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

#include <StepWiseBasicModelerOptions.hh>

Inheritance diagram for protocols::stepwise::modeler::options::StepWiseBasicModelerOptions:

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

(

)

References initialize_variables().

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

References coordinate_constraints_during_minimize_.

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

References choose_random_, dump_, protocols::stepwise::options::StepWiseBasicOptions::num_pose_minimize(), protocols::stepwise::options::StepWiseBasicOptions::set_num_pose_minimize(), skip_minimize_, use_green_packer_, verbose_, and virtualize_packable_moieties_in_screening_pose_.

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

protected

References choose_random_, coordinate_constraints_during_minimize_, disallow_realign_, dump_, skip_minimize_, use_green_packer_, verbose_, and virtualize_packable_moieties_in_screening_pose_.

Referenced by StepWiseBasicModelerOptions().

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

References coordinate_constraints_during_minimize_.

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

References virtualize_packable_moieties_in_screening_pose_.

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

References virtualize_packable_moieties_in_screening_pose_.

Member Data Documentation

bool protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::choose_random_

protected

Referenced by choose_random(), initialize_from_command_line(), initialize_variables(), and set_choose_random().

bool protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::coordinate_constraints_during_minimize_

protected

Referenced by coordinate_constraints_during_minimize(), initialize_variables(), and set_coordinate_constraints_during_minimize().

bool protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::disallow_realign_

protected

Referenced by disallow_realign(), initialize_variables(), and set_disallow_realign().

bool protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::dump_

protected

Referenced by dump(), initialize_from_command_line(), initialize_variables(), and set_dump().

bool protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::skip_minimize_

protected

Referenced by initialize_from_command_line(), initialize_variables(), set_skip_minimize(), and skip_minimize().

bool protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::use_green_packer_

protected

Referenced by initialize_from_command_line(), initialize_variables(), set_use_green_packer(), and use_green_packer().

bool protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::verbose_

protected

Referenced by initialize_from_command_line(), initialize_variables(), set_verbose(), and verbose().

bool protocols::stepwise::modeler::options::StepWiseBasicModelerOptions::virtualize_packable_moieties_in_screening_pose_

protected

Referenced by initialize_from_command_line(), initialize_variables(), set_virtualize_packable_moieties_in_screening_pose(), and virtualize_packable_moieties_in_screening_pose().

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

• src/protocols/stepwise/modeler/options/StepWiseBasicModelerOptions.hh
• src/protocols/stepwise/modeler/options/StepWiseBasicModelerOptions.cc