#include <RNA_DeNovoSetup.hh>

Inheritance diagram for core::import_pose::RNA_DeNovoSetup:

Public Member Functions
	RNA_DeNovoSetup ()

	~RNA_DeNovoSetup () override

void	initialize_from_options (utility::options::OptionCollection const &opts)

void	initialize_from_command_line ()

core::import_pose::options::RNA_DeNovoProtocolOptionsCOP	options () const

core::import_pose::RNA_DeNovoParametersCOP	rna_params () const

void	initialize_inputs_from_options (utility::options::OptionCollection const &opts)
	Initialize particular inputs first – like PDB files. More...

void	set_fasta_files (utility::vector1< std::string > const &fasta_files)

void	set_input_pdbs (utility::vector1< std::string > const &input_pdbs)

void	set_input_silent_files (utility::vector1< std::string > const &input_silent_files)

void	set_sequence_strings (utility::vector1< std::string > const &sequence_strings)

void	set_minimize_rna (bool const minimize_rna)

void	set_native_pose (core::pose::PoseOP native_pose)

void	set_align_pdb (std::string const &align_pdb)

void	set_nstruct (Size const nstruct)

void	set_silent_file (std::string const &silent_file)

utility::vector1< core::pose::PoseOP > const &	refine_pose_list () const

core::pose::PoseOP	pose ()

core::pose::PoseCOP	native_pose ()

Static Public Member Functions
static void	list_options_read (utility::options::OptionKeyList &opts)

Private Member Functions
void	de_novo_setup_from_command_line ()

void	de_novo_setup_from_options (utility::options::OptionCollection const &opts)

void	de_novo_setup_from_command_line_legacy ()

void	setup_refine_pose_list (utility::options::OptionCollection const &opts)

utility::vector1< core::pose::PoseOP >	get_refine_pose_list (std::string const &input_silent_file, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &output_res_and_chain_segid, core::chemical::ResidueTypeSetCOP rsd_set) const

utility::vector1< core::Size >	working_res_map (utility::vector1< core::Size > const &vec, utility::vector1< core::Size > const &working_res, bool const leave_out_last_working_residue=false) const

std::string	working_res_map (std::string const &seq, utility::vector1< core::Size > const &working_res, bool const annotations_in_brackets=true) const

core::pose::rna::RNA_SecStruct	working_res_map (core::pose::rna::RNA_SecStruct const &seq, utility::vector1< core::Size > const &working_res) const

void	get_seq_and_resnum (std::string const &pdb, std::string &seq, utility::vector1< int > &resnum, utility::vector1< char > &chain, utility::vector1< std::string > &segid) const

std::string	get_silent_seq (std::string const &silent_file) const

std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > >	get_silent_resnum (std::string const &silent_file) const

bool	already_listed_in_obligate_pair (utility::vector1< core::Size > const &new_pair, utility::vector1< core::Size > const &obligate_pair) const

bool	already_listed_in_obligate_pair (utility::vector1< Size > const &new_pair, utility::vector1< Size > const &obligate_pair, utility::vector1< Size > const &obligate_pair_explicit) const

void	update_working_obligate_pairs_with_stems (utility::vector1< core::pose::rna::BasePair > &working_obligate_pairs, utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > const &working_stems, utility::vector1< core::Size > const &working_input_res) const

Private Attributes
core::import_pose::options::RNA_DeNovoProtocolOptionsOP	options_

core::import_pose::RNA_DeNovoParametersOP	rna_params_

core::chemical::ResidueTypeSetCOP	rsd_set_

core::pose::PoseOP	pose_

core::pose::PoseOP	native_pose_

utility::vector1< core::pose::PoseOP >	refine_pose_list_

utility::vector1< std::string >	fasta_files_

utility::vector1< std::string >	input_pdbs_

utility::vector1< std::string >	input_silent_files_

utility::vector1< std::string >	sequence_strings_

bool	minimize_rna_

bool	minimize_rna_has_been_specified_ = false

utility::vector1< std::string >	helical_substructs_

utility::vector1< std::string >	dock_chunks_

utility::vector1< std::string >	input_initialization_pdbs_

Constructor & Destructor Documentation

◆ RNA_DeNovoSetup()

core::import_pose::RNA_DeNovoSetup::RNA_DeNovoSetup ( )

◆ ~RNA_DeNovoSetup()

core::import_pose::RNA_DeNovoSetup::~RNA_DeNovoSetup ( )

overridedefault

Member Function Documentation

◆ already_listed_in_obligate_pair() [1/2]

bool core::import_pose::RNA_DeNovoSetup::already_listed_in_obligate_pair	(	utility::vector1< core::Size > const &	new_pair,
		utility::vector1< core::Size > const &	obligate_pair
	)		const

private

Referenced by de_novo_setup_from_options().

◆ already_listed_in_obligate_pair() [2/2]

bool core::import_pose::RNA_DeNovoSetup::already_listed_in_obligate_pair	(	utility::vector1< Size > const &	new_pair,
		utility::vector1< Size > const &	obligate_pair,
		utility::vector1< Size > const &	obligate_pair_explicit
	)		const

private

◆ de_novo_setup_from_command_line()

void core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_command_line ( )

private

References de_novo_setup_from_options().

◆ de_novo_setup_from_command_line_legacy()

void core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_command_line_legacy ( )

private

References core::io::rna::RNA_DataReader::fill_rna_data_info(), core::pose::make_pose_from_sequence(), native_pose(), native_pose_, protocols::hybridization::path, core::import_pose::PDB_file, pose_, core::import_pose::pose_from_file(), core::sequence::read_fasta_file_return_str(), rna_params_, rsd_set_, and core::import_pose::TR().

◆ de_novo_setup_from_options()

void core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options ( utility::options::OptionCollection const & opts )

private

References core::pose::addVirtualResAsRoot(), already_listed_in_obligate_pair(), core::chemical::rna::ANTIPARALLEL, core::chemical::rna::ANY_BASE_DOUBLET_ORIENTATION, core::chemical::rna::ANY_BASE_EDGE, core::pose::rna::RNA_SecStruct::base_pairs(), core::pose::rna::RNA_SecStruct::blank(), core::pose::rna::RNA_SecStruct::check_compatible_with_sequence(), chr_chains(), core::pose::full_model_info::CUTPOINT_OPEN, dock_chunks_, core::import_pose::dump_stems(), core::pose::full_model_info::EXTRA_MINIMIZE, fasta_files_, core::io::rna::RNA_DataReader::fill_rna_data_info(), core::pose::copydofs::FIXED_DOMAIN, core::pose::rna::get_base_doublet_orientation_from_LW(), core::chemical::rna::get_edge_from_char(), core::import_pose::get_extra_cutpoints_from_names(), core::chemical::rna::get_LW_orientation_from_char(), core::chemical::rna::get_orientation_from_char(), get_seq_and_resnum(), core::import_pose::get_sequence_information(), get_silent_resnum(), get_silent_seq(), helical_substructs_, core::import_pose::initialize_native_and_align_pose(), core::pose::full_model_info::INPUT_DOMAIN, input_initialization_pdbs_, input_pdbs_, input_silent_files_, core::pose::make_pose_from_sequence(), protocols::mean_field::max(), protocols::mean_field::min(), minimize_rna_, minimize_rna_has_been_specified_, core::conformation::named_atom_id_to_atom_id(), native_pose_, options_, core::sequence::parse_out_non_standard_residues(), protocols::hybridization::path, core::import_pose::PDB_file, core::pose::pdbslice(), pose_, core::import_pose::pose_from_file(), core::chemical::rings::q, refine_pose_list(), core::pose::rna::RNA_SecStruct::remove_pair(), core::pose::full_model_info::RNA_ANTI_CHI, core::pose::full_model_info::RNA_BLOCK_STACK_ABOVE, core::pose::full_model_info::RNA_BLOCK_STACK_BELOW, rna_params_, core::pose::full_model_info::RNA_SYN_CHI, rsd_set_, core::pose::rna::RNA_SecStruct::secstruct(), sequence_strings_, core::pose::full_model_info::set_full_model_info(), core::pose::set_output_res_and_chain(), core::pose::rna::RNA_SecStruct::stems(), core::sequence::strip_spacers(), core::import_pose::TR(), update_working_obligate_pairs_with_stems(), core::chemical::rna::WATSON_CRICK, and working_res_map().

Referenced by de_novo_setup_from_command_line(), and initialize_from_options().

◆ get_refine_pose_list()

vector1< pose::PoseOP > core::import_pose::RNA_DeNovoSetup::get_refine_pose_list	(	std::string const &	input_silent_file,
		std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &	output_res_and_chain_segid,
		core::chemical::ResidueTypeSetCOP	rsd_set
	)		const

private

References refine_pose_list(), and core::pose::set_output_res_and_chain().

Referenced by setup_refine_pose_list().

◆ get_seq_and_resnum()

void core::import_pose::RNA_DeNovoSetup::get_seq_and_resnum	(	std::string const &	pdb,
		std::string &	seq,
		utility::vector1< int > &	resnum,
		utility::vector1< char > &	chain,
		utility::vector1< std::string > &	segid
	)		const

private

References pose(), and core::import_pose::pose_from_file().

Referenced by de_novo_setup_from_options().

◆ get_silent_resnum()

std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > core::import_pose::RNA_DeNovoSetup::get_silent_resnum ( std::string const & silent_file ) const

private

References core::io::silent::SilentFileData::get_resnum().

Referenced by de_novo_setup_from_options().

◆ get_silent_seq()

std::string core::import_pose::RNA_DeNovoSetup::get_silent_seq ( std::string const & silent_file ) const

private

References core::io::silent::SilentFileData::get_sequence().

Referenced by de_novo_setup_from_options().

◆ initialize_from_command_line()

void core::import_pose::RNA_DeNovoSetup::initialize_from_command_line ( )

References initialize_from_options().

◆ initialize_from_options()

void core::import_pose::RNA_DeNovoSetup::initialize_from_options ( utility::options::OptionCollection const & opts )

References de_novo_setup_from_options(), core::chemical::FA_STANDARD, initialize_inputs_from_options(), options_, pose_, rsd_set_, core::pose::set_output_res_and_chain(), and setup_refine_pose_list().

Referenced by initialize_from_command_line().

◆ initialize_inputs_from_options()

void core::import_pose::RNA_DeNovoSetup::initialize_inputs_from_options ( utility::options::OptionCollection const & opts )

Initialize particular inputs first – like PDB files.

the idea is that these are most likely to be unspecified on the command line in a pyrosetta type of context, and this way we could re-spec them later.

References dock_chunks_, fasta_files_, helical_substructs_, input_initialization_pdbs_, input_pdbs_, input_silent_files_, minimize_rna_, minimize_rna_has_been_specified_, and sequence_strings_.

Referenced by initialize_from_options().

◆ list_options_read()

void core::import_pose::RNA_DeNovoSetup::list_options_read ( utility::options::OptionKeyList & opts )

static

References core::import_pose::dump_stems(), and protocols::hybridization::path.

◆ native_pose()

core::pose::PoseCOP core::import_pose::RNA_DeNovoSetup::native_pose ( )

inline

References native_pose_.

Referenced by de_novo_setup_from_command_line_legacy(), and set_native_pose().

◆ options()

core::import_pose::options::RNA_DeNovoProtocolOptionsCOP core::import_pose::RNA_DeNovoSetup::options ( ) const

inline

References options_.

◆ pose()

core::pose::PoseOP core::import_pose::RNA_DeNovoSetup::pose ( )

inline

References pose_.

Referenced by get_seq_and_resnum().

◆ refine_pose_list()

utility::vector1< core::pose::PoseOP > const& core::import_pose::RNA_DeNovoSetup::refine_pose_list ( ) const

inline

References refine_pose_list_.

Referenced by de_novo_setup_from_options(), and get_refine_pose_list().

◆ rna_params()

core::import_pose::RNA_DeNovoParametersCOP core::import_pose::RNA_DeNovoSetup::rna_params ( ) const

inline

References rna_params_.

◆ set_align_pdb()

void core::import_pose::RNA_DeNovoSetup::set_align_pdb ( std::string const & align_pdb )

References options_.

◆ set_fasta_files()

void core::import_pose::RNA_DeNovoSetup::set_fasta_files ( utility::vector1< std::string > const & fasta_files )

inline

References fasta_files_.

◆ set_input_pdbs()

void core::import_pose::RNA_DeNovoSetup::set_input_pdbs ( utility::vector1< std::string > const & input_pdbs )

References input_pdbs_, and options_.

◆ set_input_silent_files()

void core::import_pose::RNA_DeNovoSetup::set_input_silent_files ( utility::vector1< std::string > const & input_silent_files )

References input_silent_files_, and options_.

◆ set_minimize_rna()

void core::import_pose::RNA_DeNovoSetup::set_minimize_rna ( bool const minimize_rna )

inline

References minimize_rna_, and minimize_rna_has_been_specified_.

◆ set_native_pose()

void core::import_pose::RNA_DeNovoSetup::set_native_pose ( core::pose::PoseOP native_pose )

inline

References native_pose(), and native_pose_.

◆ set_nstruct()

void core::import_pose::RNA_DeNovoSetup::set_nstruct ( Size const nstruct )

References options_.

◆ set_sequence_strings()

void core::import_pose::RNA_DeNovoSetup::set_sequence_strings ( utility::vector1< std::string > const & sequence_strings )

inline

References sequence_strings_.

◆ set_silent_file()

void core::import_pose::RNA_DeNovoSetup::set_silent_file ( std::string const & silent_file )

References options_.

◆ setup_refine_pose_list()

void core::import_pose::RNA_DeNovoSetup::setup_refine_pose_list ( utility::options::OptionCollection const & opts )

private

References get_refine_pose_list(), options_, pose_, refine_pose_list_, and rsd_set_.

Referenced by initialize_from_options().

◆ update_working_obligate_pairs_with_stems()

void core::import_pose::RNA_DeNovoSetup::update_working_obligate_pairs_with_stems	(	utility::vector1< core::pose::rna::BasePair > &	working_obligate_pairs,
		utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > const &	working_stems,
		utility::vector1< core::Size > const &	working_input_res
	)		const

private

References core::chemical::rna::ANTIPARALLEL, core::scoring::pair, and core::chemical::rna::WATSON_CRICK.

Referenced by de_novo_setup_from_options().

◆ working_res_map() [1/3]

core::pose::rna::RNA_SecStruct core::import_pose::RNA_DeNovoSetup::working_res_map	(	core::pose::rna::RNA_SecStruct const &	seq,
		utility::vector1< core::Size > const &	working_res
	)		const

private

◆ working_res_map() [2/3]

std::string core::import_pose::RNA_DeNovoSetup::working_res_map	(	std::string const &	seq,
		utility::vector1< core::Size > const &	working_res,
		bool const	annotations_in_brackets = `true`
	)		const

private

◆ working_res_map() [3/3]

utility::vector1< core::Size > core::import_pose::RNA_DeNovoSetup::working_res_map	(	utility::vector1< core::Size > const &	vec,
		utility::vector1< core::Size > const &	working_res,
		bool const	leave_out_last_working_residue = `false`
	)		const

private

Referenced by de_novo_setup_from_options().

Member Data Documentation

◆ dock_chunks_

utility::vector1< std::string > core::import_pose::RNA_DeNovoSetup::dock_chunks_

private

Referenced by de_novo_setup_from_options(), and initialize_inputs_from_options().

◆ fasta_files_

utility::vector1< std::string > core::import_pose::RNA_DeNovoSetup::fasta_files_

private

Referenced by de_novo_setup_from_options(), initialize_inputs_from_options(), and set_fasta_files().

◆ helical_substructs_

utility::vector1< std::string > core::import_pose::RNA_DeNovoSetup::helical_substructs_

private

Referenced by de_novo_setup_from_options(), and initialize_inputs_from_options().

◆ input_initialization_pdbs_

utility::vector1< std::string > core::import_pose::RNA_DeNovoSetup::input_initialization_pdbs_

private

Referenced by de_novo_setup_from_options(), and initialize_inputs_from_options().

◆ input_pdbs_

utility::vector1< std::string > core::import_pose::RNA_DeNovoSetup::input_pdbs_

private

Referenced by de_novo_setup_from_options(), initialize_inputs_from_options(), and set_input_pdbs().

◆ input_silent_files_

utility::vector1< std::string > core::import_pose::RNA_DeNovoSetup::input_silent_files_

private

Referenced by de_novo_setup_from_options(), initialize_inputs_from_options(), and set_input_silent_files().

◆ minimize_rna_

bool core::import_pose::RNA_DeNovoSetup::minimize_rna_

private

Referenced by de_novo_setup_from_options(), initialize_inputs_from_options(), and set_minimize_rna().

◆ minimize_rna_has_been_specified_

bool core::import_pose::RNA_DeNovoSetup::minimize_rna_has_been_specified_ = false

private

Referenced by de_novo_setup_from_options(), initialize_inputs_from_options(), and set_minimize_rna().

◆ native_pose_

core::pose::PoseOP core::import_pose::RNA_DeNovoSetup::native_pose_

private

Referenced by de_novo_setup_from_command_line_legacy(), de_novo_setup_from_options(), native_pose(), and set_native_pose().

◆ options_

core::import_pose::options::RNA_DeNovoProtocolOptionsOP core::import_pose::RNA_DeNovoSetup::options_

private

Referenced by de_novo_setup_from_options(), initialize_from_options(), options(), set_align_pdb(), set_input_pdbs(), set_input_silent_files(), set_nstruct(), set_silent_file(), and setup_refine_pose_list().

◆ pose_

core::pose::PoseOP core::import_pose::RNA_DeNovoSetup::pose_

private

Referenced by de_novo_setup_from_command_line_legacy(), de_novo_setup_from_options(), initialize_from_options(), pose(), and setup_refine_pose_list().

◆ refine_pose_list_

utility::vector1< core::pose::PoseOP > core::import_pose::RNA_DeNovoSetup::refine_pose_list_

private

Referenced by refine_pose_list(), and setup_refine_pose_list().

◆ rna_params_

core::import_pose::RNA_DeNovoParametersOP core::import_pose::RNA_DeNovoSetup::rna_params_

private

Referenced by de_novo_setup_from_command_line_legacy(), de_novo_setup_from_options(), and rna_params().

◆ rsd_set_

core::chemical::ResidueTypeSetCOP core::import_pose::RNA_DeNovoSetup::rsd_set_

private

Referenced by de_novo_setup_from_command_line_legacy(), de_novo_setup_from_options(), initialize_from_options(), and setup_refine_pose_list().

◆ sequence_strings_

utility::vector1< std::string > core::import_pose::RNA_DeNovoSetup::sequence_strings_

private

Referenced by de_novo_setup_from_options(), initialize_inputs_from_options(), and set_sequence_strings().

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

src/core/import_pose/RNA_DeNovoSetup.hh
src/core/import_pose/RNA_DeNovoSetup.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ RNA_DeNovoSetup()

◆ ~RNA_DeNovoSetup()

Member Function Documentation

◆ already_listed_in_obligate_pair() [1/2]

◆ already_listed_in_obligate_pair() [2/2]

◆ de_novo_setup_from_command_line()

◆ de_novo_setup_from_command_line_legacy()

◆ de_novo_setup_from_options()

◆ get_refine_pose_list()

◆ get_seq_and_resnum()

◆ get_silent_resnum()

◆ get_silent_seq()

◆ initialize_from_command_line()

◆ initialize_from_options()

◆ initialize_inputs_from_options()

◆ list_options_read()

◆ native_pose()

◆ options()

◆ pose()

◆ refine_pose_list()

◆ rna_params()

◆ set_align_pdb()

◆ set_fasta_files()

◆ set_input_pdbs()

◆ set_input_silent_files()

◆ set_minimize_rna()

◆ set_native_pose()

◆ set_nstruct()

◆ set_sequence_strings()

◆ set_silent_file()

◆ setup_refine_pose_list()

◆ update_working_obligate_pairs_with_stems()

◆ working_res_map() [1/3]

◆ working_res_map() [2/3]

◆ working_res_map() [3/3]

Member Data Documentation

◆ dock_chunks_

◆ fasta_files_

◆ helical_substructs_

◆ input_initialization_pdbs_

◆ input_pdbs_

◆ input_silent_files_

◆ minimize_rna_

◆ minimize_rna_has_been_specified_

◆ native_pose_

◆ options_

◆ pose_

◆ refine_pose_list_

◆ rna_params_

◆ rsd_set_

◆ sequence_strings_