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Rosetta
2020.50
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#include <StepWiseMonteCarloOptions.hh>
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static void | list_options_read (utility::options::OptionKeyList &opts) |
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static void | list_options_read (utility::options::OptionKeyList &opt) |
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static void | list_options_read (utility::options::OptionKeyList &opts) |
Additional Inherited Members | |
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void | initialize_from_command_line () |
void | initialize_from_options_collection (utility::options::OptionCollection const &options) |
void | initialize_variables () |
protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::StepWiseMonteCarloOptions | ( | ) |
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References add_proposal_density_factor_.
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References allow_split_off_.
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References allow_virtual_o2prime_hydrogens_.
Referenced by setup_modeler_options().
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References allow_virtual_side_chains_.
Referenced by setup_modeler_options().
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References chainbreak_weight_.
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References checkpoint_.
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References checkpointing_frequency_.
StepWiseMonteCarloOptionsOP protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::clone | ( | ) | const |
clone the options
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References continue_until_none_missing_.
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References cycles_.
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References designing_with_noncanonicals_.
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References enumerate_.
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References erraser_.
Referenced by setup_modeler_options().
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References eval_base_pairs_.
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References exclude_submotifs_.
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References filter_native_big_bins_.
Referenced by setup_modeler_options().
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References force_centroid_interaction_.
Referenced by setup_modeler_options().
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References force_moving_res_for_erraser_.
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References force_phosphate_instantiation_.
Referenced by setup_modeler_options().
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::initialize_from_command_line | ( | ) |
References initialize_from_options_collection().
void protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::initialize_from_options_collection | ( | utility::options::OptionCollection const & | options | ) |
References allow_virtual_o2prime_hydrogens_, allow_virtual_side_chains_, checkpoint_, checkpointing_frequency_, continue_until_none_missing_, designing_with_noncanonicals_, enumerate_, eval_base_pairs_, exclude_submotifs_, filter_native_big_bins_, force_centroid_interaction_, force_moving_res_for_erraser_, force_phosphate_instantiation_, force_submotif_without_intervening_bulge_, local_redock_only_, n_sample_, new_move_selector_, o2prime_legacy_mode_, pack_protein_side_chains_, preminimize_, protein_prepack_, rebuild_bulge_mode_, recover_low_, sampler_max_centroid_distance_, sampler_perform_phosphate_pack_, save_times_, set_add_proposal_density_factor(), set_allow_split_off(), set_cycles(), set_erraser(), set_force_centroid_interaction(), set_integration_test_mode(), set_just_min_after_mutation_frequency(), set_make_movie(), set_minimize_after_delete(), set_minimize_single_res_frequency(), protocols::stepwise::options::StepWiseBasicOptions::set_num_pose_minimize(), protocols::stepwise::options::StepWiseBasicOptions::set_num_random_samples(), protocols::stepwise::options::StepWiseBasicOptions::set_silent_file(), set_temperature(), set_use_phenix_geo(), set_verbose_scores(), set_virtual_sugar_do_minimize(), set_virtual_sugar_keep_base_fixed(), skip_coord_constraints_, skip_preminimize_, superimpose_over_all_, test_all_moves_, tether_jump_, use_first_jump_for_submotif_, use_precomputed_library_, and virtualize_packable_moieties_in_screening_pose_.
Referenced by initialize_from_command_line().
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References integration_test_mode_.
Referenced by setup_modeler_options().
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References just_min_after_mutation_frequency_.
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References local_redock_only_.
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References make_movie_.
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References max_missing_weight_.
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References minimize_after_delete_.
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References minimize_single_res_frequency_.
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References n_sample_.
Referenced by setup_modeler_options().
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References new_move_selector_.
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References o2prime_legacy_mode_.
Referenced by setup_modeler_options().
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References pack_protein_side_chains_.
Referenced by setup_modeler_options().
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Initialize from the recursive "tag" structure.
Reimplemented from protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions.
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References preminimize_.
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References protein_prepack_.
Referenced by setup_modeler_options().
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References rebuild_bulge_mode_.
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References recover_low_.
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References sampler_max_centroid_distance_.
Referenced by setup_modeler_options().
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References sampler_perform_phosphate_pack_.
Referenced by setup_modeler_options().
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References save_times_.
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References add_proposal_density_factor_.
Referenced by initialize_from_options_collection().
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References allow_split_off_.
Referenced by initialize_from_options_collection().
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References allow_virtual_o2prime_hydrogens_.
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References allow_virtual_side_chains_.
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References chainbreak_weight_.
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References checkpoint_.
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References checkpointing_frequency_.
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References continue_until_none_missing_.
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References cycles_.
Referenced by initialize_from_options_collection().
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References designing_with_noncanonicals_.
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References enumerate_.
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References erraser_.
Referenced by initialize_from_options_collection().
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References eval_base_pairs_.
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References exclude_submotifs_.
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References filter_native_big_bins_.
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References force_centroid_interaction_.
Referenced by initialize_from_options_collection().
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References force_moving_res_for_erraser_.
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References force_phosphate_instantiation_.
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References integration_test_mode_.
Referenced by initialize_from_options_collection().
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References just_min_after_mutation_frequency_.
Referenced by initialize_from_options_collection().
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References local_redock_only_.
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References make_movie_.
Referenced by initialize_from_options_collection().
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References max_missing_weight_.
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References minimize_after_delete_.
Referenced by initialize_from_options_collection().
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References minimize_single_res_frequency_.
Referenced by initialize_from_options_collection().
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References n_sample_.
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References new_move_selector_.
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References o2prime_legacy_mode_.
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References pack_protein_side_chains_.
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References preminimize_.
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References protein_prepack_.
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References rebuild_bulge_mode_.
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References recover_low_.
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References sampler_max_centroid_distance_.
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References sampler_perform_phosphate_pack_.
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References save_times_.
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References skip_coord_constraints_.
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References skip_deletions_.
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References skip_preminimize_.
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References superimpose_over_all_.
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References temperature_.
Referenced by initialize_from_options_collection().
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References test_all_moves_.
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References tether_jump_.
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References use_first_jump_for_submotif_.
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References use_phenix_geo_.
Referenced by initialize_from_options_collection().
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References use_precomputed_library_.
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References verbose_scores_.
Referenced by initialize_from_options_collection().
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References virtual_sugar_do_minimize_.
Referenced by initialize_from_options_collection().
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References virtual_sugar_keep_base_fixed_.
Referenced by initialize_from_options_collection().
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References virtualize_packable_moieties_in_screening_pose_.
protocols::stepwise::modeler::options::StepWiseModelerOptionsOP protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::setup_modeler_options | ( | ) | const |
References allow_virtual_o2prime_hydrogens(), allow_virtual_side_chains(), protocols::stepwise::options::StepWiseBasicOptions::atr_rep_screen(), enumerate_, erraser(), filter_native_big_bins(), force_centroid_interaction(), force_phosphate_instantiation(), integration_test_mode(), n_sample(), protocols::stepwise::options::StepWiseBasicOptions::num_pose_minimize(), protocols::stepwise::options::StepWiseBasicOptions::num_random_samples(), o2prime_legacy_mode(), pack_protein_side_chains(), preminimize_, protein_prepack(), rebuild_bulge_mode_, protocols::stepwise::options::StepWiseBasicOptions::rmsd_screen(), sampler_max_centroid_distance(), sampler_perform_phosphate_pack(), protocols::stepwise::options::StepWiseBasicOptions::set_num_pose_minimize(), skip_coord_constraints(), tether_jump(), use_phenix_geo(), protocols::stepwise::options::StepWiseBasicOptions::VDW_rep_screen_info(), virtual_sugar_do_minimize(), virtual_sugar_keep_base_fixed(), and virtualize_packable_moieties_in_screening_pose().
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Describe this instance to a given output stream.
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References skip_coord_constraints_.
Referenced by setup_modeler_options().
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References skip_deletions_.
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References skip_preminimize_.
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References superimpose_over_all_.
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References temperature_.
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References test_all_moves_.
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References tether_jump_.
Referenced by setup_modeler_options().
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The class name (its type) for a particular instance. This function allows for better error message delivery.
Reimplemented from protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions.
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References use_first_jump_for_submotif_.
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References use_phenix_geo_.
Referenced by setup_modeler_options().
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References use_precomputed_library_.
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References verbose_scores_.
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References virtual_sugar_do_minimize_.
Referenced by setup_modeler_options().
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References virtual_sugar_keep_base_fixed_.
Referenced by setup_modeler_options().
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References virtualize_packable_moieties_in_screening_pose_.
Referenced by setup_modeler_options().
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Referenced by add_proposal_density_factor(), and set_add_proposal_density_factor().
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Referenced by allow_split_off(), and set_allow_split_off().
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Referenced by chainbreak_weight(), and set_chainbreak_weight().
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Referenced by checkpoint(), initialize_from_options_collection(), and set_checkpoint().
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Referenced by checkpointing_frequency(), initialize_from_options_collection(), and set_checkpointing_frequency().
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Referenced by cycles(), and set_cycles().
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Referenced by enumerate(), initialize_from_options_collection(), set_enumerate(), and setup_modeler_options().
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Referenced by erraser(), and set_erraser().
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Referenced by eval_base_pairs(), initialize_from_options_collection(), and set_eval_base_pairs().
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Referenced by exclude_submotifs(), initialize_from_options_collection(), and set_exclude_submotifs().
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Referenced by filter_native_big_bins(), initialize_from_options_collection(), and set_filter_native_big_bins().
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Referenced by initialize_from_options_collection().
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Referenced by integration_test_mode(), and set_integration_test_mode().
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Referenced by just_min_after_mutation_frequency(), and set_just_min_after_mutation_frequency().
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Referenced by initialize_from_options_collection(), local_redock_only(), and set_local_redock_only().
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Referenced by make_movie(), and set_make_movie().
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Referenced by max_missing_weight(), and set_max_missing_weight().
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Referenced by minimize_after_delete(), and set_minimize_after_delete().
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Referenced by minimize_single_res_frequency(), and set_minimize_single_res_frequency().
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Referenced by initialize_from_options_collection(), n_sample(), and set_n_sample().
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Referenced by initialize_from_options_collection(), new_move_selector(), and set_new_move_selector().
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Referenced by initialize_from_options_collection(), o2prime_legacy_mode(), and set_o2prime_legacy_mode().
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Referenced by initialize_from_options_collection(), pack_protein_side_chains(), and set_pack_protein_side_chains().
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Referenced by initialize_from_options_collection(), preminimize(), set_preminimize(), and setup_modeler_options().
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Referenced by initialize_from_options_collection(), protein_prepack(), and set_protein_prepack().
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Referenced by initialize_from_options_collection(), recover_low(), and set_recover_low().
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Referenced by initialize_from_options_collection(), save_times(), and set_save_times().
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Referenced by initialize_from_options_collection(), set_skip_coord_constraints(), and skip_coord_constraints().
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Referenced by set_skip_deletions(), and skip_deletions().
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Referenced by initialize_from_options_collection(), set_skip_preminimize(), and skip_preminimize().
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Referenced by initialize_from_options_collection(), set_superimpose_over_all(), and superimpose_over_all().
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Referenced by set_temperature(), and temperature().
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Referenced by initialize_from_options_collection(), set_test_all_moves(), and test_all_moves().
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Referenced by initialize_from_options_collection(), set_tether_jump(), and tether_jump().
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Referenced by set_use_phenix_geo(), and use_phenix_geo().
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Referenced by initialize_from_options_collection(), set_use_precomputed_library(), and use_precomputed_library().
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Referenced by set_verbose_scores(), and verbose_scores().
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Referenced by set_virtual_sugar_do_minimize(), and virtual_sugar_do_minimize().
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Referenced by set_virtual_sugar_keep_base_fixed(), and virtual_sugar_keep_base_fixed().
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