protocols::recces::options::RECCES_Options Class Reference

#include <RECCES_Options.hh>

Inheritance diagram for protocols::recces::options::RECCES_Options:

Public Member Functions
	RECCES_Options ()
RECCES_OptionsOP	clone () const
	clone the options More...
virtual void	parse_my_tag (utility::tag::TagCOP)
	Initialize from the recursive "tag" structure. More...
virtual std::string	type () const
	The class name (its type) for a particular ResourceOptions instance. This function allows for better error message delivery. More...
void	initialize_from_command_line ()
void	set_n_cycle (core::Size const &setting)
core::Size	n_cycle () const
void	set_n_dump (core::Size const &setting)
core::Size	n_dump () const
void	set_a_form_range (core::Real const &setting)
core::Real	a_form_range () const
void	set_base_pair_rmsd_cutoff (core::Real const &setting)
core::Real	base_pair_rmsd_cutoff () const
void	set_base_pair_rotation_mag (core::Real const &setting)
core::Real	base_pair_rotation_mag () const
void	set_base_pair_translation_mag (core::Real const &setting)
core::Real	base_pair_translation_mag () const
void	set_legacy_turner_mode (bool const &setting)
bool	legacy_turner_mode () const
void	set_dump_pdb (bool const &setting)
bool	dump_pdb () const
void	set_save_scores (bool const &setting)
bool	save_scores () const
void	set_block_stack (bool const &setting)
bool	block_stack () const
void	set_dump_freq (core::Size const &setting)
core::Size	dump_freq () const
void	set_dump_silent (bool const &setting)
bool	dump_silent () const
void	set_out_torsions (bool const &setting)
bool	out_torsions () const
void	set_setup_base_pair_constraints (bool const &setting)
bool	setup_base_pair_constraints () const
void	set_seq1 (std::string const &setting)
std::string	seq1 () const
void	set_seq2 (std::string const &setting)
std::string	seq2 () const
void	set_infile (std::string const &setting)
std::string	infile () const
void	set_xyz_file (std::string const &setting)
std::string	xyz_file () const
void	set_out_prefix (std::string const &setting)
std::string	out_prefix () const
void	set_temperatures (utility::vector1< core::Real > const &setting)
utility::vector1< core::Real >	temperatures () const
void	set_st_weights (utility::vector1< core::Real > const &setting)
utility::vector1< core::Real >	st_weights () const
void	set_sample_residues (utility::vector1< core::Size > const &setting)
utility::vector1< core::Size >	sample_residues () const
void	set_free_residues (utility::vector1< core::Size > const &setting)
utility::vector1< core::Size >	free_residues () const
void	set_loop_residues (utility::vector1< core::Size > const &setting)
utility::vector1< core::Size >	loop_residues () const
void	set_angle_range_bb (core::Real const &setting)
core::Real	angle_range_bb () const
void	set_angle_range_free_bb (core::Real const &setting)
core::Real	angle_range_free_bb () const
void	set_angle_range_chi (core::Real const &setting)
core::Real	angle_range_chi () const
void	set_angle_range_free_chi (core::Real const &setting)
core::Real	angle_range_free_chi () const
void	set_chi_stdev (core::Real const &setting)
core::Real	chi_stdev () const
void	set_bb_stdev (core::Real const &setting)
core::Real	bb_stdev () const
void	set_standard_bb_stdev (core::Real const &setting)
core::Real	standard_bb_stdev () const
void	set_silent_file (std::string const &setting)
std::string	silent_file () const
void	set_histogram_min (core::Real const &setting)
core::Real	histogram_min () const
void	set_histogram_max (core::Real const &setting)
core::Real	histogram_max () const
void	set_histogram_spacing (core::Real const &setting)
core::Real	histogram_spacing () const
void	set_thermal_sampler_mode (bool const &setting)
bool	thermal_sampler_mode () const
void	set_blank_score_terms (bool const &setting)
bool	blank_score_terms () const
void	set_skip_last_accept (bool const &setting)
bool	skip_last_accept () const
void	set_suppress_sampler_display (bool const &setting)
bool	suppress_sampler_display () const
void	set_prefix_each_output_pdb (bool const &setting)
bool	prefix_each_output_pdb () const
void	set_show_more_pose_scores (bool const &setting)
bool	show_more_pose_scores () const
void	set_output_simple_text_files (bool const &setting)
bool	output_simple_text_files () const
void	set_accept_no_op_moves (bool const &setting)
bool	accept_no_op_moves () const
void	set_sample_jump (bool const &setting)
bool	sample_jump () const
void	set_rna_secstruct (core::pose::rna::RNA_SecStruct const &setting)
core::pose::rna::RNA_SecStruct	rna_secstruct () const

Private Attributes
core::Size	n_cycle_
core::Size	n_dump_
core::Real	a_form_range_
core::Real	base_pair_rmsd_cutoff_
core::Real	base_pair_rotation_mag_
core::Real	base_pair_translation_mag_
bool	legacy_turner_mode_
bool	dump_pdb_
bool	save_scores_
bool	block_stack_
core::Size	dump_freq_
bool	dump_silent_
bool	out_torsions_
bool	setup_base_pair_constraints_
std::string	seq1_
std::string	seq2_
std::string	infile_
std::string	out_prefix_
std::string	xyz_file_
utility::vector1< core::Real >	temperatures_
utility::vector1< core::Real >	st_weights_
core::Real	histogram_min_
core::Real	histogram_max_
core::Real	histogram_spacing_
core::Real	angle_range_bb_
core::Real	angle_range_free_bb_
core::Real	angle_range_chi_
core::Real	angle_range_free_chi_
core::Real	chi_stdev_
core::Real	bb_stdev_
core::Real	standard_bb_stdev_
std::string	silent_file_
utility::vector1< core::Size >	sample_residues_
utility::vector1< core::Size >	free_residues_
utility::vector1< core::Size >	loop_residues_
bool	thermal_sampler_mode_
bool	blank_score_terms_
bool	skip_last_accept_
bool	suppress_sampler_display_
bool	prefix_each_output_pdb_
bool	show_more_pose_scores_
bool	output_simple_text_files_
bool	accept_no_op_moves_
bool	sample_jump_
core::pose::rna::RNA_SecStruct	rna_secstruct_

Constructor & Destructor Documentation

protocols::recces::options::RECCES_Options::RECCES_Options

(

)

Member Function Documentation

core::Real protocols::recces::options::RECCES_Options::a_form_range ( ) const

inline

References a_form_range_.

Referenced by protocols::recces::sampler::initialize_sampler().

bool protocols::recces::options::RECCES_Options::accept_no_op_moves ( ) const

inline

References accept_no_op_moves_.

core::Real protocols::recces::options::RECCES_Options::angle_range_bb ( ) const

inline

References angle_range_bb_.

Referenced by protocols::recces::sampler::initialize_thermal_sampler().

core::Real protocols::recces::options::RECCES_Options::angle_range_chi ( ) const

inline

References angle_range_chi_.

Referenced by protocols::recces::sampler::initialize_thermal_sampler().

core::Real protocols::recces::options::RECCES_Options::angle_range_free_bb ( ) const

inline

References angle_range_free_bb_.

Referenced by protocols::recces::sampler::initialize_thermal_sampler().

core::Real protocols::recces::options::RECCES_Options::angle_range_free_chi ( ) const

inline

References angle_range_free_chi_.

Referenced by protocols::recces::sampler::initialize_thermal_sampler().

core::Real protocols::recces::options::RECCES_Options::base_pair_rmsd_cutoff ( ) const

inline

References base_pair_rmsd_cutoff_.

Referenced by protocols::recces::sampler::initialize_jump_sampler().

core::Real protocols::recces::options::RECCES_Options::base_pair_rotation_mag ( ) const

inline

References base_pair_rotation_mag_.

Referenced by protocols::recces::sampler::initialize_jump_sampler().

core::Real protocols::recces::options::RECCES_Options::base_pair_translation_mag ( ) const

inline

References base_pair_translation_mag_.

Referenced by protocols::recces::sampler::initialize_jump_sampler().

core::Real protocols::recces::options::RECCES_Options::bb_stdev ( ) const

inline

References bb_stdev_.

bool protocols::recces::options::RECCES_Options::blank_score_terms ( ) const

inline

References blank_score_terms_.

bool protocols::recces::options::RECCES_Options::block_stack ( ) const

inline

References block_stack_.

Referenced by protocols::recces::pose_setup_from_file().

core::Real protocols::recces::options::RECCES_Options::chi_stdev ( ) const

inline

References chi_stdev_.

RECCES_OptionsOP protocols::recces::options::RECCES_Options::clone

(

)

const

clone the options

core::Size protocols::recces::options::RECCES_Options::dump_freq ( ) const

inline

References dump_freq_.

bool protocols::recces::options::RECCES_Options::dump_pdb ( ) const

inline

References dump_pdb_.

bool protocols::recces::options::RECCES_Options::dump_silent ( ) const

inline

References dump_silent_.

utility::vector1< core::Size > protocols::recces::options::RECCES_Options::free_residues ( ) const

inline

References free_residues_.

Referenced by protocols::recces::sampler::initialize_thermal_sampler(), and protocols::recces::set_gaussian_stdevs_thermal_sampler().

core::Real protocols::recces::options::RECCES_Options::histogram_max ( ) const

inline

References histogram_max_.

core::Real protocols::recces::options::RECCES_Options::histogram_min ( ) const

inline

References histogram_min_.

core::Real protocols::recces::options::RECCES_Options::histogram_spacing ( ) const

inline

References histogram_spacing_.

std::string protocols::recces::options::RECCES_Options::infile ( ) const

inline

References infile_.

Referenced by protocols::recces::pose_setup_from_file(), and protocols::recces::recces_pose_setup().

void protocols::recces::options::RECCES_Options::initialize_from_command_line

(

)

References core::io::pdb::dump_pdb(), legacy_turner_mode(), legacy_turner_mode_, protocols::hybridization::path, rna_secstruct_, seq1(), set_a_form_range(), set_angle_range_bb(), set_angle_range_chi(), set_angle_range_free_bb(), set_angle_range_free_chi(), set_base_pair_rmsd_cutoff(), set_base_pair_rotation_mag(), set_base_pair_translation_mag(), set_bb_stdev(), set_block_stack(), set_chi_stdev(), set_dump_freq(), set_dump_pdb(), set_dump_silent(), set_free_residues(), set_histogram_max(), set_histogram_min(), set_histogram_spacing(), set_infile(), set_loop_residues(), set_n_cycle(), set_n_dump(), set_out_prefix(), set_out_torsions(), set_sample_jump(), set_sample_residues(), set_save_scores(), set_seq1(), set_seq2(), set_setup_base_pair_constraints(), set_silent_file(), set_st_weights(), set_standard_bb_stdev(), set_temperatures(), set_thermal_sampler_mode(), set_xyz_file(), and core::pose::rna::setup_base_pair_constraints().

bool protocols::recces::options::RECCES_Options::legacy_turner_mode ( ) const

inline

References legacy_turner_mode_.

Referenced by initialize_from_command_line(), protocols::recces::sampler::initialize_sampler(), protocols::recces::recces_pose_setup(), and protocols::recces::set_sampler_gaussian_stdev().

utility::vector1< core::Size > protocols::recces::options::RECCES_Options::loop_residues ( ) const

inline

References loop_residues_.

core::Size protocols::recces::options::RECCES_Options::n_cycle ( ) const

inline

References n_cycle_.

core::Size protocols::recces::options::RECCES_Options::n_dump ( ) const

inline

References n_dump_.

std::string protocols::recces::options::RECCES_Options::out_prefix ( ) const

inline

References out_prefix_.

bool protocols::recces::options::RECCES_Options::out_torsions ( ) const

inline

References out_torsions_.

bool protocols::recces::options::RECCES_Options::output_simple_text_files ( ) const

inline

References output_simple_text_files_.

virtual void protocols::recces::options::RECCES_Options::parse_my_tag ( utility::tag::TagCOP  )

inlinevirtual

Initialize from the recursive "tag" structure.

bool protocols::recces::options::RECCES_Options::prefix_each_output_pdb ( ) const

inline

References prefix_each_output_pdb_.

core::pose::rna::RNA_SecStruct protocols::recces::options::RECCES_Options::rna_secstruct ( ) const

inline

References rna_secstruct_.

Referenced by protocols::recces::sampler::initialize_sampler(), protocols::recces::recces_pose_setup(), and protocols::recces::set_sampler_gaussian_stdev().

bool protocols::recces::options::RECCES_Options::sample_jump ( ) const

inline

References sample_jump_.

Referenced by protocols::recces::sampler::initialize_sampler(), and protocols::recces::sampler::initialize_thermal_sampler().

utility::vector1< core::Size > protocols::recces::options::RECCES_Options::sample_residues ( ) const

inline

References sample_residues_.

Referenced by protocols::recces::sampler::initialize_sampler(), protocols::recces::sampler::initialize_thermal_sampler(), and protocols::recces::set_gaussian_stdevs_thermal_sampler().

bool protocols::recces::options::RECCES_Options::save_scores ( ) const

inline

References save_scores_.

std::string protocols::recces::options::RECCES_Options::seq1 ( ) const

inline

References seq1_.

Referenced by initialize_from_command_line(), and protocols::recces::recces_pose_setup().

std::string protocols::recces::options::RECCES_Options::seq2 ( ) const

inline

References seq2_.

Referenced by protocols::recces::recces_pose_setup().

void protocols::recces::options::RECCES_Options::set_a_form_range ( core::Real const &  setting )

inline

References a_form_range_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_accept_no_op_moves ( bool const &  setting )

inline

References accept_no_op_moves_.

void protocols::recces::options::RECCES_Options::set_angle_range_bb ( core::Real const &  setting )

inline

References angle_range_bb_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_angle_range_chi ( core::Real const &  setting )

inline

References angle_range_chi_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_angle_range_free_bb ( core::Real const &  setting )

inline

References angle_range_free_bb_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_angle_range_free_chi ( core::Real const &  setting )

inline

References angle_range_free_chi_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_base_pair_rmsd_cutoff ( core::Real const &  setting )

inline

References base_pair_rmsd_cutoff_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_base_pair_rotation_mag ( core::Real const &  setting )

inline

References base_pair_rotation_mag_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_base_pair_translation_mag ( core::Real const &  setting )

inline

References base_pair_translation_mag_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_bb_stdev ( core::Real const &  setting )

inline

References bb_stdev_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_blank_score_terms ( bool const &  setting )

inline

References blank_score_terms_.

void protocols::recces::options::RECCES_Options::set_block_stack ( bool const &  setting )

inline

References block_stack_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_chi_stdev ( core::Real const &  setting )

inline

References chi_stdev_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_dump_freq ( core::Size const &  setting )

inline

References dump_freq_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_dump_pdb ( bool const &  setting )

inline

References dump_pdb_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_dump_silent ( bool const &  setting )

inline

References dump_silent_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_free_residues ( utility::vector1< core::Size > const &  setting )

inline

References free_residues_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_histogram_max ( core::Real const &  setting )

inline

References histogram_max_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_histogram_min ( core::Real const &  setting )

inline

References histogram_min_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_histogram_spacing ( core::Real const &  setting )

inline

References histogram_spacing_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_infile ( std::string const &  setting )

inline

References infile_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_legacy_turner_mode ( bool const &  setting )

inline

References legacy_turner_mode_.

void protocols::recces::options::RECCES_Options::set_loop_residues ( utility::vector1< core::Size > const &  setting )

inline

References loop_residues_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_n_cycle ( core::Size const &  setting )

inline

References n_cycle_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_n_dump ( core::Size const &  setting )

inline

References n_dump_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_out_prefix ( std::string const &  setting )

inline

References out_prefix_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_out_torsions ( bool const &  setting )

inline

References out_torsions_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_output_simple_text_files ( bool const &  setting )

inline

References output_simple_text_files_.

void protocols::recces::options::RECCES_Options::set_prefix_each_output_pdb ( bool const &  setting )

inline

References prefix_each_output_pdb_.

void protocols::recces::options::RECCES_Options::set_rna_secstruct ( core::pose::rna::RNA_SecStruct const &  setting )

inline

References rna_secstruct_.

void protocols::recces::options::RECCES_Options::set_sample_jump ( bool const &  setting )

inline

References sample_jump_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_sample_residues ( utility::vector1< core::Size > const &  setting )

inline

References sample_residues_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_save_scores ( bool const &  setting )

inline

References save_scores_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_seq1 ( std::string const &  setting )

inline

References seq1_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_seq2 ( std::string const &  setting )

inline

References seq2_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_setup_base_pair_constraints ( bool const &  setting )

inline

References setup_base_pair_constraints_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_show_more_pose_scores ( bool const &  setting )

inline

References show_more_pose_scores_.

void protocols::recces::options::RECCES_Options::set_silent_file ( std::string const &  setting )

inline

References silent_file_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_skip_last_accept ( bool const &  setting )

inline

References skip_last_accept_.

void protocols::recces::options::RECCES_Options::set_st_weights ( utility::vector1< core::Real > const &  setting )

inline

References st_weights_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_standard_bb_stdev ( core::Real const &  setting )

inline

References standard_bb_stdev_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_suppress_sampler_display ( bool const &  setting )

inline

References suppress_sampler_display_.

void protocols::recces::options::RECCES_Options::set_temperatures ( utility::vector1< core::Real > const &  setting )

inline

References temperatures_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_thermal_sampler_mode ( bool const &  setting )

inline

References thermal_sampler_mode_.

Referenced by initialize_from_command_line().

void protocols::recces::options::RECCES_Options::set_xyz_file ( std::string const &  setting )

inline

References xyz_file_.

Referenced by initialize_from_command_line().

bool protocols::recces::options::RECCES_Options::setup_base_pair_constraints ( ) const

inline

References setup_base_pair_constraints_.

Referenced by protocols::recces::recces_pose_setup().

bool protocols::recces::options::RECCES_Options::show_more_pose_scores ( ) const

inline

References show_more_pose_scores_.

std::string protocols::recces::options::RECCES_Options::silent_file ( ) const

inline

References silent_file_.

bool protocols::recces::options::RECCES_Options::skip_last_accept ( ) const

inline

References skip_last_accept_.

utility::vector1< core::Real > protocols::recces::options::RECCES_Options::st_weights ( ) const

inline

References st_weights_.

core::Real protocols::recces::options::RECCES_Options::standard_bb_stdev ( ) const

inline

References standard_bb_stdev_.

bool protocols::recces::options::RECCES_Options::suppress_sampler_display ( ) const

inline

References suppress_sampler_display_.

Referenced by protocols::recces::sampler::initialize_sampler().

utility::vector1< core::Real > protocols::recces::options::RECCES_Options::temperatures ( ) const

inline

References temperatures_.

bool protocols::recces::options::RECCES_Options::thermal_sampler_mode ( ) const

inline

References thermal_sampler_mode_.

Referenced by protocols::recces::sampler::initialize_sampler(), and protocols::recces::set_sampler_gaussian_stdev().

virtual std::string protocols::recces::options::RECCES_Options::type ( ) const

inlinevirtual

The class name (its type) for a particular ResourceOptions instance. This function allows for better error message delivery.

std::string protocols::recces::options::RECCES_Options::xyz_file ( ) const

inline

References xyz_file_.

Referenced by protocols::recces::sampler::initialize_sampler().

Member Data Documentation

core::Real protocols::recces::options::RECCES_Options::a_form_range_

private

Referenced by a_form_range(), and set_a_form_range().

bool protocols::recces::options::RECCES_Options::accept_no_op_moves_

private

Referenced by accept_no_op_moves(), and set_accept_no_op_moves().

core::Real protocols::recces::options::RECCES_Options::angle_range_bb_

private

Referenced by angle_range_bb(), and set_angle_range_bb().

core::Real protocols::recces::options::RECCES_Options::angle_range_chi_

private

Referenced by angle_range_chi(), and set_angle_range_chi().

core::Real protocols::recces::options::RECCES_Options::angle_range_free_bb_

private

Referenced by angle_range_free_bb(), and set_angle_range_free_bb().

core::Real protocols::recces::options::RECCES_Options::angle_range_free_chi_

private

Referenced by angle_range_free_chi(), and set_angle_range_free_chi().

core::Real protocols::recces::options::RECCES_Options::base_pair_rmsd_cutoff_

private

Referenced by base_pair_rmsd_cutoff(), and set_base_pair_rmsd_cutoff().

core::Real protocols::recces::options::RECCES_Options::base_pair_rotation_mag_

private

Referenced by base_pair_rotation_mag(), and set_base_pair_rotation_mag().

core::Real protocols::recces::options::RECCES_Options::base_pair_translation_mag_

private

Referenced by base_pair_translation_mag(), and set_base_pair_translation_mag().

core::Real protocols::recces::options::RECCES_Options::bb_stdev_

private

Referenced by bb_stdev(), and set_bb_stdev().

bool protocols::recces::options::RECCES_Options::blank_score_terms_

private

Referenced by blank_score_terms(), and set_blank_score_terms().

bool protocols::recces::options::RECCES_Options::block_stack_

private

Referenced by block_stack(), and set_block_stack().

core::Real protocols::recces::options::RECCES_Options::chi_stdev_

private

Referenced by chi_stdev(), and set_chi_stdev().

core::Size protocols::recces::options::RECCES_Options::dump_freq_

private

Referenced by dump_freq(), and set_dump_freq().

bool protocols::recces::options::RECCES_Options::dump_pdb_

private

Referenced by dump_pdb(), and set_dump_pdb().

bool protocols::recces::options::RECCES_Options::dump_silent_

private

Referenced by dump_silent(), and set_dump_silent().

utility::vector1< core::Size > protocols::recces::options::RECCES_Options::free_residues_

private

Referenced by free_residues(), and set_free_residues().

core::Real protocols::recces::options::RECCES_Options::histogram_max_

private

Referenced by histogram_max(), and set_histogram_max().

core::Real protocols::recces::options::RECCES_Options::histogram_min_

private

Referenced by histogram_min(), and set_histogram_min().

core::Real protocols::recces::options::RECCES_Options::histogram_spacing_

private

Referenced by histogram_spacing(), and set_histogram_spacing().

std::string protocols::recces::options::RECCES_Options::infile_

private

Referenced by infile(), and set_infile().

bool protocols::recces::options::RECCES_Options::legacy_turner_mode_

private

Referenced by initialize_from_command_line(), legacy_turner_mode(), and set_legacy_turner_mode().

utility::vector1< core::Size > protocols::recces::options::RECCES_Options::loop_residues_

private

Referenced by loop_residues(), and set_loop_residues().

core::Size protocols::recces::options::RECCES_Options::n_cycle_

private

Referenced by n_cycle(), and set_n_cycle().

core::Size protocols::recces::options::RECCES_Options::n_dump_

private

Referenced by n_dump(), and set_n_dump().

std::string protocols::recces::options::RECCES_Options::out_prefix_

private

Referenced by out_prefix(), and set_out_prefix().

bool protocols::recces::options::RECCES_Options::out_torsions_

private

Referenced by out_torsions(), and set_out_torsions().

bool protocols::recces::options::RECCES_Options::output_simple_text_files_

private

Referenced by output_simple_text_files(), and set_output_simple_text_files().

bool protocols::recces::options::RECCES_Options::prefix_each_output_pdb_

private

Referenced by prefix_each_output_pdb(), and set_prefix_each_output_pdb().

core::pose::rna::RNA_SecStruct protocols::recces::options::RECCES_Options::rna_secstruct_

private

Referenced by initialize_from_command_line(), rna_secstruct(), and set_rna_secstruct().

bool protocols::recces::options::RECCES_Options::sample_jump_

private

Referenced by sample_jump(), and set_sample_jump().

utility::vector1< core::Size > protocols::recces::options::RECCES_Options::sample_residues_

private

Referenced by sample_residues(), and set_sample_residues().

bool protocols::recces::options::RECCES_Options::save_scores_

private

Referenced by save_scores(), and set_save_scores().

std::string protocols::recces::options::RECCES_Options::seq1_

private

Referenced by seq1(), and set_seq1().

std::string protocols::recces::options::RECCES_Options::seq2_

private

Referenced by seq2(), and set_seq2().

bool protocols::recces::options::RECCES_Options::setup_base_pair_constraints_

private

Referenced by set_setup_base_pair_constraints(), and setup_base_pair_constraints().

bool protocols::recces::options::RECCES_Options::show_more_pose_scores_

private

Referenced by set_show_more_pose_scores(), and show_more_pose_scores().

std::string protocols::recces::options::RECCES_Options::silent_file_

private

Referenced by set_silent_file(), and silent_file().

bool protocols::recces::options::RECCES_Options::skip_last_accept_

private

Referenced by set_skip_last_accept(), and skip_last_accept().

utility::vector1< core::Real > protocols::recces::options::RECCES_Options::st_weights_

private

Referenced by set_st_weights(), and st_weights().

core::Real protocols::recces::options::RECCES_Options::standard_bb_stdev_

private

Referenced by set_standard_bb_stdev(), and standard_bb_stdev().

bool protocols::recces::options::RECCES_Options::suppress_sampler_display_

private

Referenced by set_suppress_sampler_display(), and suppress_sampler_display().

utility::vector1< core::Real > protocols::recces::options::RECCES_Options::temperatures_

private

Referenced by set_temperatures(), and temperatures().

bool protocols::recces::options::RECCES_Options::thermal_sampler_mode_

private

Referenced by set_thermal_sampler_mode(), and thermal_sampler_mode().

std::string protocols::recces::options::RECCES_Options::xyz_file_

private

Referenced by set_xyz_file(), and xyz_file().

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

• src/protocols/recces/options/RECCES_Options.hh
• src/protocols/recces/options/RECCES_Options.cc