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protocols::stepwise::modeler::rna Namespace Reference

Namespaces

 bulge
 
 checker
 
 o2prime
 
 phosphate
 
 rigid_body
 
 sugar
 

Classes

class  Jump_point
 
struct  Torsion_Info
 
struct  output_data_struct
 
class  InternalWorkingResidueParameter
 
class  StepWiseRNA_CountStruct
 
class  Combine_Tags_Info
 
class  Filterer_Count
 
class  StepWiseRNA_CombineLongLoopFilterer
 
struct  Residue_info
 

Typedefs

typedef utility::pointer::shared_ptr< StepWiseRNA_CombineLongLoopFilterer > StepWiseRNA_CombineLongLoopFiltererOP
 
typedef utility::pointer::shared_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_, bool const NAT_rmsd)
 
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_, bool const NAT_rmsd)
 
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)
 
void output_res_map (std::map< core::Size, core::Size > const &my_map, core::Size const max_seq_num)
 
utility::vector1< Residue_info > get_copy_dofs_from_fasta (std::string const &full_fasta_sequence)
 
bool contain_residue_at_seq_num (core::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)
 
Residue_info get_residue_from_seq_num (core::Size const &seq_num, utility::vector1< Residue_info > const &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< core::Size > apply_full_to_sub_mapping (utility::vector1< core::Size > const &res_vector, utility::vector1< core::Size > const &is_working_res, std::map< core::Size, core::Size > const &full_to_sub)
 
utility::vector1< core::Size > apply_full_to_sub_mapping (utility::vector1< core::Size > const &res_vector, working_parameters::StepWiseWorkingParametersCOP working_parameters)
 
utility::vector1< core::Size > apply_sub_to_full_mapping (utility::vector1< core::Size > const &working_res_vector, working_parameters::StepWiseWorkingParametersCOP working_parameters)
 
void ensure_valid_full_seq_num (core::Size const full_seq_num, working_parameters::StepWiseWorkingParametersCOP const &working_parameters)
 
bool check_is_working_res (core::Size const full_seq_num, working_parameters::StepWiseWorkingParametersCOP const &working_parameters)
 
core::Size check_validity_and_get_working_res (core::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 const &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, core::Size const res_num_1, core::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, core::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, core::Size const base_res_1, core::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_legacy (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)
 
void remove_file (std::string const &file_name)
 
void output_rotamer (utility::vector1< Real > &rotamer)
 
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, core::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< core::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 (core::Size const &suite_num_1, core::Size const &suite_num_2, pose::Pose const &pose1, pose::Pose const &pose2)
 
Real atom_square_deviation (conformation::Residue const &rsd_1, conformation::Residue const &rsd_2, core::Size const &atomno_1, core::Size const &atomno_2, bool verbose)
 
void base_atoms_square_deviation (pose::Pose const &pose1, pose::Pose const &pose2, core::Size const &moving_res_1, core::Size const &moving_res_2, core::Size &atom_count, Real &sum_sd, bool verbose, bool const)
 
void phosphate_square_deviation (pose::Pose const &pose1, pose::Pose const &pose2, core::Size const &moving_res_1, core::Size const &moving_res_2, core::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, core::Size const &moving_res_num, bool const ignore_virtual_atom)
 
void phosphate_base_phosphate_square_deviation (pose::Pose const &pose1, pose::Pose const &pose2, core::Size const &moving_res_1, core::Size const &moving_res_2, core::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, core::Size const &moving_res_1, core::Size const &moving_res_2, core::Size &atom_count, Real &sum_sd, bool verbose, bool const ignore_virtual_atom)
 
void freeze_sugar_torsions (core::kinematics::MoveMap &mm, core::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, core::Size const cutpoint)
 
void remove_chain_break_variants (core::pose::Pose &pose, core::Size const &cutpoint)
 
utility::vector1< bool > get_partition_definition_floating_base (pose::Pose const &pose, core::Size const &moving_res)
 
Size get_anchor_res (core::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, core::Size const five_prime_res)
 
void print_atom_info (pose::Pose const &pose, core::Size const seq_num, std::string const &pose_name)
 
void print_individual_atom_info (core::conformation::Residue const &rsd, core::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)
 
utility::vector1< std::string > possible_rts (utility::tools::make_vector1("RAD", "RGU", "RCY", "URA", "OMA", "OMC", "OMG", "OMU", "PSU", "H2U", "PUR", "1MA", "NPU", "8OG", "6MG", "5IU", "5FC", "5FU"))
 
std::string choose_randomly_from_allowed_at_position (core::pose::Pose const &, core::Size const)
 
bool mutate_res_if_allowed (pose::Pose &pose, core::Size const mutate_res, Real const mutation_frequency)
 
std::string create_tag (std::string const &prestring, core::Size const i)
 
std::string create_torsion_value_string (core::Real const &torsion_value)
 
std::string create_rotamer_string (core::pose::Pose const &pose, core::Size const moving_res, bool const is_prepend)
 
std::string create_rotamer_string (core::pose::Pose const &pose, core::Size const moving_res, core::Size const reference_res)
 
void add_fade_chain_break_constraint_across_gap (pose::Pose &pose, core::Size const five_prime_res, core::Size const three_prime_res, core::Size const gap_size)
 
void add_harmonic_chain_break_constraint (pose::Pose &pose, core::Size const five_prime_res)
 
void get_possible_O3prime_C5prime_distance_range (core::Size const gap_size_, Distance &min_dist, Distance &max_dist)
 
void remove_all_virtual_phosphates (core::pose::Pose &pose)
 
utility::vector1< core::Size > just_rna (utility::vector1< core::Size > const &res_list, pose::Pose const &pose)
 
void figure_out_moving_rna_chain_breaks (pose::Pose const &pose, utility::vector1< core::Size > const &moving_partition_res, utility::vector1< core::Size > &rna_cutpoints_closed, utility::vector1< core::Size > &rna_five_prime_chain_breaks, utility::vector1< core::Size > &rna_three_prime_chain_breaks, utility::vector1< core::Size > &rna_chain_break_gap_sizes)
 

Typedef Documentation

◆ StepWiseRNA_CombineLongLoopFiltererOP

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

◆ StepWiseRNA_CombineLongLoopFiltererpCOP

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

Function Documentation

◆ add_fade_chain_break_constraint_across_gap()

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

References core::conformation::Residue::atom_index(), core::pose::Pose::constraint_set(), GAP_SIZE_DUMMY, get_possible_O3prime_C5prime_distance_range(), core::conformation::Residue::has(), and core::pose::Pose::residue().

Referenced by protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::setup_sugar_conformations().

◆ add_harmonic_chain_break_constraint()

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

References core::conformation::Residue::atom_index(), core::pose::Pose::constraint_set(), core::chemical::ResidueType::is_NA(), core::pose::Pose::residue(), and core::pose::Pose::residue_type().

Referenced by protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::bulge_chain_closure_legacy(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_pose(), and protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::setup_sugar_conformations().

◆ align_poses()

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

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().

◆ apply_full_to_sub_mapping() [1/2]

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

References core::pose::full_model_info::full_to_sub().

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_silent_file_and_tag_list(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::get_user_input_alignment_res_list(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_fixed_res(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_native_alignment_res(), protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters::setup(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::setup_native_pose(), and protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_using_user_input_VDW_pose().

◆ apply_full_to_sub_mapping() [2/2]

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

References core::pose::full_model_info::full_to_sub().

◆ apply_protonated_H1_adenosine_variant_type()

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::chemical::PROTONATED_N1, core::pose::Pose::residue(), core::pose::Pose::size(), core::chemical::rna::TR(), and core::chemical::VIRTUAL_RNA_RESIDUE.

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().

◆ apply_sub_to_full_mapping()

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

References core::pose::full_model_info::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().

◆ atom_square_deviation()

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

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

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

◆ base_atoms_square_deviation()

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

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

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

◆ check_for_messed_up_structure()

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

References core::conformation::Residue::chi(), core::chemical::rna::DELTA, core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_RNA(), core::conformation::Residue::mainchain_torsion(), core::pose::Pose::residue(), core::pose::Pose::size(), core::chemical::rna::TR(), core::chemical::VIRTUAL_RIBOSE, and core::chemical::VIRTUAL_RNA_RESIDUE.

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

◆ check_instantiated_O2Prime_hydrogen()

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

References core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::chemical::VIRTUAL_O2PRIME_HYDROGEN.

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

◆ check_is_working_res()

bool protocols::stepwise::modeler::rna::check_is_working_res ( core::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::VirtualSugarSamplerFromStringList::setup_sugar_modeling_list().

◆ check_validity_and_get_working_res()

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

References check_is_working_res(), core::pose::full_model_info::full_to_sub(), and core::pose::rna::remove_bracketed().

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

◆ choose_random_if_unspecified_nucleotide()

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

References core::scoring::rg, and core::chemical::rna::TR().

Referenced by protocols::stepwise::monte_carlo::mover::FromScratchMover::apply(), protocols::stepwise::monte_carlo::mover::AddMover::create_residue_to_add(), and mutate_res_if_allowed().

◆ choose_randomly_from_allowed_at_position()

std::string protocols::stepwise::modeler::rna::choose_randomly_from_allowed_at_position ( core::pose::Pose const &  ,
core::Size const   
)

References possible_rts(), and core::scoring::rg.

Referenced by protocols::stepwise::monte_carlo::mover::AddMover::create_residue_to_add().

◆ contain_residue_at_seq_num()

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

References core::pose::copydofs::copy_dofs().

Referenced by set_difference(), and set_union().

◆ copy_all_o2prime_torsions()

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(), core::pose::Pose::set_torsion(), core::pose::Pose::size(), and core::pose::Pose::torsion().

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

◆ copy_dofs_sort_criterion()

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().

◆ create_alignment_id_map_legacy()

id::AtomID_Map< id::AtomID > protocols::stepwise::modeler::rna::create_alignment_id_map_legacy ( 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::AtomID::BOGUS_ATOM_ID(), core::pose::initialize_atomid_map(), core::pose::Pose::residue(), core::pose::Pose::sequence(), setup_suite_atom_id_map(), core::pose::Pose::size(), and core::chemical::rna::TR().

Referenced by align_poses(), protocols::stepwise::modeler::align::create_alignment_id_map_legacy(), and protocols::stepwise::modeler::align::superimpose_pose_legacy().

◆ create_full_to_input_res_map()

std::map< core::Size, core::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().

◆ create_rotamer_string() [1/2]

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

References create_rotamer_string().

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

◆ create_rotamer_string() [2/2]

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

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

Referenced by create_rotamer_string().

◆ create_standard_o2prime_pack_task()

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(), core::chemical::ResidueTypeBase::has_variant_type(), core::conformation::Residue::is_RNA(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::chemical::VIRTUAL_O2PRIME_HYDROGEN.

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

◆ create_strand_list()

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

References core::pose::copydofs::copy_dofs(), and sort_copy_dofs().

◆ create_tag()

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

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

◆ create_torsion_value_string()

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

Referenced by create_rotamer_string().

◆ ensure_valid_full_seq_num()

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

Referenced by check_is_working_res().

◆ figure_out_moving_rna_chain_breaks()

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

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

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

◆ freeze_sugar_torsions()

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

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

◆ get_anchor_res()

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

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

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_split_move_elements().

◆ get_binary_rna_silent_struct_safe()

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 check_for_messed_up_structure(), protocols::stepwise::sampler::rigid_body::EulerAngles::convert_to_rotation_matrix(), core::pose::Pose::dump_pdb(), core::chemical::FA_STANDARD, core::conformation::Residue::is_virtual(), core::conformation::Residue::natoms(), RADS_PER_DEG, core::io::silent::SilentFileData::read_file(), remove_file(), core::pose::Pose::residue(), 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::size(), TR(), core::io::silent::SilentFileData::write_silent_struct(), core::pose::Pose::xyz(), and core::conformation::Residue::xyz().

Referenced by get_binary_rna_silent_struct_safe_wrapper().

◆ 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().

◆ get_copy_dofs_from_fasta()

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, and protocols::stepwise::modeler::rna::Residue_info::seq_num.

◆ get_modeler_scorefxn()

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

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::chainbreak, core::scoring::fa_rep, and protocols::denovo_design::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::VirtualSugarSampler::restore_pose_variants_after_chain_closure().

◆ get_partition_definition_floating_base()

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

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

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

◆ get_possible_O3prime_C5prime_distance_range()

void protocols::stepwise::modeler::rna::get_possible_O3prime_C5prime_distance_range ( core::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().

◆ get_residue_from_seq_num()

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

◆ get_surrounding_O2prime_hydrogen()

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

References core::chemical::ResidueType::atom_index(), core::conformation::Residue::first_sidechain_atom(), core::chemical::ResidueTypeBase::is_RNA(), core::chemical::ResidueType::is_virtual(), core::conformation::Residue::is_virtual(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), core::chemical::rna::TR(), core::chemical::VIRTUAL_RIBOSE, core::chemical::VIRTUAL_RNA_RESIDUE, and core::conformation::Residue::xyz().

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

◆ is_residues_in_contact()

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 core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), core::conformation::Residue::is_virtual(), core::chemical::AtomType::lj_radius(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::chemical::rna::TR(), and core::conformation::Residue::xyz().

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().

◆ is_virtual_base()

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

References core::conformation::Residue::aa(), core::conformation::Residue::atom_type(), core::chemical::BULGE, core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_NA(), core::conformation::Residue::is_virtual(), core::chemical::AtomType::name(), core::chemical::name_from_aa(), core::conformation::Residue::nheavyatoms(), core::pose::rna::output_boolean(), core::conformation::Residue::seqpos(), core::chemical::rna::TR(), and core::chemical::VIRTUAL_RNA_RESIDUE.

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

◆ just_rna()

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

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

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

◆ minimize_with_constraints()

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(), core::pose::Pose::constraint_set(), and core::optimization::AtomTreeMinimizer::run().

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

◆ mutate_res_if_allowed()

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

References choose_random_if_unspecified_nucleotide(), core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::FullModelInfo::full_sequence(), core::pose::full_model_info::get_res_list_from_full_model_info(), core::pose::rna::mutate_position(), core::scoring::rg, core::pose::Pose::sequence(), and core::pose::full_model_info::sub_to_full().

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

◆ o2prime_trials() [1/2]

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::ResidueTypeBase::is_RNA(), o2prime_trials(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

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

◆ o2prime_trials() [2/2]

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().

◆ output_data() [1/2]

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_,
bool const  NAT_rmsd 
)

References core::io::silent::SilentStruct::add_energy(), align_poses(), core::pose::full_model_info::full_to_sub(), core::io::silent::SilentStruct::has_energy(), phosphate_base_phosphate_rmsd(), core::scoring::rms_at_corresponding_heavy_atoms(), rmsd_over_residue_list(), suite_rmsd(), and core::io::silent::SilentFileData::write_silent_struct().

Referenced by output_data().

◆ output_data() [2/2]

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_,
bool const  NAT_rmsd 
)

References output_data().

Referenced by protocols::stepwise::modeler::StepWiseMinimizer::output_minimized_pose_list(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::output_pose_data_list(), and protocols::features::serialize_residue_xyz_coords().

◆ output_res_map()

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

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

◆ output_rotamer()

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

References core::chemical::rna::TR().

◆ output_seq_num_list()

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 protocols::comparative_modeling::features::A, core::chemical::element::I, and sort_seq_num_list().

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_terminal_res_repulsion(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::correctly_copy_HO2prime_positions(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_silent_file_and_tag_list(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::figure_out_appended_and_prepended_res_list(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_best_working_alignment(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_is_prepend_map(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_partition_definition(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_prepend_internal(), protocols::stepwise::legacy::modeler::rna::full_length_rmsd_over_residue_list(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::get_previously_closed_cutpoint_from_imported_silent_file(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::get_user_input_alignment_res_list(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::initialize_quick_alignment_pose(), o2prime_trials(), protocols::stepwise::legacy::modeler::rna::print_WorkingParameters_info(), rmsd_over_residue_list(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_fixed_res(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_native_alignment_res(), protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters::setup(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_additional_cutpoint_closed(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::setup_native_pose(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_using_user_input_VDW_pose(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::StepWiseWorkingParametersSetup(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::update_VDW_screen_bin(), and protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen_with_act_pose().

◆ output_title_text()

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

Referenced by protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::align_all_pose(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::align_VDW_rep_screen_pose(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::apply(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::apply(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::apply(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::bulge_chain_closure_legacy(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::bulge_chain_minimize_legacy(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::cluster(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::correctly_copy_HO2prime_positions(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_large_cluster_centers_member_list(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_silent_file_and_tag_list(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_tags_map(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::do_some_filtering(), protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::do_the_modeler(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::FARFAR_setup_using_user_input_VDW_pose(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_best_working_alignment(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_chain_boundaries(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_is_prepend_map(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_is_residue_prepend(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_jump_partners(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_prepend_internal(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_working_sequence_and_mapping(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::filter(), protocols::stepwise::legacy::modeler::rna::full_length_rmsd_over_residue_list(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::stepwise::legacy::modeler::rna::get_silent_file_tags(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::get_user_input_alignment_res_list(), protocols::stepwise::modeler::rna::sugar::minimize_all_sampled_floating_bases(), protocols::stepwise::legacy::modeler::rna::print_WorkingParameters_info(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::reroot_fold_tree(), rmsd_over_residue_list(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_fixed_res(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::set_native_alignment_res(), protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters::setup(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_additional_cutpoint_closed(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_fold_tree(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::setup_native_pose(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::setup_sugar_conformations(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_using_user_input_VDW_pose(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_using_working_pose(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::StepWiseWorkingParametersSetup(), and protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::two_stage_clustering().

◆ phosphate_base_phosphate_rmsd()

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

References protocols::mean_field::max(), phosphate_base_phosphate_square_deviation(), and core::chemical::rna::TR().

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().

◆ phosphate_base_phosphate_square_deviation()

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

References core::conformation::Residue::aa(), atom_square_deviation(), core::chemical::ResidueType::atom_type(), core::chemical::AtomType::element(), core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::is_virtual(), core::conformation::Residue::is_virtual_residue(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::conformation::Residue::type().

Referenced by phosphate_base_phosphate_rmsd().

◆ phosphate_square_deviation()

void protocols::stepwise::modeler::rna::phosphate_square_deviation ( pose::Pose const &  pose1,
pose::Pose const &  pose2,
core::Size const &  moving_res_1,
core::Size const &  moving_res_2,
core::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(), and core::chemical::rna::TR().

Referenced by protocols::stepwise::legacy::modeler::rna::full_length_rmsd_over_residue_list().

◆ possible_rts()

utility::vector1< std::string > protocols::stepwise::modeler::rna::possible_rts ( utility::tools::make_vector1("RAD", "RGU", "RCY", "URA", "OMA", "OMC", "OMG", "OMU", "PSU", "H2U", "PUR", "1MA", "NPU", "8OG", "6MG", "5IU", "5FC", "5FU")  )

Referenced by choose_randomly_from_allowed_at_position().

◆ print_atom_info()

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

References 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().

◆ print_base_state()

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::sequence::left, core::chemical::rna::NO_CHI, and core::chemical::rna::SYN.

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

◆ print_heavy_atoms()

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

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

◆ print_individual_atom_info()

void protocols::stepwise::modeler::rna::print_individual_atom_info ( core::conformation::Residue const &  rsd,
core::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().

◆ print_sugar_pucker_state()

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::sequence::left, core::chemical::rna::NO_PUCKER, core::chemical::rna::NORTH, and core::chemical::rna::SOUTH.

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().

◆ print_torsion_info()

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::chemical::ResidueType::atom_name(), core::conformation::Residue::atom_type(), core::conformation::Residue::atom_type_index(), core::conformation::Residue::atomic_charge(), core::id::AtomID::atomno(), core::id::BB, core::conformation::Residue::chi(), core::id::CHI, core::pose::Pose::conformation(), core::conformation::Conformation::get_torsion_angle_atom_ids(), core::conformation::Residue::mainchain_torsion(), core::chemical::AtomType::name(), core::pose::Pose::residue(), core::id::AtomID::rsd(), TR(), and core::conformation::Residue::type().

◆ remove_all_variant_types()

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

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::chemical::ResidueProperties::get_list_of_variants(), core::chemical::ResidueProperties::get_variant_from_string(), core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueTypeBase::properties(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::type().

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file().

◆ remove_all_virtual_phosphates()

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

References core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::size(), and core::chemical::VIRTUAL_PHOSPHATE.

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

◆ remove_chain_break_variants()

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

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

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

◆ remove_file()

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

References protocols::pack_daemon::error_message.

Referenced by get_binary_rna_silent_struct_safe().

◆ remove_virtual_O2Prime_hydrogen()

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

References core::chemical::ResidueTypeBase::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(), core::pose::Pose::size(), and core::chemical::VIRTUAL_O2PRIME_HYDROGEN.

◆ rescale_scorefxn()

core::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 smart 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::n_score_types, show_scorefxn_weight_lines(), and core::chemical::rna::TR().

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

◆ rmsd_over_residue_list() [1/2]

Real protocols::stepwise::modeler::rna::rmsd_over_residue_list ( pose::Pose const &  pose1,
pose::Pose const &  pose2,
utility::vector1< core::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::pose::full_model_info::full_to_sub(), core::conformation::Residue::has_variant_type(), protocols::mean_field::max(), core::pose::rna::output_boolean(), output_seq_num_list(), output_title_text(), core::pose::Pose::residue(), suite_square_deviation(), core::chemical::rna::TR(), and core::chemical::VIRTUAL_RNA_RESIDUE.

Referenced by 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(), and protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::setup_fail_triangle_inequailty_list().

◆ rmsd_over_residue_list() [2/2]

core::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 core::pose::full_model_info::full_to_sub().

◆ score_sort_criterion()

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().

◆ seq_num_sort_criterion()

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().

◆ set_CCD_torsions_to_zero()

void protocols::stepwise::modeler::rna::set_CCD_torsions_to_zero ( core::pose::Pose &  pose,
core::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().

◆ set_difference()

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().

◆ set_union()

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().

Referenced by protocols::indexed_structure_store::SSHashedFragmentStore::potential_valid_ss_strings(), and core::scoring::BondOrderParser::vector_union().

◆ setup_chain_break_variants()

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

References core::pose::correctly_add_cutpoint_variants().

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

◆ setup_suite_atom_id_map() [1/4]

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

References 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::conformation::Residue::name1(), core::conformation::Residue::nheavyatoms(), core::id::AtomID_Map< T >::set(), and core::conformation::Residue::type().

◆ setup_suite_atom_id_map() [2/4]

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().

◆ setup_suite_atom_id_map() [3/4]

void protocols::stepwise::modeler::rna::setup_suite_atom_id_map ( pose::Pose const &  pose_1,
pose::Pose const &  pose_2,
core::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().

◆ setup_suite_atom_id_map() [4/4]

void protocols::stepwise::modeler::rna::setup_suite_atom_id_map ( pose::Pose const &  pose_1,
pose::Pose const &  pose_2,
core::Size const  base_res_1,
core::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_legacy(), protocols::stepwise::modeler::align::create_alignment_id_map_legacy(), and setup_suite_atom_id_map().

◆ show_scorefxn_weight_lines()

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

References core::chemical::element::F, core::scoring::sasa::LJ, core::scoring::n_score_types, and core::chemical::rna::TR().

Referenced by rescale_scorefxn().

◆ sleep()

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::wum::WorkUnit_Wait::run(), and protocols::jd2::WriteFileSFB::WriteFileSFB().

◆ sort_copy_dofs()

void protocols::stepwise::modeler::rna::sort_copy_dofs ( utility::vector1< Residue_info > &  copy_dofs)

References core::pose::copydofs::copy_dofs(), and copy_dofs_sort_criterion().

Referenced by create_strand_list().

◆ sort_seq_num_list()

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().

◆ string_to_int()

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

References core::pose::rna::string_to_int().

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::VirtualSugarSamplerFromStringList::setup_sugar_modeling_list(), and protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_using_user_input_VDW_pose().

◆ string_to_real()

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

References core::conformation::membrane::in, and core::conformation::membrane::out.

◆ suite_rmsd()

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

References protocols::mean_field::max(), suite_square_deviation(), and core::chemical::rna::TR().

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().

◆ suite_square_deviation()

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

References core::chemical::ResidueTypeBase::aa(), atom_square_deviation(), core::chemical::ResidueType::first_sidechain_atom(), core::conformation::Residue::first_sidechain_atom(), core::chemical::ResidueType::is_NA(), core::conformation::Residue::is_virtual(), core::chemical::ResidueType::is_virtual_residue(), core::chemical::ResidueType::nheavyatoms(), core::pose::Pose::residue(), and core::pose::Pose::residue_type().

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

◆ tokenize()

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

References protocols::kinmatch::str(), and core::pose::rna::tokenize().

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::StepWiseRNA_CombineLongLoopFilterer::is_sibling_sugar_rotamer_pose(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::setup_sugar_modeling_list(), and protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_using_user_input_VDW_pose().

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