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

#include <StepWiseBasicOptions.hh>

Inheritance diagram for protocols::stepwise::options::StepWiseBasicOptions:

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

References atr_rep_screen_.

Referenced by protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::setup_modeler_options().

bool protocols::stepwise::options::StepWiseBasicOptions::atr_rep_screen_for_docking ( ) const

inline

References atr_rep_screen_for_docking_.

bool protocols::stepwise::options::StepWiseBasicOptions::boltzmann_choice_post_enumerated_minimize ( ) const

inline

References boltzmann_choice_post_enumerated_minimize_.

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

References disallow_pack_polar_hydrogens_.

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

References protocols::stepwise::modeler::THERMAL_SAMPLER, and protocols::stepwise::modeler::TRADITIONAL_MINIMIZER.

void protocols::stepwise::options::StepWiseBasicOptions::initialize_variables ( )

protected

References protocols::stepwise::modeler::TRADITIONAL_MINIMIZER.

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

References max_tries_multiplier_for_ccd_.

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

References num_pose_minimize_.

Referenced by protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::initialize_from_command_line(), and protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::setup_modeler_options().

core::Size protocols::stepwise::options::StepWiseBasicOptions::num_random_samples ( ) const

inline

References num_random_samples_.

Referenced by protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::setup_modeler_options().

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

References output_minimized_pose_list_.

virtual void protocols::stepwise::options::StepWiseBasicOptions::parse_my_tag ( utility::tag::TagCOP  )

inlinevirtual

Initialize from the recursive "tag" structure.

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

core::Real protocols::stepwise::options::StepWiseBasicOptions::rmsd_screen ( ) const

inline

References rmsd_screen_.

Referenced by protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::setup_modeler_options().

bool protocols::stepwise::options::StepWiseBasicOptions::sample_pH ( ) const

inline

References sample_pH_.

core::Size protocols::stepwise::options::StepWiseBasicOptions::sampler_num_pose_kept ( ) const

inline

References sampler_num_pose_kept_.

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

References atr_rep_screen_for_docking_.

void protocols::stepwise::options::StepWiseBasicOptions::set_boltzmann_choice_post_enumerated_minimize ( bool const  setting )

inline

References boltzmann_choice_post_enumerated_minimize_.

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

References disallow_pack_polar_hydrogens_.

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

References max_tries_multiplier_for_ccd_.

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

References num_pose_minimize_.

Referenced by protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::initialize_from_command_line(), protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::initialize_from_options_collection(), and protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::setup_modeler_options().

void protocols::stepwise::options::StepWiseBasicOptions::set_num_random_samples ( core::Size const &  setting )

inline

References num_random_samples_.

Referenced by protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::initialize_from_options_collection().

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

References output_minimized_pose_list_.

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

References sampler_num_pose_kept_.

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

References silent_file_.

Referenced by protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::initialize_from_options_collection(), and protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::StepWiseMonteCarloOptions().

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

inline

References test_all_mg_hydration_frames_.

void protocols::stepwise::options::StepWiseBasicOptions::set_thermal_sampler_output_min_pose ( bool const  setting )

inline

References thermal_sampler_output_min_pose_.

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

inline

References use_packer_instead_of_rotamer_trials_.

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

inline

References vary_polar_hydrogen_geometry_.

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

inline

References vary_rna_bond_geometry_.

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

References test_all_mg_hydration_frames_.

bool protocols::stepwise::options::StepWiseBasicOptions::thermal_sampler_output_min_pose ( ) const

inline

References thermal_sampler_output_min_pose_.

core::Real protocols::stepwise::options::StepWiseBasicOptions::thermal_sampler_temperature ( ) const

inline

References thermal_sampler_temperature_.

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

References use_packer_instead_of_rotamer_trials_.

bool protocols::stepwise::options::StepWiseBasicOptions::vary_polar_hydrogen_geometry ( ) const

inline

References vary_polar_hydrogen_geometry_.

bool protocols::stepwise::options::StepWiseBasicOptions::vary_rna_bond_geometry ( ) const

inline

References vary_rna_bond_geometry_.

utility::vector1< std::string > const& protocols::stepwise::options::StepWiseBasicOptions::VDW_rep_screen_info ( ) const

inline

References VDW_rep_screen_info_.

Referenced by protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions::setup_modeler_options().

bool protocols::stepwise::options::StepWiseBasicOptions::verbose_sampler ( ) const

inline

References verbose_sampler_.

Member Data Documentation

bool protocols::stepwise::options::StepWiseBasicOptions::atr_rep_screen_

private

Referenced by atr_rep_screen(), and set_atr_rep_screen().

bool protocols::stepwise::options::StepWiseBasicOptions::atr_rep_screen_for_docking_

private

Referenced by atr_rep_screen_for_docking(), and set_atr_rep_screen_for_docking().

bool protocols::stepwise::options::StepWiseBasicOptions::boltzmann_choice_post_enumerated_minimize_ = false

private

Referenced by boltzmann_choice_post_enumerated_minimize(), and set_boltzmann_choice_post_enumerated_minimize().

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

Referenced by disallow_pack_polar_hydrogens(), and set_disallow_pack_polar_hydrogens().

bool protocols::stepwise::options::StepWiseBasicOptions::hydrate_magnesiums_

private

Referenced by hydrate_magnesiums(), and set_hydrate_magnesiums().

bool protocols::stepwise::options::StepWiseBasicOptions::lores_

private

Referenced by lores(), and set_lores().

bool protocols::stepwise::options::StepWiseBasicOptions::mapfile_activated_

private

Referenced by mapfile_activated(), and set_mapfile_activated().

core::Size protocols::stepwise::options::StepWiseBasicOptions::max_tries_multiplier_for_ccd_

private

Referenced by max_tries_multiplier_for_ccd(), and set_max_tries_multiplier_for_ccd().

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

Referenced by minimize_waters(), and set_minimize_waters().

modeler::MinimizerMode protocols::stepwise::options::StepWiseBasicOptions::minimizer_mode_

private

Referenced by minimizer_mode(), and set_minimizer_mode().

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

Referenced by num_pose_minimize(), and set_num_pose_minimize().

core::Size protocols::stepwise::options::StepWiseBasicOptions::num_random_samples_

private

Referenced by num_random_samples(), and set_num_random_samples().

bool protocols::stepwise::options::StepWiseBasicOptions::output_cluster_size_

private

Referenced by output_cluster_size(), and set_output_cluster_size().

bool protocols::stepwise::options::StepWiseBasicOptions::output_minimized_pose_list_

private

Referenced by output_minimized_pose_list(), and set_output_minimized_pose_list().

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

Referenced by sampler_num_pose_kept(), and set_sampler_num_pose_kept().

std::string protocols::stepwise::options::StepWiseBasicOptions::sampler_silent_file_

private

Referenced by sampler_silent_file(), and set_sampler_silent_file().

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

Referenced by set_test_all_mg_hydration_frames(), and test_all_mg_hydration_frames().

bool protocols::stepwise::options::StepWiseBasicOptions::thermal_sampler_output_min_pose_

private

Referenced by set_thermal_sampler_output_min_pose(), and thermal_sampler_output_min_pose().

core::Real protocols::stepwise::options::StepWiseBasicOptions::thermal_sampler_temperature_

private

Referenced by thermal_sampler_temperature().

bool protocols::stepwise::options::StepWiseBasicOptions::use_packer_instead_of_rotamer_trials_

private

Referenced by set_use_packer_instead_of_rotamer_trials(), and use_packer_instead_of_rotamer_trials().

bool protocols::stepwise::options::StepWiseBasicOptions::vary_polar_hydrogen_geometry_

private

Referenced by set_vary_polar_hydrogen_geometry(), and vary_polar_hydrogen_geometry().

bool protocols::stepwise::options::StepWiseBasicOptions::vary_rna_bond_geometry_

private

Referenced by set_vary_rna_bond_geometry(), and vary_rna_bond_geometry().

utility::vector1< std::string > protocols::stepwise::options::StepWiseBasicOptions::VDW_rep_screen_info_

private

Referenced by set_VDW_rep_screen_info(), and VDW_rep_screen_info().

bool protocols::stepwise::options::StepWiseBasicOptions::verbose_sampler_

private

Referenced by set_verbose_sampler(), and verbose_sampler().

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

• src/protocols/stepwise/options/StepWiseBasicOptions.hh
• src/protocols/stepwise/options/StepWiseBasicOptions.cc