#include <RECCES_Options.hh>
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 |
Constructor & Destructor Documentation
◆ RECCES_Options()
| protocols::recces::options::RECCES_Options::RECCES_Options | ( | ) |
Member Function Documentation
◆ a_form_range()
|
inline |
References a_form_range_.
Referenced by protocols::recces::sampler::initialize_sampler().
◆ accept_no_op_moves()
|
inline |
References accept_no_op_moves_.
◆ angle_range_bb()
|
inline |
References angle_range_bb_.
Referenced by protocols::recces::sampler::initialize_thermal_sampler().
◆ angle_range_chi()
|
inline |
References angle_range_chi_.
Referenced by protocols::recces::sampler::initialize_thermal_sampler().
◆ angle_range_free_bb()
|
inline |
References angle_range_free_bb_.
Referenced by protocols::recces::sampler::initialize_thermal_sampler().
◆ angle_range_free_chi()
|
inline |
References angle_range_free_chi_.
Referenced by protocols::recces::sampler::initialize_thermal_sampler().
◆ base_pair_rmsd_cutoff()
|
inline |
References base_pair_rmsd_cutoff_.
Referenced by protocols::recces::sampler::initialize_jump_sampler().
◆ base_pair_rotation_mag()
|
inline |
References base_pair_rotation_mag_.
Referenced by protocols::recces::sampler::initialize_jump_sampler().
◆ base_pair_translation_mag()
|
inline |
References base_pair_translation_mag_.
Referenced by protocols::recces::sampler::initialize_jump_sampler().
◆ bb_stdev()
|
inline |
References bb_stdev_.
◆ blank_score_terms()
|
inline |
References blank_score_terms_.
◆ block_stack()
|
inline |
References block_stack_.
Referenced by protocols::recces::pose_setup_from_file().
◆ chi_stdev()
|
inline |
References chi_stdev_.
◆ clone()
| RECCES_OptionsOP protocols::recces::options::RECCES_Options::clone | ( | ) | const |
clone the options
◆ dump_freq()
|
inline |
References dump_freq_.
◆ dump_pdb()
|
inline |
References dump_pdb_.
◆ dump_silent()
|
inline |
References dump_silent_.
◆ free_residues()
|
inline |
References free_residues_.
Referenced by protocols::recces::sampler::initialize_thermal_sampler(), and protocols::recces::set_gaussian_stdevs_thermal_sampler().
◆ histogram_max()
|
inline |
References histogram_max_.
◆ histogram_min()
|
inline |
References histogram_min_.
◆ histogram_spacing()
|
inline |
References histogram_spacing_.
◆ infile()
|
inline |
References infile_.
Referenced by protocols::recces::pose_setup_from_file(), and protocols::recces::recces_pose_setup().
◆ initialize_from_command_line()
| 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().
◆ legacy_turner_mode()
|
inline |
◆ loop_residues()
|
inline |
References loop_residues_.
◆ n_cycle()
|
inline |
References n_cycle_.
◆ n_dump()
|
inline |
References n_dump_.
◆ out_prefix()
|
inline |
References out_prefix_.
◆ out_torsions()
|
inline |
References out_torsions_.
◆ output_simple_text_files()
|
inline |
References output_simple_text_files_.
◆ parse_my_tag()
|
inlinevirtual |
Initialize from the recursive "tag" structure.
◆ prefix_each_output_pdb()
|
inline |
References prefix_each_output_pdb_.
◆ rna_secstruct()
|
inline |
◆ sample_jump()
|
inline |
References sample_jump_.
Referenced by protocols::recces::sampler::initialize_sampler(), and protocols::recces::sampler::initialize_thermal_sampler().
◆ sample_residues()
|
inline |
◆ save_scores()
|
inline |
References save_scores_.
◆ seq1()
|
inline |
References seq1_.
Referenced by initialize_from_command_line(), and protocols::recces::recces_pose_setup().
◆ seq2()
|
inline |
References seq2_.
Referenced by protocols::recces::recces_pose_setup().
◆ set_a_form_range()
|
inline |
References a_form_range_.
Referenced by initialize_from_command_line().
◆ set_accept_no_op_moves()
|
inline |
References accept_no_op_moves_.
◆ set_angle_range_bb()
|
inline |
References angle_range_bb_.
Referenced by initialize_from_command_line().
◆ set_angle_range_chi()
|
inline |
References angle_range_chi_.
Referenced by initialize_from_command_line().
◆ set_angle_range_free_bb()
|
inline |
References angle_range_free_bb_.
Referenced by initialize_from_command_line().
◆ set_angle_range_free_chi()
|
inline |
References angle_range_free_chi_.
Referenced by initialize_from_command_line().
◆ set_base_pair_rmsd_cutoff()
|
inline |
References base_pair_rmsd_cutoff_.
Referenced by initialize_from_command_line().
◆ set_base_pair_rotation_mag()
|
inline |
References base_pair_rotation_mag_.
Referenced by initialize_from_command_line().
◆ set_base_pair_translation_mag()
|
inline |
References base_pair_translation_mag_.
Referenced by initialize_from_command_line().
◆ set_bb_stdev()
|
inline |
References bb_stdev_.
Referenced by initialize_from_command_line().
◆ set_blank_score_terms()
|
inline |
References blank_score_terms_.
◆ set_block_stack()
|
inline |
References block_stack_.
Referenced by initialize_from_command_line().
◆ set_chi_stdev()
|
inline |
References chi_stdev_.
Referenced by initialize_from_command_line().
◆ set_dump_freq()
|
inline |
References dump_freq_.
Referenced by initialize_from_command_line().
◆ set_dump_pdb()
|
inline |
References dump_pdb_.
Referenced by initialize_from_command_line().
◆ set_dump_silent()
|
inline |
References dump_silent_.
Referenced by initialize_from_command_line().
◆ set_free_residues()
|
inline |
References free_residues_.
Referenced by initialize_from_command_line().
◆ set_histogram_max()
|
inline |
References histogram_max_.
Referenced by initialize_from_command_line().
◆ set_histogram_min()
|
inline |
References histogram_min_.
Referenced by initialize_from_command_line().
◆ set_histogram_spacing()
|
inline |
References histogram_spacing_.
Referenced by initialize_from_command_line().
◆ set_infile()
|
inline |
References infile_.
Referenced by initialize_from_command_line().
◆ set_legacy_turner_mode()
|
inline |
References legacy_turner_mode_.
◆ set_loop_residues()
|
inline |
References loop_residues_.
Referenced by initialize_from_command_line().
◆ set_n_cycle()
|
inline |
References n_cycle_.
Referenced by initialize_from_command_line().
◆ set_n_dump()
|
inline |
References n_dump_.
Referenced by initialize_from_command_line().
◆ set_out_prefix()
|
inline |
References out_prefix_.
Referenced by initialize_from_command_line().
◆ set_out_torsions()
|
inline |
References out_torsions_.
Referenced by initialize_from_command_line().
◆ set_output_simple_text_files()
|
inline |
References output_simple_text_files_.
◆ set_prefix_each_output_pdb()
|
inline |
References prefix_each_output_pdb_.
◆ set_rna_secstruct()
|
inline |
References rna_secstruct_.
◆ set_sample_jump()
|
inline |
References sample_jump_.
Referenced by initialize_from_command_line().
◆ set_sample_residues()
|
inline |
References sample_residues_.
Referenced by initialize_from_command_line().
◆ set_save_scores()
|
inline |
References save_scores_.
Referenced by initialize_from_command_line().
◆ set_seq1()
|
inline |
References seq1_.
Referenced by initialize_from_command_line().
◆ set_seq2()
|
inline |
References seq2_.
Referenced by initialize_from_command_line().
◆ set_setup_base_pair_constraints()
|
inline |
References setup_base_pair_constraints_.
Referenced by initialize_from_command_line().
◆ set_show_more_pose_scores()
|
inline |
References show_more_pose_scores_.
◆ set_silent_file()
|
inline |
References silent_file_.
Referenced by initialize_from_command_line().
◆ set_skip_last_accept()
|
inline |
References skip_last_accept_.
◆ set_st_weights()
|
inline |
References st_weights_.
Referenced by initialize_from_command_line().
◆ set_standard_bb_stdev()
|
inline |
References standard_bb_stdev_.
Referenced by initialize_from_command_line().
◆ set_suppress_sampler_display()
|
inline |
References suppress_sampler_display_.
◆ set_temperatures()
|
inline |
References temperatures_.
Referenced by initialize_from_command_line().
◆ set_thermal_sampler_mode()
|
inline |
References thermal_sampler_mode_.
Referenced by initialize_from_command_line().
◆ set_xyz_file()
|
inline |
References xyz_file_.
Referenced by initialize_from_command_line().
◆ setup_base_pair_constraints()
|
inline |
References setup_base_pair_constraints_.
Referenced by protocols::recces::recces_pose_setup().
◆ show_more_pose_scores()
|
inline |
References show_more_pose_scores_.
◆ silent_file()
|
inline |
References silent_file_.
◆ skip_last_accept()
|
inline |
References skip_last_accept_.
◆ st_weights()
|
inline |
References st_weights_.
◆ standard_bb_stdev()
|
inline |
References standard_bb_stdev_.
◆ suppress_sampler_display()
|
inline |
References suppress_sampler_display_.
Referenced by protocols::recces::sampler::initialize_sampler().
◆ temperatures()
|
inline |
References temperatures_.
◆ thermal_sampler_mode()
|
inline |
References thermal_sampler_mode_.
Referenced by protocols::recces::sampler::initialize_sampler(), and protocols::recces::set_sampler_gaussian_stdev().
◆ type()
|
inlinevirtual |
The class name (its type) for a particular ResourceOptions instance. This function allows for better error message delivery.
◆ xyz_file()
|
inline |
References xyz_file_.
Referenced by protocols::recces::sampler::initialize_sampler().
Member Data Documentation
◆ a_form_range_
|
private |
Referenced by a_form_range(), and set_a_form_range().
◆ accept_no_op_moves_
|
private |
Referenced by accept_no_op_moves(), and set_accept_no_op_moves().
◆ angle_range_bb_
|
private |
Referenced by angle_range_bb(), and set_angle_range_bb().
◆ angle_range_chi_
|
private |
Referenced by angle_range_chi(), and set_angle_range_chi().
◆ angle_range_free_bb_
|
private |
Referenced by angle_range_free_bb(), and set_angle_range_free_bb().
◆ angle_range_free_chi_
|
private |
Referenced by angle_range_free_chi(), and set_angle_range_free_chi().
◆ base_pair_rmsd_cutoff_
|
private |
Referenced by base_pair_rmsd_cutoff(), and set_base_pair_rmsd_cutoff().
◆ base_pair_rotation_mag_
|
private |
Referenced by base_pair_rotation_mag(), and set_base_pair_rotation_mag().
◆ base_pair_translation_mag_
|
private |
Referenced by base_pair_translation_mag(), and set_base_pair_translation_mag().
◆ bb_stdev_
|
private |
Referenced by bb_stdev(), and set_bb_stdev().
◆ blank_score_terms_
|
private |
Referenced by blank_score_terms(), and set_blank_score_terms().
◆ block_stack_
|
private |
Referenced by block_stack(), and set_block_stack().
◆ chi_stdev_
|
private |
Referenced by chi_stdev(), and set_chi_stdev().
◆ dump_freq_
|
private |
Referenced by dump_freq(), and set_dump_freq().
◆ dump_pdb_
|
private |
Referenced by dump_pdb(), and set_dump_pdb().
◆ dump_silent_
|
private |
Referenced by dump_silent(), and set_dump_silent().
◆ free_residues_
|
private |
Referenced by free_residues(), and set_free_residues().
◆ histogram_max_
|
private |
Referenced by histogram_max(), and set_histogram_max().
◆ histogram_min_
|
private |
Referenced by histogram_min(), and set_histogram_min().
◆ histogram_spacing_
|
private |
Referenced by histogram_spacing(), and set_histogram_spacing().
◆ infile_
|
private |
Referenced by infile(), and set_infile().
◆ legacy_turner_mode_
|
private |
Referenced by initialize_from_command_line(), legacy_turner_mode(), and set_legacy_turner_mode().
◆ loop_residues_
|
private |
Referenced by loop_residues(), and set_loop_residues().
◆ n_cycle_
|
private |
Referenced by n_cycle(), and set_n_cycle().
◆ n_dump_
|
private |
Referenced by n_dump(), and set_n_dump().
◆ out_prefix_
|
private |
Referenced by out_prefix(), and set_out_prefix().
◆ out_torsions_
|
private |
Referenced by out_torsions(), and set_out_torsions().
◆ output_simple_text_files_
|
private |
Referenced by output_simple_text_files(), and set_output_simple_text_files().
◆ prefix_each_output_pdb_
|
private |
Referenced by prefix_each_output_pdb(), and set_prefix_each_output_pdb().
◆ rna_secstruct_
|
private |
Referenced by initialize_from_command_line(), rna_secstruct(), and set_rna_secstruct().
◆ sample_jump_
|
private |
Referenced by sample_jump(), and set_sample_jump().
◆ sample_residues_
|
private |
Referenced by sample_residues(), and set_sample_residues().
◆ save_scores_
|
private |
Referenced by save_scores(), and set_save_scores().
◆ seq1_
|
private |
Referenced by seq1(), and set_seq1().
◆ seq2_
|
private |
Referenced by seq2(), and set_seq2().
◆ setup_base_pair_constraints_
|
private |
Referenced by set_setup_base_pair_constraints(), and setup_base_pair_constraints().
◆ show_more_pose_scores_
|
private |
Referenced by set_show_more_pose_scores(), and show_more_pose_scores().
◆ silent_file_
|
private |
Referenced by set_silent_file(), and silent_file().
◆ skip_last_accept_
|
private |
Referenced by set_skip_last_accept(), and skip_last_accept().
◆ st_weights_
|
private |
Referenced by set_st_weights(), and st_weights().
◆ standard_bb_stdev_
|
private |
Referenced by set_standard_bb_stdev(), and standard_bb_stdev().
◆ suppress_sampler_display_
|
private |
Referenced by set_suppress_sampler_display(), and suppress_sampler_display().
◆ temperatures_
|
private |
Referenced by set_temperatures(), and temperatures().
◆ thermal_sampler_mode_
|
private |
Referenced by set_thermal_sampler_mode(), and thermal_sampler_mode().
◆ xyz_file_
|
private |
Referenced by set_xyz_file(), and xyz_file().
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
