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protocols::stepwise::modeler::options::StepWiseModelerOptions Class Reference

#include <StepWiseModelerOptions.hh>

Inheritance diagram for protocols::stepwise::modeler::options::StepWiseModelerOptions:
Inheritance graph
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Public Member Functions

 StepWiseModelerOptions ()
 
StepWiseModelerOptionsOP clone () const
 clone the options More...
 
void show (std::ostream &) const override
 Describe this instance to a given output stream. More...
 
void parse_my_tag (utility::tag::TagCOP) override
 Initialize from the recursive "tag" structure. More...
 
std::string type () const override
 The class name (its type) for a particular instance. This function allows for better error message delivery. More...
 
void initialize_from_command_line ()
 
void setup_options_for_VDW_bin_checker (rna::checker::RNA_VDW_BinCheckerOP user_input_VDW_bin_checker) const
 
StepWiseModelerOptionsOP get_sampler_options () const
 
- Public Member Functions inherited from protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
 StepWiseBasicModelerOptions ()
 
StepWiseBasicModelerOptionsOP clone () const
 clone the options More...
 
bool use_green_packer () const
 
void set_use_green_packer (bool const &setting)
 
bool verbose () const
 
void set_verbose (bool const &setting)
 
bool choose_random () const
 
void set_choose_random (bool const &setting)
 
void set_dump (bool const &setting)
 
bool dump () const
 
void set_skip_minimize (bool const &setting)
 
bool skip_minimize () const
 
bool disallow_realign () const
 
void set_disallow_realign (bool const setting)
 
bool coordinate_constraints_during_minimize () const
 
void set_coordinate_constraints_during_minimize (bool const setting)
 
bool virtualize_packable_moieties_in_screening_pose () const
 
void set_virtualize_packable_moieties_in_screening_pose (bool const setting)
 
- Public Member Functions inherited from protocols::stepwise::options::StepWiseBasicOptions
 StepWiseBasicOptions ()
 
StepWiseBasicOptionsOP clone () const
 clone the options More...
 
std::string const & silent_file () const
 
void set_silent_file (std::string const &setting)
 
std::string const & sampler_silent_file () const
 
void set_sampler_silent_file (std::string const &setting)
 
core::Size sampler_num_pose_kept () const
 
void set_sampler_num_pose_kept (core::Size const &setting)
 
core::Real cluster_rmsd () const
 
void set_cluster_rmsd (core::Real const &setting)
 
core::Size num_pose_minimize () const
 
void set_num_pose_minimize (core::Size const &setting)
 
core::Size num_random_samples () const
 
void set_num_random_samples (core::Size const &setting)
 
core::Size max_tries_multiplier_for_ccd () const
 
void set_max_tries_multiplier_for_ccd (core::Size const &setting)
 
void set_atr_rep_screen (bool const &setting)
 
bool atr_rep_screen () const
 
void set_atr_rep_screen_for_docking (bool const &setting)
 
bool atr_rep_screen_for_docking () const
 
utility::vector1< std::string >
const & 
VDW_rep_screen_info () const
 
void set_VDW_rep_screen_info (utility::vector1< std::string > const &setting)
 
void set_rmsd_screen (core::Real const &setting)
 
core::Real rmsd_screen () const
 
bool output_minimized_pose_list () const
 
void set_output_minimized_pose_list (bool const &setting)
 
bool output_cluster_size () const
 
void set_output_cluster_size (bool const &setting)
 
void set_min_type (std::string const &setting)
 
std::string min_type () const
 
void set_min_tolerance (core::Real const &setting)
 
core::Real min_tolerance () const
 
bool vary_rna_bond_geometry () const
 
void set_vary_rna_bond_geometry (bool const &setting)
 
bool vary_polar_hydrogen_geometry () const
 
void set_vary_polar_hydrogen_geometry (bool const &setting)
 
void set_disallow_pack_polar_hydrogens (bool const &setting)
 
bool disallow_pack_polar_hydrogens () const
 
void set_use_packer_instead_of_rotamer_trials (bool const &setting)
 
bool use_packer_instead_of_rotamer_trials () const
 
bool mapfile_activated () const
 
void set_mapfile_activated (bool const &setting)
 
void set_lores (bool const &setting)
 
bool lores () const
 
void set_verbose_sampler (bool const &setting)
 
bool verbose_sampler () const
 
void set_minimize_waters (bool const &setting)
 
bool minimize_waters () const
 
void set_hydrate_magnesiums (bool const &setting)
 
bool hydrate_magnesiums () const
 
void set_test_all_mg_hydration_frames (bool const &setting)
 
bool test_all_mg_hydration_frames () const
 
modeler::MinimizerMode const & minimizer_mode () const
 
void set_minimizer_mode (modeler::MinimizerMode const &setting)
 
core::Size n_cycles () const
 
void set_n_cycles (core::Size const setting)
 
core::Real thermal_sampler_temperature () const
 
void set_thermal_sampler_output_min_pose (bool const setting)
 
bool thermal_sampler_output_min_pose () const
 
void set_sample_pH (bool const setting)
 
bool sample_pH () const
 
bool boltzmann_choice_post_enumerated_minimize () const
 
void set_boltzmann_choice_post_enumerated_minimize (bool const setting)
 
- Public Member Functions inherited from protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
 StepWiseProteinModelerOptions ()
 
StepWiseProteinModelerOptionsOP clone () const
 clone the options More...
 
void initialize_from_command_line ()
 
void set_global_optimize (bool const &setting)
 
bool global_optimize () const
 
void set_sample_beta (bool const &setting)
 
bool sample_beta () const
 
void set_move_jumps_between_chains (bool const &setting)
 
bool move_jumps_between_chains () const
 
void set_disable_sampling_of_loop_takeoff (bool const &setting)
 
bool disable_sampling_of_loop_takeoff () const
 
void set_cart_min (bool const &setting)
 
bool cart_min () const
 
void set_n_sample (core::Size const &setting)
 
core::Size n_sample () const
 
void set_filter_native_big_bins (bool const &setting)
 
bool filter_native_big_bins () const
 
void set_allow_virtual_side_chains (bool const &setting)
 
bool allow_virtual_side_chains () const
 
void set_prepack (bool const &setting)
 
bool prepack () const
 
void set_pack_protein_side_chains (bool const &setting)
 
bool pack_protein_side_chains () const
 
void set_centroid_output (bool const &setting)
 
bool centroid_output () const
 
void set_centroid_screen (bool const &setting)
 
bool centroid_screen () const
 
void set_centroid_score_diff_cut (core::Real const &setting)
 
core::Real centroid_score_diff_cut () const
 
void set_centroid_weights (std::string const &setting)
 
std::string centroid_weights () const
 
void set_nstruct_centroid (core::Size const &setting)
 
core::Size nstruct_centroid () const
 
void set_ghost_loops (bool const &setting)
 
bool ghost_loops () const
 
void set_ccd_close (bool const &setting)
 
bool ccd_close () const
 
void set_cluster_by_all_atom_rmsd (bool const &setting)
 
bool cluster_by_all_atom_rmsd () const
 
void set_pack_weights (std::string const &setting)
 
std::string pack_weights () const
 
bool const & expand_loop_takeoff () const
 
void set_expand_loop_takeoff (bool const &setting)
 
bool const & skip_coord_constraints () const
 
void set_skip_coord_constraints (bool const &setting)
 
void set_frag_files (utility::vector1< std::string > const &setting)
 
utility::vector1< std::string > frag_files () const
 
void set_bridge_res (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Sizebridge_res () const
 
- Public Member Functions inherited from protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
 StepWiseRNA_ModelerOptions ()
 
StepWiseRNA_ModelerOptionsOP clone () const
 clone the options More...
 
void initialize_from_command_line ()
 
core::Real const & native_edensity_score_cutoff () const
 
void set_native_edensity_score_cutoff (core::Real const &setting)
 
bool const & o2prime_legacy_mode () const
 
void set_o2prime_legacy_mode (bool const &setting)
 
bool const & allow_virtual_o2prime_hydrogens () const
 
void set_allow_virtual_o2prime_hydrogens (bool const &setting)
 
bool const & sampler_perform_phosphate_pack () const
 
void set_sampler_perform_phosphate_pack (bool const &setting)
 
bool const & force_phosphate_instantiation () const
 
void set_force_phosphate_instantiation (bool const &setting)
 
bool const & distinguish_pucker () const
 
void set_distinguish_pucker (bool const &setting)
 
bool const & finer_sampling_at_chain_closure () const
 
void set_finer_sampling_at_chain_closure (bool const &setting)
 
bool const & PBP_clustering_at_chain_closure () const
 
void set_PBP_clustering_at_chain_closure (bool const &setting)
 
bool const & allow_syn_pyrimidine () const
 
void set_allow_syn_pyrimidine (bool const &setting)
 
bool const & extra_chi () const
 
void set_extra_chi (bool const &setting)
 
void set_sample_all_chi (bool const &setting)
 
bool sample_all_chi () const
 
bool const & use_phenix_geo () const
 
void set_use_phenix_geo (bool const &setting)
 
bool const & virtual_sugar_legacy_mode () const
 
void set_virtual_sugar_legacy_mode (bool const &setting)
 
bool const & virtual_sugar_keep_base_fixed () const
 
void set_virtual_sugar_keep_base_fixed (bool const &setting)
 
bool const & virtual_sugar_do_minimize () const
 
void set_virtual_sugar_do_minimize (bool const &setting)
 
bool const & virtual_sugar_do_screens () const
 
void set_virtual_sugar_do_screens (bool const &setting)
 
bool const & kic_modeler_if_relevant () const
 
void set_kic_modeler_if_relevant (bool const &setting)
 
bool const & force_centroid_interaction () const
 
void set_force_centroid_interaction (bool const &setting)
 
bool const & minimize_and_score_sugar () const
 
void set_minimize_and_score_sugar (bool const &setting)
 
bool const & minimize_and_score_native_pose () const
 
void set_minimize_and_score_native_pose (bool const &setting)
 
bool const & rm_virt_phosphate () const
 
void set_rm_virt_phosphate (bool const &setting)
 
core::Real const & VDW_rep_alignment_RMSD_CUTOFF () const
 
void set_VDW_rep_alignment_RMSD_CUTOFF (core::Real const &setting)
 
core::Real const & sampler_max_centroid_distance () const
 
void set_sampler_max_centroid_distance (core::Real const &setting)
 
utility::vector1< std::string >
const & 
VDW_rep_delete_matching_res () const
 
void set_VDW_rep_delete_matching_res (utility::vector1< std::string > const &setting)
 
bool const & VDW_rep_screen_physical_pose_clash_dist_cutoff () const
 
void set_VDW_rep_screen_physical_pose_clash_dist_cutoff (bool const &setting)
 
bool const & integration_test_mode () const
 
void set_integration_test_mode (bool const &setting)
 
bool const & allow_bulge_at_chainbreak () const
 
void set_allow_bulge_at_chainbreak (bool const &setting)
 
bool const & parin_favorite_output () const
 
void set_parin_favorite_output (bool const &setting)
 
bool const & reinitialize_CCD_torsions () const
 
void set_reinitialize_CCD_torsions (bool const &setting)
 
bool const & sampler_extra_epsilon_rotamer () const
 
void set_sampler_extra_epsilon_rotamer (bool const &setting)
 
bool const & sampler_extra_beta_rotamer () const
 
void set_sampler_extra_beta_rotamer (bool const &setting)
 
bool const & sampler_include_torsion_value_in_tag () const
 
void set_sampler_include_torsion_value_in_tag (bool const &setting)
 
bool const & combine_long_loop_mode () const
 
void set_combine_long_loop_mode (bool const &setting)
 
bool const & do_not_sample_multiple_virtual_sugar () const
 
void set_do_not_sample_multiple_virtual_sugar (bool const &setting)
 
bool const & sample_ONLY_multiple_virtual_sugar () const
 
void set_sample_ONLY_multiple_virtual_sugar (bool const &setting)
 
bool const & sampler_assert_no_virt_sugar_sampling () const
 
void set_sampler_assert_no_virt_sugar_sampling (bool const &setting)
 
bool const & sampler_try_sugar_instantiation () const
 
void set_sampler_try_sugar_instantiation (bool const &setting)
 
bool const & allow_base_pair_only_centroid_screen () const
 
void set_allow_base_pair_only_centroid_screen (bool const &setting)
 
bool const & minimizer_rename_tag () const
 
void set_minimizer_rename_tag (bool const &setting)
 
bool const & tether_jump () const
 
void set_tether_jump (bool const &setting)
 
bool const & turn_off_rna_chem_map_during_optimize () const
 
void set_turn_off_rna_chem_map_during_optimize (bool const &setting)
 
bool const & rna_legacy_output_mode () const
 
void set_rna_legacy_output_mode (bool const &setting)
 
bool const & allow_rebuild_bulge_mode () const
 
void set_allow_rebuild_bulge_mode (bool const &setting)
 

Private Member Functions

void initialize_variables ()
 

Additional Inherited Members

- Static Public Member Functions inherited from protocols::stepwise::options::StepWiseBasicOptions
static void list_options_read (utility::options::OptionKeyList &opt)
 
- Protected Member Functions inherited from protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
void initialize_from_command_line ()
 
void initialize_variables ()
 
- Protected Member Functions inherited from protocols::stepwise::options::StepWiseBasicOptions
void initialize_from_command_line ()
 
void initialize_from_options_collection (utility::options::OptionCollection const &options)
 
void initialize_variables ()
 
- Protected Member Functions inherited from protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
void initialize_variables ()
 
- Protected Member Functions inherited from protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
void initialize_variables ()
 
- Protected Attributes inherited from protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
bool use_green_packer_
 
bool verbose_
 
bool choose_random_
 
bool dump_
 
bool skip_minimize_
 
bool disallow_realign_
 
bool coordinate_constraints_during_minimize_
 
bool virtualize_packable_moieties_in_screening_pose_
 

Constructor & Destructor Documentation

protocols::stepwise::modeler::options::StepWiseModelerOptions::StepWiseModelerOptions ( )

Member Function Documentation

StepWiseModelerOptionsOP protocols::stepwise::modeler::options::StepWiseModelerOptions::clone ( ) const

clone the options

StepWiseModelerOptionsOP protocols::stepwise::modeler::options::StepWiseModelerOptions::get_sampler_options ( ) const
void protocols::stepwise::modeler::options::StepWiseModelerOptions::initialize_from_command_line ( )
void protocols::stepwise::modeler::options::StepWiseModelerOptions::initialize_variables ( )
private
void protocols::stepwise::modeler::options::StepWiseModelerOptions::parse_my_tag ( utility::tag::TagCOP  )
inlineoverridevirtual

Initialize from the recursive "tag" structure.

Reimplemented from protocols::stepwise::modeler::options::StepWiseBasicModelerOptions.

void protocols::stepwise::modeler::options::StepWiseModelerOptions::setup_options_for_VDW_bin_checker ( rna::checker::RNA_VDW_BinCheckerOP  user_input_VDW_bin_checker) const
void protocols::stepwise::modeler::options::StepWiseModelerOptions::show ( std::ostream &  ) const
inlineoverridevirtual

Describe this instance to a given output stream.

Reimplemented from protocols::stepwise::modeler::options::StepWiseProteinModelerOptions.

std::string protocols::stepwise::modeler::options::StepWiseModelerOptions::type ( ) const
inlineoverridevirtual

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

Reimplemented from protocols::stepwise::modeler::options::StepWiseBasicModelerOptions.


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