Rosetta 3.4
Classes | Typedefs | Enumerations | Functions
protocols::swa::rna Namespace Reference

Classes

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

Typedefs

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

Enumerations

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

Functions

bool sort_criteria2 (pose_data_struct2 pose_data_1, pose_data_struct2 pose_data_2)
bool score_sort_citeria (Combine_Tags_Info tag_info_1, Combine_Tags_Info tag_info_2)
bool Is_base_stack (core::kinematics::Stub const &moving_res_base, utility::vector1< core::kinematics::Stub > const &other_residues_base_list, core::Real const base_axis_CUTOFF, core::Real const base_planarity_CUTOFF)
bool Is_base_pair (core::kinematics::Stub const &moving_res_base, utility::vector1< core::kinematics::Stub > const &other_residues_base_list, core::Real const base_axis_CUTOFF, core::Real const base_planarity_CUTOFF)
bool Is_strong_base_stack (core::kinematics::Stub const &moving_res_base, utility::vector1< core::kinematics::Stub > const &other_residues_base_list)
bool Is_medium_base_stack_and_medium_base_pair (core::kinematics::Stub const &moving_res_base, utility::vector1< core::kinematics::Stub > const &other_residues_base_list)
bool Base_centroid_screening (core::kinematics::Stub const &moving_res_base, utility::vector1< core::kinematics::Stub > const &other_residues_base_list, Size const num_nucleotides, SillyCountStruct &count_data, bool const allow_base_pair_only_screen)
core::kinematics::Stub Get_ribose_stub (conformation::Residue const &rsd, bool const Is_prepend, bool const verbose)
Base_bin Get_euler_stub_bin (numeric::xyzVector< core::Real > const &centriod, Euler_angles const &euler_angles)
int DOF_bin_value (std::map< Base_bin, int, compare_base_bin >::const_iterator const &base_bin_it, std::string const &DOF)
Real DOF_bin_size (std::string const &DOF)
void Analyze_base_bin_map (std::map< Base_bin, int, compare_base_bin > const &base_bin_map, std::string const &DOF_one, std::string const &DOF_two, std::string const foldername)
void Analyze_base_bin_map (std::map< Base_bin, int, compare_base_bin > const &base_bin_map, std::string const foldername)
Euler_angles Get_euler_angles (numeric::xyzMatrix< core::Real > const &coordinate_matrix)
void convert_euler_to_coordinate_matrix (Euler_angles const &E, numeric::xyzMatrix< core::Real > &coordinate_matrix)
void translate_then_rotate_pose (core::pose::Pose &pose, numeric::xyzVector< core::Real > const &vector, numeric::xyzMatrix< core::Real > const matrix, bool const verbose)
void set_to_origin (pose::Pose &pose, Size const seq_num, bool verbose)
void get_specific_atom_coordinate (std::string const &atom_name, numeric::xyzVector< core::Real > &atom_pos, core::conformation::Residue const &rsd_at_origin, core::kinematics::Stub const &moving_res_base_stub)
core::Real get_max_centroid_to_atom_distance (utility::vector1< core::conformation::ResidueOP > const &rsd_at_origin_list, std::string const atom_name)
utility::vector1
< core::conformation::ResidueOP
setup_residue_at_origin_list (pose::Pose const &pose, Size const &moving_res, bool const extra_anti_chi_rotamer, bool const extra_syn_chi_rotamer, std::string const pose_name)
bool check_floating_base_chain_closable (core::Size const &reference_res, utility::vector1< pose_data_struct2 > pose_data_list, utility::vector1< core::conformation::ResidueOP > const &rsd_at_origin_list, core::kinematics::Stub const &moving_res_base_stub, bool const Is_prepend, core::Size const gap_size)
bool check_floating_base_chain_closable (core::Size const &reference_res, core::pose::Pose const &pose, utility::vector1< core::conformation::ResidueOP > const &rsd_at_origin_list, core::kinematics::Stub const &moving_res_base_stub, bool const Is_prepend, Size const gap_size)
void set_base_coordinate_frame (pose::Pose &pose, Size const &seq_num, core::conformation::Residue const &rsd_at_origin, core::kinematics::Stub const &moving_res_base_stub)
bool Is_medium_stack_base_and_medium_stack_base (core::kinematics::Stub const &moving_res_base, utility::vector1< core::kinematics::Stub > const &other_residues_base_list)
void Analyze_base_bin_map (std::map< Base_bin, int, compare_base_bin > const &base_bin_map, std::string const &DOF_one, std::string const &DOF_two)
void Analyze_base_bin_map_old (std::map< Base_bin, int, compare_base_bin > const &base_bin_map, bool const Is_dinucleotide)
bool possible_root (core::kinematics::FoldTree const &f, Size const &n)
bool minimizer_sort_criteria (pose_data_struct2 pose_data_1, pose_data_struct2 pose_data_2)
core::io::silent::BinaryRNASilentStruct get_binary_rna_silent_struct_safe (pose::Pose const &const_pose, std::string const &tag, std::string const &silent_file)
core::io::silent::BinaryRNASilentStruct get_binary_rna_silent_struct_safe_wrapper (pose::Pose const &const_pose, std::string const &tag, std::string const &silent_file, bool const write_score_only)
void Output_data (core::io::silent::SilentFileData &silent_file_data, std::string const &silent_file, std::string const &tag, bool const write_score_only, pose::Pose const &pose, core::pose::PoseCOP native_poseCOP, StepWiseRNA_JobParametersCOP job_parameters_)
void Print_torsion_info (core::pose::Pose const &pose, core::Size const seq_num, core::Size const rna_torsion_number, std::string const type)
utility::vector1< Residue_infoConvert_rebuild_residue_string_to_list (std::string const &rebuild_residue_string)
void Output_residue_struct (Residue_info const &residue)
std::string Get_one_letter_name (std::string const &three_letter_name)
std::string Get_three_letter_name (std::string const &one_letter_name)
Size get_max_seq_num_from_res_map (std::map< core::Size, core::Size > const &my_map)
void output_res_map (std::map< core::Size, core::Size > const &my_map, Size const max_seq_num)
void Output_residue_list (utility::vector1< Residue_info > residue_list)
utility::vector1< Residue_infoGet_residue_list_from_fasta (std::string const full_fasta_sequence)
Residue_info Get_residue_from_seq_num (Size const &seq_num, utility::vector1< Residue_info > const &residue_list)
bool Contain_residue_at_seq_num (Size seq_num, utility::vector1< Residue_info > const &residue_list)
utility::vector1
< utility::vector1
< Residue_info > > 
Create_strand_list (utility::vector1< Residue_info > const &residue_list)
utility::vector1< Residue_infoSet_Difference (utility::vector1< Residue_info > const &residue_list_1, utility::vector1< Residue_info > const &residue_list_2)
utility::vector1< Residue_infoSet_Union (utility::vector1< Residue_info > const &residue_list_1, utility::vector1< Residue_info > const &residue_list_2)
bool residue_list_sort_citeria (Residue_info residue_info_1, Residue_info residue_info_2)
void sort_residue_list (utility::vector1< Residue_info > &residue_list)
void output_is_prepend_map (std::map< core::Size, bool > const &my_map, core::Size const max_seq_num)
bool sort_criteria (pose_data_struct2 pose_data_1, pose_data_struct2 pose_data_2)
bool Is_O1P_atom (std::string const &atom_name)
bool Is_O2P_atom (std::string const &atom_name)
bool Is_P_atom (std::string const &atom_name)
bool Is_O2star_atom (std::string const &atom_name)
bool Is_O3star_atom (std::string const &atom_name)
bool Is_O4star_atom (std::string const &atom_name)
bool Is_O5star_atom (std::string const &atom_name)
bool Is_C2star_atom (std::string const &atom_name)
bool Is_C3star_atom (std::string const &atom_name)
bool Is_C4star_atom (std::string const &atom_name)
bool Is_C5star_atom (std::string const &atom_name)
bool Is_1H5star_atom (std::string const &atom_name)
bool Is_2H5star_atom (std::string const &atom_name)
bool Is_H3star_atom (std::string const &atom_name)
bool Is_H4star_atom (std::string const &atom_name)
bool Is_three_prime_phosphate_atom (std::string const &atom_name)
bool Is_five_prime_phosphate_atom (std::string const &atom_name)
bool Is_phosphate_atom (std::string const &atom_name)
void minimize_with_constraints (core::pose::Pose &pose, core::kinematics::MoveMap const &mm, core::scoring::ScoreFunctionOP const &scorefxn, core::optimization::MinimizerOptions const &options)
bool assert_can_prepend (utility::vector1< core::Size > const &seq_num_list)
bool assert_can_append (utility::vector1< core::Size > const &seq_num_list)
void apply_protonated_H1_adenosine_variant_type (core::pose::Pose &pose, core::Size const &seq_num, bool const apply_check)
void apply_virtual_rna_residue_variant_type (core::pose::Pose &pose, core::Size const &seq_num, bool const apply_check)
void apply_virtual_rna_residue_variant_type (core::pose::Pose &pose, core::Size const &seq_num, utility::vector1< core::Size > const &working_cutpoint_closed_list, bool const apply_check)
void remove_virtual_rna_residue_variant_type (pose::Pose &pose, Size const &seq_num)
bool has_virtual_rna_residue_variant_type (pose::Pose &pose, Size const &seq_num)
void remove_all_variant_types (pose::Pose &pose)
utility::vector1< Sizeapply_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< Sizeapply_full_to_sub_mapping (utility::vector1< Size > const &res_vector, StepWiseRNA_JobParametersCOP job_parameters)
utility::vector1< Sizeapply_sub_to_full_mapping (utility::vector1< Size > const &working_res_vector, StepWiseRNA_JobParametersCOP job_parameters)
void ensure_valid_full_seq_num (Size const full_seq_num, StepWiseRNA_JobParametersCOP const &job_parameters)
bool check_is_working_res (Size const full_seq_num, StepWiseRNA_JobParametersCOP const &job_parameters)
core::Size check_validity_and_get_working_res (Size const full_seq_num, StepWiseRNA_JobParametersCOP const &job_parameters)
std::map< core::Size, core::Sizecreate_full_to_input_res_map (utility::vector1< core::Size > const &input_res_vector)
core::Size string_to_int (std::string const input_string)
core::Real string_to_real (std::string const input_string)
utility::vector1< std::string > Tokenize (std::string const str, std::string delimiters)
bool Contain_seq_num (Size const &seq_num, utility::vector1< std::pair< core::Size, core::Size > > const &residue_pair_list)
bool Contain_seq_num (Size const &seq_num, utility::vector1< core::Size > const &residue_list)
bool Is_virtual_base (conformation::Residue const &rsd)
void setup_suite_atom_id_map (conformation::Residue const &rsd_1, conformation::Residue const &rsd_2, id::AtomID_Map< id::AtomID > &atom_ID_map, bool const base_only)
void setup_suite_atom_id_map (conformation::Residue const &rsd_1, conformation::Residue const &rsd_2, Size const res_num_1, Size const res_num_2, id::AtomID_Map< id::AtomID > &atom_ID_map, bool const base_only)
void setup_suite_atom_id_map (pose::Pose const &pose_1, pose::Pose const &pose_2, Size const base_res, id::AtomID_Map< id::AtomID > &atom_ID_map, bool const base_only)
void setup_suite_atom_id_map (pose::Pose const &pose_1, pose::Pose const &pose_2, Size const base_res_1, Size const base_res_2, id::AtomID_Map< id::AtomID > &atom_ID_map, bool const base_only)
id::AtomID_Map< id::AtomIDcreate_alignment_id_map (pose::Pose &mod_pose, pose::Pose const &ref_pose, utility::vector1< core::Size > const &rmsd_residue_list, bool const base_only)
void align_poses (core::pose::Pose &moving_pose, std::string const moving_tag, core::pose::Pose const &static_pose, std::string const static_tag, utility::vector1< core::Size > const &working_best_alignment, bool const base_only)
void output_pair_size (std::pair< Size, Size > const &pair_size)
void output_pair_size_vector (utility::vector1< std::pair< Size, Size > > const &pair_size_vector, std::string const &output_string, core::Size const spacing)
bool pair_sort_citeria (std::pair< Size, Size > pair_one, std::pair< Size, Size > pair_two)
void Sort_pair_list (utility::vector1< std::pair< Size, Size > > pair_list)
bool seq_num_sort_citeria (core::Size seq_num_1, core::Size seq_num_2)
void sort_seq_num_list (utility::vector1< core::Size > &seq_num_list)
void Output_seq_num_list (std::string const tag, utility::vector1< core::Size > const &seq_num_list, core::Size const spacing)
bool Is_equivalent_vector (utility::vector1< core::Size > const &seq_num_list_1, utility::vector1< core::Size > const &seq_num_list_2)
void Output_is_prepend_map (std::string const tag, std::map< core::Size, bool > const &my_map, core::Size const max_seq_num, core::Size const tag_spacing)
void Output_bool_list (std::string const tag, utility::vector1< Size > const &size_list, core::Size const spacing)
void Output_bool_list (std::string const tag, utility::vector1< bool > const &bool_list, core::Size const spacing)
void Output_size_list (std::string const tag, utility::vector1< Size > const &size_list, core::Size const spacing)
bool Is_close_chain_break (pose::Pose const &pose)
void Add_harmonic_chainbreak_constraint (pose::Pose &pose, Size const five_prime_res)
void Output_title_text (std::string const title)
void Output_fold_tree_info (kinematics::FoldTree const &fold_tree, std::string const pose_name)
void Output_fold_tree_info (pose::Pose const &pose, std::string pose_name)
bool file_exists (std::string const &file_name)
void remove_file (std::string const &file_name)
void output_rotamer (utility::vector1< Real > &rotamer)
void Add_virtual_O2Star_hydrogen (core::pose::Pose &pose)
bool Remove_virtual_O2Star_hydrogen (pose::Pose &pose)
Real suite_rmsd (pose::Pose const &pose1, pose::Pose const &pose2, Size const &moving_res_num, bool const prepend_res, bool const ignore_virtual_atom)
core::Real full_length_rmsd_over_residue_list (pose::Pose const &pose1, pose::Pose const &pose2, utility::vector1< Size > const &residue_list, std::string const &full_sequence, bool const verbose, bool const ignore_virtual_atom)
Real rmsd_over_residue_list (pose::Pose const &pose1, pose::Pose const &pose2, utility::vector1< Size > const &residue_list, std::map< core::Size, core::Size > const &full_to_sub, std::map< core::Size, bool > const &Is_prepend_map, bool const verbose, bool const ignore_virtual_atom)
Real rmsd_over_residue_list (pose::Pose const &pose1, pose::Pose const &pose2, StepWiseRNA_JobParametersCOP job_parameters_, bool const ignore_virtual_atom)
void Print_heavy_atoms (Size const &suite_num_1, Size const &suite_num_2, pose::Pose const &pose1, pose::Pose const &pose2)
Size Get_num_side_chain_atom_from_res_name (chemical::AA const &res_aa, bool const verbose)
Real atom_square_deviation (conformation::Residue const &rsd_1, conformation::Residue const &rsd_2, Size const &atomno_1, Size const &atomno_2, bool verbose)
void base_atoms_square_deviation (pose::Pose const &pose1, pose::Pose const &pose2, Size const &moving_res_1, Size const &moving_res_2, Size &atom_count, Real &sum_sd, bool verbose, bool const ignore_virtual_atom)
void phosphate_square_deviation (pose::Pose const &pose1, pose::Pose const &pose2, Size const &moving_res_1, Size const &moving_res_2, Size &atom_count, Real &sum_sd, bool verbose, bool const ignore_virtual_atom)
core::Real phosphate_base_phosphate_rmsd (pose::Pose const &pose1, pose::Pose const &pose2, Size const &moving_res_num, bool const ignore_virtual_atom)
void phosphate_base_phosphate_square_deviation (pose::Pose const &pose1, pose::Pose const &pose2, Size const &moving_res_1, Size const &moving_res_2, Size &atom_count, Real &sum_sd, bool verbose, bool const ignore_virtual_atom)
void suite_square_deviation (pose::Pose const &pose1, pose::Pose const &pose2, bool const &prepend_res, Size const &moving_res_1, Size const &moving_res_2, Size &atom_count, Real &sum_sd, bool verbose, bool const ignore_virtual_atom)
bool Check_chain_closable (pose::Pose const &pose, Size const five_prime_chain_break_res, Size const gap_size)
bool Check_chain_closable (numeric::xyzVector< core::Real > const &xyz_1, numeric::xyzVector< core::Real > const &xyz_2, core::Size const gap_size)
bool Check_chain_closable_floating_base (pose::Pose const &five_prime_pose, pose::Pose const &three_prime_pose, Size const five_prime_chain_break_res, Size const gap_size)
void get_C4_C3_distance_range (conformation::Residue const &five_prime_rsd, conformation::Residue const &three_prime_rsd, Distance &C4_C3_dist_min, Distance &C4_C3_dist_max)
void Freeze_sugar_torsions (core::kinematics::MoveMap &mm, Size const total_residue)
void Output_boolean (std::string const &tag, bool boolean)
void Output_boolean (bool boolean)
void Output_movemap (kinematics::MoveMap const &mm, core::pose::Pose const &pose)
utility::vector1< core::Sizeget_surrounding_O2star_hydrogen (pose::Pose const &pose, utility::vector1< core::Size > const &moving_res, bool verbose)
void o2star_minimize (pose::Pose &pose, core::scoring::ScoreFunctionOP const &packer_scorefxn)
void o2star_minimize (pose::Pose &pose, core::scoring::ScoreFunctionOP const &packer_scorefxn, utility::vector1< core::Size > const &O2star_pack_seq_num)
pack::task::PackerTaskOP create_standard_o2star_pack_task (pose::Pose const &pose, utility::vector1< core::Size > const &O2star_pack_seq_num)
void print_backbone_torsions (pose::Pose const &pose, Size const five_prime_chainbreak)
void Correctly_position_cutpoint_phosphate_torsions (pose::Pose &current_pose, Size const five_prime_chainbreak, bool verbose)
void copy_torsions_FROM_TO (core::id::TorsionID const start_torsion_ID, core::id::TorsionID const end_torsion_ID, core::pose::Pose const &template_pose, core::pose::Pose &pose)
core::Size setup_chain_break_jump_point (core::pose::Pose &pose, core::Size const jump_point_one, core::Size const jump_point_two, core::Size const five_prime_cutpoint, bool const verbose)
void remove_chain_break_jump_point (core::pose::Pose &pose, core::Size const five_prime_cutpoint, core::kinematics::FoldTree const fold_tree_without_cutpoint)
core::Size setup_bulge_jump_point (pose::Pose &pose, Size const &moving_base, Size const &reference_base, bool const verbose)
Size make_cut_at_moving_suite (core::kinematics::FoldTree &fold_tree, Size const &moving_suite)
Size make_cut_at_moving_suite (pose::Pose &pose, Size const &moving_suite)
void apply_rotamer (pose::Pose &pose, utility::vector1< Torsion_Info > const &rotamer_list)
bool check_for_messed_up_structure (core::pose::Pose const &pose, std::string const &tag)
BaseState Get_residue_base_state (core::pose::Pose const &pose, Size const seq_num)
PuckerState Get_residue_pucker_state (core::pose::Pose const &pose, Size const seq_num, bool const verbose)
bool Is_same_ribose_pucker (core::pose::Pose const &current_pose, core::pose::Pose const &cluster_center_pose, Size const seq_num)
void sleep (core::Size mseconds)
void setup_simple_fold_tree (core::pose::Pose &pose)
void get_atom_coordinates (utility::vector1< std::pair< id::AtomID, numeric::xyzVector< core::Real > > > &xyz_list, Size const &seq_num, core::conformation::Residue const &rsd_at_origin, core::kinematics::Stub const &moving_res_base_stub)
void import_pose_from_silent_file (core::pose::Pose &import_pose, std::string const &silent_file, std::string const &input_tag)
std::string path_basename (std::string const full_path)
bool Is_residues_in_contact (core::Size const &res_ONE, core::pose::Pose const &pose_ONE, core::Size const &res_TWO, core::pose::Pose const &pose_TWO, core::Real const atom_atom_overlap_dist_cutoff, core::Size const num_atom_contacts_cutoff, bool const verbose)
void set_CCD_torsions_to_zero (core::pose::Pose &pose, Size const five_prime_res)
core::Size virtualize_energetically_unfavorable_nucleotides (core::pose::Pose &input_pose, utility::vector1< core::Size > const &allow_bulge_res_list, core::scoring::ScoreFunctionOP const &scorefxn, std::string const &tag, bool const allow_pre_virtualize, bool const allow_consecutive_bulges, bool const verbose)
std::string get_tag_from_pdb_filename (std::string const pdb_filename)
void move_jump_atom_to_base (core::kinematics::FoldTree &fold_tree, std::string const &working_sequence)
void print_JobParameters_info (StepWiseRNA_JobParametersCOP const &const_JP, std::string const JP_name, bool const Is_simple_full_length_JP)
void set_nucleotide_to_A_form (pose::Pose &pose, Size const seq_num)
void print_atom_info (pose::Pose const &pose, Size const seq_num, std::string const pose_name)
void print_individual_atom_info (core::conformation::Residue const &rsd, Size const atomno, std::string const rsd_name)
void print_base_state (std::string const tag, BaseState const base_state)
void print_ribose_pucker_state (std::string const tag, PuckerState const pucker_state)
void initialize_common_scorefxns (core::scoring::ScoreFunctionOP const &scorefxn_, core::scoring::ScoreFunctionOP &sampling_scorefxn_, core::scoring::ScoreFunctionOP &atr_rep_screening_scorefxn_, core::scoring::ScoreFunctionOP &chainbreak_scorefxn_, core::scoring::ScoreFunctionOP &o2star_pack_scorefxn_)
void copy_all_o2star_torsions (core::pose::Pose &mod_pose, core::pose::Pose const &template_pose)
core::scoring::ScoreFunctionOP rescale_scorefxn (core::scoring::ScoreFunctionOP const &starting_scorefxn, Real const scaling_factor)
void show_scorefxn_weight_lines (core::scoring::ScoreFunctionOP const &scorefxn, std::string const title)
core::Size get_matching_atom_name (std::string const &atom_name, core::conformation::Residue const &rsd)
void output_pair_size (std::pair< core::Size, core::Size > const &pair_size)
void output_pair_size_vector (utility::vector1< std::pair< core::Size, core::Size > > const &pair_size_vector, std::string const &output_string, core::Size const spacing=40)
bool pair_sort_citeria (std::pair< core::Size, core::Size > pair_one, std::pair< core::Size, core::Size > pair_two)
bool seq_num_list_sort_citeria (core::Size seq_num_1, Residue_info seq_num_2)
void Sort_pair_list (utility::vector1< std::pair< core::Size, core::Size > > pair_list)
void get_atom_coordinates (utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > &xyz_list, core::Size const &seq_num, core::conformation::Residue const &rsd_at_origin, core::kinematics::Stub const &moving_res_base_stub)
bool fast_full_atom_VDW_repulsion_screen (core::pose::Pose const &pose, core::Size const res_1, core::Size const res_2, bool const Is_prepend)
bool floating_base_full_atom_van_der_Waals_screening (core::pose::Pose &current_pose_screen, core::Real const &base_rep_score, core::scoring::ScoreFunctionOP const &atr_rep_screening_scorefxn, SillyCountStruct &count_data, bool const verbose)
bool floating_base_chain_break_screening (core::pose::Pose &chain_break_screening_pose, core::scoring::ScoreFunctionOP const &chainbreak_scorefxn, SillyCountStruct &count_data, core::Size const &five_prime_res, std::string const &tag, bool const verbose)
utility::vector1< FB_Pose_Datafloating_base_chain_closure_setup (utility::vector1< pose_data_struct2 > const &input_pose_data_list, FloatingBaseChainClosureJobParameter const &FB_job_params, core::scoring::ScoreFunctionOP const &atr_rep_screening_scorefxn, core::scoring::ScoreFunctionOP const &full_scorefxn, pose::Pose &viewer_pose, bool const do_minimize)
void floating_base_chain_closure_sampling (utility::vector1< FB_Pose_Data > &pose_data_list, core::pose::Pose &viewer_pose, FloatingBaseChainClosureJobParameter const &FB_job_params, core::scoring::ScoreFunctionOP const &chainbreak_scorefxn, core::scoring::ScoreFunctionOP const &atr_rep_screening_scorefxn, StepWiseRNA_VDW_Bin_ScreenerOP const &VDW_bin_screener, bool const CCD_grid_index_screen)
utility::vector1
< pose_data_struct2
floating_base_chain_closure_post_process (utility::vector1< FB_Pose_Data > &pose_data_list, core::pose::Pose &viewer_pose, core::scoring::ScoreFunctionOP const &sampling_scorefxn, FloatingBaseChainClosureJobParameter const &FB_job_params, bool const rm_chain_break_jump_point)
void minimize_all_sampled_floating_bases (core::pose::Pose &viewer_pose, utility::vector1< FloatingBaseChainClosureJobParameter > const &FB_JP_list, utility::vector1< pose_data_struct2 > &pose_data_list, core::scoring::ScoreFunctionOP const &sampling_scorefxn, StepWiseRNA_JobParametersCOP const &job_parameters, bool const virtual_ribose_is_from_prior_step)
bool Is_ribose_virtual (core::pose::Pose const &pose, core::Size const ribose_res, core::Size const bulge_res)
void copy_bulge_res_and_ribose_torsion (FloatingBaseChainClosureJobParameter const &FB_job_params, core::pose::Pose &pose, core::pose::Pose const &template_pose)
bool sort_pose_data_by_score (pose_data_struct2 pose_data_1, pose_data_struct2 pose_data_2)
utility::vector1
< pose_data_struct2
sample_virtual_ribose_and_bulge_and_close_chain (pose::Pose &viewer_pose, FloatingBaseChainClosureJobParameter const &FB_job_params, std::string const name, core::scoring::ScoreFunctionOP const &scorefxn, core::scoring::ScoreFunctionOP const &sampling_scorefxn, core::scoring::ScoreFunctionOP const &atr_rep_screening_scorefxn, core::scoring::ScoreFunctionOP const &chainbreak_scorefxn, StepWiseRNA_JobParametersCOP &job_parameters, bool const virtual_ribose_is_from_prior_step)
void enumerate_starting_pose_data_list (utility::vector1< pose_data_struct2 > &starting_pose_data_list, utility::vector1< FloatingBaseChainClosureJobParameter > const &FB_CC_JP_list, core::pose::Pose const &pose)
utility::vector1
< FloatingBaseChainClosureJobParameter
setup_FB_CC_JP_list (pose::Pose const &pose, utility::vector1< std::string > const &sample_virtual_ribose_string_list, StepWiseRNA_JobParametersCOP &job_parameters)
void sample_user_specified_virtual_riboses (pose::Pose &pose, utility::vector1< std::string > const &sample_virtual_ribose_string_list, StepWiseRNA_JobParametersCOP &job_parameters, core::scoring::ScoreFunctionOP const &scorefxn, std::string const silent_file_out, std::string const input_tag)

Typedef Documentation


Enumeration Type Documentation

Enumerator:
BOTH 
ANTI 
SYN 
NONE 
Enumerator:
ALL 
NORTH 
SOUTH 

Function Documentation

void protocols::swa::rna::Add_harmonic_chainbreak_constraint ( pose::Pose pose,
Size const  five_prime_res 
)
void protocols::swa::rna::Add_virtual_O2Star_hydrogen ( core::pose::Pose pose)
void protocols::swa::rna::align_poses ( core::pose::Pose moving_pose,
std::string const  moving_tag,
core::pose::Pose const &  static_pose,
std::string const  static_tag,
utility::vector1< core::Size > const &  working_best_alignment,
bool const  base_only 
)
void protocols::swa::rna::Analyze_base_bin_map ( std::map< Base_bin, int, compare_base_bin > const &  base_bin_map,
std::string const &  DOF_one,
std::string const &  DOF_two,
std::string const  foldername 
)
void protocols::swa::rna::Analyze_base_bin_map ( std::map< Base_bin, int, compare_base_bin > const &  base_bin_map,
std::string const  foldername 
)
void protocols::swa::rna::Analyze_base_bin_map ( std::map< Base_bin, int, compare_base_bin > const &  base_bin_map,
std::string const &  DOF_one,
std::string const &  DOF_two 
)
void protocols::swa::rna::Analyze_base_bin_map_old ( std::map< Base_bin, int, compare_base_bin > const &  base_bin_map,
bool const  Is_dinucleotide 
)
utility::vector1< core::Size > protocols::swa::rna::apply_full_to_sub_mapping ( utility::vector1< Size > const &  res_vector,
StepWiseRNA_JobParametersCOP  job_parameters 
)
utility::vector1< core::Size > protocols::swa::rna::apply_full_to_sub_mapping ( utility::vector1< Size > const &  res_vector,
utility::vector1< core::Size > const &  is_working_res,
std::map< core::Size, core::Size > const &  full_to_sub 
)
void protocols::swa::rna::apply_protonated_H1_adenosine_variant_type ( core::pose::Pose pose,
core::Size const &  seq_num,
bool const  apply_check 
)
void protocols::swa::rna::apply_rotamer ( pose::Pose pose,
utility::vector1< Torsion_Info > const &  rotamer_list 
)
utility::vector1< core::Size > protocols::swa::rna::apply_sub_to_full_mapping ( utility::vector1< Size > const &  working_res_vector,
StepWiseRNA_JobParametersCOP  job_parameters 
)
void protocols::swa::rna::apply_virtual_rna_residue_variant_type ( core::pose::Pose pose,
core::Size const &  seq_num,
bool const  apply_check 
)
void protocols::swa::rna::apply_virtual_rna_residue_variant_type ( core::pose::Pose pose,
core::Size const &  seq_num,
utility::vector1< core::Size > const &  working_cutpoint_closed_list,
bool const  apply_check 
)
bool protocols::swa::rna::assert_can_append ( utility::vector1< core::Size > const &  seq_num_list)
bool protocols::swa::rna::assert_can_prepend ( utility::vector1< core::Size > const &  seq_num_list)
core::Real protocols::swa::rna::atom_square_deviation ( conformation::Residue const &  rsd_1,
conformation::Residue const &  rsd_2,
Size const &  atomno_1,
Size const &  atomno_2,
bool  verbose 
)
void protocols::swa::rna::base_atoms_square_deviation ( pose::Pose const &  pose1,
pose::Pose const &  pose2,
Size const &  moving_res_1,
Size const &  moving_res_2,
Size atom_count,
Real sum_sd,
bool  verbose,
bool const  ignore_virtual_atom 
)
bool protocols::swa::rna::Base_centroid_screening ( core::kinematics::Stub const &  moving_res_base,
utility::vector1< core::kinematics::Stub > const &  other_residues_base_list,
Size const  num_nucleotides,
SillyCountStruct &  count_data,
bool const  allow_base_pair_only_screen 
)
bool protocols::swa::rna::Check_chain_closable ( pose::Pose const &  pose,
Size const  five_prime_chain_break_res,
Size const  gap_size 
)
bool protocols::swa::rna::Check_chain_closable ( numeric::xyzVector< core::Real > const &  xyz_1,
numeric::xyzVector< core::Real > const &  xyz_2,
core::Size const  gap_size 
)
bool protocols::swa::rna::Check_chain_closable_floating_base ( pose::Pose const &  five_prime_pose,
pose::Pose const &  three_prime_pose,
Size const  five_prime_chain_break_res,
Size const  gap_size 
)
bool protocols::swa::rna::check_floating_base_chain_closable ( core::Size const &  reference_res,
utility::vector1< pose_data_struct2 >  pose_data_list,
utility::vector1< core::conformation::ResidueOP > const &  rsd_at_origin_list,
core::kinematics::Stub const &  moving_res_base_stub,
bool const  Is_prepend,
core::Size const  gap_size 
)
bool protocols::swa::rna::check_floating_base_chain_closable ( core::Size const &  reference_res,
core::pose::Pose const &  pose,
utility::vector1< core::conformation::ResidueOP > const &  rsd_at_origin_list,
core::kinematics::Stub const &  moving_res_base_stub,
bool const  Is_prepend,
Size const  gap_size 
)
bool protocols::swa::rna::check_for_messed_up_structure ( core::pose::Pose const &  pose,
std::string const &  tag 
)
bool protocols::swa::rna::check_is_working_res ( Size const  full_seq_num,
StepWiseRNA_JobParametersCOP const &  job_parameters 
)
core::Size protocols::swa::rna::check_validity_and_get_working_res ( Size const  full_seq_num,
StepWiseRNA_JobParametersCOP const &  job_parameters 
)

References check_is_working_res().

Referenced by setup_FB_CC_JP_list().

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

Referenced by Set_Difference(), and Set_Union().

bool protocols::swa::rna::Contain_seq_num ( Size const &  seq_num,
utility::vector1< std::pair< core::Size, core::Size > > const &  residue_pair_list 
)
bool protocols::swa::rna::Contain_seq_num ( Size const &  seq_num,
utility::vector1< core::Size > const &  residue_list 
)
void protocols::swa::rna::convert_euler_to_coordinate_matrix ( Euler_angles const &  E,
numeric::xyzMatrix< core::Real > &  coordinate_matrix 
)
utility::vector1< Residue_info > protocols::swa::rna::Convert_rebuild_residue_string_to_list ( std::string const &  rebuild_residue_string)
void protocols::swa::rna::copy_all_o2star_torsions ( core::pose::Pose mod_pose,
core::pose::Pose const &  template_pose 
)
void protocols::swa::rna::copy_bulge_res_and_ribose_torsion ( FloatingBaseChainClosureJobParameter const &  FB_job_params,
core::pose::Pose pose,
core::pose::Pose const &  template_pose 
)
void protocols::swa::rna::copy_torsions_FROM_TO ( core::id::TorsionID const  start_torsion_ID,
core::id::TorsionID const  end_torsion_ID,
core::pose::Pose const &  template_pose,
core::pose::Pose pose 
)
void protocols::swa::rna::Correctly_position_cutpoint_phosphate_torsions ( pose::Pose current_pose,
Size const  five_prime_chainbreak,
bool  verbose 
)
core::id::AtomID_Map< core::id::AtomID > protocols::swa::rna::create_alignment_id_map ( pose::Pose mod_pose,
pose::Pose const &  ref_pose,
utility::vector1< core::Size > const &  rmsd_residue_list,
bool const  base_only 
)
std::map< core::Size, core::Size > protocols::swa::rna::create_full_to_input_res_map ( utility::vector1< core::Size > const &  input_res_vector)
core::pack::task::PackerTaskOP protocols::swa::rna::create_standard_o2star_pack_task ( pose::Pose const &  pose,
utility::vector1< core::Size > const &  O2star_pack_seq_num 
)
utility::vector1< utility::vector1< Residue_info > > protocols::swa::rna::Create_strand_list ( utility::vector1< Residue_info > const &  residue_list)

References sort_residue_list().

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

Referenced by Analyze_base_bin_map().

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

Referenced by check_is_working_res().

void protocols::swa::rna::enumerate_starting_pose_data_list ( utility::vector1< pose_data_struct2 > &  starting_pose_data_list,
utility::vector1< FloatingBaseChainClosureJobParameter > const &  FB_CC_JP_list,
core::pose::Pose const &  pose 
)
bool protocols::swa::rna::fast_full_atom_VDW_repulsion_screen ( core::pose::Pose const &  pose,
core::Size const  res_1,
core::Size const  res_2,
bool const  Is_prepend 
)
bool protocols::swa::rna::file_exists ( std::string const &  file_name)

Referenced by protocols::canonical_sampling::MetropolisHastingsMover::add_shear_mover(), protocols::canonical_sampling::MetropolisHastingsMover::add_small_mover(), protocols::protein_interface_design::movers::HotspotHasherMover::apply(), protocols::canonical_sampling::CanonicalSamplingMover::apply(), protocols::jobdist::AtomTreeDiffJobDistributor::AtomTreeDiffJobDistributor(), protocols::dna::checkpoint_cleanup(), protocols::jobdist::BaseJobDistributor::checkpoint_clear(), protocols::jd2::BOINCJobDistributor::checkpoint_clear(), protocols::jobdist::BaseJobDistributor::checkpoint_read(), protocols::jd2::BOINCJobDistributor::checkpoint_read(), protocols::constraints_additional::ConstraintEvaluator::ConstraintEvaluator(), protocols::simple_filters::EvaluatedTrialMover::dump_file(), protocols::jobdist::PlainPdbJobDistributor::dump_pose_and_map(), protocols::enzdes::EnzdesJobOutputter::EnzdesJobOutputter(), protocols::simple_filters::ExternalEvaluator::ExternalEvaluator(), protocols::jd2::archive::ArchiveManager::finalize_batch(), protocols::abinitio::IterativeBase::gen_noe_assignments(), get_binary_rna_silent_struct_safe(), protocols::jd2::FileSystemJobDistributor::get_new_job_id(), protocols::motifs::get_targetconformers_user(), protocols::MakeRotLib::init_rotamers_centroids(), protocols::jobdist::PlainPdbJobDistributor::is_finished(), protocols::abinitio::IterativeBase::IterativeBase(), protocols::jd2::PDBJobOutputter::job_has_completed(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::load_lib(), protocols::jobdist::load_s_and_l(), protocols::dna::make_subdirs(), protocols::motifs::MotifLibrary::MotifLibrary(), protocols::jobdist::PlainRawJobDistributor::PlainRawJobDistributor(), protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::pool_exists(), protocols::comparative_modeling::poses_from_cmd_line(), protocols::constraints_additional::SequenceCouplingConstraint::read_def(), protocols::constraints_additional::SequenceCoupling1BDConstraint::read_def(), core::scoring::constraints::SequenceProfileConstraint::read_def(), protocols::jd2::archive::ArchiveManager::read_existing_batches(), core::chemical::read_topology_file(), protocols::checkpoint::CheckPointer::recover_checkpoint(), protocols::enzdes::EnzdesFlexBBProtocol::recover_loops_from_file(), remove_file(), protocols::genetic_algorithm::GeneticAlgorithm::rename_checkpoint_files(), protocols::jd2::archive::ArchiveBase::restore_from_file(), protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::RestrictConservedLowDdgOperation(), protocols::motifs::LigandMotifSearch::run(), protocols::jd2::MpiFileBuffer::run(), protocols::jd2::archive::ArchiveBase::save_to_file(), core::sequence::SequenceFactory::seq_from_file(), protocols::toolbox::task_operations::SeqprofConsensusOperation::SeqprofConsensusOperation(), protocols::jd2::archive::ArchiveManager::start_new_batch(), protocols::jobdist::PlainSilentFileJobDistributor::startup(), protocols::jobdist::universal_main(), core::io::raw_data::RawFileData::write_all(), core::conformation::symmetry::SymmetryInfo::write_silent_struct(), core::io::raw_data::ScoreFileData::write_struct(), core::io::raw_data::DecoyFileData::write_struct(), and protocols::jd2::WriteFileSFB::WriteFileSFB().

bool protocols::swa::rna::floating_base_chain_break_screening ( core::pose::Pose chain_break_screening_pose,
core::scoring::ScoreFunctionOP const &  chainbreak_scorefxn,
SillyCountStruct &  count_data,
core::Size const &  five_prime_res,
std::string const &  tag,
bool const  verbose 
)
utility::vector1< pose_data_struct2 > protocols::swa::rna::floating_base_chain_closure_post_process ( utility::vector1< FB_Pose_Data > &  pose_data_list,
core::pose::Pose viewer_pose,
core::scoring::ScoreFunctionOP const &  sampling_scorefxn,
FloatingBaseChainClosureJobParameter const &  FB_job_params,
bool const  rm_chain_break_jump_point 
)
void protocols::swa::rna::floating_base_chain_closure_sampling ( utility::vector1< FB_Pose_Data > &  pose_data_list,
core::pose::Pose viewer_pose,
FloatingBaseChainClosureJobParameter const &  FB_job_params,
core::scoring::ScoreFunctionOP const &  chainbreak_scorefxn,
core::scoring::ScoreFunctionOP const &  atr_rep_screening_scorefxn,
StepWiseRNA_VDW_Bin_ScreenerOP const &  VDW_bin_screener,
bool const  CCD_grid_index_screen 
)
utility::vector1< FB_Pose_Data > protocols::swa::rna::floating_base_chain_closure_setup ( utility::vector1< pose_data_struct2 > const &  input_pose_data_list,
FloatingBaseChainClosureJobParameter const &  FB_job_params,
core::scoring::ScoreFunctionOP const &  atr_rep_screening_scorefxn,
core::scoring::ScoreFunctionOP const &  full_scorefxn,
pose::Pose viewer_pose,
bool const  do_minimize 
)

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

Referenced by sample_virtual_ribose_and_bulge_and_close_chain().

bool protocols::swa::rna::floating_base_full_atom_van_der_Waals_screening ( core::pose::Pose current_pose_screen,
core::Real const &  base_rep_score,
core::scoring::ScoreFunctionOP const &  atr_rep_screening_scorefxn,
SillyCountStruct &  count_data,
bool const  verbose 
)
void protocols::swa::rna::Freeze_sugar_torsions ( core::kinematics::MoveMap mm,
Size const  total_residue 
)
core::Real protocols::swa::rna::full_length_rmsd_over_residue_list ( pose::Pose const &  pose1,
pose::Pose const &  pose2,
utility::vector1< Size > const &  residue_list,
std::string const &  full_sequence,
bool const  verbose,
bool const  ignore_virtual_atom 
)
void protocols::swa::rna::get_atom_coordinates ( utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > &  xyz_list,
core::Size const &  seq_num,
core::conformation::Residue const &  rsd_at_origin,
core::kinematics::Stub const &  moving_res_base_stub 
)
void protocols::swa::rna::get_atom_coordinates ( utility::vector1< std::pair< id::AtomID, numeric::xyzVector< core::Real > > > &  xyz_list,
Size const &  seq_num,
core::conformation::Residue const &  rsd_at_origin,
core::kinematics::Stub const &  moving_res_base_stub 
)
core::io::silent::BinaryRNASilentStruct protocols::swa::rna::get_binary_rna_silent_struct_safe ( pose::Pose const &  const_pose,
std::string const &  tag,
std::string const &  silent_file 
)
core::io::silent::BinaryRNASilentStruct protocols::swa::rna::get_binary_rna_silent_struct_safe_wrapper ( pose::Pose const &  const_pose,
std::string const &  tag,
std::string const &  silent_file,
bool const  write_score_only 
)
void protocols::swa::rna::get_C4_C3_distance_range ( conformation::Residue const &  five_prime_rsd,
conformation::Residue const &  three_prime_rsd,
Distance C4_C3_dist_min,
Distance C4_C3_dist_max 
)
Euler_angles protocols::swa::rna::Get_euler_angles ( numeric::xyzMatrix< core::Real > const &  coordinate_matrix)
Base_bin protocols::swa::rna::Get_euler_stub_bin ( numeric::xyzVector< core::Real > const &  centriod,
Euler_angles const &  euler_angles 
)
core::Size protocols::swa::rna::get_matching_atom_name ( std::string const &  atom_name,
core::conformation::Residue const &  rsd 
)
core::Real protocols::swa::rna::get_max_centroid_to_atom_distance ( utility::vector1< core::conformation::ResidueOP > const &  rsd_at_origin_list,
std::string const  atom_name 
)
core::Size protocols::swa::rna::get_max_seq_num_from_res_map ( std::map< core::Size, core::Size > const &  my_map)
core::Size protocols::swa::rna::Get_num_side_chain_atom_from_res_name ( chemical::AA const &  res_aa,
bool const  verbose 
)
std::string protocols::swa::rna::Get_one_letter_name ( std::string const &  three_letter_name)

Referenced by Output_residue_struct().

BaseState protocols::swa::rna::Get_residue_base_state ( core::pose::Pose const &  pose,
Size const  seq_num 
)
Residue_info protocols::swa::rna::Get_residue_from_seq_num ( Size const &  seq_num,
utility::vector1< Residue_info > const &  residue_list 
)
utility::vector1< Residue_info > protocols::swa::rna::Get_residue_list_from_fasta ( std::string const  full_fasta_sequence)
PuckerState protocols::swa::rna::Get_residue_pucker_state ( core::pose::Pose const &  pose,
Size const  seq_num,
bool const  verbose 
)
core::kinematics::Stub protocols::swa::rna::Get_ribose_stub ( conformation::Residue const &  rsd,
bool const  Is_prepend,
bool const  verbose 
)
void protocols::swa::rna::get_specific_atom_coordinate ( std::string const &  atom_name,
numeric::xyzVector< core::Real > &  atom_pos,
core::conformation::Residue const &  rsd_at_origin,
core::kinematics::Stub const &  moving_res_base_stub 
)
utility::vector1< core::Size > protocols::swa::rna::get_surrounding_O2star_hydrogen ( pose::Pose const &  pose,
utility::vector1< core::Size > const &  moving_res,
bool  verbose 
)
std::string protocols::swa::rna::get_tag_from_pdb_filename ( std::string const  pdb_filename)
std::string protocols::swa::rna::Get_three_letter_name ( std::string const &  one_letter_name)
bool protocols::swa::rna::has_virtual_rna_residue_variant_type ( pose::Pose pose,
Size const &  seq_num 
)
void protocols::swa::rna::import_pose_from_silent_file ( core::pose::Pose import_pose,
std::string const &  silent_file,
std::string const &  input_tag 
)
void protocols::swa::rna::initialize_common_scorefxns ( core::scoring::ScoreFunctionOP const &  scorefxn_,
core::scoring::ScoreFunctionOP sampling_scorefxn_,
core::scoring::ScoreFunctionOP atr_rep_screening_scorefxn_,
core::scoring::ScoreFunctionOP chainbreak_scorefxn_,
core::scoring::ScoreFunctionOP o2star_pack_scorefxn_ 
)
bool protocols::swa::rna::Is_1H5star_atom ( std::string const &  atom_name)
bool protocols::swa::rna::Is_2H5star_atom ( std::string const &  atom_name)
bool protocols::swa::rna::Is_base_pair ( core::kinematics::Stub const &  moving_res_base,
utility::vector1< core::kinematics::Stub > const &  other_residues_base_list,
core::Real const  base_axis_CUTOFF,
core::Real const  base_planarity_CUTOFF 
)
bool protocols::swa::rna::Is_base_stack ( core::kinematics::Stub const &  moving_res_base,
utility::vector1< core::kinematics::Stub > const &  other_residues_base_list,
core::Real const  base_axis_CUTOFF,
core::Real const  base_planarity_CUTOFF 
)
bool protocols::swa::rna::Is_C2star_atom ( std::string const &  atom_name)
bool protocols::swa::rna::Is_C3star_atom ( std::string const &  atom_name)
bool protocols::swa::rna::Is_C4star_atom ( std::string const &  atom_name)
bool protocols::swa::rna::Is_C5star_atom ( std::string const &  atom_name)
bool protocols::swa::rna::Is_close_chain_break ( pose::Pose const &  pose)
bool protocols::swa::rna::Is_equivalent_vector ( utility::vector1< core::Size > const &  seq_num_list_1,
utility::vector1< core::Size > const &  seq_num_list_2 
)

References sort_seq_num_list().

bool protocols::swa::rna::Is_five_prime_phosphate_atom ( std::string const &  atom_name)
bool protocols::swa::rna::Is_H3star_atom ( std::string const &  atom_name)
bool protocols::swa::rna::Is_H4star_atom ( std::string const &  atom_name)
bool protocols::swa::rna::Is_medium_base_stack_and_medium_base_pair ( core::kinematics::Stub const &  moving_res_base,
utility::vector1< core::kinematics::Stub > const &  other_residues_base_list 
)

References Is_base_pair(), and Is_base_stack().

Referenced by Base_centroid_screening().

bool protocols::swa::rna::Is_medium_stack_base_and_medium_stack_base ( core::kinematics::Stub const &  moving_res_base,
utility::vector1< core::kinematics::Stub > const &  other_residues_base_list 
)
bool protocols::swa::rna::Is_O1P_atom ( std::string const &  atom_name)
bool protocols::swa::rna::Is_O2P_atom ( std::string const &  atom_name)
bool protocols::swa::rna::Is_O2star_atom ( std::string const &  atom_name)
bool protocols::swa::rna::Is_O3star_atom ( std::string const &  atom_name)
bool protocols::swa::rna::Is_O4star_atom ( std::string const &  atom_name)
bool protocols::swa::rna::Is_O5star_atom ( std::string const &  atom_name)
bool protocols::swa::rna::Is_P_atom ( std::string const &  atom_name)
bool protocols::swa::rna::Is_phosphate_atom ( std::string const &  atom_name)
bool protocols::swa::rna::Is_residues_in_contact ( core::Size const &  res_ONE,
core::pose::Pose const &  pose_ONE,
core::Size const &  res_TWO,
core::pose::Pose const &  pose_TWO,
core::Real const  atom_atom_overlap_dist_cutoff,
core::Size const  num_atom_contacts_cutoff,
bool const  verbose 
)
bool protocols::swa::rna::Is_ribose_virtual ( core::pose::Pose const &  pose,
core::Size const  ribose_res,
core::Size const  bulge_res 
)
bool protocols::swa::rna::Is_same_ribose_pucker ( core::pose::Pose const &  current_pose,
core::pose::Pose const &  cluster_center_pose,
Size const  seq_num 
)
bool protocols::swa::rna::Is_strong_base_stack ( core::kinematics::Stub const &  moving_res_base,
utility::vector1< core::kinematics::Stub > const &  other_residues_base_list 
)

References Is_base_stack().

Referenced by Base_centroid_screening().

bool protocols::swa::rna::Is_three_prime_phosphate_atom ( std::string const &  atom_name)

References Is_O3star_atom().

Referenced by Is_phosphate_atom().

bool protocols::swa::rna::Is_virtual_base ( conformation::Residue const &  rsd)
core::Size protocols::swa::rna::make_cut_at_moving_suite ( pose::Pose pose,
Size const &  moving_suite 
)
core::Size protocols::swa::rna::make_cut_at_moving_suite ( core::kinematics::FoldTree fold_tree,
Size const &  moving_suite 
)
void protocols::swa::rna::minimize_all_sampled_floating_bases ( core::pose::Pose viewer_pose,
utility::vector1< FloatingBaseChainClosureJobParameter > const &  FB_JP_list,
utility::vector1< pose_data_struct2 > &  pose_data_list,
core::scoring::ScoreFunctionOP const &  sampling_scorefxn,
StepWiseRNA_JobParametersCOP const &  job_parameters,
bool const  virtual_ribose_is_from_prior_step 
)
void protocols::swa::rna::minimize_with_constraints ( core::pose::Pose pose,
core::kinematics::MoveMap const &  mm,
core::scoring::ScoreFunctionOP const &  scorefxn,
core::optimization::MinimizerOptions const &  options 
)
bool protocols::swa::rna::minimizer_sort_criteria ( pose_data_struct2  pose_data_1,
pose_data_struct2  pose_data_2 
)
void protocols::swa::rna::move_jump_atom_to_base ( core::kinematics::FoldTree fold_tree,
std::string const &  working_sequence 
)
void protocols::swa::rna::o2star_minimize ( pose::Pose pose,
core::scoring::ScoreFunctionOP const &  packer_scorefxn,
utility::vector1< core::Size > const &  O2star_pack_seq_num 
)
void protocols::swa::rna::o2star_minimize ( pose::Pose pose,
core::scoring::ScoreFunctionOP const &  packer_scorefxn 
)
void protocols::swa::rna::Output_bool_list ( std::string const  tag,
utility::vector1< Size > const &  size_list,
core::Size const  spacing 
)
void protocols::swa::rna::Output_bool_list ( std::string const  tag,
utility::vector1< bool > const &  bool_list,
core::Size const  spacing 
)

References Output_boolean().

void protocols::swa::rna::Output_boolean ( std::string const &  tag,
bool  boolean 
)
void protocols::swa::rna::Output_boolean ( bool  boolean)
void protocols::swa::rna::Output_data ( core::io::silent::SilentFileData silent_file_data,
std::string const &  silent_file,
std::string const &  tag,
bool const  write_score_only,
pose::Pose const &  pose,
core::pose::PoseCOP  native_poseCOP,
StepWiseRNA_JobParametersCOP  job_parameters_ 
)
void protocols::swa::rna::Output_fold_tree_info ( pose::Pose const &  pose,
std::string  pose_name 
)
void protocols::swa::rna::Output_fold_tree_info ( kinematics::FoldTree const &  fold_tree,
std::string const  pose_name 
)
void protocols::swa::rna::output_is_prepend_map ( std::map< core::Size, bool > const &  my_map,
core::Size const  max_seq_num 
)
void protocols::swa::rna::Output_is_prepend_map ( std::string const  tag,
std::map< core::Size, bool > const &  my_map,
core::Size const  max_seq_num,
core::Size const  tag_spacing 
)
void protocols::swa::rna::Output_movemap ( kinematics::MoveMap const &  mm,
core::pose::Pose const &  pose 
)
void protocols::swa::rna::output_pair_size ( std::pair< core::Size, core::Size > const &  pair_size)
void protocols::swa::rna::output_pair_size ( std::pair< Size, Size > const &  pair_size)
void protocols::swa::rna::output_pair_size_vector ( utility::vector1< std::pair< core::Size, core::Size > > const &  pair_size_vector,
std::string const &  output_string,
core::Size const  spacing = 40 
)
void protocols::swa::rna::output_pair_size_vector ( utility::vector1< std::pair< Size, Size > > const &  pair_size_vector,
std::string const &  output_string,
core::Size const  spacing 
)
void protocols::swa::rna::output_res_map ( std::map< core::Size, core::Size > const &  my_map,
Size const  max_seq_num 
)
void protocols::swa::rna::Output_residue_list ( utility::vector1< Residue_info >  residue_list)
void protocols::swa::rna::Output_residue_struct ( Residue_info const &  residue)
void protocols::swa::rna::output_rotamer ( utility::vector1< Real > &  rotamer)
void protocols::swa::rna::Output_seq_num_list ( std::string const  tag,
utility::vector1< core::Size > const &  seq_num_list,
core::Size const  spacing 
)
void protocols::swa::rna::Output_size_list ( std::string const  tag,
utility::vector1< Size > const &  size_list,
core::Size const  spacing 
)
void protocols::swa::rna::Output_title_text ( std::string const  title)

Referenced by protocols::swa::rna::StepWiseRNA_JobParameters_Setup::apply(), protocols::swa::rna::StepWiseRNA_PoseSetup::apply(), protocols::swa::rna::StepWiseRNA_ResidueSampler::apply(), protocols::swa::rna::StepWiseRNA_Minimizer::apply(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::apply(), protocols::swa::rna::StepWiseRNA_Clusterer::cluster(), Correctly_position_cutpoint_phosphate_torsions(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::FARFAR_setup_using_user_input_VDW_pose(), protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::filter(), floating_base_chain_closure_post_process(), floating_base_chain_closure_sampling(), floating_base_chain_closure_setup(), full_length_rmsd_over_residue_list(), protocols::swa::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file(), protocols::swa::rna::StepWiseRNA_RotamerGenerator::initialize_rotamer_generator(), protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::initialize_rotamer_generator_list(), minimize_all_sampled_floating_bases(), protocols::swa::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file(), rmsd_over_residue_list(), sample_user_specified_virtual_riboses(), sample_virtual_ribose_and_bulge_and_close_chain(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_fixed_res(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::set_native_alignment_res(), protocols::swa::rna::SlicedPoseJobParameters::setup(), protocols::swa::rna::StepWiseRNA_PoseSetup::setup_native_pose(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::setup_using_user_input_VDW_pose(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::setup_using_working_pose(), and protocols::swa::rna::StepWiseRNA_JobParameters_Setup::StepWiseRNA_JobParameters_Setup().

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

Referenced by Sort_pair_list().

bool protocols::swa::rna::pair_sort_citeria ( std::pair< core::Size, core::Size pair_one,
std::pair< core::Size, core::Size pair_two 
)
std::string protocols::swa::rna::path_basename ( std::string const  full_path)
core::Real protocols::swa::rna::phosphate_base_phosphate_rmsd ( pose::Pose const &  pose1,
pose::Pose const &  pose2,
Size const &  moving_res_num,
bool const  ignore_virtual_atom 
)
void protocols::swa::rna::phosphate_base_phosphate_square_deviation ( pose::Pose const &  pose1,
pose::Pose const &  pose2,
Size const &  moving_res_1,
Size const &  moving_res_2,
Size atom_count,
Real sum_sd,
bool  verbose,
bool const  ignore_virtual_atom 
)
void protocols::swa::rna::phosphate_square_deviation ( pose::Pose const &  pose1,
pose::Pose const &  pose2,
Size const &  moving_res_1,
Size const &  moving_res_2,
Size atom_count,
Real sum_sd,
bool  verbose,
bool const  ignore_virtual_atom 
)
bool protocols::swa::rna::possible_root ( core::kinematics::FoldTree const &  f,
Size const &  n 
)
void protocols::swa::rna::print_atom_info ( pose::Pose const &  pose,
Size const  seq_num,
std::string const  pose_name 
)
void protocols::swa::rna::print_backbone_torsions ( pose::Pose const &  pose,
Size const  five_prime_chainbreak 
)
void protocols::swa::rna::print_base_state ( std::string const  tag,
BaseState const  base_state 
)
void protocols::swa::rna::Print_heavy_atoms ( Size const &  suite_num_1,
Size const &  suite_num_2,
pose::Pose const &  pose1,
pose::Pose const &  pose2 
)
void protocols::swa::rna::print_individual_atom_info ( core::conformation::Residue const &  rsd,
Size const  atomno,
std::string const  rsd_name 
)
void protocols::swa::rna::print_JobParameters_info ( StepWiseRNA_JobParametersCOP const &  const_JP,
std::string const  JP_name,
bool const  Is_simple_full_length_JP 
)
void protocols::swa::rna::print_ribose_pucker_state ( std::string const  tag,
PuckerState const  pucker_state 
)
void protocols::swa::rna::Print_torsion_info ( core::pose::Pose const &  pose,
core::Size const  seq_num,
core::Size const  rna_torsion_number,
std::string const  type 
)
void protocols::swa::rna::remove_all_variant_types ( pose::Pose pose)
void protocols::swa::rna::remove_chain_break_jump_point ( core::pose::Pose pose,
core::Size const  five_prime_cutpoint,
core::kinematics::FoldTree const  fold_tree_without_cutpoint 
)
void protocols::swa::rna::remove_file ( std::string const &  file_name)
bool protocols::swa::rna::Remove_virtual_O2Star_hydrogen ( pose::Pose pose)
void protocols::swa::rna::remove_virtual_rna_residue_variant_type ( pose::Pose pose,
Size const &  seq_num 
)
core::scoring::ScoreFunctionOP protocols::swa::rna::rescale_scorefxn ( core::scoring::ScoreFunctionOP const &  starting_scorefxn,
Real const  scaling_factor 
)

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

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

Referenced by floating_base_chain_closure_setup().

bool protocols::swa::rna::residue_list_sort_citeria ( Residue_info  residue_info_1,
Residue_info  residue_info_2 
)
core::Real protocols::swa::rna::rmsd_over_residue_list ( pose::Pose const &  pose1,
pose::Pose const &  pose2,
StepWiseRNA_JobParametersCOP  job_parameters_,
bool const  ignore_virtual_atom 
)
core::Real protocols::swa::rna::rmsd_over_residue_list ( pose::Pose const &  pose1,
pose::Pose const &  pose2,
utility::vector1< Size > const &  residue_list,
std::map< core::Size, core::Size > const &  full_to_sub,
std::map< core::Size, bool > const &  Is_prepend_map,
bool const  verbose,
bool const  ignore_virtual_atom 
)
void protocols::swa::rna::sample_user_specified_virtual_riboses ( pose::Pose pose,
utility::vector1< std::string > const &  sample_virtual_ribose_string_list,
StepWiseRNA_JobParametersCOP &  job_parameters,
core::scoring::ScoreFunctionOP const &  scorefxn,
std::string const  silent_file_out,
std::string const  input_tag 
)
utility::vector1< pose_data_struct2 > protocols::swa::rna::sample_virtual_ribose_and_bulge_and_close_chain ( pose::Pose viewer_pose,
FloatingBaseChainClosureJobParameter const &  FB_job_params,
std::string const  name,
core::scoring::ScoreFunctionOP const &  scorefxn,
core::scoring::ScoreFunctionOP const &  sampling_scorefxn,
core::scoring::ScoreFunctionOP const &  atr_rep_screening_scorefxn,
core::scoring::ScoreFunctionOP const &  chainbreak_scorefxn,
StepWiseRNA_JobParametersCOP &  job_parameters,
bool const  virtual_ribose_is_from_prior_step 
)
bool protocols::swa::rna::score_sort_citeria ( Combine_Tags_Info  tag_info_1,
Combine_Tags_Info  tag_info_2 
)
bool protocols::swa::rna::seq_num_list_sort_citeria ( core::Size  seq_num_1,
Residue_info  seq_num_2 
)
bool protocols::swa::rna::seq_num_sort_citeria ( core::Size  seq_num_1,
core::Size  seq_num_2 
)

Referenced by sort_seq_num_list().

void protocols::swa::rna::set_base_coordinate_frame ( pose::Pose pose,
Size const &  seq_num,
core::conformation::Residue const &  rsd_at_origin,
core::kinematics::Stub const &  moving_res_base_stub 
)
void protocols::swa::rna::set_CCD_torsions_to_zero ( core::pose::Pose pose,
Size const  five_prime_res 
)
utility::vector1< Residue_info > protocols::swa::rna::Set_Difference ( utility::vector1< Residue_info > const &  residue_list_1,
utility::vector1< Residue_info > const &  residue_list_2 
)
void protocols::swa::rna::set_nucleotide_to_A_form ( pose::Pose pose,
Size const  seq_num 
)
void protocols::swa::rna::set_to_origin ( pose::Pose pose,
Size const  seq_num,
bool  verbose 
)
utility::vector1< Residue_info > protocols::swa::rna::Set_Union ( utility::vector1< Residue_info > const &  residue_list_1,
utility::vector1< Residue_info > const &  residue_list_2 
)
core::Size protocols::swa::rna::setup_bulge_jump_point ( pose::Pose pose,
Size const &  moving_base,
Size const &  reference_base,
bool const  verbose 
)
core::Size protocols::swa::rna::setup_chain_break_jump_point ( core::pose::Pose pose,
core::Size const  jump_point_one,
core::Size const  jump_point_two,
core::Size const  five_prime_cutpoint,
bool const  verbose 
)
utility::vector1< FloatingBaseChainClosureJobParameter > protocols::swa::rna::setup_FB_CC_JP_list ( pose::Pose const &  pose,
utility::vector1< std::string > const &  sample_virtual_ribose_string_list,
StepWiseRNA_JobParametersCOP &  job_parameters 
)
utility::vector1< core::conformation::ResidueOP > protocols::swa::rna::setup_residue_at_origin_list ( pose::Pose const &  pose,
Size const &  moving_res,
bool const  extra_anti_chi_rotamer,
bool const  extra_syn_chi_rotamer,
std::string const  pose_name 
)
void protocols::swa::rna::setup_simple_fold_tree ( core::pose::Pose pose)
void protocols::swa::rna::setup_suite_atom_id_map ( conformation::Residue const &  rsd_1,
conformation::Residue const &  rsd_2,
id::AtomID_Map< id::AtomID > &  atom_ID_map,
bool const  base_only 
)
void protocols::swa::rna::setup_suite_atom_id_map ( 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(), and setup_suite_atom_id_map().

void protocols::swa::rna::setup_suite_atom_id_map ( conformation::Residue const &  rsd_1,
conformation::Residue const &  rsd_2,
Size const  res_num_1,
Size const  res_num_2,
id::AtomID_Map< id::AtomID > &  atom_ID_map,
bool const  base_only 
)
void protocols::swa::rna::setup_suite_atom_id_map ( pose::Pose const &  pose_1,
pose::Pose const &  pose_2,
Size const  base_res,
id::AtomID_Map< id::AtomID > &  atom_ID_map,
bool const  base_only 
)
void protocols::swa::rna::show_scorefxn_weight_lines ( core::scoring::ScoreFunctionOP const &  scorefxn,
std::string const  title 
)
void protocols::swa::rna::sleep ( core::Size  mseconds)
bool protocols::swa::rna::sort_criteria ( pose_data_struct2  pose_data_1,
pose_data_struct2  pose_data_2 
)
bool protocols::swa::rna::sort_criteria2 ( pose_data_struct2  pose_data_1,
pose_data_struct2  pose_data_2 
)
void protocols::swa::rna::Sort_pair_list ( utility::vector1< std::pair< core::Size, core::Size > >  pair_list)
void protocols::swa::rna::Sort_pair_list ( utility::vector1< std::pair< Size, Size > >  pair_list)
bool protocols::swa::rna::sort_pose_data_by_score ( pose_data_struct2  pose_data_1,
pose_data_struct2  pose_data_2 
)
void protocols::swa::rna::sort_residue_list ( utility::vector1< Residue_info > &  residue_list)
void protocols::swa::rna::sort_seq_num_list ( utility::vector1< core::Size > &  seq_num_list)
core::Size protocols::swa::rna::string_to_int ( std::string const  input_string)
core::Real protocols::swa::rna::string_to_real ( std::string const  input_string)
core::Real protocols::swa::rna::suite_rmsd ( pose::Pose const &  pose1,
pose::Pose const &  pose2,
Size const &  moving_res_num,
bool const  prepend_res,
bool const  ignore_virtual_atom 
)

References suite_square_deviation().

Referenced by Output_data().

void protocols::swa::rna::suite_square_deviation ( pose::Pose const &  pose1,
pose::Pose const &  pose2,
bool const &  prepend_res,
Size const &  moving_res_1,
Size const &  moving_res_2,
Size atom_count,
Real sum_sd,
bool  verbose,
bool const  ignore_virtual_atom 
)
utility::vector1< std::string > protocols::swa::rna::Tokenize ( std::string const  str,
std::string  delimiters 
)
void protocols::swa::rna::translate_then_rotate_pose ( core::pose::Pose pose,
numeric::xyzVector< core::Real > const &  vector,
numeric::xyzMatrix< core::Real > const  matrix,
bool const  verbose 
)
core::Size protocols::swa::rna::virtualize_energetically_unfavorable_nucleotides ( core::pose::Pose input_pose,
utility::vector1< core::Size > const &  allow_bulge_res_list,
core::scoring::ScoreFunctionOP const &  scorefxn,
std::string const &  tag,
bool const  allow_pre_virtualize,
bool const  allow_consecutive_bulges,
bool const  verbose 
)
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines