Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::farna::RNA_StructureParameters Class Reference

#include <RNA_StructureParameters.hh>

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 (core::Real const setting)
 
void set_bps_moves (Size const setting)
 
bool check_base_pairs (core::pose::Pose &pose) const
 
std::map< Size, Sizeconnections () const
 
std::list< Sizeget_stem_residues (core::pose::Pose const &pose) const
 
void setup_base_pair_constraints (core::pose::Pose &pose)
 
void setup_virtual_phosphate_variants (core::pose::Pose &pose)
 
utility::vector1< BasePairStepget_base_pair_steps () const
 
utility::vector1
< utility::vector1< core::Size > > 
get_obligate_pairing_sets ()
 
RNA_PairingList get_rna_pairing_list ()
 

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 save_res_lists_to_chain_connections_and_clear (utility::vector1< Size > &res_list1, utility::vector1< Size > &res_list2)
 
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 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
 
Size check_in_pairing_sets (utility::vector1< utility::vector1< core::Size > > pairing_sets, RNA_Pairing const &rna_pairing_check) 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 > > 
stem_pairing_sets_
 
utility::vector1< std::pair
< utility::vector1< core::Size >
, utility::vector1< core::Size > > > 
chain_connections_
 
utility::vector1< core::Sizecutpoints_open_
 
utility::vector1< core::Sizecutpoints_closed_
 
utility::vector1< core::Sizevirtual_anchor_attachment_points_
 
bool secstruct_defined_
 
std::string rna_secstruct_
 
bool assume_non_stem_is_loop
 
bool bps_moves_
 
bool allow_cuts_inside_base_pair_steps_
 
bool add_virtual_anchor_
 
bool root_at_first_rigid_body_
 
core::Real suppress_bp_constraint_
 
utility::vector1< core::Sizeallow_insert_res_
 
toolbox::AllowInsertOP allow_insert_
 

Constructor & Destructor Documentation

protocols::farna::RNA_StructureParameters::RNA_StructureParameters ( )
protocols::farna::RNA_StructureParameters::~RNA_StructureParameters ( )
virtual

Member Function Documentation

void protocols::farna::RNA_StructureParameters::add_new_RNA_jump ( core::pose::Pose pose,
core::Size const &  which_jump,
bool success 
) const
private
toolbox::AllowInsertOP protocols::farna::RNA_StructureParameters::allow_insert ( )
void protocols::farna::RNA_StructureParameters::append_virtual_anchor ( core::pose::Pose pose)
private
bool protocols::farna::RNA_StructureParameters::check_base_pairs ( core::pose::Pose pose) const
bool protocols::farna::RNA_StructureParameters::check_forward_backward ( core::pose::Pose pose,
core::Size const  jump_pos 
) const
private
Size protocols::farna::RNA_StructureParameters::check_in_chain_connections ( core::Size const &  pos1,
core::Size const &  pos2 
) const
private
Size protocols::farna::RNA_StructureParameters::check_in_pairing_sets ( utility::vector1< utility::vector1< core::Size > >  pairing_sets,
RNA_Pairing const &  rna_pairing_check 
) const
private
std::map< Size, Size > protocols::farna::RNA_StructureParameters::connections ( ) const
void protocols::farna::RNA_StructureParameters::fill_in_default_jump_atoms ( core::kinematics::FoldTree f,
core::pose::Pose const &  pose 
) const
private
utility::vector1< BasePairStep > protocols::farna::RNA_StructureParameters::get_base_pair_steps ( ) const
utility::vector1< utility::vector1 <core::Size > > protocols::farna::RNA_StructureParameters::get_obligate_pairing_sets ( )
inline
void protocols::farna::RNA_StructureParameters::get_pairings_from_line ( std::istringstream &  line_stream,
bool const  in_stem 
)
private
RNA_PairingList protocols::farna::RNA_StructureParameters::get_rna_pairing_list ( )
inline

References rna_pairing_list_.

std::list< Size > protocols::farna::RNA_StructureParameters::get_stem_residues ( core::pose::Pose const &  pose) const
void protocols::farna::RNA_StructureParameters::initialize ( core::pose::Pose pose,
std::string const  rna_params_file,
std::string const  jump_library_file,
bool const  ignore_secstruct 
)
void protocols::farna::RNA_StructureParameters::initialize_allow_insert ( core::pose::Pose pose)
private
void protocols::farna::RNA_StructureParameters::initialize_secstruct ( core::pose::Pose pose)
private
void protocols::farna::RNA_StructureParameters::insert_base_pair_jumps ( core::pose::Pose pose,
bool success 
) const
private
void protocols::farna::RNA_StructureParameters::override_secstruct ( core::pose::Pose pose)
private
bool protocols::farna::RNA_StructureParameters::random_jump_change ( core::pose::Pose pose) const
void protocols::farna::RNA_StructureParameters::read_chain_connection ( std::istringstream &  line_stream)
private
void protocols::farna::RNA_StructureParameters::read_parameters_from_file ( std::string const &  pairing_file)
private
std::string const protocols::farna::RNA_StructureParameters::read_secstruct_from_file ( std::string const &  rna_secstruct_file)
private
void protocols::farna::RNA_StructureParameters::sample_alternative_chain_connection ( core::pose::Pose pose,
core::Size const &  which_jump 
) const
private
void protocols::farna::RNA_StructureParameters::save_res_lists_to_chain_connections_and_clear ( utility::vector1< Size > &  res_list1,
utility::vector1< Size > &  res_list2 
)
private
void protocols::farna::RNA_StructureParameters::set_allow_insert ( toolbox::AllowInsertOP  allow_insert)

References allow_insert_.

void protocols::farna::RNA_StructureParameters::set_bps_moves ( Size const  setting)
inline
void protocols::farna::RNA_StructureParameters::set_jump_library ( RNA_JumpLibraryOP  rna_jump_library)
private

References rna_jump_library_.

void protocols::farna::RNA_StructureParameters::set_root_at_first_rigid_body ( bool const  setting)
inline
void protocols::farna::RNA_StructureParameters::set_suppress_bp_constraint ( core::Real const  setting)
inline
void protocols::farna::RNA_StructureParameters::setup_base_pair_constraints ( core::pose::Pose pose)
void protocols::farna::RNA_StructureParameters::setup_chainbreak_variants ( core::pose::Pose pose)
private
void protocols::farna::RNA_StructureParameters::setup_fold_tree_and_jumps_and_variants ( core::pose::Pose pose)
void protocols::farna::RNA_StructureParameters::setup_jumps ( core::pose::Pose pose)
private
void protocols::farna::RNA_StructureParameters::setup_virtual_phosphate_variants ( core::pose::Pose pose)

Member Data Documentation

bool protocols::farna::RNA_StructureParameters::add_virtual_anchor_
private
bool protocols::farna::RNA_StructureParameters::allow_cuts_inside_base_pair_steps_
private
toolbox::AllowInsertOP protocols::farna::RNA_StructureParameters::allow_insert_
private
utility::vector1< core::Size > protocols::farna::RNA_StructureParameters::allow_insert_res_
private
bool protocols::farna::RNA_StructureParameters::assume_non_stem_is_loop
private

Referenced by initialize_secstruct().

bool protocols::farna::RNA_StructureParameters::bps_moves_
private
utility::vector1< std::pair< utility::vector1 <core::Size >, utility::vector1 <core::Size > > > protocols::farna::RNA_StructureParameters::chain_connections_
private
utility::vector1<core::Size > protocols::farna::RNA_StructureParameters::cutpoints_closed_
private
utility::vector1<core::Size > protocols::farna::RNA_StructureParameters::cutpoints_open_
private
utility::vector1< utility::vector1 <core::Size > > protocols::farna::RNA_StructureParameters::obligate_pairing_sets_
private
RNA_JumpLibraryOP protocols::farna::RNA_StructureParameters::rna_jump_library_
private
RNA_PairingList protocols::farna::RNA_StructureParameters::rna_pairing_list_
private
std::string protocols::farna::RNA_StructureParameters::rna_secstruct_
private
bool protocols::farna::RNA_StructureParameters::root_at_first_rigid_body_
private
bool protocols::farna::RNA_StructureParameters::secstruct_defined_
private
utility::vector1< utility::vector1 <core::Size > > protocols::farna::RNA_StructureParameters::stem_pairing_sets_
private
core::Real protocols::farna::RNA_StructureParameters::suppress_bp_constraint_
private
utility::vector1<core::Size > protocols::farna::RNA_StructureParameters::virtual_anchor_attachment_points_
private

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