Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | List of all members
protocols::stepwise::modeler::options::StepWiseModelerOptions Class Reference

#include <StepWiseModelerOptions.hh>

Public Member Functions

 StepWiseModelerOptions ()
 
 StepWiseModelerOptions (StepWiseModelerOptions const &src)
 copy constructor More...
 
 ~StepWiseModelerOptions ()
 
StepWiseModelerOptionsOP clone () const
 clone the options More...
 
StepWiseModelerOptionsoperator= (StepWiseModelerOptions const &src)
 
virtual void show (std::ostream &) const
 Describe this instance to a given output stream. 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 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 ()
 
 StepWiseBasicModelerOptions (StepWiseBasicModelerOptions const &src)
 copy constructor More...
 
 ~StepWiseBasicModelerOptions ()
 
StepWiseBasicModelerOptionsOP clone () const
 clone the options More...
 
StepWiseBasicModelerOptionsoperator= (StepWiseBasicModelerOptions const &src)
 
core::Size const & sampler_num_pose_kept () const
 
void set_sampler_num_pose_kept (core::Size const &setting)
 
bool const & use_green_packer () const
 
void set_use_green_packer (bool const &setting)
 
bool const & verbose () const
 
void set_verbose (bool const &setting)
 
bool const & choose_random () const
 
void set_choose_random (bool const &setting)
 
void set_dump (bool const &setting)
 
bool dump () const
 
core::Real const & cluster_rmsd () const
 
void set_cluster_rmsd (core::Real const &setting)
 
void set_skip_minimize (bool const &setting)
 
bool skip_minimize () const
 
bool const & disallow_realign () const
 
void set_disallow_realign (bool const &setting)
 
- Public Member Functions inherited from protocols::stepwise::options::StepWiseBasicOptions
 StepWiseBasicOptions ()
 
 StepWiseBasicOptions (StepWiseBasicOptions const &src)
 copy constructor More...
 
 ~StepWiseBasicOptions ()
 
StepWiseBasicOptionsOP clone () const
 clone the options More...
 
StepWiseBasicOptionsoperator= (StepWiseBasicOptions const &src)
 
bool const & output_minimized_pose_list () const
 
void set_output_minimized_pose_list (bool const &setting)
 
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 const & num_pose_minimize () const
 
void set_num_pose_minimize (core::Size const &setting)
 
core::Size const & num_random_samples () const
 
void set_num_random_samples (core::Size const &setting)
 
void set_atr_rep_screen (bool const &setting)
 
bool atr_rep_screen () const
 
void set_rmsd_screen (core::Real const &setting)
 
core::Real rmsd_screen () const
 
- Public Member Functions inherited from protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
 StepWiseProteinModelerOptions ()
 
 StepWiseProteinModelerOptions (StepWiseProteinModelerOptions const &src)
 copy constructor More...
 
 ~StepWiseProteinModelerOptions ()
 
StepWiseProteinModelerOptionsOP clone () const
 clone the options More...
 
StepWiseProteinModelerOptionsoperator= (StepWiseProteinModelerOptions const &src)
 
void initialize_from_command_line ()
 
void set_global_optimize (bool const &setting)
 
bool global_optimize () const
 
void set_mapfile_activated (bool const &setting)
 
bool mapfile_activated () 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 (Size const &setting)
 
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_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 (Real const &setting)
 
Real centroid_score_diff_cut () const
 
void set_centroid_weights (std::string const &setting)
 
std::string centroid_weights () const
 
void set_nstruct_centroid (Size const &setting)
 
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
 
void set_use_packer_instead_of_rotamer_trials (bool const &setting)
 
bool use_packer_instead_of_rotamer_trials () const
 
void set_min_type (std::string const &setting)
 
std::string min_type () const
 
void set_min_tolerance (Real const &setting)
 
Real min_tolerance () 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::stringfrag_files () const
 
void set_bridge_res (utility::vector1< Size > const &setting)
 
utility::vector1< Sizebridge_res () const
 
- Public Member Functions inherited from protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
 StepWiseRNA_ModelerOptions ()
 
 StepWiseRNA_ModelerOptions (StepWiseRNA_ModelerOptions const &src)
 copy constructor More...
 
 ~StepWiseRNA_ModelerOptions ()
 
StepWiseRNA_ModelerOptionsOP clone () const
 clone the options More...
 
StepWiseRNA_ModelerOptionsoperator= (StepWiseRNA_ModelerOptions const &src)
 
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 & sampler_perform_phosphate_pack () const
 
void set_sampler_perform_phosphate_pack (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)
 
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 & 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)
 
utility::vector1< std::string >
const & 
VDW_rep_screen_info () const
 
void set_VDW_rep_screen_info (utility::vector1< std::string > 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 & minimizer_allow_variable_bond_geometry () const
 
void set_minimizer_allow_variable_bond_geometry (bool const &setting)
 
core::Real const & minimizer_vary_bond_geometry_frequency () const
 
void set_minimizer_vary_bond_geometry_frequency (core::Real 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)
 

Private Member Functions

void initialize_variables ()
 

Additional Inherited Members

- 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_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
core::Size sampler_num_pose_kept_
 
bool use_green_packer_
 
bool verbose_
 
bool choose_random_
 
bool dump_
 
core::Real cluster_rmsd_
 
bool skip_minimize_
 
bool disallow_realign_
 

Constructor & Destructor Documentation

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

Referenced by clone().

protocols::stepwise::modeler::options::StepWiseModelerOptions::StepWiseModelerOptions ( StepWiseModelerOptions const &  src)

copy constructor

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

Member Function Documentation

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

clone the options

References StepWiseModelerOptions().

Referenced by get_sampler_options().

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

References clone().

void protocols::stepwise::modeler::options::StepWiseModelerOptions::initialize_from_command_line ( )
void protocols::stepwise::modeler::options::StepWiseModelerOptions::initialize_variables ( )
private
StepWiseModelerOptions & protocols::stepwise::modeler::options::StepWiseModelerOptions::operator= ( StepWiseModelerOptions const &  src)
virtual void protocols::stepwise::modeler::options::StepWiseModelerOptions::parse_my_tag ( utility::tag::TagCOP  )
inlinevirtual

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
virtual void protocols::stepwise::modeler::options::StepWiseModelerOptions::show ( std::ostream &  ) const
inlinevirtual

Describe this instance to a given output stream.

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

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

The class name (its type) for a particular ResourceOptions 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: