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protocols::stepwise::modeler::options::StepWiseBasicModelerOptions Class Reference

#include <StepWiseBasicModelerOptions.hh>

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

 StepWiseBasicModelerOptions ()
 
StepWiseBasicModelerOptionsOP clone () const
 clone the options 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...
 
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)
 

Protected Member Functions

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 Attributes

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_
 

Additional Inherited Members

- Static Public Member Functions inherited from protocols::stepwise::options::StepWiseBasicOptions
static void list_options_read (utility::options::OptionKeyList &opt)
 

Constructor & Destructor Documentation

protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::StepWiseBasicModelerOptions ( )

Member Function Documentation

bool protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::choose_random ( ) const
inline

References choose_random_.

StepWiseBasicModelerOptionsOP protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::clone ( ) const

clone the options

bool protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::coordinate_constraints_during_minimize ( ) const
inline
bool protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::disallow_realign ( ) const
inline

References disallow_realign_.

bool protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::dump ( ) const
inline

References dump_.

void protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::initialize_from_command_line ( )
protected
void protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::initialize_variables ( )
protected
void protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::parse_my_tag ( utility::tag::TagCOP  )
inlineoverridevirtual

Initialize from the recursive "tag" structure.

Reimplemented from protocols::stepwise::options::StepWiseBasicOptions.

Reimplemented in protocols::stepwise::modeler::options::StepWiseModelerOptions.

void protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::set_choose_random ( bool const &  setting)
inline

References choose_random_.

void protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::set_coordinate_constraints_during_minimize ( bool const  setting)
inline
void protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::set_disallow_realign ( bool const  setting)
inline

References disallow_realign_.

void protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::set_dump ( bool const &  setting)
inline

References dump_.

void protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::set_skip_minimize ( bool const &  setting)
inline

References skip_minimize_.

void protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::set_use_green_packer ( bool const &  setting)
inline

References use_green_packer_.

void protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::set_verbose ( bool const &  setting)
inline

References verbose_.

void protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::set_virtualize_packable_moieties_in_screening_pose ( bool const  setting)
inline
bool protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::skip_minimize ( ) const
inline

References skip_minimize_.

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

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

Reimplemented from protocols::stepwise::options::StepWiseBasicOptions.

Reimplemented in protocols::stepwise::modeler::options::StepWiseModelerOptions.

bool protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::use_green_packer ( ) const
inline

References use_green_packer_.

bool protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::verbose ( ) const
inline

References verbose_.

bool protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::virtualize_packable_moieties_in_screening_pose ( ) const
inline

Member Data Documentation

bool protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::choose_random_
protected
bool protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::coordinate_constraints_during_minimize_
protected
bool protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::disallow_realign_
protected
bool protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::dump_
protected
bool protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::skip_minimize_
protected
bool protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::use_green_packer_
protected
bool protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::verbose_
protected
bool protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::virtualize_packable_moieties_in_screening_pose_
protected

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