core::io::silent::SilentFileOptions Class Reference

#include <SilentFileOptions.hh>

Inheritance diagram for core::io::silent::SilentFileOptions:

Public Member Functions
	SilentFileOptions ()
	SilentFileOptions (utility::options::OptionCollection const &options)
void	read_from_global_options ()
void	read_from_options (utility::options::OptionCollection const &options)
void	read_from_tag (utility::tag::TagCOP tag)
bool	keep_input_scores () const
bool	out_user_tag_set () const
std::string	out_user_tag () const
bool	out_weight_silent_scores () const
std::string	in_silent_score_prefix () const
bool	in_silent_scores_wanted_set () const
utility::vector1< std::string >	in_silent_scores_wanted () const
bool	in_fullatom () const
bool	write_failures_set () const
bool	write_failures () const
bool	in_silent_struct_type_set () const
std::string	in_silent_struct_type () const
bool	out_silent_struct_type_set () const
std::string	out_silent_struct_type () const
bool	read_through_errors () const
bool	select_random_set () const
int	select_random () const
int	select_range_start () const
int	select_range_len () const
int	select_range_mul () const
bool	force_silent_bitflip_on_read_set () const
bool	force_silent_bitflip_on_read () const
bool	print_all_score_headers () const
bool	binary_output () const
void	keep_input_scores (bool setting)
void	out_user_tag (std::string setting)
void	out_weight_silent_scores (bool setting)
void	in_silent_score_prefix (std::string setting)
void	in_silent_scores_wanted (utility::vector1< std::string > const &setting)
void	in_fullatom (bool setting)
void	write_failures (bool setting)
void	in_silent_struct_type (std::string setting)
void	out_silent_struct_type (std::string setting)
void	read_through_errors (bool setting)
void	select_random (int setting)
void	select_range_start (int setting)
void	select_range_len (int setting)
void	select_range_mul (int setting)
void	force_silent_bitflip_on_read (bool setting)
void	print_all_score_headers (bool setting)
void	set_binary_output (bool setting)

Static Public Member Functions
static void	list_read_options (utility::options::OptionKeyList &read_options)
static void	append_attributes_for_tag_parsing (utility::tag::XMLSchemaDefinition &xsd, utility::tag::AttributeList &attributes)

Private Attributes
bool	keep_input_scores_
bool	out_user_tag_set_
std::string	out_user_tag_
bool	out_weight_silent_scores_
std::string	in_silent_score_prefix_
bool	in_silent_scores_wanted_set_
utility::vector1< std::string >	in_silent_scores_wanted_
bool	in_fullatom_
bool	write_failures_set_
bool	write_failures_
bool	in_silent_struct_type_set_
std::string	in_silent_struct_type_
bool	out_silent_struct_type_set_
std::string	out_silent_struct_type_
bool	binary_output_ = true
bool	read_through_errors_
bool	select_random_set_
int	select_random_
int	select_range_start_
int	select_range_len_
int	select_range_mul_
bool	force_silent_bitflip_on_read_set_
bool	force_silent_bitflip_on_read_
bool	print_all_score_headers_

Constructor & Destructor Documentation

core::io::silent::SilentFileOptions::SilentFileOptions

(

)

References read_from_global_options().

core::io::silent::SilentFileOptions::SilentFileOptions

(

utility::options::OptionCollection const &

options

)

References read_from_options().

Member Function Documentation

void core::io::silent::SilentFileOptions::append_attributes_for_tag_parsing ( utility::tag::XMLSchemaDefinition &  xsd, utility::tag::AttributeList &  attributes  )

static

Referenced by core::import_pose::PoseResourceLoader::provide_xml_schema(), protocols::jd3::full_model_inputters::SilentFileFullModelInputter::provide_xml_schema(), protocols::jd3::pose_inputters::SilentFilePoseInputter::provide_xml_schema(), protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::provide_xml_schema(), and protocols::jd3::pose_outputters::SilentFilePoseOutputter::provide_xml_schema().

bool core::io::silent::SilentFileOptions::binary_output ( ) const

inline

References binary_output_.

Referenced by core::io::silent::SilentStructFactory::get_silent_struct_out().

bool core::io::silent::SilentFileOptions::force_silent_bitflip_on_read

(

)

const

References force_silent_bitflip_on_read_.

Referenced by core::io::silent::SilentFileData::read_stream().

void core::io::silent::SilentFileOptions::force_silent_bitflip_on_read

(

bool

setting

)

References force_silent_bitflip_on_read_, and force_silent_bitflip_on_read_set_.

bool core::io::silent::SilentFileOptions::force_silent_bitflip_on_read_set

(

)

const

References force_silent_bitflip_on_read_set_.

bool core::io::silent::SilentFileOptions::in_fullatom

(

)

const

References in_fullatom_.

Referenced by core::io::silent::BinarySilentStruct::init_from_lines(), and protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::run().

void core::io::silent::SilentFileOptions::in_fullatom

(

bool

setting

)

References in_fullatom_.

std::string core::io::silent::SilentFileOptions::in_silent_score_prefix

(

)

const

References in_silent_score_prefix_.

Referenced by core::io::silent::SilentStruct::energies_into_pose().

void core::io::silent::SilentFileOptions::in_silent_score_prefix

(

std::string

setting

)

References in_silent_score_prefix_.

utility::vector1< std::string > core::io::silent::SilentFileOptions::in_silent_scores_wanted

(

)

const

References in_silent_scores_wanted_.

Referenced by core::io::silent::SilentStruct::energies_into_pose().

void core::io::silent::SilentFileOptions::in_silent_scores_wanted

(

utility::vector1< std::string > const &

setting

)

References in_silent_scores_wanted_, and in_silent_scores_wanted_set_.

bool core::io::silent::SilentFileOptions::in_silent_scores_wanted_set

(

)

const

References in_silent_scores_wanted_set_.

Referenced by core::io::silent::SilentStruct::energies_into_pose().

std::string core::io::silent::SilentFileOptions::in_silent_struct_type

(

)

const

References in_silent_struct_type_.

Referenced by core::io::silent::SilentStructFactory::get_silent_struct_in().

void core::io::silent::SilentFileOptions::in_silent_struct_type

(

std::string

setting

)

References in_silent_struct_type_.

bool core::io::silent::SilentFileOptions::in_silent_struct_type_set

(

)

const

References in_silent_struct_type_set_.

bool core::io::silent::SilentFileOptions::keep_input_scores

(

)

const

References keep_input_scores_.

Referenced by core::io::silent::SilentStruct::finish_pose().

void core::io::silent::SilentFileOptions::keep_input_scores

(

bool

setting

)

References keep_input_scores_.

void core::io::silent::SilentFileOptions::list_read_options ( utility::options::OptionKeyList &  read_options )

static

Referenced by protocols::jd3::full_model_inputters::SilentFileFullModelInputter::list_options_read(), protocols::jd3::pose_inputters::SilentFilePoseInputter::list_options_read(), protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::list_options_read(), and protocols::jd3::pose_outputters::SilentFilePoseOutputter::list_options_read().

std::string core::io::silent::SilentFileOptions::out_silent_struct_type

(

)

const

References out_silent_struct_type_.

Referenced by core::io::silent::SilentStructFactory::get_silent_struct_out().

void core::io::silent::SilentFileOptions::out_silent_struct_type

(

std::string

setting

)

References out_silent_struct_type_.

bool core::io::silent::SilentFileOptions::out_silent_struct_type_set

(

)

const

References out_silent_struct_type_set_.

Referenced by core::io::silent::SilentStructFactory::get_silent_struct_out().

std::string core::io::silent::SilentFileOptions::out_user_tag

(

)

const

References out_user_tag_.

Referenced by core::io::silent::SilentStruct::print_score_header(), and core::io::silent::SilentStruct::print_scores().

void core::io::silent::SilentFileOptions::out_user_tag

(

std::string

setting

)

References out_user_tag_, and out_user_tag_set_.

bool core::io::silent::SilentFileOptions::out_user_tag_set

(

)

const

References out_user_tag_set_.

Referenced by core::io::silent::SilentStruct::print_score_header(), and core::io::silent::SilentStruct::print_scores().

bool core::io::silent::SilentFileOptions::out_weight_silent_scores

(

)

const

References out_weight_silent_scores_.

Referenced by core::io::silent::SilentStruct::print_scores().

void core::io::silent::SilentFileOptions::out_weight_silent_scores

(

bool

setting

)

References out_weight_silent_scores_.

bool core::io::silent::SilentFileOptions::print_all_score_headers

(

)

const

References print_all_score_headers_.

Referenced by core::io::silent::SilentFileData::write_silent_struct().

void core::io::silent::SilentFileOptions::print_all_score_headers

(

bool

setting

)

References print_all_score_headers_.

void core::io::silent::SilentFileOptions::read_from_global_options

(

)

References read_from_options().

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::go(), and SilentFileOptions().

void core::io::silent::SilentFileOptions::read_from_options

(

utility::options::OptionCollection const &

options

)

References binary_output_, force_silent_bitflip_on_read_, force_silent_bitflip_on_read_set_, in_fullatom_, in_silent_score_prefix_, in_silent_scores_wanted_, in_silent_scores_wanted_set_, in_silent_struct_type_, in_silent_struct_type_set_, keep_input_scores_, out_silent_struct_type_, out_silent_struct_type_set_, out_user_tag_, out_user_tag_set_, out_weight_silent_scores_, print_all_score_headers_, read_through_errors_, select_random_, select_random_set_, select_range_len_, select_range_mul_, select_range_start_, write_failures_, and write_failures_set_.

Referenced by read_from_global_options(), and SilentFileOptions().

void core::io::silent::SilentFileOptions::read_from_tag

(

utility::tag::TagCOP

tag

)

References binary_output_, force_silent_bitflip_on_read_, force_silent_bitflip_on_read_set_, in_fullatom_, in_silent_score_prefix_, in_silent_scores_wanted_, in_silent_scores_wanted_set_, in_silent_struct_type_, in_silent_struct_type_set_, keep_input_scores_, out_silent_struct_type_, out_silent_struct_type_set_, out_user_tag_, out_user_tag_set_, out_weight_silent_scores_, print_all_score_headers_, read_through_errors_, select_random_, select_random_set_, select_range_len_, select_range_mul_, select_range_start_, write_failures_, and write_failures_set_.

Referenced by protocols::jd3::pose_outputters::SilentFilePoseOutputter::create_output_specification().

bool core::io::silent::SilentFileOptions::read_through_errors

(

)

const

References read_through_errors_.

Referenced by protocols::indexed_structure_store::SilentStructureStoreBackend::load_store(), and core::io::silent::SilentFileData::read_file().

void core::io::silent::SilentFileOptions::read_through_errors

(

bool

setting

)

References read_through_errors_.

int core::io::silent::SilentFileOptions::select_random

(

)

const

References select_random_.

Referenced by core::io::silent::SilentFileData::_read_file().

void core::io::silent::SilentFileOptions::select_random

(

int

setting

)

References select_random_.

bool core::io::silent::SilentFileOptions::select_random_set

(

)

const

References select_random_set_.

Referenced by core::io::silent::SilentFileData::_read_file().

int core::io::silent::SilentFileOptions::select_range_len

(

)

const

References select_range_len_.

Referenced by core::io::silent::SilentFileData::_read_file().

void core::io::silent::SilentFileOptions::select_range_len

(

int

setting

)

References select_range_len_.

int core::io::silent::SilentFileOptions::select_range_mul

(

)

const

References select_range_mul_.

Referenced by core::io::silent::SilentFileData::_read_file().

void core::io::silent::SilentFileOptions::select_range_mul

(

int

setting

)

References select_range_mul_.

int core::io::silent::SilentFileOptions::select_range_start

(

)

const

References select_range_start_.

Referenced by core::io::silent::SilentFileData::_read_file().

void core::io::silent::SilentFileOptions::select_range_start

(

int

setting

)

References select_range_start_.

void core::io::silent::SilentFileOptions::set_binary_output ( bool  setting )

inline

References binary_output_.

bool core::io::silent::SilentFileOptions::write_failures

(

)

const

References write_failures_.

void core::io::silent::SilentFileOptions::write_failures

(

bool

setting

)

References write_failures_, and write_failures_set_.

bool core::io::silent::SilentFileOptions::write_failures_set

(

)

const

References write_failures_set_.

Member Data Documentation

bool core::io::silent::SilentFileOptions::binary_output_ = true

private

Referenced by binary_output(), read_from_options(), read_from_tag(), and set_binary_output().

bool core::io::silent::SilentFileOptions::force_silent_bitflip_on_read_

private

Referenced by force_silent_bitflip_on_read(), read_from_options(), and read_from_tag().

bool core::io::silent::SilentFileOptions::force_silent_bitflip_on_read_set_

private

Referenced by force_silent_bitflip_on_read(), force_silent_bitflip_on_read_set(), read_from_options(), and read_from_tag().

bool core::io::silent::SilentFileOptions::in_fullatom_

private

Referenced by in_fullatom(), read_from_options(), and read_from_tag().

std::string core::io::silent::SilentFileOptions::in_silent_score_prefix_

private

Referenced by in_silent_score_prefix(), read_from_options(), and read_from_tag().

utility::vector1< std::string > core::io::silent::SilentFileOptions::in_silent_scores_wanted_

private

Referenced by in_silent_scores_wanted(), read_from_options(), and read_from_tag().

bool core::io::silent::SilentFileOptions::in_silent_scores_wanted_set_

private

Referenced by in_silent_scores_wanted(), in_silent_scores_wanted_set(), read_from_options(), and read_from_tag().

std::string core::io::silent::SilentFileOptions::in_silent_struct_type_

private

Referenced by in_silent_struct_type(), read_from_options(), and read_from_tag().

bool core::io::silent::SilentFileOptions::in_silent_struct_type_set_

private

Referenced by in_silent_struct_type_set(), read_from_options(), and read_from_tag().

bool core::io::silent::SilentFileOptions::keep_input_scores_

private

Referenced by keep_input_scores(), read_from_options(), and read_from_tag().

std::string core::io::silent::SilentFileOptions::out_silent_struct_type_

private

Referenced by out_silent_struct_type(), read_from_options(), and read_from_tag().

bool core::io::silent::SilentFileOptions::out_silent_struct_type_set_

private

Referenced by out_silent_struct_type_set(), read_from_options(), and read_from_tag().

std::string core::io::silent::SilentFileOptions::out_user_tag_

private

Referenced by out_user_tag(), read_from_options(), and read_from_tag().

bool core::io::silent::SilentFileOptions::out_user_tag_set_

private

Referenced by out_user_tag(), out_user_tag_set(), read_from_options(), and read_from_tag().

bool core::io::silent::SilentFileOptions::out_weight_silent_scores_

private

Referenced by out_weight_silent_scores(), read_from_options(), and read_from_tag().

bool core::io::silent::SilentFileOptions::print_all_score_headers_

private

Referenced by print_all_score_headers(), read_from_options(), and read_from_tag().

bool core::io::silent::SilentFileOptions::read_through_errors_

private

Referenced by read_from_options(), read_from_tag(), and read_through_errors().

int core::io::silent::SilentFileOptions::select_random_

private

Referenced by read_from_options(), read_from_tag(), and select_random().

bool core::io::silent::SilentFileOptions::select_random_set_

private

Referenced by read_from_options(), read_from_tag(), and select_random_set().

int core::io::silent::SilentFileOptions::select_range_len_

private

Referenced by read_from_options(), read_from_tag(), and select_range_len().

int core::io::silent::SilentFileOptions::select_range_mul_

private

Referenced by read_from_options(), read_from_tag(), and select_range_mul().

int core::io::silent::SilentFileOptions::select_range_start_

private

Referenced by read_from_options(), read_from_tag(), and select_range_start().

bool core::io::silent::SilentFileOptions::write_failures_

private

Referenced by read_from_options(), read_from_tag(), and write_failures().

bool core::io::silent::SilentFileOptions::write_failures_set_

private

Referenced by read_from_options(), read_from_tag(), write_failures(), and write_failures_set().

---

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

• src/core/io/silent/SilentFileOptions.hh
• src/core/io/silent/SilentFileOptions.cc