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

#include <RECCES_Options.hh>

Inheritance diagram for protocols::recces::options::RECCES_Options:
Inheritance graph
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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::Realtemperatures () const
 
void set_st_weights (utility::vector1< core::Real > const &setting)
 
utility::vector1< core::Realst_weights () const
 
void set_sample_residues (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Sizesample_residues () const
 
void set_free_residues (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Sizefree_residues () const
 
void set_loop_residues (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Sizeloop_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::Realtemperatures_
 
utility::vector1< core::Realst_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::Sizesample_residues_
 
utility::vector1< core::Sizefree_residues_
 
utility::vector1< core::Sizeloop_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
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
core::Real protocols::recces::options::RECCES_Options::angle_range_chi ( ) const
inline
core::Real protocols::recces::options::RECCES_Options::angle_range_free_bb ( ) const
inline
core::Real protocols::recces::options::RECCES_Options::angle_range_free_chi ( ) const
inline
core::Real protocols::recces::options::RECCES_Options::base_pair_rmsd_cutoff ( ) const
inline
core::Real protocols::recces::options::RECCES_Options::base_pair_rotation_mag ( ) const
inline
core::Real protocols::recces::options::RECCES_Options::base_pair_translation_mag ( ) const
inline
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
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
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
void protocols::recces::options::RECCES_Options::initialize_from_command_line ( )
bool protocols::recces::options::RECCES_Options::legacy_turner_mode ( ) const
inline
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
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
core::pose::rna::RNA_SecStruct protocols::recces::options::RECCES_Options::rna_secstruct ( ) const
inline
bool protocols::recces::options::RECCES_Options::sample_jump ( ) const
inline
utility::vector1< core::Size > protocols::recces::options::RECCES_Options::sample_residues ( ) const
inline
bool protocols::recces::options::RECCES_Options::save_scores ( ) const
inline

References save_scores_.

std::string protocols::recces::options::RECCES_Options::seq1 ( ) const
inline
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
void protocols::recces::options::RECCES_Options::set_angle_range_free_bb ( core::Real const &  setting)
inline
void protocols::recces::options::RECCES_Options::set_angle_range_free_chi ( core::Real const &  setting)
inline
void protocols::recces::options::RECCES_Options::set_base_pair_rmsd_cutoff ( core::Real const &  setting)
inline
void protocols::recces::options::RECCES_Options::set_base_pair_rotation_mag ( core::Real const &  setting)
inline
void protocols::recces::options::RECCES_Options::set_base_pair_translation_mag ( core::Real const &  setting)
inline
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
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
void protocols::recces::options::RECCES_Options::set_prefix_each_output_pdb ( bool const &  setting)
inline
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
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
void protocols::recces::options::RECCES_Options::set_show_more_pose_scores ( bool const &  setting)
inline
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
void protocols::recces::options::RECCES_Options::set_suppress_sampler_display ( bool const &  setting)
inline
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
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
bool protocols::recces::options::RECCES_Options::show_more_pose_scores ( ) const
inline
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
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
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

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
core::Real protocols::recces::options::RECCES_Options::angle_range_bb_
private
core::Real protocols::recces::options::RECCES_Options::angle_range_chi_
private
core::Real protocols::recces::options::RECCES_Options::angle_range_free_bb_
private
core::Real protocols::recces::options::RECCES_Options::angle_range_free_chi_
private
core::Real protocols::recces::options::RECCES_Options::base_pair_rmsd_cutoff_
private
core::Real protocols::recces::options::RECCES_Options::base_pair_rotation_mag_
private
core::Real protocols::recces::options::RECCES_Options::base_pair_translation_mag_
private
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
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
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
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
bool protocols::recces::options::RECCES_Options::prefix_each_output_pdb_
private
core::pose::rna::RNA_SecStruct protocols::recces::options::RECCES_Options::rna_secstruct_
private
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
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
bool protocols::recces::options::RECCES_Options::show_more_pose_scores_
private
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
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
bool protocols::recces::options::RECCES_Options::suppress_sampler_display_
private
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
std::string protocols::recces::options::RECCES_Options::xyz_file_
private

Referenced by set_xyz_file(), and xyz_file().


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