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protocols::stepwise::options::StepWiseBasicOptions Class Reference

#include <StepWiseBasicOptions.hh>

Inheritance diagram for protocols::stepwise::options::StepWiseBasicOptions:
Inheritance graph
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Public Member Functions

 StepWiseBasicOptions ()
 
StepWiseBasicOptionsOP 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...
 
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)
 

Static Public Member Functions

static void list_options_read (utility::options::OptionKeyList &opt)
 

Protected Member Functions

void initialize_from_command_line ()
 
void initialize_from_options_collection (utility::options::OptionCollection const &options)
 
void initialize_variables ()
 

Private Attributes

std::string silent_file_
 
core::Size sampler_num_pose_kept_
 
core::Real cluster_rmsd_
 
core::Size num_pose_minimize_
 
core::Size num_random_samples_
 
core::Size max_tries_multiplier_for_ccd_
 
bool atr_rep_screen_
 
bool atr_rep_screen_for_docking_
 
core::Real rmsd_screen_
 
utility::vector1< std::string > VDW_rep_screen_info_
 
bool output_minimized_pose_list_
 
bool output_cluster_size_
 
std::string min_type_
 
core::Real min_tolerance_
 
bool vary_rna_bond_geometry_
 
bool vary_polar_hydrogen_geometry_
 
bool disallow_pack_polar_hydrogens_
 
bool use_packer_instead_of_rotamer_trials_
 
bool lores_
 
bool verbose_sampler_
 
std::string sampler_silent_file_
 
bool minimize_waters_
 
bool hydrate_magnesiums_
 
bool test_all_mg_hydration_frames_
 
bool mapfile_activated_
 
modeler::MinimizerMode minimizer_mode_
 
core::Size n_cycles_
 
core::Real thermal_sampler_temperature_
 
bool thermal_sampler_output_min_pose_
 
bool sample_pH_
 
bool boltzmann_choice_post_enumerated_minimize_ = false
 

Constructor & Destructor Documentation

protocols::stepwise::options::StepWiseBasicOptions::StepWiseBasicOptions ( )

Member Function Documentation

bool protocols::stepwise::options::StepWiseBasicOptions::atr_rep_screen ( ) const
inline
bool protocols::stepwise::options::StepWiseBasicOptions::atr_rep_screen_for_docking ( ) const
inline
bool protocols::stepwise::options::StepWiseBasicOptions::boltzmann_choice_post_enumerated_minimize ( ) const
inline
StepWiseBasicOptionsOP protocols::stepwise::options::StepWiseBasicOptions::clone ( ) const

clone the options

core::Real protocols::stepwise::options::StepWiseBasicOptions::cluster_rmsd ( ) const
inline

References cluster_rmsd_.

bool protocols::stepwise::options::StepWiseBasicOptions::disallow_pack_polar_hydrogens ( ) const
inline
bool protocols::stepwise::options::StepWiseBasicOptions::hydrate_magnesiums ( ) const
inline

References hydrate_magnesiums_.

void protocols::stepwise::options::StepWiseBasicOptions::initialize_from_command_line ( )
protected
void protocols::stepwise::options::StepWiseBasicOptions::initialize_from_options_collection ( utility::options::OptionCollection const &  options)
protected
void protocols::stepwise::options::StepWiseBasicOptions::initialize_variables ( )
protected
void protocols::stepwise::options::StepWiseBasicOptions::list_options_read ( utility::options::OptionKeyList &  opt)
static
bool protocols::stepwise::options::StepWiseBasicOptions::lores ( ) const
inline

References lores_.

bool protocols::stepwise::options::StepWiseBasicOptions::mapfile_activated ( ) const
inline

References mapfile_activated_.

core::Size protocols::stepwise::options::StepWiseBasicOptions::max_tries_multiplier_for_ccd ( ) const
inline
core::Real protocols::stepwise::options::StepWiseBasicOptions::min_tolerance ( ) const
inline

References min_tolerance_.

std::string protocols::stepwise::options::StepWiseBasicOptions::min_type ( ) const
inline

References min_type_.

bool protocols::stepwise::options::StepWiseBasicOptions::minimize_waters ( ) const
inline

References minimize_waters_.

modeler::MinimizerMode const& protocols::stepwise::options::StepWiseBasicOptions::minimizer_mode ( ) const
inline

References minimizer_mode_.

core::Size protocols::stepwise::options::StepWiseBasicOptions::n_cycles ( ) const
inline

References n_cycles_.

core::Size protocols::stepwise::options::StepWiseBasicOptions::num_pose_minimize ( ) const
inline
core::Size protocols::stepwise::options::StepWiseBasicOptions::num_random_samples ( ) const
inline
bool protocols::stepwise::options::StepWiseBasicOptions::output_cluster_size ( ) const
inline

References output_cluster_size_.

bool protocols::stepwise::options::StepWiseBasicOptions::output_minimized_pose_list ( ) const
inline
virtual void protocols::stepwise::options::StepWiseBasicOptions::parse_my_tag ( utility::tag::TagCOP  )
inlinevirtual
core::Real protocols::stepwise::options::StepWiseBasicOptions::rmsd_screen ( ) const
inline
bool protocols::stepwise::options::StepWiseBasicOptions::sample_pH ( ) const
inline

References sample_pH_.

core::Size protocols::stepwise::options::StepWiseBasicOptions::sampler_num_pose_kept ( ) const
inline
std::string const& protocols::stepwise::options::StepWiseBasicOptions::sampler_silent_file ( ) const
inline

References sampler_silent_file_.

void protocols::stepwise::options::StepWiseBasicOptions::set_atr_rep_screen ( bool const &  setting)
inline

References atr_rep_screen_.

void protocols::stepwise::options::StepWiseBasicOptions::set_atr_rep_screen_for_docking ( bool const &  setting)
inline
void protocols::stepwise::options::StepWiseBasicOptions::set_boltzmann_choice_post_enumerated_minimize ( bool const  setting)
inline
void protocols::stepwise::options::StepWiseBasicOptions::set_cluster_rmsd ( core::Real const &  setting)
inline

References cluster_rmsd_.

void protocols::stepwise::options::StepWiseBasicOptions::set_disallow_pack_polar_hydrogens ( bool const &  setting)
inline
void protocols::stepwise::options::StepWiseBasicOptions::set_hydrate_magnesiums ( bool const &  setting)
inline

References hydrate_magnesiums_.

void protocols::stepwise::options::StepWiseBasicOptions::set_lores ( bool const &  setting)
inline

References lores_.

void protocols::stepwise::options::StepWiseBasicOptions::set_mapfile_activated ( bool const &  setting)
inline

References mapfile_activated_.

void protocols::stepwise::options::StepWiseBasicOptions::set_max_tries_multiplier_for_ccd ( core::Size const &  setting)
inline
void protocols::stepwise::options::StepWiseBasicOptions::set_min_tolerance ( core::Real const &  setting)
inline

References min_tolerance_.

void protocols::stepwise::options::StepWiseBasicOptions::set_min_type ( std::string const &  setting)
inline

References min_type_.

void protocols::stepwise::options::StepWiseBasicOptions::set_minimize_waters ( bool const &  setting)
inline

References minimize_waters_.

void protocols::stepwise::options::StepWiseBasicOptions::set_minimizer_mode ( modeler::MinimizerMode const &  setting)
inline

References minimizer_mode_.

void protocols::stepwise::options::StepWiseBasicOptions::set_n_cycles ( core::Size const  setting)
inline

References n_cycles_.

void protocols::stepwise::options::StepWiseBasicOptions::set_num_pose_minimize ( core::Size const &  setting)
inline
void protocols::stepwise::options::StepWiseBasicOptions::set_num_random_samples ( core::Size const &  setting)
inline
void protocols::stepwise::options::StepWiseBasicOptions::set_output_cluster_size ( bool const &  setting)
inline

References output_cluster_size_.

void protocols::stepwise::options::StepWiseBasicOptions::set_output_minimized_pose_list ( bool const &  setting)
inline
void protocols::stepwise::options::StepWiseBasicOptions::set_rmsd_screen ( core::Real const &  setting)
inline

References rmsd_screen_.

void protocols::stepwise::options::StepWiseBasicOptions::set_sample_pH ( bool const  setting)
inline

References sample_pH_.

void protocols::stepwise::options::StepWiseBasicOptions::set_sampler_num_pose_kept ( core::Size const &  setting)
inline
void protocols::stepwise::options::StepWiseBasicOptions::set_sampler_silent_file ( std::string const &  setting)
inline

References sampler_silent_file_.

void protocols::stepwise::options::StepWiseBasicOptions::set_silent_file ( std::string const &  setting)
inline
void protocols::stepwise::options::StepWiseBasicOptions::set_test_all_mg_hydration_frames ( bool const &  setting)
inline
void protocols::stepwise::options::StepWiseBasicOptions::set_thermal_sampler_output_min_pose ( bool const  setting)
inline
void protocols::stepwise::options::StepWiseBasicOptions::set_use_packer_instead_of_rotamer_trials ( bool const &  setting)
inline
void protocols::stepwise::options::StepWiseBasicOptions::set_vary_polar_hydrogen_geometry ( bool const &  setting)
inline
void protocols::stepwise::options::StepWiseBasicOptions::set_vary_rna_bond_geometry ( bool const &  setting)
inline
void protocols::stepwise::options::StepWiseBasicOptions::set_VDW_rep_screen_info ( utility::vector1< std::string > const &  setting)
inline

References VDW_rep_screen_info_.

void protocols::stepwise::options::StepWiseBasicOptions::set_verbose_sampler ( bool const &  setting)
inline

References verbose_sampler_.

std::string const& protocols::stepwise::options::StepWiseBasicOptions::silent_file ( ) const
inline

References silent_file_.

bool protocols::stepwise::options::StepWiseBasicOptions::test_all_mg_hydration_frames ( ) const
inline
bool protocols::stepwise::options::StepWiseBasicOptions::thermal_sampler_output_min_pose ( ) const
inline
core::Real protocols::stepwise::options::StepWiseBasicOptions::thermal_sampler_temperature ( ) const
inline
virtual std::string protocols::stepwise::options::StepWiseBasicOptions::type ( ) const
inlinevirtual

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

Reimplemented in protocols::stepwise::modeler::options::StepWiseModelerOptions, protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions, and protocols::stepwise::modeler::options::StepWiseBasicModelerOptions.

bool protocols::stepwise::options::StepWiseBasicOptions::use_packer_instead_of_rotamer_trials ( ) const
inline
bool protocols::stepwise::options::StepWiseBasicOptions::vary_polar_hydrogen_geometry ( ) const
inline
bool protocols::stepwise::options::StepWiseBasicOptions::vary_rna_bond_geometry ( ) const
inline
utility::vector1< std::string > const& protocols::stepwise::options::StepWiseBasicOptions::VDW_rep_screen_info ( ) const
inline
bool protocols::stepwise::options::StepWiseBasicOptions::verbose_sampler ( ) const
inline

References verbose_sampler_.

Member Data Documentation

bool protocols::stepwise::options::StepWiseBasicOptions::atr_rep_screen_
private
bool protocols::stepwise::options::StepWiseBasicOptions::atr_rep_screen_for_docking_
private
bool protocols::stepwise::options::StepWiseBasicOptions::boltzmann_choice_post_enumerated_minimize_ = false
private
core::Real protocols::stepwise::options::StepWiseBasicOptions::cluster_rmsd_
private

Referenced by cluster_rmsd(), and set_cluster_rmsd().

bool protocols::stepwise::options::StepWiseBasicOptions::disallow_pack_polar_hydrogens_
private
bool protocols::stepwise::options::StepWiseBasicOptions::hydrate_magnesiums_
private
bool protocols::stepwise::options::StepWiseBasicOptions::lores_
private

Referenced by lores(), and set_lores().

bool protocols::stepwise::options::StepWiseBasicOptions::mapfile_activated_
private
core::Size protocols::stepwise::options::StepWiseBasicOptions::max_tries_multiplier_for_ccd_
private
core::Real protocols::stepwise::options::StepWiseBasicOptions::min_tolerance_
private

Referenced by min_tolerance(), and set_min_tolerance().

std::string protocols::stepwise::options::StepWiseBasicOptions::min_type_
private

Referenced by min_type(), and set_min_type().

bool protocols::stepwise::options::StepWiseBasicOptions::minimize_waters_
private
modeler::MinimizerMode protocols::stepwise::options::StepWiseBasicOptions::minimizer_mode_
private
core::Size protocols::stepwise::options::StepWiseBasicOptions::n_cycles_
private

Referenced by n_cycles(), and set_n_cycles().

core::Size protocols::stepwise::options::StepWiseBasicOptions::num_pose_minimize_
private
core::Size protocols::stepwise::options::StepWiseBasicOptions::num_random_samples_
private
bool protocols::stepwise::options::StepWiseBasicOptions::output_cluster_size_
private
bool protocols::stepwise::options::StepWiseBasicOptions::output_minimized_pose_list_
private
core::Real protocols::stepwise::options::StepWiseBasicOptions::rmsd_screen_
private

Referenced by rmsd_screen(), and set_rmsd_screen().

bool protocols::stepwise::options::StepWiseBasicOptions::sample_pH_
private

Referenced by sample_pH(), and set_sample_pH().

core::Size protocols::stepwise::options::StepWiseBasicOptions::sampler_num_pose_kept_
private
std::string protocols::stepwise::options::StepWiseBasicOptions::sampler_silent_file_
private
std::string protocols::stepwise::options::StepWiseBasicOptions::silent_file_
private

Referenced by set_silent_file(), and silent_file().

bool protocols::stepwise::options::StepWiseBasicOptions::test_all_mg_hydration_frames_
private
bool protocols::stepwise::options::StepWiseBasicOptions::thermal_sampler_output_min_pose_
private
core::Real protocols::stepwise::options::StepWiseBasicOptions::thermal_sampler_temperature_
private
bool protocols::stepwise::options::StepWiseBasicOptions::use_packer_instead_of_rotamer_trials_
private
bool protocols::stepwise::options::StepWiseBasicOptions::vary_polar_hydrogen_geometry_
private
bool protocols::stepwise::options::StepWiseBasicOptions::vary_rna_bond_geometry_
private
utility::vector1< std::string > protocols::stepwise::options::StepWiseBasicOptions::VDW_rep_screen_info_
private
bool protocols::stepwise::options::StepWiseBasicOptions::verbose_sampler_
private

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