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protocols::rna::RNA_StructureParameters Class Reference

#include <RNA_StructureParameters.hh>

Inheritance diagram for protocols::rna::RNA_StructureParameters:
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Collaboration diagram for protocols::rna::RNA_StructureParameters:
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Public Member Functions

 RNA_StructureParameters ()
 
virtual ~RNA_StructureParameters ()
 
void initialize (core::pose::Pose &pose, std::string const rna_params_file, std::string const jump_library_file, bool const ignore_secstruct)
 
void setup_fold_tree_and_jumps_and_variants (core::pose::Pose &pose)
 
bool random_jump_change (core::pose::Pose &pose) const
 
toolbox::AllowInsertOP allow_insert ()
 
void set_allow_insert (toolbox::AllowInsertOP allow_insert)
 
void set_root_at_first_rigid_body (bool const setting)
 
void set_suppress_bp_constraint (bool const setting)
 
bool check_base_pairs (core::pose::Pose &pose) const
 
std::map< Size, Size > connections () const
 
std::list< Size > get_stem_residues (core::pose::Pose const &pose) const
 
void setup_base_pair_constraints (core::pose::Pose &pose)
 

Private Member Functions

void initialize_secstruct (core::pose::Pose &pose)
 
void override_secstruct (core::pose::Pose &pose)
 
void append_virtual_anchor (core::pose::Pose &pose)
 
void initialize_allow_insert (core::pose::Pose &pose)
 
void get_pairings_from_line (std::istringstream &line_stream, bool const in_stem)
 
void read_chain_connection (std::istringstream &line_stream)
 
void read_parameters_from_file (std::string const &pairing_file)
 
void setup_jumps (core::pose::Pose &pose)
 
void setup_chainbreak_variants (core::pose::Pose &pose)
 
void setup_virtual_phosphate_variants (core::pose::Pose &pose)
 
void setup_virtual_phosphate_variants_OLD (core::pose::Pose &pose)
 
void set_jump_library (RNA_JumpLibraryOP rna_jump_library)
 
std::string const read_secstruct_from_file (std::string const &rna_secstruct_file)
 
core::Size check_in_chain_connections (core::Size const &pos1, core::Size const &pos2) const
 
bool check_forward_backward (core::pose::Pose &pose, core::Size const jump_pos) const
 
void add_new_RNA_jump (core::pose::Pose &pose, core::Size const &which_jump, bool &success) const
 
void sample_alternative_chain_connection (core::pose::Pose &pose, core::Size const &which_jump) const
 
void insert_base_pair_jumps (core::pose::Pose &pose, bool &success) const
 
void fill_in_default_jump_atoms (core::kinematics::FoldTree &f, core::pose::Pose const &pose) const
 

Private Attributes

RNA_JumpLibraryOP rna_jump_library_
 
RNA_PairingList rna_pairing_list_
 
utility::vector1
< utility::vector1< core::Size > > 		obligate_pairing_sets_
 
utility::vector1
< utility::vector1< core::Size > > 		possible_pairing_sets_
 
utility::vector1< std::pair
< utility::vector1< core::Size >
, utility::vector1< core::Size > > > 		chain_connections_
 
utility::vector1< core::Size > cutpoints_open_
 
utility::vector1< core::Size > cutpoints_closed_
 
utility::vector1< core::Size > virtual_anchor_attachment_points_
 
bool secstruct_defined_
 
std::string rna_secstruct_
 
bool assume_non_stem_is_loop
 
bool add_virtual_anchor_
 
bool root_at_first_rigid_body_
 
bool suppress_bp_constraint_
 
utility::vector1< core::Size > allow_insert_res_
 
toolbox::AllowInsertOP allow_insert_
 

Detailed Description

Definition at line 53 of file RNA_StructureParameters.hh.

Constructor & Destructor Documentation

protocols::rna::RNA_StructureParameters::RNA_StructureParameters ( )

Definition at line 83 of file RNA_StructureParameters.cc.

protocols::rna::RNA_StructureParameters::~RNA_StructureParameters ( )
virtual

Definition at line 90 of file RNA_StructureParameters.cc.

Member Function Documentation

void protocols::rna::RNA_StructureParameters::add_new_RNA_jump ( core::pose::Pose &  pose,
core::Size const &  which_jump,
bool &  success 
) const
private

Definition at line 538 of file RNA_StructureParameters.cc.

References check_forward_backward(), check_in_chain_connections(), protocols::rna::RNA_Pairing::edge1, protocols::rna::RNA_Pairing::edge2, core::pose::Pose::fold_tree(), core::conformation::Residue::is_RNA(), core::conformation::Residue::name1(), protocols::rna::RNA_Pairing::orientation, protocols::rna::RNA_Pairing::pos1, protocols::rna::RNA_Pairing::pos2, core::pose::Pose::residue(), rna_jump_library_, rna_pairing_list_, and core::pose::Pose::set_jump().

Referenced by insert_base_pair_jumps(), and random_jump_change().

toolbox::AllowInsertOP protocols::rna::RNA_StructureParameters::allow_insert ( )

Definition at line 1200 of file RNA_StructureParameters.cc.

References allow_insert_.

void protocols::rna::RNA_StructureParameters::append_virtual_anchor ( core::pose::Pose &  pose)
private

Definition at line 129 of file RNA_StructureParameters.cc.

References allow_insert_, core::pose::Pose::annotated_sequence(), core::pose::Pose::append_residue_by_jump(), core::conformation::ResidueFactory::create_residue(), cutpoints_open_, protocols::rna::RNA_Pairing::edge1, protocols::rna::RNA_Pairing::edge2, core::chemical::ResidueTypeSet::name3_map(), obligate_pairing_sets_, protocols::rna::RNA_Pairing::orientation, protocols::rna::RNA_Pairing::pos1, protocols::rna::RNA_Pairing::pos2, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::chemical::ResidueType::residue_type_set(), rna_pairing_list_, core::pose::Pose::total_residue(), and virtual_anchor_attachment_points_.

Referenced by initialize().

bool protocols::rna::RNA_StructureParameters::check_base_pairs ( core::pose::Pose &  pose) const

Definition at line 1095 of file RNA_StructureParameters.cc.

References allow_insert_, protocols::rna::RNA_Pairing::edge1, protocols::rna::RNA_Pairing::edge2, core::scoring::rna::is_cutpoint_open(), core::conformation::named_atom_id_to_atom_id(), protocols::rna::RNA_Pairing::orientation, protocols::rna::RNA_Pairing::pos1, protocols::rna::RNA_Pairing::pos2, rna_pairing_list_, and protocols::rna::tr().

bool protocols::rna::RNA_StructureParameters::check_forward_backward ( core::pose::Pose &  pose,
core::Size const  jump_pos 
) const
private

Definition at line 517 of file RNA_StructureParameters.cc.

References core::kinematics::AtomTree::atom(), core::conformation::Residue::atom_index(), core::pose::Pose::atom_tree(), core::conformation::Residue::is_coarse(), core::conformation::Residue::is_RNA(), and core::pose::Pose::residue().

Referenced by add_new_RNA_jump().

Size protocols::rna::RNA_StructureParameters::check_in_chain_connections ( core::Size const &  pos1,
core::Size const &  pos2 
) const
private

Definition at line 499 of file RNA_StructureParameters.cc.

References chain_connections_, and protocols::rna::in_list().

Referenced by add_new_RNA_jump(), and sample_alternative_chain_connection().

std::map< Size, Size > protocols::rna::RNA_StructureParameters::connections ( ) const

Definition at line 1179 of file RNA_StructureParameters.cc.

References protocols::rna::RNA_Pairing::pos1, protocols::rna::RNA_Pairing::pos2, and rna_pairing_list_.

void protocols::rna::RNA_StructureParameters::fill_in_default_jump_atoms ( core::kinematics::FoldTree &  f,
core::pose::Pose const &  pose 
) const
private

Definition at line 915 of file RNA_StructureParameters.cc.

References core::scoring::rna::default_jump_atom(), core::kinematics::FoldTree::downstream_jump_residue(), core::kinematics::FoldTree::num_jump(), core::pose::Pose::residue(), core::kinematics::FoldTree::set_jump_atoms(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by sample_alternative_chain_connection(), and setup_jumps().

void protocols::rna::RNA_StructureParameters::get_pairings_from_line ( std::istringstream &  line_stream,
bool const  in_stem 
)
private

Definition at line 272 of file RNA_StructureParameters.cc.

References protocols::match::upstream::b, protocols::rna::RNA_Pairing::edge1, protocols::rna::RNA_Pairing::edge2, obligate_pairing_sets_, protocols::rna::RNA_Pairing::orientation, protocols::rna::RNA_Pairing::pos1, protocols::rna::RNA_Pairing::pos2, possible_pairing_sets_, and rna_pairing_list_.

Referenced by read_parameters_from_file().

std::list< Size > protocols::rna::RNA_StructureParameters::get_stem_residues ( core::pose::Pose const &  pose) const

Definition at line 209 of file RNA_StructureParameters.cc.

References core::conformation::Residue::aa(), protocols::rna::RNA_Pairing::edge1, protocols::rna::RNA_Pairing::edge2, protocols::rna::RNA_Pairing::orientation, protocols::rna::RNA_Pairing::pos1, protocols::rna::RNA_Pairing::pos2, core::scoring::rna::possibly_canonical(), core::pose::Pose::residue(), and rna_pairing_list_.

void protocols::rna::RNA_StructureParameters::initialize ( core::pose::Pose &  pose,
std::string const  rna_params_file,
std::string const  jump_library_file,
bool const  ignore_secstruct 
)

Definition at line 94 of file RNA_StructureParameters.cc.

References append_virtual_anchor(), chain_connections_, initialize_allow_insert(), initialize_secstruct(), override_secstruct(), read_parameters_from_file(), rna_jump_library_, rna_pairing_list_, setup_virtual_phosphate_variants(), and virtual_anchor_attachment_points_.

void protocols::rna::RNA_StructureParameters::initialize_allow_insert ( core::pose::Pose &  pose)
private

Definition at line 233 of file RNA_StructureParameters.cc.

References allow_insert_, allow_insert_res_, and core::pose::Pose::total_residue().

Referenced by initialize().

void protocols::rna::RNA_StructureParameters::initialize_secstruct ( core::pose::Pose &  pose)
private

Definition at line 178 of file RNA_StructureParameters.cc.

References core::conformation::Residue::aa(), assume_non_stem_is_loop, protocols::rna::RNA_Pairing::edge1, protocols::rna::RNA_Pairing::edge2, protocols::rna::RNA_Pairing::orientation, protocols::rna::RNA_Pairing::pos1, protocols::rna::RNA_Pairing::pos2, core::scoring::rna::possibly_canonical(), core::pose::Pose::residue(), rna_pairing_list_, rna_secstruct_, secstruct_defined_, protocols::rna::set_rna_secstruct(), and core::pose::Pose::total_residue().

Referenced by initialize().

void protocols::rna::RNA_StructureParameters::insert_base_pair_jumps ( core::pose::Pose &  pose,
bool &  success 
) const
private

Definition at line 683 of file RNA_StructureParameters.cc.

References add_new_RNA_jump(), allow_insert_, core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::pose::Pose::num_jump(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by setup_jumps().

void protocols::rna::RNA_StructureParameters::override_secstruct ( core::pose::Pose &  pose)
private

Definition at line 122 of file RNA_StructureParameters.cc.

References rna_secstruct_, protocols::rna::set_rna_secstruct(), and core::pose::Pose::total_residue().

Referenced by initialize().

bool protocols::rna::RNA_StructureParameters::random_jump_change ( core::pose::Pose &  pose) const

Definition at line 1041 of file RNA_StructureParameters.cc.

References add_new_RNA_jump(), allow_insert_, core::scoring::rna::default_jump_atom(), core::pose::Pose::fold_tree(), core::pose::Pose::num_jump(), core::pose::Pose::residue(), protocols::rna::RG(), sample_alternative_chain_connection(), and core::kinematics::FoldTree::upstream_jump_residue().

void protocols::rna::RNA_StructureParameters::read_chain_connection ( std::istringstream &  line_stream)
private

Definition at line 337 of file RNA_StructureParameters.cc.

References chain_connections_.

Referenced by read_parameters_from_file().

void protocols::rna::RNA_StructureParameters::read_parameters_from_file ( std::string const &  pairing_file)
private

Definition at line 388 of file RNA_StructureParameters.cc.

References allow_insert_res_, cutpoints_closed_, cutpoints_open_, get_pairings_from_line(), read_chain_connection(), rna_secstruct_, secstruct_defined_, protocols::rna::tr(), and virtual_anchor_attachment_points_.

Referenced by initialize().

std::string const protocols::rna::RNA_StructureParameters::read_secstruct_from_file ( std::string const &  rna_secstruct_file)
private
void protocols::rna::RNA_StructureParameters::sample_alternative_chain_connection ( core::pose::Pose &  pose,
core::Size const &  which_jump 
) const
private

Definition at line 621 of file RNA_StructureParameters.cc.

References chain_connections_, check_in_chain_connections(), fill_in_default_jump_atoms(), core::pose::Pose::fold_tree(), protocols::rna::RG(), and core::pose::Pose::total_residue().

Referenced by random_jump_change().

void protocols::rna::RNA_StructureParameters::set_allow_insert ( toolbox::AllowInsertOP  allow_insert)

Definition at line 1193 of file RNA_StructureParameters.cc.

References allow_insert_.

void protocols::rna::RNA_StructureParameters::set_jump_library ( RNA_JumpLibraryOP  rna_jump_library)
private

Definition at line 1204 of file RNA_StructureParameters.cc.

References rna_jump_library_.

void protocols::rna::RNA_StructureParameters::set_root_at_first_rigid_body ( bool const  setting)
inline

Definition at line 79 of file RNA_StructureParameters.hh.

References root_at_first_rigid_body_.

void protocols::rna::RNA_StructureParameters::set_suppress_bp_constraint ( bool const  setting)
inline

Definition at line 82 of file RNA_StructureParameters.hh.

References suppress_bp_constraint_.

void protocols::rna::RNA_StructureParameters::setup_base_pair_constraints ( core::pose::Pose &  pose)

Definition at line 1143 of file RNA_StructureParameters.cc.

References allow_insert_, protocols::rna::RNA_Pairing::edge1, protocols::rna::RNA_Pairing::edge2, core::conformation::Residue::is_RNA(), core::conformation::named_atom_id_to_atom_id(), protocols::rna::RNA_Pairing::orientation, protocols::rna::RNA_Pairing::pos1, protocols::rna::RNA_Pairing::pos2, core::pose::Pose::residue(), rna_pairing_list_, protocols::rna::setup_base_pair_constraints(), suppress_bp_constraint_, and protocols::rna::tr().

void protocols::rna::RNA_StructureParameters::setup_chainbreak_variants ( core::pose::Pose &  pose)
private

Definition at line 931 of file RNA_StructureParameters.cc.

References core::pose::add_variant_type_to_pose_residue(), allow_insert_, core::id::BB, protocols::swa::rna::Correctly_position_cutpoint_phosphate_torsions(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, cutpoints_open_, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::mainchain_torsions(), core::pose::Pose::residue(), core::pose::Pose::set_torsion(), core::pose::Pose::torsion(), and core::pose::Pose::total_residue().

Referenced by setup_fold_tree_and_jumps_and_variants().

void protocols::rna::RNA_StructureParameters::setup_fold_tree_and_jumps_and_variants ( core::pose::Pose &  pose)

Definition at line 709 of file RNA_StructureParameters.cc.

References core::pose::Pose::annotated_sequence(), core::pose::Pose::fold_tree(), setup_chainbreak_variants(), setup_jumps(), and protocols::rna::tr().

void protocols::rna::RNA_StructureParameters::setup_jumps ( core::pose::Pose &  pose)
private

Definition at line 724 of file RNA_StructureParameters.cc.

References allow_insert_, chain_connections_, cutpoints_closed_, cutpoints_open_, fill_in_default_jump_atoms(), core::pose::Pose::fold_tree(), protocols::rna::get_rigid_body_jumps(), protocols::rna::get_rna_secstruct(), insert_base_pair_jumps(), core::conformation::Residue::is_RNA(), core::conformation::named_atom_id_to_atom_id(), obligate_pairing_sets_, possible_pairing_sets_, protocols::rna::possible_root(), core::kinematics::FoldTree::random_tree_from_jump_points(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), protocols::rna::RG(), rna_pairing_list_, root_at_first_rigid_body_, core::pose::Pose::total_residue(), core::kinematics::FoldTree::upstream_jump_residue(), and virtual_anchor_attachment_points_.

Referenced by setup_fold_tree_and_jumps_and_variants().

void protocols::rna::RNA_StructureParameters::setup_virtual_phosphate_variants ( core::pose::Pose &  pose)
private

Definition at line 1003 of file RNA_StructureParameters.cc.

References core::pose::add_variant_type_to_pose_residue(), allow_insert_, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, cutpoints_open_, core::chemical::ResidueType::has_variant_type(), core::chemical::ResidueType::is_RNA(), core::conformation::Residue::is_RNA(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and core::chemical::VIRTUAL_PHOSPHATE.

Referenced by initialize().

void protocols::rna::RNA_StructureParameters::setup_virtual_phosphate_variants_OLD ( core::pose::Pose &  pose)
private

Definition at line 972 of file RNA_StructureParameters.cc.

References core::pose::add_variant_type_to_pose_residue(), allow_insert_, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::chemical::ResidueType::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::chemical::ResidueType::is_RNA(), core::conformation::Residue::is_RNA(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and core::chemical::VIRTUAL_PHOSPHATE.

Member Data Documentation

bool protocols::rna::RNA_StructureParameters::add_virtual_anchor_
private

Definition at line 182 of file RNA_StructureParameters.hh.

toolbox::AllowInsertOP protocols::rna::RNA_StructureParameters::allow_insert_
private

Definition at line 187 of file RNA_StructureParameters.hh.

Referenced by allow_insert(), append_virtual_anchor(), check_base_pairs(), initialize_allow_insert(), insert_base_pair_jumps(), random_jump_change(), set_allow_insert(), setup_base_pair_constraints(), setup_chainbreak_variants(), setup_jumps(), setup_virtual_phosphate_variants(), and setup_virtual_phosphate_variants_OLD().

utility::vector1< core::Size > protocols::rna::RNA_StructureParameters::allow_insert_res_
private

Definition at line 186 of file RNA_StructureParameters.hh.

Referenced by initialize_allow_insert(), and read_parameters_from_file().

bool protocols::rna::RNA_StructureParameters::assume_non_stem_is_loop
private

Definition at line 180 of file RNA_StructureParameters.hh.

Referenced by initialize_secstruct().

utility::vector1< std::pair< utility::vector1 <core::Size >, utility::vector1 <core::Size > > > protocols::rna::RNA_StructureParameters::chain_connections_
private

Definition at line 170 of file RNA_StructureParameters.hh.

Referenced by check_in_chain_connections(), initialize(), read_chain_connection(), sample_alternative_chain_connection(), and setup_jumps().

utility::vector1<core::Size > protocols::rna::RNA_StructureParameters::cutpoints_closed_
private

Definition at line 175 of file RNA_StructureParameters.hh.

Referenced by read_parameters_from_file(), and setup_jumps().

utility::vector1<core::Size > protocols::rna::RNA_StructureParameters::cutpoints_open_
private

Definition at line 174 of file RNA_StructureParameters.hh.

Referenced by append_virtual_anchor(), read_parameters_from_file(), setup_chainbreak_variants(), setup_jumps(), and setup_virtual_phosphate_variants().

utility::vector1< utility::vector1 <core::Size > > protocols::rna::RNA_StructureParameters::obligate_pairing_sets_
private

Definition at line 167 of file RNA_StructureParameters.hh.

Referenced by append_virtual_anchor(), get_pairings_from_line(), and setup_jumps().

utility::vector1< utility::vector1 <core::Size > > protocols::rna::RNA_StructureParameters::possible_pairing_sets_
private

Definition at line 168 of file RNA_StructureParameters.hh.

Referenced by get_pairings_from_line(), and setup_jumps().

RNA_JumpLibraryOP protocols::rna::RNA_StructureParameters::rna_jump_library_
private

Definition at line 164 of file RNA_StructureParameters.hh.

Referenced by add_new_RNA_jump(), initialize(), and set_jump_library().

RNA_PairingList protocols::rna::RNA_StructureParameters::rna_pairing_list_
private

Definition at line 165 of file RNA_StructureParameters.hh.

Referenced by add_new_RNA_jump(), append_virtual_anchor(), check_base_pairs(), connections(), get_pairings_from_line(), get_stem_residues(), initialize(), initialize_secstruct(), setup_base_pair_constraints(), and setup_jumps().

std::string protocols::rna::RNA_StructureParameters::rna_secstruct_
private

Definition at line 179 of file RNA_StructureParameters.hh.

Referenced by initialize_secstruct(), override_secstruct(), and read_parameters_from_file().

bool protocols::rna::RNA_StructureParameters::root_at_first_rigid_body_
private

Definition at line 183 of file RNA_StructureParameters.hh.

Referenced by set_root_at_first_rigid_body(), and setup_jumps().

bool protocols::rna::RNA_StructureParameters::secstruct_defined_
private

Definition at line 178 of file RNA_StructureParameters.hh.

Referenced by initialize_secstruct(), and read_parameters_from_file().

bool protocols::rna::RNA_StructureParameters::suppress_bp_constraint_
private

Definition at line 184 of file RNA_StructureParameters.hh.

Referenced by set_suppress_bp_constraint(), and setup_base_pair_constraints().

utility::vector1<core::Size > protocols::rna::RNA_StructureParameters::virtual_anchor_attachment_points_
private

Definition at line 176 of file RNA_StructureParameters.hh.

Referenced by append_virtual_anchor(), initialize(), read_parameters_from_file(), and setup_jumps().

The documentation for this class was generated from the following files:
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