protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions Class Reference

#include <StepWiseMonteCarloOptions.hh>

Public Member Functions
	StepWiseMonteCarloOptions ()
	~StepWiseMonteCarloOptions ()
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 ()
protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptionsOP	setup_rna_modeler_options () const
protocols::stepwise::sampling::protein::StepWiseProteinModelerOptionsOP	setup_protein_modeler_options () const
std::string const &	silent_file () const
void	set_silent_file (std::string const &setting)
bool const &	verbose_scores () const
void	set_verbose_scores (bool const &setting)
bool const &	integration_test_mode () const
void	set_integration_test_mode (bool const &setting)
bool const &	force_centroid_interaction () const
void	set_force_centroid_interaction (bool const &setting)
core::Real const &	sampler_max_centroid_distance () const
void	set_sampler_max_centroid_distance (core::Real const &setting)
bool const &	use_phenix_geo () const
void	set_use_phenix_geo (bool const &setting)
bool const &	skip_deletions () const
void	set_skip_deletions (bool const &setting)
bool const &	erraser () const
void	set_erraser (bool const &setting)
bool const &	allow_internal_hinge_moves () const
void	set_allow_internal_hinge_moves (bool const &setting)
bool const &	allow_internal_local_moves () const
void	set_allow_internal_local_moves (bool const &setting)
core::Size const &	num_random_samples () const
void	set_num_random_samples (core::Size const &setting)
core::Size const &	num_pose_minimize () const
void	set_num_pose_minimize (core::Size const &setting)
core::Size const &	cycles () const
void	set_cycles (core::Size const &setting)
core::Real const &	add_delete_frequency () const
void	set_add_delete_frequency (core::Real const &setting)
core::Real const &	intermolecular_frequency () const
void	set_intermolecular_frequency (core::Real const &setting)
core::Real const &	minimize_single_res_frequency () const
void	set_minimize_single_res_frequency (core::Real 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)
core::Real const &	switch_focus_frequency () const
void	set_switch_focus_frequency (core::Real const &setting)
core::Real const &	just_min_after_mutation_frequency () const
void	set_just_min_after_mutation_frequency (core::Real const &setting)
core::Real const &	temperature () const
void	set_temperature (core::Real const &setting)
utility::vector1< core::Size > const &	bulge_res () const
void	set_bulge_res (utility::vector1< core::Size > const &setting)
core::Real const &	max_missing_weight () const
void	set_max_missing_weight (core::Real const &setting)
core::Real const &	chainbreak_weight () const
void	set_chainbreak_weight (core::Real const &setting)
bool const &	allow_skip_bulge () const
void	set_allow_skip_bulge (bool const &setting)
core::Real const &	from_scratch_frequency () const
void	set_from_scratch_frequency (core::Real const &setting)
bool const &	allow_split_off () const
void	set_allow_split_off (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 &	make_movie () const
void	set_make_movie (bool const &setting)
utility::vector1< core::Size > const &	extra_minimize_res () const
void	set_extra_minimize_res (utility::vector1< core::Size > const &setting)
utility::vector1< core::Size > const &	syn_chi_res_list () const
void	set_syn_chi_res_list (utility::vector1< core::Size > const &setting)
utility::vector1< core::Size > const &	terminal_res () const
void	set_terminal_res (utility::vector1< core::Size > const &setting)
bool const &	sampler_perform_phosphate_pack () const
void	set_sampler_perform_phosphate_pack (bool const &setting)
bool const &	rebuild_bulge_mode () const
void	set_rebuild_bulge_mode (bool const &setting)
bool const &	unified_framework () const
void	set_unified_framework (bool const &setting)
bool const &	tether_jump () const
void	set_tether_jump (bool const &setting)
bool const &	local_redock_only () const
void	set_local_redock_only (bool const &setting)
bool const &	skip_coord_constraints () const
void	set_skip_coord_constraints (bool const &setting)
bool const &	output_minimized_pose_list () const
void	set_output_minimized_pose_list (bool const &setting)
bool const &	filter_native_big_bins () const
void	set_filter_native_big_bins (bool const &setting)
bool const &	allow_virtual_side_chains () const
void	set_allow_virtual_side_chains (bool const &setting)
bool const &	protein_prepack () const
void	set_protein_prepack (bool const &setting)
bool const &	protein_atr_rep_screen () const
void	set_protein_atr_rep_screen (bool const &setting)
core::Real const &	rmsd_screen () const
void	set_rmsd_screen (core::Real const &setting)

Private Attributes
std::string	silent_file_
bool	verbose_scores_
bool	integration_test_mode_
bool	force_centroid_interaction_
core::Real	sampler_max_centroid_distance_
bool	use_phenix_geo_
bool	skip_deletions_
bool	erraser_
bool	allow_internal_hinge_moves_
bool	allow_internal_local_moves_
core::Size	num_random_samples_
core::Size	num_pose_minimize_
core::Size	cycles_
core::Real	add_delete_frequency_
core::Real	intermolecular_frequency_
core::Real	minimize_single_res_frequency_
bool	minimizer_allow_variable_bond_geometry_
core::Real	minimizer_vary_bond_geometry_frequency_
core::Real	switch_focus_frequency_
core::Real	just_min_after_mutation_frequency_
core::Real	temperature_
utility::vector1< core::Size >	bulge_res_
core::Real	max_missing_weight_
core::Real	chainbreak_weight_
bool	allow_skip_bulge_
core::Real	from_scratch_frequency_
bool	allow_split_off_
bool	virtual_sugar_keep_base_fixed_
bool	virtual_sugar_do_minimize_
bool	make_movie_
bool	sampler_perform_phosphate_pack_
bool	rebuild_bulge_mode_
bool	unified_framework_
bool	tether_jump_
bool	local_redock_only_
bool	skip_coord_constraints_
bool	output_minimized_pose_list_
bool	filter_native_big_bins_
bool	allow_virtual_side_chains_
bool	protein_prepack_
bool	protein_atr_rep_screen_
core::Real	rmsd_screen_
utility::vector1< core::Size >	extra_minimize_res_
utility::vector1< core::Size >	syn_chi_res_list_
utility::vector1< core::Size >	terminal_res_

Constructor & Destructor Documentation

protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::StepWiseMonteCarloOptions

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protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::~StepWiseMonteCarloOptions

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Member Function Documentation

core::Real const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::add_delete_frequency ( ) const

inline

bool const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::allow_internal_hinge_moves ( ) const

inline

bool const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::allow_internal_local_moves ( ) const

inline

bool const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::allow_skip_bulge ( ) const

inline

bool const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::allow_split_off ( ) const

inline

bool const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::allow_virtual_side_chains ( ) const

inline

Referenced by setup_protein_modeler_options().

utility::vector1< core::Size > const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::bulge_res ( ) const

inline

core::Real const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::chainbreak_weight ( ) const

inline

core::Size const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::cycles ( ) const

inline

bool const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::erraser ( ) const

inline

Referenced by setup_rna_modeler_options().

utility::vector1< core::Size > const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::extra_minimize_res ( ) const

inline

bool const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::filter_native_big_bins ( ) const

inline

Referenced by setup_protein_modeler_options().

bool const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::force_centroid_interaction ( ) const

inline

Referenced by setup_rna_modeler_options().

core::Real const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::from_scratch_frequency ( ) const

inline

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::initialize_from_command_line

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)

References allow_virtual_side_chains_, basic::options::OptionKeys::stepwise::rna::bulge_res, filter_native_big_bins_, force_centroid_interaction_, local_redock_only_, option, protein_atr_rep_screen_, protein_prepack_, rebuild_bulge_mode_, basic::options::OptionKeys::stepwise::protein::rmsd_screen, rmsd_screen_, sampler_max_centroid_distance_, sampler_perform_phosphate_pack_, set_add_delete_frequency(), set_allow_internal_hinge_moves(), set_allow_internal_local_moves(), set_allow_skip_bulge(), set_allow_split_off(), set_bulge_res(), set_cycles(), set_erraser(), set_force_centroid_interaction(), set_from_scratch_frequency(), set_integration_test_mode(), set_intermolecular_frequency(), set_just_min_after_mutation_frequency(), set_make_movie(), set_minimize_single_res_frequency(), set_minimizer_allow_variable_bond_geometry(), set_num_pose_minimize(), set_num_random_samples(), set_silent_file(), set_skip_deletions(), set_switch_focus_frequency(), set_syn_chi_res_list(), set_temperature(), set_terminal_res(), set_use_phenix_geo(), set_verbose_scores(), set_virtual_sugar_do_minimize(), set_virtual_sugar_keep_base_fixed(), skip_coord_constraints_, tether_jump_, unified_framework_, and user.

bool const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::integration_test_mode ( ) const

inline

Referenced by setup_rna_modeler_options().

core::Real const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::intermolecular_frequency ( ) const

inline

core::Real const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::just_min_after_mutation_frequency ( ) const

inline

bool const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::local_redock_only ( ) const

inline

bool const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::make_movie ( ) const

inline

core::Real const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::max_missing_weight ( ) const

inline

core::Real const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::minimize_single_res_frequency ( ) const

inline

bool const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::minimizer_allow_variable_bond_geometry ( ) const

inline

Referenced by setup_rna_modeler_options().

core::Real const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::minimizer_vary_bond_geometry_frequency ( ) const

inline

Referenced by setup_rna_modeler_options().

core::Size const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::num_pose_minimize ( ) const

inline

Referenced by setup_protein_modeler_options(), and setup_rna_modeler_options().

core::Size const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::num_random_samples ( ) const

inline

Referenced by setup_protein_modeler_options(), and setup_rna_modeler_options().

bool const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::output_minimized_pose_list ( ) const

inline

Referenced by setup_protein_modeler_options().

virtual void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::parse_my_tag ( utility::tag::TagCOP  )

inlinevirtual

Initialize from the recursive "tag" structure.

Implements basic::resource_manager::ResourceOptions.

bool const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::protein_atr_rep_screen ( ) const

inline

Referenced by setup_protein_modeler_options().

bool const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::protein_prepack ( ) const

inline

Referenced by setup_protein_modeler_options().

bool const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::rebuild_bulge_mode ( ) const

inline

core::Real const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::rmsd_screen ( ) const

inline

Referenced by setup_protein_modeler_options().

core::Real const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::sampler_max_centroid_distance ( ) const

inline

Referenced by setup_rna_modeler_options().

bool const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::sampler_perform_phosphate_pack ( ) const

inline

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_add_delete_frequency ( core::Real const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_allow_internal_hinge_moves ( bool const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_allow_internal_local_moves ( bool const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_allow_skip_bulge ( bool const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_allow_split_off ( bool const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_allow_virtual_side_chains ( bool const &  setting )

inline

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_bulge_res ( utility::vector1< core::Size > const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_chainbreak_weight ( core::Real const &  setting )

inline

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_cycles ( core::Size const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_erraser ( bool const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_extra_minimize_res ( utility::vector1< core::Size > const &  setting )

inline

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_filter_native_big_bins ( bool const &  setting )

inline

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_force_centroid_interaction ( bool const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_from_scratch_frequency ( core::Real const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_integration_test_mode ( bool const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_intermolecular_frequency ( core::Real const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_just_min_after_mutation_frequency ( core::Real const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_local_redock_only ( bool const &  setting )

inline

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_make_movie ( bool const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_max_missing_weight ( core::Real const &  setting )

inline

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_minimize_single_res_frequency ( core::Real const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_minimizer_allow_variable_bond_geometry ( bool const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_minimizer_vary_bond_geometry_frequency ( core::Real const &  setting )

inline

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_num_pose_minimize ( core::Size const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_num_random_samples ( core::Size const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_output_minimized_pose_list ( bool const &  setting )

inline

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_protein_atr_rep_screen ( bool const &  setting )

inline

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_protein_prepack ( bool const &  setting )

inline

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_rebuild_bulge_mode ( bool const &  setting )

inline

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_rmsd_screen ( core::Real const &  setting )

inline

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_sampler_max_centroid_distance ( core::Real const &  setting )

inline

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_sampler_perform_phosphate_pack ( bool const &  setting )

inline

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_silent_file ( std::string const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_skip_coord_constraints ( bool const &  setting )

inline

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_skip_deletions ( bool const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_switch_focus_frequency ( core::Real const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_syn_chi_res_list ( utility::vector1< core::Size > const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_temperature ( core::Real const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_terminal_res ( utility::vector1< core::Size > const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_tether_jump ( bool const &  setting )

inline

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_unified_framework ( bool const &  setting )

inline

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_use_phenix_geo ( bool const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_verbose_scores ( bool const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_virtual_sugar_do_minimize ( bool const &  setting )

inline

Referenced by initialize_from_command_line().

void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::set_virtual_sugar_keep_base_fixed ( bool const &  setting )

inline

Referenced by initialize_from_command_line().

StepWiseProteinModelerOptionsOP protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::setup_protein_modeler_options

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)

const

References allow_virtual_side_chains(), filter_native_big_bins(), num_pose_minimize(), num_random_samples(), output_minimized_pose_list(), protein_atr_rep_screen(), protein_prepack(), rmsd_screen(), silent_file_, and skip_coord_constraints().

StepWiseRNA_ModelerOptionsOP protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::setup_rna_modeler_options

(

)

const

References erraser(), force_centroid_interaction(), integration_test_mode(), minimizer_allow_variable_bond_geometry(), minimizer_vary_bond_geometry_frequency(), num_pose_minimize(), num_random_samples(), rebuild_bulge_mode_, sampler_max_centroid_distance(), protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_choose_random(), protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_force_centroid_interaction(), protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_integration_test_mode(), protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_kic_sampling_if_relevant(), protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_minimizer_allow_variable_bond_geometry(), protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_minimizer_vary_bond_geometry_frequency(), protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_num_pose_minimize(), protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_num_random_samples(), protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_sampler_max_centroid_distance(), protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_silent_file(), protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_tether_jump(), protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_unified_framework(), protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_use_phenix_geo(), protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_virtual_sugar_do_minimize(), protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::set_virtual_sugar_keep_base_fixed(), silent_file_, tether_jump(), unified_framework(), use_phenix_geo(), virtual_sugar_do_minimize(), and virtual_sugar_keep_base_fixed().

virtual void protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::show ( std::ostream &  ) const

inlinevirtual

Describe this instance to a given output stream.

std::string const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::silent_file ( ) const

inline

bool const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::skip_coord_constraints ( ) const

inline

Referenced by setup_protein_modeler_options().

bool const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::skip_deletions ( ) const

inline

core::Real const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::switch_focus_frequency ( ) const

inline

utility::vector1< core::Size > const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::syn_chi_res_list ( ) const

inline

core::Real const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::temperature ( ) const

inline

utility::vector1< core::Size > const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::terminal_res ( ) const

inline

bool const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::tether_jump ( ) const

inline

Referenced by setup_rna_modeler_options().

virtual std::string protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::type ( ) const

inlinevirtual

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

Implements basic::resource_manager::ResourceOptions.

bool const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::unified_framework ( ) const

inline

Referenced by setup_rna_modeler_options().

bool const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::use_phenix_geo ( ) const

inline

Referenced by setup_rna_modeler_options().

bool const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::verbose_scores ( ) const

inline

bool const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::virtual_sugar_do_minimize ( ) const

inline

Referenced by setup_rna_modeler_options().

bool const& protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::virtual_sugar_keep_base_fixed ( ) const

inline

Referenced by setup_rna_modeler_options().

Member Data Documentation

core::Real protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::add_delete_frequency_

private

bool protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::allow_internal_hinge_moves_

private

bool protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::allow_internal_local_moves_

private

bool protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::allow_skip_bulge_

private

bool protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::allow_split_off_

private

bool protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::allow_virtual_side_chains_

private

Referenced by initialize_from_command_line().

utility::vector1< core::Size > protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::bulge_res_

private

core::Real protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::chainbreak_weight_

private

core::Size protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::cycles_

private

bool protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::erraser_

private

utility::vector1< core::Size > protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::extra_minimize_res_

private

bool protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::filter_native_big_bins_

private

Referenced by initialize_from_command_line().

bool protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::force_centroid_interaction_

private

Referenced by initialize_from_command_line().

core::Real protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::from_scratch_frequency_

private

bool protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::integration_test_mode_

private

core::Real protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::intermolecular_frequency_

private

core::Real protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::just_min_after_mutation_frequency_

private

bool protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::local_redock_only_

private

Referenced by initialize_from_command_line().

bool protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::make_movie_

private

core::Real protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::max_missing_weight_

private

core::Real protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::minimize_single_res_frequency_

private

bool protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::minimizer_allow_variable_bond_geometry_

private

core::Real protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::minimizer_vary_bond_geometry_frequency_

private

core::Size protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::num_pose_minimize_

private

core::Size protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::num_random_samples_

private

bool protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::output_minimized_pose_list_

private

bool protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::protein_atr_rep_screen_

private

Referenced by initialize_from_command_line().

bool protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::protein_prepack_

private

Referenced by initialize_from_command_line().

bool protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::rebuild_bulge_mode_

private

Referenced by initialize_from_command_line(), and setup_rna_modeler_options().

core::Real protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::rmsd_screen_

private

Referenced by initialize_from_command_line().

core::Real protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::sampler_max_centroid_distance_

private

Referenced by initialize_from_command_line().

bool protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::sampler_perform_phosphate_pack_

private

Referenced by initialize_from_command_line().

std::string protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::silent_file_

private

Referenced by setup_protein_modeler_options(), and setup_rna_modeler_options().

bool protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::skip_coord_constraints_

private

Referenced by initialize_from_command_line().

bool protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::skip_deletions_

private

core::Real protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::switch_focus_frequency_

private

utility::vector1< core::Size > protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::syn_chi_res_list_

private

core::Real protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::temperature_

private

utility::vector1< core::Size > protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::terminal_res_

private

bool protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::tether_jump_

private

Referenced by initialize_from_command_line().

bool protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::unified_framework_

private

Referenced by initialize_from_command_line().

bool protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::use_phenix_geo_

private

bool protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::verbose_scores_

private

bool protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::virtual_sugar_do_minimize_

private

bool protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions::virtual_sugar_keep_base_fixed_

private

---

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

• symlinks/rosetta/src/protocols/stepwise/monte_carlo/StepWiseMonteCarloOptions.hh
• symlinks/rosetta/src/protocols/stepwise/monte_carlo/StepWiseMonteCarloOptions.cc