiseRNA_CombineLongLoopFiltererpCOP

Functions
bool	score_sort_criterion (Combine_Tags_Info tag_info_1, Combine_Tags_Info tag_info_2)

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, working_parameters::StepWiseWorkingParametersCOP working_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, working_parameters::StepWiseWorkingParametersCOP working_parameters_)

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	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)

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

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

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, working_parameters::StepWiseWorkingParametersCOP working_parameters)

utility::vector1< Size >	apply_sub_to_full_mapping (utility::vector1< Size > const &working_res_vector, working_parameters::StepWiseWorkingParametersCOP working_parameters)

void	ensure_valid_full_seq_num (Size const full_seq_num, working_parameters::StepWiseWorkingParametersCOP const &working_parameters)

bool	check_is_working_res (Size const full_seq_num, working_parameters::StepWiseWorkingParametersCOP const &working_parameters)

core::Size	check_validity_and_get_working_res (Size const full_seq_num, working_parameters::StepWiseWorkingParametersCOP const &working_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)

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)

void	output_title_text (std::string const title, 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)

void	check_instantiated_O2Prime_hydrogen (core::pose::Pose const &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)

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, working_parameters::StepWiseWorkingParametersCOP working_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)

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::ScoreFunctionCOP const &packer_scorefxn, bool const pack_virtual_o2prime_hydrogen)

void	o2prime_trials (pose::Pose &pose, core::scoring::ScoreFunctionCOP const &packer_scorefxn, utility::vector1< core::Size > const &O2prime_pack_seq_num, bool const pack_virtual_o2prime_hydrogen)

pack::task::PackerTaskOP	create_standard_o2prime_pack_task (pose::Pose const &pose, utility::vector1< core::Size > const &O2prime_pack_seq_num, bool const pack_virtual_o2prime_hydrogen)

void	setup_chain_break_variants (core::pose::Pose &pose, Size const cutpoint)

void	remove_chain_break_variants (core::pose::Pose &pose, Size const &cutpoint)

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)

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

void	sleep (core::Size mseconds)

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	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_modeler_scorefxn (scoring::ScoreFunctionCOP 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	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)

void	remove_all_virtual_phosphates (core::pose::Pose &pose)

utility::vector1< Size >	just_rna (utility::vector1< Size > const &res_list, pose::Pose const &pose)

void	figure_out_moving_rna_chain_breaks (pose::Pose const &pose, utility::vector1< Size > const &moving_partition_res, utility::vector1< Size > &rna_cutpoints_closed, utility::vector1< Size > &rna_five_prime_chain_breaks, utility::vector1< Size > &rna_three_prime_chain_breaks, utility::vector1< Size > &rna_chain_break_gap_sizes)

Typedef Documentation

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

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

Function Documentation

void protocols::stepwise::modeler::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::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler::setup_sugar_conformations().

void protocols::stepwise::modeler::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::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler::bulge_chain_closure_legacy(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_pose(), protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::reinstantiate_backbone_and_add_constraint_at_moving_res(), and protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler::setup_sugar_conformations().

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

References 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::modeler::rna::checker::RNA_VDW_BinChecker::create_VDW_rep_screen_pose(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::FARFAR_setup_using_user_input_VDW_pose(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_checkers(), protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::initialize_poses_and_checkers(), and protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_using_user_input_VDW_pose().

void protocols::stepwise::modeler::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::legacy::modeler::rna::StepWiseRNA_Clusterer::align_to_quick_alignment_pose(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_large_cluster_centers_member_list(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::is_new_cluster_center_with_working_parameters(), output_data(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::setup_fail_triangle_inequailty_list(), and protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::setup_native_pose().

utility::vector1< Size > protocols::stepwise::modeler::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.

utility::vector1< Size > protocols::stepwise::modeler::rna::apply_full_to_sub_mapping	(	utility::vector1< Size > const &	res_vector,
		working_parameters::StepWiseWorkingParametersCOP	working_parameters
	)

References full_to_sub().

void protocols::stepwise::modeler::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::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_protonated_H1_adenosine_variants(), and protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::do_checks_and_apply_protonated_H1_adenosine_variant().

utility::vector1< Size > protocols::stepwise::modeler::rna::apply_sub_to_full_mapping	(	utility::vector1< Size > const &	working_res_vector,
		working_parameters::StepWiseWorkingParametersCOP	working_parameters
	)

References runtime_assert, and sub_to_full().

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

Real protocols::stepwise::modeler::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::modeler::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::modeler::rna::checker::RNA_VDW_BinChecker::align_VDW_rep_screen_pose().

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

References 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.

void protocols::stepwise::modeler::rna::check_instantiated_O2Prime_hydrogen ( core::pose::Pose const & pose )

References core::chemical::ResidueType::has_variant_type(), core::chemical::ResidueType::is_RNA(), core::pose::Pose::residue_type(), runtime_assert, and core::pose::Pose::total_residue().

Referenced by protocols::stepwise::modeler::packer::StepWiseMasterPacker::initialize().

bool protocols::stepwise::modeler::rna::check_is_working_res	(	Size const	full_seq_num,
		working_parameters::StepWiseWorkingParametersCOP const &	working_parameters
	)

References ensure_valid_full_seq_num().

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

Size protocols::stepwise::modeler::rna::check_validity_and_get_working_res	(	Size const	full_seq_num,
		working_parameters::StepWiseWorkingParametersCOP const &	working_parameters
	)

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

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

void protocols::stepwise::modeler::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::mover::AddMover::append_residue(), protocols::stepwise::monte_carlo::mover::FromScratchMover::apply(), mutate_res_if_allowed(), and protocols::stepwise::monte_carlo::mover::AddMover::prepend_residue().

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

Referenced by set_difference(), and set_union().

utility::vector1< Residue_info > protocols::stepwise::modeler::rna::Convert_rebuild_residue_string_to_list ( std::string const & rebuild_residue_string )

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

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

References core::id::CHI, core::conformation::Residue::is_RNA(), core::pose::Pose::residue(), runtime_assert, core::pose::Pose::set_torsion(), core::pose::Pose::torsion(), and core::pose::Pose::total_residue().

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

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

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

Referenced by sort_copy_dofs().

id::AtomID_Map< id::AtomID > protocols::stepwise::modeler::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::modeler::rna::create_full_to_input_res_map ( utility::vector1< core::Size > const & input_res_vector )

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

std::string protocols::stepwise::modeler::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::screener::TagDefinition::check_screen().

std::string protocols::stepwise::modeler::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::modeler::rna::create_standard_o2prime_pack_task	(	pose::Pose const &	pose,
		utility::vector1< core::Size > const &	O2prime_pack_seq_num,
		bool const	pack_virtual_o2prime_hydrogen
	)

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

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

utility::vector1< utility::vector1< Residue_info > > protocols::stepwise::modeler::rna::create_strand_list ( utility::vector1< Residue_info > const & copy_dofs )

References sort_copy_dofs().

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

References tag.

Referenced by protocols::stepwise::screener::TagDefinition::check_screen().

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

References numeric::principal_angle_degrees().

Referenced by create_rotamer_string().

void protocols::stepwise::modeler::rna::ensure_valid_full_seq_num	(	Size const	full_seq_num,
		working_parameters::StepWiseWorkingParametersCOP const &	working_parameters
	)

References runtime_assert.

Referenced by check_is_working_res().

void protocols::stepwise::modeler::rna::figure_out_moving_rna_chain_breaks	(	pose::Pose const &	pose,
		utility::vector1< Size > const &	moving_partition_res,
		utility::vector1< Size > &	rna_cutpoints_closed,
		utility::vector1< Size > &	rna_five_prime_chain_breaks,
		utility::vector1< Size > &	rna_three_prime_chain_breaks,
		utility::vector1< Size > &	rna_chain_break_gap_sizes
	)

References protocols::stepwise::modeler::figure_out_moving_chain_breaks(), core::chemical::ResidueType::is_RNA(), just_rna(), core::pose::Pose::residue_type(), and runtime_assert.

Referenced by protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_useful_info().

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

References file_exists().

void protocols::stepwise::modeler::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.

Size protocols::stepwise::modeler::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::modeler::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().

core::io::silent::BinarySilentStruct protocols::stepwise::modeler::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::stepwise::sampler::rigid_body::EulerAngles::convert_to_rotation_matrix(), end, core::io::silent::SilentFileData::end(), core::chemical::FA_RNA, 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, rotation_matrix(), protocols::stepwise::sampler::rigid_body::EulerAngles::set_alpha(), protocols::stepwise::sampler::rigid_body::EulerAngles::set_gamma(), core::pose::Pose::set_xyz(), protocols::stepwise::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::modeler::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.

utility::vector1< Residue_info > protocols::stepwise::modeler::rna::get_copy_dofs_from_fasta ( std::string const full_fasta_sequence )

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

core::Size protocols::stepwise::modeler::rna::get_max_seq_num_from_res_map ( std::map< core::Size, core::Size > const & my_map )

References TR.

scoring::ScoreFunctionOP protocols::stepwise::modeler::rna::get_modeler_scorefxn ( scoring::ScoreFunctionCOP scorefxn )

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

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::initialize_modeler_scorefxn(), protocols::stepwise::modeler::rna::sugar::minimize_all_sampled_floating_bases(), and protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler::restore_pose_variants_after_chain_closure().

Size protocols::stepwise::modeler::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::modeler::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::modeler::rna::get_partition_definition_floating_base	(	pose::Pose const &	pose,
		Size const &	moving_res
	)

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

Referenced by protocols::stepwise::modeler::working_parameters::setup_working_parameters_explicit().

void protocols::stepwise::modeler::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::modeler::rna::checker::RNA_ChainClosableGeometryChecker::initialize_distance_range().

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

References exit, and TR.

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

References 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(), runtime_assert, 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::legacy::modeler::rna::StepWiseRNA_Minimizer::apply(), and protocols::stepwise::modeler::rna::o2prime::O2PrimePacker::initialize_o2prime_packer_task().

std::string protocols::stepwise::modeler::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::modeler::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::screener::ResidueContactScreener::check_screen(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::previously_builded_res_VDW_filter(), and protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen_with_act_pose().

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

Referenced by align_poses(), protocols::stepwise::modeler::rna::bulge::BulgeApplyMover::apply(), and protocols::stepwise::modeler::rna::bulge::BulgeUnApplyMover::apply().

utility::vector1< core::Size > protocols::stepwise::modeler::rna::just_rna	(	utility::vector1< Size > const &	res_list,
		pose::Pose const &	pose
	)

References core::chemical::ResidueType::is_RNA(), and core::pose::Pose::residue_type().

Referenced by protocols::stepwise::modeler::StepWiseMinimizer::close_chainbreaks(), and figure_out_moving_rna_chain_breaks().

void protocols::stepwise::modeler::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(), and core::pose::Pose::constraint_set().

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

bool protocols::stepwise::modeler::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::mover::ResampleMover::apply().

void protocols::stepwise::modeler::rna::o2prime_trials	(	pose::Pose &	pose,
		core::scoring::ScoreFunctionCOP const &	packer_scorefxn,
		bool const	pack_virtual_o2prime_hydrogen
	)

References core::chemical::ResidueType::is_RNA(), o2prime_trials(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

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

void protocols::stepwise::modeler::rna::o2prime_trials	(	pose::Pose &	pose,
		core::scoring::ScoreFunctionCOP const &	packer_scorefxn,
		utility::vector1< core::Size > const &	O2prime_pack_seq_num,
		bool const	pack_virtual_o2prime_hydrogen
	)

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::modeler::rna::output_copy_dofs ( utility::vector1< Residue_info > copy_dofs )

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

void protocols::stepwise::modeler::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,
		working_parameters::StepWiseWorkingParametersCOP	working_parameters_
	)

References output_data().

Referenced by protocols::stepwise::legacy::screener::RNA_LegacyPoseSelectionScreener::check_screen(), protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList::output_pose_data_list(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::output_pose_wrapper(), and protocols::features::serialize_residue_xyz_coords().

void protocols::stepwise::modeler::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,
		working_parameters::StepWiseWorkingParametersCOP	working_parameters_
	)

References align_poses(), calc_rms_res, full_to_sub(), 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::modeler::rna::output_res_map	(	std::map< core::Size, core::Size > const &	my_map,
		Size const	max_seq_num
	)

References spacing, and TR.

void protocols::stepwise::modeler::rna::output_residue_struct ( Residue_info const & residue )

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

Referenced by output_copy_dofs().

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

References spacing, and core::chemical::rna::TR.

void protocols::stepwise::modeler::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 I, and sort_seq_num_list().

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

Real protocols::stepwise::modeler::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::legacy::modeler::rna::StepWiseRNA_PoseSelection::cluster_pose_list(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::is_old_individual_suite_cluster(), and output_data().

void protocols::stepwise::modeler::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::pose::Pose::residue(), and runtime_assert.

Referenced by phosphate_base_phosphate_rmsd().

void protocols::stepwise::modeler::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 protocols::stepwise::legacy::modeler::rna::full_length_rmsd_over_residue_list().

void protocols::stepwise::modeler::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::modeler::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::modeler::rna::sugar::SugarModeling::set_base_and_pucker_state().

void protocols::stepwise::modeler::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.

void protocols::stepwise::modeler::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::modeler::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::legacy::modeler::rna::StepWiseRNA_PoseSelection::cluster_pose_list(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::is_old_individual_suite_cluster(), and protocols::stepwise::modeler::rna::sugar::SugarModeling::set_base_and_pucker_state().

void protocols::stepwise::modeler::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(), print_torsion_info(), core::pose::Pose::residue(), and TR.

void protocols::stepwise::modeler::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::legacy::modeler::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file().

void protocols::stepwise::modeler::rna::remove_all_virtual_phosphates ( core::pose::Pose & pose )

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

Referenced by protocols::stepwise::modeler::StepWiseMinimizer::do_full_minimizing().

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

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

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

void protocols::stepwise::modeler::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::modeler::rna::remove_virtual_O2Prime_hydrogen ( pose::Pose & pose )

References 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::legacy::modeler::rna::StepWiseRNA_Minimizer::apply(), and protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::initialize_poses_and_checkers().

scoring::ScoreFunctionOP protocols::stepwise::modeler::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 n_score_types, show_scorefxn_weight_lines(), and core::chemical::rna::TR.

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

Real protocols::stepwise::modeler::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::legacy::screener::RNA_LegacyNativeRMSD_Screener::check_screen(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_large_cluster_centers_member_list(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::is_new_cluster_center_with_working_parameters(), output_data(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::pass_all_pose_screens(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file(), and protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::setup_fail_triangle_inequailty_list().

Real protocols::stepwise::modeler::rna::rmsd_over_residue_list	(	pose::Pose const &	pose1,
		pose::Pose const &	pose2,
		working_parameters::StepWiseWorkingParametersCOP	working_parameters_,
		bool const	ignore_virtual_atom
	)

References calc_rms_res, and full_to_sub().

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

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

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

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

Referenced by sort_seq_num_list().

void protocols::stepwise::modeler::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::modeler::rna::checker::RNA_ChainClosureChecker::chain_break_screening_general().

utility::vector1< Residue_info > protocols::stepwise::modeler::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().

utility::vector1< Residue_info > protocols::stepwise::modeler::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().

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

References core::pose::correctly_add_cutpoint_variants().

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

void protocols::stepwise::modeler::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::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::align_all_pose().

void protocols::stepwise::modeler::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::modeler::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::modeler::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 protocols::stepwise::modeler::align::create_alignment_id_map(), create_alignment_id_map(), and setup_suite_atom_id_map().

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

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

Referenced by rescale_scorefxn().

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

References seq_num_sort_criterion().

Referenced by output_seq_num_list().

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

References ss, string_to_int(), and utility_exit_with_message.

Referenced by protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::FARFAR_setup_using_user_input_VDW_pose(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList::setup_sugar_modeling_list(), and protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_using_user_input_VDW_pose().

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

References ss, string_to_real(), and utility_exit_with_message.

Real protocols::stepwise::modeler::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::legacy::screener::RNA_LegacyNativeRMSD_Screener::check_screen(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::cluster_pose_list(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::is_old_individual_suite_cluster(), output_data(), and protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::pass_all_pose_screens().

void protocols::stepwise::modeler::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(), atom_square_deviation(), core::conformation::Residue::first_sidechain_atom(), get_num_side_chain_atom_from_res_name(), core::conformation::Residue::is_virtual(), core::pose::Pose::residue(), and runtime_assert.

Referenced by protocols::stepwise::legacy::modeler::rna::full_length_rmsd_over_residue_list(), rmsd_over_residue_list(), and suite_rmsd().

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

Namespaces

Classes

Typedefs

Functions

Typedef Documentation

Function Documentation