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Public Member Functions | Private Member Functions | Private Attributes | List of all members
core::import_pose::RNA_DeNovoParameters Class Reference

#include <RNA_DeNovoParameters.hh>

Inheritance diagram for core::import_pose::RNA_DeNovoParameters:
Inheritance graph
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Public Member Functions

 RNA_DeNovoParameters (std::string const &filename)
 
 RNA_DeNovoParameters ()
 
 ~RNA_DeNovoParameters () override
 
void set_rna_pairing_list (core::pose::rna::RNA_BasePairList const &setting)
 
core::pose::rna::RNA_BasePairList const & rna_pairing_list () const
 
void set_stem_pairing_sets (utility::vector1< utility::vector1< core::Size > > const &setting)
 
utility::vector1< utility::vector1< core::Size > > const & stem_pairing_sets () const
 
void set_obligate_pairing_sets (utility::vector1< utility::vector1< core::Size > > const &setting)
 
utility::vector1< utility::vector1< core::Size > > const & obligate_pairing_sets () const
 
void set_cutpoints_open (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Sizecutpoints_open () const
 
void set_cutpoints_closed (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Sizecutpoints_closed () const
 
void set_fiveprime_cap (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Sizefiveprime_cap () const
 
void set_cutpoints_cyclize (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Sizecutpoints_cyclize () const
 
void set_twoprime (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Sizetwoprime () const
 
void set_block_stack_above_res (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Sizeblock_stack_above_res () const
 
void set_block_stack_below_res (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Sizeblock_stack_below_res () const
 
void set_virtual_anchor_attachment_points (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Sizevirtual_anchor_attachment_points () const
 
void set_allow_insert_res (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Sizeallow_insert_res () const
 
void set_chain_connections (utility::vector1< std::pair< utility::vector1< core::Size >, utility::vector1< core::Size > > > const &setting)
 
utility::vector1< std::pair< utility::vector1< core::Size >, utility::vector1< core::Size > > > const & chain_connections () const
 
void set_rna_secstruct_legacy (std::string const &setting)
 
std::string rna_secstruct_legacy () const
 
void set_rna_and_protein (bool const &setting)
 
bool is_rna_and_protein () const
 
void add_cutpoint_open (Size const n)
 
void add_rna_pairing (core::pose::rna::BasePair const &rna_pairing)
 
void add_obligate_pairing_set (utility::vector1< core::Size > const &set)
 
bool const & secstruct_defined () const
 
Size check_in_pairing_sets (utility::vector1< utility::vector1< core::Size > > pairing_sets, core::pose::rna::BasePair const &rna_pairing_check) const
 
void set_use_fold_tree_from_silent_file (bool const &setting)
 
bool use_fold_tree_from_silent_file () const
 
void set_fold_tree_from_silent_file (core::kinematics::FoldTree const &fold_tree)
 
core::kinematics::FoldTree fold_tree_from_silent_file () const
 

Private Member Functions

void read_parameters_from_file (std::string const &filename)
 
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 get_pairings_from_line (std::istringstream &line_stream, bool const in_stem)
 

Private Attributes

std::string const filename_
 
core::pose::rna::RNA_BasePairList 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::Sizecutpoints_cyclize_
 
utility::vector1< core::Sizetwoprime_
 
utility::vector1< core::Sizeblock_stack_above_res_
 
utility::vector1< core::Sizeblock_stack_below_res_
 
utility::vector1< core::Sizevirtual_anchor_attachment_points_
 
utility::vector1< core::Sizefiveprime_cap_
 
utility::vector1< core::Sizeallow_insert_res_
 
std::string rna_secstruct_legacy_
 
bool secstruct_defined_
 
bool is_rna_and_protein_
 
bool use_fold_tree_from_silent_file_
 
core::kinematics::FoldTree fold_tree_from_silent_file_
 

Constructor & Destructor Documentation

◆ RNA_DeNovoParameters() [1/2]

core::import_pose::RNA_DeNovoParameters::RNA_DeNovoParameters ( std::string const &  filename)

◆ RNA_DeNovoParameters() [2/2]

core::import_pose::RNA_DeNovoParameters::RNA_DeNovoParameters ( )

◆ ~RNA_DeNovoParameters()

core::import_pose::RNA_DeNovoParameters::~RNA_DeNovoParameters ( )
overridedefault

Member Function Documentation

◆ add_cutpoint_open()

void core::import_pose::RNA_DeNovoParameters::add_cutpoint_open ( Size const  n)
inline

◆ add_obligate_pairing_set()

void core::import_pose::RNA_DeNovoParameters::add_obligate_pairing_set ( utility::vector1< core::Size > const &  set)
inline

◆ add_rna_pairing()

void core::import_pose::RNA_DeNovoParameters::add_rna_pairing ( core::pose::rna::BasePair const &  rna_pairing)
inline

◆ allow_insert_res()

utility::vector1<core::Size > core::import_pose::RNA_DeNovoParameters::allow_insert_res ( ) const
inline

References allow_insert_res_.

◆ block_stack_above_res()

utility::vector1<core::Size > core::import_pose::RNA_DeNovoParameters::block_stack_above_res ( ) const
inline

◆ block_stack_below_res()

utility::vector1<core::Size > core::import_pose::RNA_DeNovoParameters::block_stack_below_res ( ) const
inline

◆ chain_connections()

utility::vector1< std::pair< utility::vector1 <core::Size >, utility::vector1 <core::Size > > > const& core::import_pose::RNA_DeNovoParameters::chain_connections ( ) const
inline

◆ check_in_pairing_sets()

Size core::import_pose::RNA_DeNovoParameters::check_in_pairing_sets ( utility::vector1< utility::vector1< core::Size > >  pairing_sets,
core::pose::rna::BasePair const &  rna_pairing_check 
) const

◆ cutpoints_closed()

utility::vector1<core::Size > core::import_pose::RNA_DeNovoParameters::cutpoints_closed ( ) const
inline

◆ cutpoints_cyclize()

utility::vector1<core::Size > core::import_pose::RNA_DeNovoParameters::cutpoints_cyclize ( ) const
inline

◆ cutpoints_open()

utility::vector1<core::Size > core::import_pose::RNA_DeNovoParameters::cutpoints_open ( ) const
inline

◆ fiveprime_cap()

utility::vector1< core::Size > core::import_pose::RNA_DeNovoParameters::fiveprime_cap ( ) const
inline

◆ fold_tree_from_silent_file()

core::kinematics::FoldTree core::import_pose::RNA_DeNovoParameters::fold_tree_from_silent_file ( ) const
inline

◆ get_pairings_from_line()

void core::import_pose::RNA_DeNovoParameters::get_pairings_from_line ( std::istringstream &  line_stream,
bool const  in_stem 
)
private

◆ is_rna_and_protein()

bool core::import_pose::RNA_DeNovoParameters::is_rna_and_protein ( ) const
inline

References is_rna_and_protein_.

◆ obligate_pairing_sets()

utility::vector1< utility::vector1 <core::Size > > const& core::import_pose::RNA_DeNovoParameters::obligate_pairing_sets ( ) const
inline

◆ read_chain_connection()

void core::import_pose::RNA_DeNovoParameters::read_chain_connection ( std::istringstream &  line_stream)
private

◆ read_parameters_from_file()

void core::import_pose::RNA_DeNovoParameters::read_parameters_from_file ( std::string const &  filename)
private

◆ rna_pairing_list()

core::pose::rna::RNA_BasePairList const& core::import_pose::RNA_DeNovoParameters::rna_pairing_list ( ) const
inline

◆ rna_secstruct_legacy()

std::string core::import_pose::RNA_DeNovoParameters::rna_secstruct_legacy ( ) const
inline

◆ save_res_lists_to_chain_connections_and_clear()

void core::import_pose::RNA_DeNovoParameters::save_res_lists_to_chain_connections_and_clear ( utility::vector1< Size > &  res_list1,
utility::vector1< Size > &  res_list2 
)
private

References chain_connections_.

Referenced by read_chain_connection().

◆ secstruct_defined()

bool const& core::import_pose::RNA_DeNovoParameters::secstruct_defined ( ) const
inline

◆ set_allow_insert_res()

void core::import_pose::RNA_DeNovoParameters::set_allow_insert_res ( utility::vector1< core::Size > const &  setting)
inline

References allow_insert_res_.

◆ set_block_stack_above_res()

void core::import_pose::RNA_DeNovoParameters::set_block_stack_above_res ( utility::vector1< core::Size > const &  setting)
inline

◆ set_block_stack_below_res()

void core::import_pose::RNA_DeNovoParameters::set_block_stack_below_res ( utility::vector1< core::Size > const &  setting)
inline

◆ set_chain_connections()

void core::import_pose::RNA_DeNovoParameters::set_chain_connections ( utility::vector1< std::pair< utility::vector1< core::Size >, utility::vector1< core::Size > > > const &  setting)
inline

References chain_connections_.

◆ set_cutpoints_closed()

void core::import_pose::RNA_DeNovoParameters::set_cutpoints_closed ( utility::vector1< core::Size > const &  setting)
inline

References cutpoints_closed_.

◆ set_cutpoints_cyclize()

void core::import_pose::RNA_DeNovoParameters::set_cutpoints_cyclize ( utility::vector1< core::Size > const &  setting)
inline

References cutpoints_cyclize_.

◆ set_cutpoints_open()

void core::import_pose::RNA_DeNovoParameters::set_cutpoints_open ( utility::vector1< core::Size > const &  setting)
inline

References cutpoints_open_.

◆ set_fiveprime_cap()

void core::import_pose::RNA_DeNovoParameters::set_fiveprime_cap ( utility::vector1< core::Size > const &  setting)
inline

References fiveprime_cap_.

◆ set_fold_tree_from_silent_file()

void core::import_pose::RNA_DeNovoParameters::set_fold_tree_from_silent_file ( core::kinematics::FoldTree const &  fold_tree)
inline

◆ set_obligate_pairing_sets()

void core::import_pose::RNA_DeNovoParameters::set_obligate_pairing_sets ( utility::vector1< utility::vector1< core::Size > > const &  setting)
inline

◆ set_rna_and_protein()

void core::import_pose::RNA_DeNovoParameters::set_rna_and_protein ( bool const &  setting)
inline

References is_rna_and_protein_.

◆ set_rna_pairing_list()

void core::import_pose::RNA_DeNovoParameters::set_rna_pairing_list ( core::pose::rna::RNA_BasePairList const &  setting)
inline

References rna_pairing_list_.

◆ set_rna_secstruct_legacy()

void core::import_pose::RNA_DeNovoParameters::set_rna_secstruct_legacy ( std::string const &  setting)
inline

◆ set_stem_pairing_sets()

void core::import_pose::RNA_DeNovoParameters::set_stem_pairing_sets ( utility::vector1< utility::vector1< core::Size > > const &  setting)
inline

References stem_pairing_sets_.

◆ set_twoprime()

void core::import_pose::RNA_DeNovoParameters::set_twoprime ( utility::vector1< core::Size > const &  setting)
inline

References twoprime_.

◆ set_use_fold_tree_from_silent_file()

void core::import_pose::RNA_DeNovoParameters::set_use_fold_tree_from_silent_file ( bool const &  setting)
inline

◆ set_virtual_anchor_attachment_points()

void core::import_pose::RNA_DeNovoParameters::set_virtual_anchor_attachment_points ( utility::vector1< core::Size > const &  setting)
inline

◆ stem_pairing_sets()

utility::vector1< utility::vector1 <core::Size > > const& core::import_pose::RNA_DeNovoParameters::stem_pairing_sets ( ) const
inline

◆ twoprime()

utility::vector1<core::Size > core::import_pose::RNA_DeNovoParameters::twoprime ( ) const
inline

◆ use_fold_tree_from_silent_file()

bool core::import_pose::RNA_DeNovoParameters::use_fold_tree_from_silent_file ( ) const
inline

◆ virtual_anchor_attachment_points()

utility::vector1<core::Size > core::import_pose::RNA_DeNovoParameters::virtual_anchor_attachment_points ( ) const
inline

Member Data Documentation

◆ allow_insert_res_

utility::vector1< core::Size > core::import_pose::RNA_DeNovoParameters::allow_insert_res_
private

◆ block_stack_above_res_

utility::vector1<core::Size > core::import_pose::RNA_DeNovoParameters::block_stack_above_res_
private

◆ block_stack_below_res_

utility::vector1<core::Size > core::import_pose::RNA_DeNovoParameters::block_stack_below_res_
private

◆ chain_connections_

utility::vector1< std::pair< utility::vector1 <core::Size >, utility::vector1 <core::Size > > > core::import_pose::RNA_DeNovoParameters::chain_connections_
private

◆ cutpoints_closed_

utility::vector1<core::Size > core::import_pose::RNA_DeNovoParameters::cutpoints_closed_
private

◆ cutpoints_cyclize_

utility::vector1<core::Size > core::import_pose::RNA_DeNovoParameters::cutpoints_cyclize_
private

◆ cutpoints_open_

utility::vector1<core::Size > core::import_pose::RNA_DeNovoParameters::cutpoints_open_
private

◆ filename_

std::string const core::import_pose::RNA_DeNovoParameters::filename_
private

Referenced by RNA_DeNovoParameters().

◆ fiveprime_cap_

utility::vector1< core::Size > core::import_pose::RNA_DeNovoParameters::fiveprime_cap_
private

Referenced by fiveprime_cap(), and set_fiveprime_cap().

◆ fold_tree_from_silent_file_

core::kinematics::FoldTree core::import_pose::RNA_DeNovoParameters::fold_tree_from_silent_file_
private

◆ is_rna_and_protein_

bool core::import_pose::RNA_DeNovoParameters::is_rna_and_protein_
private

◆ obligate_pairing_sets_

utility::vector1< utility::vector1 <core::Size > > core::import_pose::RNA_DeNovoParameters::obligate_pairing_sets_
private

◆ rna_pairing_list_

core::pose::rna::RNA_BasePairList core::import_pose::RNA_DeNovoParameters::rna_pairing_list_
private

◆ rna_secstruct_legacy_

std::string core::import_pose::RNA_DeNovoParameters::rna_secstruct_legacy_
private

◆ secstruct_defined_

bool core::import_pose::RNA_DeNovoParameters::secstruct_defined_
private

◆ stem_pairing_sets_

utility::vector1< utility::vector1 <core::Size > > core::import_pose::RNA_DeNovoParameters::stem_pairing_sets_
private

◆ twoprime_

utility::vector1<core::Size > core::import_pose::RNA_DeNovoParameters::twoprime_
private

Referenced by set_twoprime(), and twoprime().

◆ use_fold_tree_from_silent_file_

bool core::import_pose::RNA_DeNovoParameters::use_fold_tree_from_silent_file_
private

◆ virtual_anchor_attachment_points_

utility::vector1<core::Size > core::import_pose::RNA_DeNovoParameters::virtual_anchor_attachment_points_
private

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