core::import_pose::RNA_DeNovoParameters Class Reference

#include <RNA_DeNovoParameters.hh>

Inheritance diagram for core::import_pose::RNA_DeNovoParameters:

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::Size >	cutpoints_open () const
void	set_cutpoints_closed (utility::vector1< core::Size > const &setting)
utility::vector1< core::Size >	cutpoints_closed () const
void	set_fiveprime_cap (utility::vector1< core::Size > const &setting)
utility::vector1< core::Size >	fiveprime_cap () const
void	set_cutpoints_cyclize (utility::vector1< core::Size > const &setting)
utility::vector1< core::Size >	cutpoints_cyclize () const
void	set_twoprime (utility::vector1< core::Size > const &setting)
utility::vector1< core::Size >	twoprime () const
void	set_block_stack_above_res (utility::vector1< core::Size > const &setting)
utility::vector1< core::Size >	block_stack_above_res () const
void	set_block_stack_below_res (utility::vector1< core::Size > const &setting)
utility::vector1< core::Size >	block_stack_below_res () const
void	set_virtual_anchor_attachment_points (utility::vector1< core::Size > const &setting)
utility::vector1< core::Size >	virtual_anchor_attachment_points () const
void	set_allow_insert_res (utility::vector1< core::Size > const &setting)
utility::vector1< core::Size >	allow_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::Size >	cutpoints_open_
utility::vector1< core::Size >	cutpoints_closed_
utility::vector1< core::Size >	cutpoints_cyclize_
utility::vector1< core::Size >	twoprime_
utility::vector1< core::Size >	block_stack_above_res_
utility::vector1< core::Size >	block_stack_below_res_
utility::vector1< core::Size >	virtual_anchor_attachment_points_
utility::vector1< core::Size >	fiveprime_cap_
utility::vector1< core::Size >	allow_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

core::import_pose::RNA_DeNovoParameters::RNA_DeNovoParameters

(

std::string const &

filename

)

References filename_, and read_parameters_from_file().

core::import_pose::RNA_DeNovoParameters::RNA_DeNovoParameters

(

)

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

overridedefault

Member Function Documentation

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

inline

References cutpoints_open_.

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::append_virtual_anchor().

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

inline

References obligate_pairing_sets_.

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::append_virtual_anchor().

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

inline

References rna_pairing_list_.

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::append_virtual_anchor().

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

inline

References allow_insert_res_.

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

inline

References block_stack_above_res_.

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_block_stack_variants().

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

inline

References block_stack_below_res_.

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_block_stack_variants().

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

inline

References chain_connections_.

Referenced by core::import_pose::RNA_BasePairHandler::RNA_BasePairHandler(), and protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_legacy().

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

References core::pose::rna::BasePair::res1(), core::pose::rna::BasePair::res2(), and rna_pairing_list_.

Referenced by get_pairings_from_line(), and protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_legacy().

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

inline

References cutpoints_closed_.

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_legacy().

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

inline

References cutpoints_cyclize_.

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_chainbreak_variants().

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

inline

References cutpoints_open_.

Referenced by core::import_pose::RNA_BasePairHandler::RNA_BasePairHandler(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_chainbreak_variants(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_legacy(), and protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_virtual_phosphate_variants().

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

inline

References fiveprime_cap_.

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_chainbreak_variants().

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

inline

References fold_tree_from_silent_file_.

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_jumps().

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

private

References core::pose::motif::a(), core::chemical::rna::ANTIPARALLEL, core::chemical::rna::ANY_BASE_DOUBLET_ORIENTATION, core::chemical::rna::ANY_BASE_EDGE, protocols::match::upstream::b, check_in_pairing_sets(), core::pose::rna::get_base_doublet_orientation_from_LW(), core::chemical::rna::get_edge_from_char(), core::chemical::rna::get_LW_orientation_from_char(), core::chemical::rna::get_orientation_from_char(), core::chemical::element::I, obligate_pairing_sets_, rna_pairing_list_, core::pose::rna::BasePair::set_edge1(), core::pose::rna::BasePair::set_edge2(), core::pose::rna::BasePair::set_orientation(), core::pose::rna::BasePair::set_res1(), core::pose::rna::BasePair::set_res2(), stem_pairing_sets_, and core::chemical::rna::WATSON_CRICK.

Referenced by read_parameters_from_file().

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

inline

References is_rna_and_protein_.

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

inline

References obligate_pairing_sets_.

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_legacy().

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

private

References chain_connections_, and save_res_lists_to_chain_connections_and_clear().

Referenced by read_parameters_from_file().

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

private

References core::pose::motif::a(), allow_insert_res_, cutpoints_closed_, cutpoints_open_, get_pairings_from_line(), read_chain_connection(), rna_secstruct_legacy_, secstruct_defined_, core::import_pose::TR(), and virtual_anchor_attachment_points_.

Referenced by RNA_DeNovoParameters().

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

inline

References rna_pairing_list_.

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::append_virtual_anchor(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::initialize_secstruct(), core::import_pose::RNA_BasePairHandler::RNA_BasePairHandler(), and protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_legacy().

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

inline

References rna_secstruct_legacy_.

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::initialize_secstruct(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::override_secstruct(), and protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info().

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().

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

inline

References secstruct_defined_.

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::initialize_secstruct().

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

inline

References allow_insert_res_.

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

inline

References block_stack_above_res_.

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

inline

References block_stack_below_res_.

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_.

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

inline

References cutpoints_closed_.

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

inline

References cutpoints_cyclize_.

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

inline

References cutpoints_open_.

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

inline

References fiveprime_cap_.

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

inline

References fold_tree_from_silent_file_.

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

inline

References obligate_pairing_sets_.

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

inline

References is_rna_and_protein_.

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

inline

References rna_pairing_list_.

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

inline

References rna_secstruct_legacy_, and secstruct_defined_.

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::initialize_secstruct(), and protocols::rna::denovo::RNA_DeNovoPoseInitializer::override_secstruct().

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

inline

References stem_pairing_sets_.

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

inline

References twoprime_.

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

inline

References use_fold_tree_from_silent_file_.

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

inline

References virtual_anchor_attachment_points_.

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

inline

References stem_pairing_sets_.

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_legacy().

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

inline

References twoprime_.

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_chainbreak_variants().

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

inline

References use_fold_tree_from_silent_file_.

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_jumps().

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

inline

References virtual_anchor_attachment_points_.

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::append_virtual_anchor(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::initialize_for_de_novo_protocol(), and protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_jumps().

Member Data Documentation

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

private

Referenced by allow_insert_res(), read_parameters_from_file(), and set_allow_insert_res().

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

private

Referenced by block_stack_above_res(), and set_block_stack_above_res().

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

private

Referenced by block_stack_below_res(), and set_block_stack_below_res().

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

private

Referenced by chain_connections(), read_chain_connection(), save_res_lists_to_chain_connections_and_clear(), and set_chain_connections().

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

private

Referenced by cutpoints_closed(), read_parameters_from_file(), and set_cutpoints_closed().

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

private

Referenced by cutpoints_cyclize(), and set_cutpoints_cyclize().

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

private

Referenced by add_cutpoint_open(), cutpoints_open(), read_parameters_from_file(), and set_cutpoints_open().

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

private

Referenced by RNA_DeNovoParameters().

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

private

Referenced by fiveprime_cap(), and set_fiveprime_cap().

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

private

Referenced by fold_tree_from_silent_file(), and set_fold_tree_from_silent_file().

bool core::import_pose::RNA_DeNovoParameters::is_rna_and_protein_

private

Referenced by is_rna_and_protein(), and set_rna_and_protein().

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

private

Referenced by add_obligate_pairing_set(), get_pairings_from_line(), obligate_pairing_sets(), and set_obligate_pairing_sets().

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

private

Referenced by add_rna_pairing(), check_in_pairing_sets(), get_pairings_from_line(), rna_pairing_list(), and set_rna_pairing_list().

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

private

Referenced by read_parameters_from_file(), rna_secstruct_legacy(), and set_rna_secstruct_legacy().

bool core::import_pose::RNA_DeNovoParameters::secstruct_defined_

private

Referenced by read_parameters_from_file(), secstruct_defined(), and set_rna_secstruct_legacy().

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

private

Referenced by get_pairings_from_line(), set_stem_pairing_sets(), and stem_pairing_sets().

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

private

Referenced by set_twoprime(), and twoprime().

bool core::import_pose::RNA_DeNovoParameters::use_fold_tree_from_silent_file_

private

Referenced by set_use_fold_tree_from_silent_file(), and use_fold_tree_from_silent_file().

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

private

Referenced by read_parameters_from_file(), set_virtual_anchor_attachment_points(), and virtual_anchor_attachment_points().

---

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

• src/core/import_pose/RNA_DeNovoParameters.hh
• src/core/import_pose/RNA_DeNovoParameters.cc