core::import_pose::options::RNA_FragmentMonteCarloOptions Class Reference

#include <RNA_FragmentMonteCarloOptions.hh>

Inheritance diagram for core::import_pose::options::RNA_FragmentMonteCarloOptions:

Public Member Functions
	RNA_FragmentMonteCarloOptions ()
RNA_FragmentMonteCarloOptionsOP	clone () const
	clone the options More...
void	initialize_from_command_line ()
void	initialize_from_options (utility::options::OptionCollection const &opts)
void	initialize_from_tag (utility::tag::TagCOP const &tag)
void	initialize_for_farna_optimizer (core::Size const &cycles)
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...
void	set_rounds (core::Size const &setting)
core::Size	rounds () const
void	set_close_loops_after_each_move (bool const &setting)
bool	close_loops_after_each_move () const
void	set_refine_pose (bool const &setting)
bool	refine_pose () const
void	set_override_refine_pose_rounds (bool const &setting)
bool	override_refine_pose_rounds () const
void	set_refine_native_get_good_FT (bool const &setting)
bool	refine_native_get_good_FT () const
void	set_temperature (core::Real const setting)
core::Real	temperature () const
void	set_autofilter (bool const &setting)
bool	autofilter () const
void	set_autofilter_score_quantile (core::Real const &setting)
core::Real	autofilter_score_quantile () const
void	set_minimize_structure (bool const &setting)
bool	minimize_structure () const
void	set_relax_structure (bool const &setting)
bool	relax_structure () const
void	set_use_chem_shift_data (bool const &setting)
bool	use_chem_shift_data () const
void	set_superimpose_over_all (bool const &setting)
bool	superimpose_over_all () const
void	set_fixed_stems (bool const &setting)
bool	fixed_stems () const
void	set_ft_close_chains (bool const &setting)
bool	ft_close_chains () const
void	set_jump_change_frequency (core::Real const &setting)
core::Real	jump_change_frequency () const
void	set_close_loops (bool const setting)
bool	close_loops () const
void	set_allow_bulge (bool const &setting)
bool	allow_bulge () const
void	set_allow_consecutive_bulges (bool const &setting)
bool	allow_consecutive_bulges () const
void	set_simple_rmsd_cutoff_relax (bool const &setting)
bool	simple_rmsd_cutoff_relax () const
void	set_filter_lores_base_pairs (bool const setting)
bool	filter_lores_base_pairs () const
void	set_filter_lores_base_pairs_early (bool const setting)
bool	filter_lores_base_pairs_early () const
void	set_filter_chain_closure (bool const setting)
bool	filter_chain_closure () const
void	set_filter_chain_closure_distance (core::Real const setting)
core::Real	filter_chain_closure_distance () const
void	set_filter_chain_closure_halfway (bool const setting)
bool	filter_chain_closure_halfway () const
void	set_chainbreak_weight (core::Real const &setting)
core::Real	chainbreak_weight () const
void	set_linear_chainbreak_weight (core::Real const &setting)
core::Real	linear_chainbreak_weight () const
void	set_allowed_bulge_res (utility::vector1< core::Size > const &setting)
utility::vector1< core::Size > const &	allowed_bulge_res () const
void	set_filter_vdw (bool const setting)
bool	filter_vdw () const
void	set_VDW_rep_screen_info (utility::vector1< std::string > const &setting)
utility::vector1< std::string >	VDW_rep_screen_info () const
void	set_vdw_rep_screen_include_sidechains (bool const setting)
bool	vdw_rep_screen_include_sidechains () const
void	set_gradual_constraints (bool const setting)
bool	gradual_constraints () const
void	set_ramp_rnp_vdw (bool const &setting)
bool	ramp_rnp_vdw () const
void	set_grid_vdw_weight (core::Real const &setting)
core::Real	grid_vdw_weight () const
void	set_convert_protein_centroid (bool const &setting)
bool	convert_protein_centroid () const
void	set_rna_protein_docking (bool const &setting)
bool	rna_protein_docking () const
void	set_small_docking_moves (bool const &setting)
bool	small_docking_moves () const
void	set_docking_move_size (core::Real const &setting)
core::Real	docking_move_size () const
void	set_rna_protein_docking_legacy (bool const &setting)
bool	rna_protein_docking_legacy () const
void	set_rna_protein_docking_freq (core::Real const &setting)
core::Real	rna_protein_docking_freq () const
void	set_docking (bool const &setting)
bool	docking () const
void	set_randomize_init_rnp (bool const &setting)
bool	randomize_init_rnp () const
void	set_rnp_high_res_relax (bool const &setting)
bool	rnp_high_res_relax () const
void	set_rnp_high_res_cycles (core::Real const &setting)
core::Real	rnp_high_res_cycles () const
void	set_rnp_pack_first (bool const &setting)
bool	rnp_pack_first () const
void	set_rnp_ramp_rep (bool const &setting)
bool	rnp_ramp_rep () const
void	set_rnp_min_first (bool const &setting)
bool	rnp_min_first () const
void	set_dock_into_density_legacy (bool const &setting)
bool	dock_into_density_legacy () const
void	set_new_fold_tree_initializer (bool const &setting)
bool	new_fold_tree_initializer () const
void	set_initial_structures_provided (bool const &setting)
bool	initial_structures_provided () const
void	set_monte_carlo_cycles (core::Size const setting)
core::Size	monte_carlo_cycles () const
void	set_user_defined_cycles (bool const &setting)
bool	user_defined_cycles () const
void	set_ignore_secstruct (bool const &setting)
bool	ignore_secstruct () const
void	set_titrate_stack_bonus (bool const &setting)
bool	titrate_stack_bonus () const
void	set_staged_constraints (bool const &setting)
bool	staged_constraints () const
void	set_root_at_first_rigid_body (bool const &setting)
bool	root_at_first_rigid_body () const
void	set_dock_each_chunk (bool const &setting)
bool	dock_each_chunk () const
void	set_dock_each_chunk_per_chain (bool const &setting)
bool	dock_each_chunk_per_chain () const
void	set_dock_chunks (utility::vector1< std::string > const &dock_chunks)
utility::vector1< std::string > const &	dock_chunks () const
void	set_center_jumps_in_single_stranded (bool const &setting)
bool	center_jumps_in_single_stranded () const
void	set_suppress_bp_constraint (core::Real const &setting)
core::Real	suppress_bp_constraint () const
void	set_bps_moves (bool const &setting)
bool	bps_moves () const
void	set_disallow_bps_at_extra_min_res (bool const &setting)
bool	disallow_bps_at_extra_min_res () const
void	set_allow_fragment_moves_in_bps (bool const &setting)
bool	allow_fragment_moves_in_bps () const
void	set_frag_size (core::Size const &setting)
core::Size	frag_size () const
void	set_jump_library_file (std::string const &setting)
std::string	jump_library_file () const
void	set_all_rna_fragments_file (std::string const &setting)
std::string	all_rna_fragments_file () const
void	set_vall_torsions_file (std::string const &setting)
std::string	vall_torsions_file () const
void	set_chunk_pdb_files (utility::vector1< std::string > const &chunk_pdb_files)
utility::vector1< std::string > const &	chunk_pdb_files () const
void	set_helical_substructs (utility::vector1< std::string > const &setting)
utility::vector1< std::string > const &	helical_substructs () const
void	set_helical_substruct_res (utility::vector1< utility::vector1< core::Size > > const &setting)
utility::vector1 < utility::vector1< core::Size > > const &	helical_substruct_res () const
void	set_dock_chunks_res (utility::vector1< core::Size > const &setting)
utility::vector1< core::Size > const &	dock_chunks_res () const
void	set_chunk_initialization_pdb_files (utility::vector1< std::string > const &input_files)
utility::vector1< std::string > const &	chunk_initialization_pdb_files () const
void	set_chunk_silent_files (utility::vector1< std::string > const &chunk_silent_files)
utility::vector1< std::string > const &	chunk_silent_files () const
void	set_input_res (utility::vector1< Size > const &input_res)
utility::vector1< Size > const &	input_res () const
void	set_input_res_initialize (utility::vector1< Size > const &input_res)
utility::vector1< Size > const &	input_res_initialize () const
void	set_output_score_frequency (core::Size const &setting)
core::Size	output_score_frequency () const
void	set_output_score_file (std::string const &setting)
std::string	output_score_file () const
void	set_output_lores_silent_file (bool const setting)
bool	output_lores_silent_file () const
void	set_output_jump_res (utility::vector1< Size > const &output_jump_res)
utility::vector1< Size > const &	output_jump_res () const
void	set_output_jump_o3p_to_o5p (bool const &setting)
bool	output_jump_o3p_to_o5p () const
void	set_output_jump_chainbreak (bool const &setting)
bool	output_jump_chainbreak () const
void	set_save_jump_histogram (bool const &setting)
bool	save_jump_histogram () const
void	set_output_histogram_file (std::string const &setting)
std::string	output_histogram_file () const
void	set_output_rotation_vector (bool const &setting)
bool	output_rotation_vector () const
void	set_output_jump_target_xyz (core::Vector const &setting)
core::Vector	output_jump_target_xyz () const
void	set_output_jump_reference_RT_string (std::string const &setting)
std::string	output_jump_reference_RT_string () const
void	set_jump_histogram_boxsize (core::Real const &setting)
core::Real	jump_histogram_boxsize () const
void	set_jump_histogram_binwidth (core::Real const &setting)
core::Real	jump_histogram_binwidth () const
void	set_jump_histogram_binwidth_rotvector (core::Real const &setting)
core::Real	jump_histogram_binwidth_rotvector () const
void	set_rmsd_screen (core::Real const setting)
core::Real	rmsd_screen () const
void	set_disallow_realign (bool const setting)
bool	disallow_realign () const
void	set_align_pdb (std::string const &setting)
std::string	align_pdb () const
void	set_symm_hack_arity (Size const setting)
Size	symm_hack_arity () const
void	set_exhaustive_fragment_insertion (Size const setting)
Size	exhaustive_fragment_insertion () const
void	set_output_filters (bool const setting)
bool	output_filters () const
void	set_save_times (bool const setting)
bool	save_times () const
Public Member Functions inherited from core::import_pose::options::RNA_MinimizerOptions
	RNA_MinimizerOptions ()
RNA_MinimizerOptionsOP	clone () const
	clone the options More...
void	initialize_from_command_line ()
void	initialize_from_options (utility::options::OptionCollection const &opts)
void	initialize_from_tag (utility::tag::TagCOP const &tag)
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...
void	set_vary_bond_geometry (bool const &setting)
bool	vary_bond_geometry () const
void	set_extra_minimize_res (utility::vector1< Size > const &extra_minimize_res)
utility::vector1< Size > const &	extra_minimize_res () const
void	set_extra_minimize_chi_res (utility::vector1< Size > const &extra_minimize_chi_res)
utility::vector1< Size > const &	extra_minimize_chi_res () const
void	set_minimizer_use_coordinate_constraints (bool const &setting)
bool	minimizer_use_coordinate_constraints () const
void	set_min_type (std::string const &setting)
std::string	min_type () const
void	set_minimize_bps (bool const &setting)
bool	minimize_bps () const
void	set_minimize_all_protein (bool const &setting)
bool	minimize_all_protein () const
void	set_minimize_protein_sc (bool const &setting)
bool	minimize_protein_sc () const
void	set_protein_packing (bool const &setting)
bool	protein_packing () const
void	set_protein_pack_all (bool const &setting)
bool	protein_pack_all () const
void	set_protein_packing_distance (core::Real const &setting)
core::Real	protein_packing_distance () const
void	set_deriv_check (bool const &setting)
bool	deriv_check () const
void	set_skip_o2prime_trials (bool const &setting)
bool	skip_o2prime_trials () const
void	set_minimize_rounds (core::Size const &setting)
core::Size	minimize_rounds () const
void	set_use_nblist (bool const &setting)
bool	use_nblist () const
void	set_nblist_auto_update (bool const &setting)
bool	nblist_auto_update () const
void	set_max_iter (core::Size const &setting)
core::Size	max_iter () const
Public Member Functions inherited from core::import_pose::options::RNA_BasicOptions
	RNA_BasicOptions ()
RNA_BasicOptionsOP	clone () const
	clone the options More...
void	initialize_from_command_line ()
void	initialize_from_options (utility::options::OptionCollection const &opts)
void	initialize_from_tag (utility::tag::TagCOP const &tag)
void	set_dump_pdb (bool const setting)
bool	dump_pdb () const
void	set_move_first_rigid_body (bool const &setting)
bool	move_first_rigid_body () const
void	set_dock_into_density (bool const &setting)
bool	dock_into_density () const
void	set_model_with_density (bool const &setting)
bool	model_with_density () const
void	set_verbose (bool const &setting)
bool	verbose () const

Static Public Member Functions
static void	list_attributes (utility::tag::AttributeList &attlist)
static void	list_options_read (utility::options::OptionKeyList &opts)
Static Public Member Functions inherited from core::import_pose::options::RNA_MinimizerOptions
static void	list_attributes (utility::tag::AttributeList &attlist)
static void	list_options_read (utility::options::OptionKeyList &opts)
Static Public Member Functions inherited from core::import_pose::options::RNA_BasicOptions
static void	list_attributes (utility::tag::AttributeList &attlist)
static void	list_options_read (utility::options::OptionKeyList &opts)

Private Attributes
Size	rounds_ = 10
Size	monte_carlo_cycles_ = 0
bool	user_defined_cycles_ = false
bool	minimize_structure_ = false
bool	relax_structure_ = false
core::Real	temperature_ = 2.0
bool	ignore_secstruct_ = false
core::Real	chainbreak_weight_ = -1
core::Real	linear_chainbreak_weight_ = -1
bool	close_loops_ = true
bool	close_loops_after_each_move_ = false
bool	allow_bulge_ = false
bool	allow_consecutive_bulges_ = false
core::Real	jump_change_frequency_ = 0.1
bool	autofilter_ = false
core::Real	autofilter_score_quantile_ = 0.20
bool	titrate_stack_bonus_ = true
bool	root_at_first_rigid_body_ = false
bool	dock_each_chunk_ = false
bool	dock_each_chunk_per_chain_ = false
bool	center_jumps_in_single_stranded_ = false
core::Real	suppress_bp_constraint_ = 1.0
bool	filter_lores_base_pairs_ = false
bool	filter_lores_base_pairs_early_ = false
bool	filter_chain_closure_ = true
core::Real	filter_chain_closure_distance_ = 6.0
bool	filter_chain_closure_halfway_ = true
bool	staged_constraints_ = false
Size	output_score_frequency_ = 0
std::string	output_score_file_ = ""
bool	output_lores_silent_file_ = false
utility::vector1< core::Size >	output_jump_res_ = utility::vector1< core::Size >( 0 )
bool	output_jump_o3p_to_o5p_ = false
bool	output_jump_chainbreak_ = false
bool	output_rotation_vector_ = false
core::Vector	output_jump_target_xyz_ = core::Vector( 0 )
std::string	output_jump_reference_RT_string_ = ""
bool	save_jump_histogram_ = false
std::string	output_histogram_file_ = ""
core::Real	jump_histogram_boxsize_ = 0.0
core::Real	jump_histogram_binwidth_ = 0.0
core::Real	jump_histogram_binwidth_rotvector_ = 0.0
utility::vector1< core::Size >	allowed_bulge_res_
bool	output_filters_ = false
bool	filter_vdw_ = false
utility::vector1< std::string >	VDW_rep_screen_info_
bool	vdw_rep_screen_include_sidechains_ = false
bool	gradual_constraints_ = true
bool	ramp_rnp_vdw_ = false
core::Real	grid_vdw_weight_ = 1.0
bool	convert_protein_centroid_ = true
bool	rna_protein_docking_ = false
bool	small_docking_moves_ = false
core::Real	docking_move_size_ = 1.0
bool	rna_protein_docking_legacy_ = false
core::Real	rna_protein_docking_freq_ = 0.4
bool	docking_ = false
bool	randomize_init_rnp_ = true
bool	rnp_high_res_relax_ = true
core::Size	rnp_high_res_cycles_ = 10
bool	rnp_pack_first_ = false
bool	rnp_ramp_rep_ = false
bool	rnp_min_first_ = false
bool	dock_into_density_legacy_ = false
bool	new_fold_tree_initializer_ = false
bool	initial_structures_provided_ = false
bool	simple_rmsd_cutoff_relax_ = false
bool	refine_pose_ = false
bool	override_refine_pose_rounds_ = false
bool	refine_native_get_good_FT_ = false
bool	bps_moves_ = false
bool	disallow_bps_at_extra_min_res_ = false
bool	allow_fragment_moves_in_bps_ = false
Size	frag_size_ = 0
bool	use_chem_shift_data_ = false
bool	superimpose_over_all_ = false
bool	fixed_stems_ = false
bool	ft_close_chains_ = true
std::string	all_rna_fragments_file_ = ""
std::string	jump_library_file_ = ""
utility::vector1< std::string >	chunk_pdb_files_
utility::vector1< std::string >	dock_chunks_
utility::vector1< std::string >	helical_substructs_
utility::vector1 < utility::vector1< Size > >	helical_substruct_res_
utility::vector1< Size >	dock_chunks_res_
utility::vector1< std::string >	chunk_initialization_pdb_files_
utility::vector1< std::string >	chunk_silent_files_
utility::vector1< core::Size >	input_res_
utility::vector1< core::Size >	input_res_initialize_
core::Real	rmsd_screen_ = 0
bool	disallow_realign_ = true
std::string	align_pdb_ = ""
Size	symm_hack_arity_ = 1
bool	save_times_ = false
bool	exhaustive_fragment_insertion_ = false

Constructor & Destructor Documentation

core::import_pose::options::RNA_FragmentMonteCarloOptions::RNA_FragmentMonteCarloOptions

(

)

Member Function Documentation

std::string core::import_pose::options::RNA_FragmentMonteCarloOptions::align_pdb ( ) const

inline

References align_pdb_.

std::string core::import_pose::options::RNA_FragmentMonteCarloOptions::all_rna_fragments_file ( ) const

inline

References all_rna_fragments_file_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::allow_bulge ( ) const

inline

References allow_bulge_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::allow_consecutive_bulges ( ) const

inline

References allow_consecutive_bulges_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::allow_fragment_moves_in_bps ( ) const

inline

References allow_fragment_moves_in_bps_.

utility::vector1< core::Size > const& core::import_pose::options::RNA_FragmentMonteCarloOptions::allowed_bulge_res ( ) const

inline

References allowed_bulge_res_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::autofilter ( ) const

inline

References autofilter_.

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::autofilter_score_quantile ( ) const

inline

References autofilter_score_quantile_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::bps_moves ( ) const

inline

References bps_moves_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::center_jumps_in_single_stranded ( ) const

inline

References center_jumps_in_single_stranded_.

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::chainbreak_weight ( ) const

inline

References chainbreak_weight_.

utility::vector1< std::string > const& core::import_pose::options::RNA_FragmentMonteCarloOptions::chunk_initialization_pdb_files ( ) const

inline

References chunk_initialization_pdb_files_.

utility::vector1< std::string > const& core::import_pose::options::RNA_FragmentMonteCarloOptions::chunk_pdb_files ( ) const

inline

References chunk_pdb_files_.

Referenced by set_chunk_pdb_files().

utility::vector1< std::string > const& core::import_pose::options::RNA_FragmentMonteCarloOptions::chunk_silent_files ( ) const

inline

References chunk_silent_files_.

Referenced by set_chunk_silent_files().

RNA_FragmentMonteCarloOptionsOP core::import_pose::options::RNA_FragmentMonteCarloOptions::clone

(

)

const

clone the options

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::close_loops ( ) const

inline

References close_loops_.

Referenced by core::import_pose::options::RNA_DeNovoProtocolOptions::initialize_from_options().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::close_loops_after_each_move ( ) const

inline

References close_loops_after_each_move_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::convert_protein_centroid ( ) const

inline

References convert_protein_centroid_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::disallow_bps_at_extra_min_res ( ) const

inline

References disallow_bps_at_extra_min_res_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::disallow_realign ( ) const

inline

References disallow_realign_.

utility::vector1< std::string > const& core::import_pose::options::RNA_FragmentMonteCarloOptions::dock_chunks ( ) const

inline

References dock_chunks_.

Referenced by set_dock_chunks().

utility::vector1< core::Size > const& core::import_pose::options::RNA_FragmentMonteCarloOptions::dock_chunks_res ( ) const

inline

References dock_chunks_res_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::dock_each_chunk ( ) const

inline

References dock_each_chunk_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::dock_each_chunk_per_chain ( ) const

inline

References dock_each_chunk_per_chain_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::dock_into_density_legacy ( ) const

inline

References dock_into_density_legacy_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::docking ( ) const

inline

References docking_.

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::docking_move_size ( ) const

inline

References docking_move_size_.

Size core::import_pose::options::RNA_FragmentMonteCarloOptions::exhaustive_fragment_insertion ( ) const

inline

References exhaustive_fragment_insertion_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::filter_chain_closure ( ) const

inline

References filter_chain_closure_.

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::filter_chain_closure_distance ( ) const

inline

References filter_chain_closure_distance_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::filter_chain_closure_halfway ( ) const

inline

References filter_chain_closure_halfway_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::filter_lores_base_pairs ( ) const

inline

References filter_lores_base_pairs_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::filter_lores_base_pairs_early ( ) const

inline

References filter_lores_base_pairs_early_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::filter_vdw ( ) const

inline

References filter_vdw_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::fixed_stems ( ) const

inline

References fixed_stems_.

core::Size core::import_pose::options::RNA_FragmentMonteCarloOptions::frag_size ( ) const

inline

References frag_size_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::ft_close_chains ( ) const

inline

References ft_close_chains_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::gradual_constraints ( ) const

inline

References gradual_constraints_.

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::grid_vdw_weight ( ) const

inline

References grid_vdw_weight_.

utility::vector1< utility::vector1< core::Size > > const& core::import_pose::options::RNA_FragmentMonteCarloOptions::helical_substruct_res ( ) const

inline

References helical_substruct_res_.

utility::vector1< std::string > const& core::import_pose::options::RNA_FragmentMonteCarloOptions::helical_substructs ( ) const

inline

References helical_substructs_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::ignore_secstruct ( ) const

inline

References ignore_secstruct_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::initial_structures_provided ( ) const

inline

References initial_structures_provided_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::initialize_for_farna_optimizer

(

core::Size const &

cycles

)

void core::import_pose::options::RNA_FragmentMonteCarloOptions::initialize_from_command_line

(

)

void core::import_pose::options::RNA_FragmentMonteCarloOptions::initialize_from_options

(

utility::options::OptionCollection const &

opts

)

References protocols::hybridization::path.

Referenced by core::import_pose::options::RNA_DeNovoProtocolOptions::initialize_from_command_line(), core::import_pose::options::RNA_DeNovoProtocolOptions::initialize_from_options(), and core::import_pose::libraries::RNA_LibraryManager::rna_jump_library_cop().

void core::import_pose::options::RNA_FragmentMonteCarloOptions::initialize_from_tag

(

utility::tag::TagCOP const &

tag

)

References core::pose::motif::a(), protocols::match::upstream::b, and core::pack::dunbrack::c.

Referenced by core::import_pose::options::RNA_DeNovoProtocolOptions::initialize_from_tag().

utility::vector1< Size > const& core::import_pose::options::RNA_FragmentMonteCarloOptions::input_res ( ) const

inline

References input_res_.

Referenced by set_input_res(), and set_input_res_initialize().

utility::vector1< Size > const& core::import_pose::options::RNA_FragmentMonteCarloOptions::input_res_initialize ( ) const

inline

References input_res_initialize_.

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::jump_change_frequency ( ) const

inline

References jump_change_frequency_.

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::jump_histogram_binwidth ( ) const

inline

References jump_histogram_binwidth_.

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::jump_histogram_binwidth_rotvector ( ) const

inline

References jump_histogram_binwidth_rotvector_.

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::jump_histogram_boxsize ( ) const

inline

References jump_histogram_boxsize_.

std::string core::import_pose::options::RNA_FragmentMonteCarloOptions::jump_library_file ( ) const

inline

References jump_library_file_.

Referenced by core::import_pose::libraries::RNA_LibraryManager::rna_jump_library_cop().

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::linear_chainbreak_weight ( ) const

inline

References linear_chainbreak_weight_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::list_attributes ( utility::tag::AttributeList &  attlist )

static

Referenced by core::import_pose::options::RNA_DeNovoProtocolOptions::list_attributes().

void core::import_pose::options::RNA_FragmentMonteCarloOptions::list_options_read ( utility::options::OptionKeyList &  opts )

static

References protocols::hybridization::path.

Referenced by core::import_pose::options::RNA_DeNovoProtocolOptions::list_options_read().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::minimize_structure ( ) const

inline

References minimize_structure_.

core::Size core::import_pose::options::RNA_FragmentMonteCarloOptions::monte_carlo_cycles ( ) const

inline

References monte_carlo_cycles_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::new_fold_tree_initializer ( ) const

inline

References new_fold_tree_initializer_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::output_filters ( ) const

inline

References output_filters_.

std::string core::import_pose::options::RNA_FragmentMonteCarloOptions::output_histogram_file ( ) const

inline

References output_histogram_file_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::output_jump_chainbreak ( ) const

inline

References output_jump_chainbreak_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::output_jump_o3p_to_o5p ( ) const

inline

References output_jump_o3p_to_o5p_.

std::string core::import_pose::options::RNA_FragmentMonteCarloOptions::output_jump_reference_RT_string ( ) const

inline

References output_jump_reference_RT_string_.

utility::vector1< Size > const& core::import_pose::options::RNA_FragmentMonteCarloOptions::output_jump_res ( ) const

inline

References output_jump_res_.

Referenced by set_output_jump_res().

core::Vector core::import_pose::options::RNA_FragmentMonteCarloOptions::output_jump_target_xyz ( ) const

inline

References output_jump_target_xyz_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::output_lores_silent_file ( ) const

inline

References output_lores_silent_file_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::output_rotation_vector ( ) const

inline

References output_rotation_vector_.

std::string core::import_pose::options::RNA_FragmentMonteCarloOptions::output_score_file ( ) const

inline

References output_score_file_.

core::Size core::import_pose::options::RNA_FragmentMonteCarloOptions::output_score_frequency ( ) const

inline

References output_score_frequency_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::override_refine_pose_rounds ( ) const

inline

References override_refine_pose_rounds_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::parse_my_tag ( utility::tag::TagCOP  )

inlineoverridevirtual

Initialize from the recursive "tag" structure.

Reimplemented from core::import_pose::options::RNA_BasicOptions.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::ramp_rnp_vdw ( ) const

inline

References ramp_rnp_vdw_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::randomize_init_rnp ( ) const

inline

References randomize_init_rnp_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::refine_native_get_good_FT ( ) const

inline

References refine_native_get_good_FT_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::refine_pose ( ) const

inline

References refine_pose_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::relax_structure ( ) const

inline

References relax_structure_.

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::rmsd_screen ( ) const

inline

References rmsd_screen_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::rna_protein_docking ( ) const

inline

References rna_protein_docking_.

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::rna_protein_docking_freq ( ) const

inline

References rna_protein_docking_freq_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::rna_protein_docking_legacy ( ) const

inline

References rna_protein_docking_legacy_.

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::rnp_high_res_cycles ( ) const

inline

References rnp_high_res_cycles_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::rnp_high_res_relax ( ) const

inline

References rnp_high_res_relax_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::rnp_min_first ( ) const

inline

References rnp_min_first_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::rnp_pack_first ( ) const

inline

References rnp_pack_first_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::rnp_ramp_rep ( ) const

inline

References rnp_ramp_rep_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::root_at_first_rigid_body ( ) const

inline

References root_at_first_rigid_body_.

core::Size core::import_pose::options::RNA_FragmentMonteCarloOptions::rounds ( ) const

inline

References rounds_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::save_jump_histogram ( ) const

inline

References save_jump_histogram_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::save_times ( ) const

inline

References save_times_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_align_pdb ( std::string const &  setting )

inline

References align_pdb_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_all_rna_fragments_file ( std::string const &  setting )

inline

References all_rna_fragments_file_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_allow_bulge ( bool const &  setting )

inline

References allow_bulge_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_allow_consecutive_bulges ( bool const &  setting )

inline

References allow_consecutive_bulges_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_allow_fragment_moves_in_bps ( bool const &  setting )

inline

References allow_fragment_moves_in_bps_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_allowed_bulge_res ( utility::vector1< core::Size > const &  setting )

inline

References allowed_bulge_res_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_autofilter ( bool const &  setting )

inline

References autofilter_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_autofilter_score_quantile ( core::Real const &  setting )

inline

References autofilter_score_quantile_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_bps_moves ( bool const &  setting )

inline

References bps_moves_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_center_jumps_in_single_stranded ( bool const &  setting )

inline

References center_jumps_in_single_stranded_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_chainbreak_weight ( core::Real const &  setting )

inline

References chainbreak_weight_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_chunk_initialization_pdb_files ( utility::vector1< std::string > const &  input_files )

inline

References chunk_initialization_pdb_files_.

Referenced by core::import_pose::options::RNA_DeNovoProtocolOptions::initialize_from_options().

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_chunk_pdb_files ( utility::vector1< std::string > const &  chunk_pdb_files )

inline

References chunk_pdb_files(), and chunk_pdb_files_.

Referenced by core::import_pose::options::RNA_DeNovoProtocolOptions::initialize_from_options().

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_chunk_silent_files ( utility::vector1< std::string > const &  chunk_silent_files )

inline

References chunk_silent_files(), and chunk_silent_files_.

Referenced by core::import_pose::options::RNA_DeNovoProtocolOptions::initialize_from_options().

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_close_loops ( bool const  setting )

inline

References close_loops_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_close_loops_after_each_move ( bool const &  setting )

inline

References close_loops_after_each_move_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_convert_protein_centroid ( bool const &  setting )

inline

References convert_protein_centroid_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_disallow_bps_at_extra_min_res ( bool const &  setting )

inline

References disallow_bps_at_extra_min_res_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_disallow_realign ( bool const  setting )

inline

References disallow_realign_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_dock_chunks ( utility::vector1< std::string > const &  dock_chunks )

inline

References dock_chunks(), and dock_chunks_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_dock_chunks_res ( utility::vector1< core::Size > const &  setting )

inline

References dock_chunks_res_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_dock_each_chunk ( bool const &  setting )

inline

References dock_each_chunk_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_dock_each_chunk_per_chain ( bool const &  setting )

inline

References dock_each_chunk_per_chain_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_dock_into_density_legacy ( bool const &  setting )

inline

References dock_into_density_legacy_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_docking ( bool const &  setting )

inline

References docking_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_docking_move_size ( core::Real const &  setting )

inline

References docking_move_size_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_exhaustive_fragment_insertion ( Size const  setting )

inline

References exhaustive_fragment_insertion_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_filter_chain_closure ( bool const  setting )

inline

References filter_chain_closure_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_filter_chain_closure_distance ( core::Real const  setting )

inline

References filter_chain_closure_distance_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_filter_chain_closure_halfway ( bool const  setting )

inline

References filter_chain_closure_halfway_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_filter_lores_base_pairs ( bool const  setting )

inline

References filter_lores_base_pairs_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_filter_lores_base_pairs_early ( bool const  setting )

inline

References filter_lores_base_pairs_early_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_filter_vdw ( bool const  setting )

inline

References filter_vdw_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_fixed_stems ( bool const &  setting )

inline

References fixed_stems_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_frag_size ( core::Size const &  setting )

inline

References frag_size_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_ft_close_chains ( bool const &  setting )

inline

References ft_close_chains_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_gradual_constraints ( bool const  setting )

inline

References gradual_constraints_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_grid_vdw_weight ( core::Real const &  setting )

inline

References grid_vdw_weight_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_helical_substruct_res ( utility::vector1< utility::vector1< core::Size > > const &  setting )

inline

References helical_substruct_res_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_helical_substructs ( utility::vector1< std::string > const &  setting )

inline

References helical_substructs_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_ignore_secstruct ( bool const &  setting )

inline

References ignore_secstruct_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_initial_structures_provided ( bool const &  setting )

inline

References initial_structures_provided_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_input_res ( utility::vector1< Size > const &  input_res )

inline

References input_res(), and input_res_.

Referenced by core::import_pose::options::RNA_DeNovoProtocolOptions::initialize_from_options().

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_input_res_initialize ( utility::vector1< Size > const &  input_res )

inline

References input_res(), and input_res_initialize_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_jump_change_frequency ( core::Real const &  setting )

inline

References jump_change_frequency_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_jump_histogram_binwidth ( core::Real const &  setting )

inline

References jump_histogram_binwidth_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_jump_histogram_binwidth_rotvector ( core::Real const &  setting )

inline

References jump_histogram_binwidth_rotvector_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_jump_histogram_boxsize ( core::Real const &  setting )

inline

References jump_histogram_boxsize_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_jump_library_file ( std::string const &  setting )

inline

References jump_library_file_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_linear_chainbreak_weight ( core::Real const &  setting )

inline

References linear_chainbreak_weight_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_minimize_structure ( bool const &  setting )

inline

References minimize_structure_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_monte_carlo_cycles ( core::Size const  setting )

inline

References monte_carlo_cycles_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_new_fold_tree_initializer ( bool const &  setting )

inline

References new_fold_tree_initializer_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_output_filters ( bool const  setting )

inline

References output_filters_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_output_histogram_file ( std::string const &  setting )

inline

References output_histogram_file_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_output_jump_chainbreak ( bool const &  setting )

inline

References output_jump_chainbreak_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_output_jump_o3p_to_o5p ( bool const &  setting )

inline

References output_jump_o3p_to_o5p_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_output_jump_reference_RT_string ( std::string const &  setting )

inline

References output_jump_reference_RT_string_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_output_jump_res ( utility::vector1< Size > const &  output_jump_res )

inline

References output_jump_res(), and output_jump_res_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_output_jump_target_xyz ( core::Vector const &  setting )

inline

References output_jump_target_xyz_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_output_lores_silent_file ( bool const  setting )

inline

References output_lores_silent_file_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_output_rotation_vector ( bool const &  setting )

inline

References output_rotation_vector_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_output_score_file ( std::string const &  setting )

inline

References output_score_file_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_output_score_frequency ( core::Size const &  setting )

inline

References output_score_frequency_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_override_refine_pose_rounds ( bool const &  setting )

inline

References override_refine_pose_rounds_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_ramp_rnp_vdw ( bool const &  setting )

inline

References ramp_rnp_vdw_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_randomize_init_rnp ( bool const &  setting )

inline

References randomize_init_rnp_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_refine_native_get_good_FT ( bool const &  setting )

inline

References refine_native_get_good_FT_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_refine_pose ( bool const &  setting )

inline

References refine_pose_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_relax_structure ( bool const &  setting )

inline

References relax_structure_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_rmsd_screen ( core::Real const  setting )

inline

References rmsd_screen_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_rna_protein_docking ( bool const &  setting )

inline

References rna_protein_docking_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_rna_protein_docking_freq ( core::Real const &  setting )

inline

References rna_protein_docking_freq_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_rna_protein_docking_legacy ( bool const &  setting )

inline

References rna_protein_docking_legacy_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_rnp_high_res_cycles ( core::Real const &  setting )

inline

References rnp_high_res_cycles_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_rnp_high_res_relax ( bool const &  setting )

inline

References rnp_high_res_relax_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_rnp_min_first ( bool const &  setting )

inline

References rnp_min_first_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_rnp_pack_first ( bool const &  setting )

inline

References rnp_pack_first_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_rnp_ramp_rep ( bool const &  setting )

inline

References rnp_ramp_rep_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_root_at_first_rigid_body ( bool const &  setting )

inline

References root_at_first_rigid_body_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_rounds ( core::Size const &  setting )

inline

References rounds_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_save_jump_histogram ( bool const &  setting )

inline

References save_jump_histogram_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_save_times ( bool const  setting )

inline

References save_times_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_simple_rmsd_cutoff_relax ( bool const &  setting )

inline

References simple_rmsd_cutoff_relax_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_small_docking_moves ( bool const &  setting )

inline

References small_docking_moves_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_staged_constraints ( bool const &  setting )

inline

References staged_constraints_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_superimpose_over_all ( bool const &  setting )

inline

References superimpose_over_all_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_suppress_bp_constraint ( core::Real const &  setting )

inline

References suppress_bp_constraint_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_symm_hack_arity ( Size const  setting )

inline

References symm_hack_arity_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_temperature ( core::Real const  setting )

inline

References temperature_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_titrate_stack_bonus ( bool const &  setting )

inline

References titrate_stack_bonus_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_use_chem_shift_data ( bool const &  setting )

inline

References use_chem_shift_data_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_user_defined_cycles ( bool const &  setting )

inline

References user_defined_cycles_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_vall_torsions_file ( std::string const &  setting )

inline

References all_rna_fragments_file_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_vdw_rep_screen_include_sidechains ( bool const  setting )

inline

References vdw_rep_screen_include_sidechains_.

void core::import_pose::options::RNA_FragmentMonteCarloOptions::set_VDW_rep_screen_info ( utility::vector1< std::string > const &  setting )

inline

References VDW_rep_screen_info_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::simple_rmsd_cutoff_relax ( ) const

inline

References simple_rmsd_cutoff_relax_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::small_docking_moves ( ) const

inline

References small_docking_moves_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::staged_constraints ( ) const

inline

References staged_constraints_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::superimpose_over_all ( ) const

inline

References superimpose_over_all_.

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::suppress_bp_constraint ( ) const

inline

References suppress_bp_constraint_.

Size core::import_pose::options::RNA_FragmentMonteCarloOptions::symm_hack_arity ( ) const

inline

References symm_hack_arity_.

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::temperature ( ) const

inline

References temperature_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::titrate_stack_bonus ( ) const

inline

References titrate_stack_bonus_.

std::string core::import_pose::options::RNA_FragmentMonteCarloOptions::type ( ) const

inlineoverridevirtual

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

Reimplemented from core::import_pose::options::RNA_BasicOptions.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::use_chem_shift_data ( ) const

inline

References use_chem_shift_data_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::user_defined_cycles ( ) const

inline

References user_defined_cycles_.

std::string core::import_pose::options::RNA_FragmentMonteCarloOptions::vall_torsions_file ( ) const

inline

References all_rna_fragments_file_.

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::vdw_rep_screen_include_sidechains ( ) const

inline

References vdw_rep_screen_include_sidechains_.

utility::vector1< std::string > core::import_pose::options::RNA_FragmentMonteCarloOptions::VDW_rep_screen_info ( ) const

inline

References VDW_rep_screen_info_.

Member Data Documentation

std::string core::import_pose::options::RNA_FragmentMonteCarloOptions::align_pdb_ = ""

private

Referenced by align_pdb(), and set_align_pdb().

std::string core::import_pose::options::RNA_FragmentMonteCarloOptions::all_rna_fragments_file_ = ""

private

Referenced by all_rna_fragments_file(), set_all_rna_fragments_file(), set_vall_torsions_file(), and vall_torsions_file().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::allow_bulge_ = false

private

Referenced by allow_bulge(), and set_allow_bulge().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::allow_consecutive_bulges_ = false

private

Referenced by allow_consecutive_bulges(), and set_allow_consecutive_bulges().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::allow_fragment_moves_in_bps_ = false

private

Referenced by allow_fragment_moves_in_bps(), and set_allow_fragment_moves_in_bps().

utility::vector1< core::Size > core::import_pose::options::RNA_FragmentMonteCarloOptions::allowed_bulge_res_

private

Referenced by allowed_bulge_res(), and set_allowed_bulge_res().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::autofilter_ = false

private

Referenced by autofilter(), and set_autofilter().

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::autofilter_score_quantile_ = 0.20

private

Referenced by autofilter_score_quantile(), and set_autofilter_score_quantile().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::bps_moves_ = false

private

Referenced by bps_moves(), and set_bps_moves().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::center_jumps_in_single_stranded_ = false

private

Referenced by center_jumps_in_single_stranded(), and set_center_jumps_in_single_stranded().

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::chainbreak_weight_ = -1

private

Referenced by chainbreak_weight(), and set_chainbreak_weight().

utility::vector1< std::string > core::import_pose::options::RNA_FragmentMonteCarloOptions::chunk_initialization_pdb_files_

private

Referenced by chunk_initialization_pdb_files(), and set_chunk_initialization_pdb_files().

utility::vector1< std::string > core::import_pose::options::RNA_FragmentMonteCarloOptions::chunk_pdb_files_

private

Referenced by chunk_pdb_files(), and set_chunk_pdb_files().

utility::vector1< std::string > core::import_pose::options::RNA_FragmentMonteCarloOptions::chunk_silent_files_

private

Referenced by chunk_silent_files(), and set_chunk_silent_files().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::close_loops_ = true

private

Referenced by close_loops(), and set_close_loops().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::close_loops_after_each_move_ = false

private

Referenced by close_loops_after_each_move(), and set_close_loops_after_each_move().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::convert_protein_centroid_ = true

private

Referenced by convert_protein_centroid(), and set_convert_protein_centroid().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::disallow_bps_at_extra_min_res_ = false

private

Referenced by disallow_bps_at_extra_min_res(), and set_disallow_bps_at_extra_min_res().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::disallow_realign_ = true

private

Referenced by disallow_realign(), and set_disallow_realign().

utility::vector1< std::string > core::import_pose::options::RNA_FragmentMonteCarloOptions::dock_chunks_

private

Referenced by dock_chunks(), and set_dock_chunks().

utility::vector1< Size > core::import_pose::options::RNA_FragmentMonteCarloOptions::dock_chunks_res_

private

Referenced by dock_chunks_res(), and set_dock_chunks_res().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::dock_each_chunk_ = false

private

Referenced by dock_each_chunk(), and set_dock_each_chunk().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::dock_each_chunk_per_chain_ = false

private

Referenced by dock_each_chunk_per_chain(), and set_dock_each_chunk_per_chain().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::dock_into_density_legacy_ = false

private

Referenced by dock_into_density_legacy(), and set_dock_into_density_legacy().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::docking_ = false

private

Referenced by docking(), and set_docking().

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::docking_move_size_ = 1.0

private

Referenced by docking_move_size(), and set_docking_move_size().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::exhaustive_fragment_insertion_ = false

private

Referenced by exhaustive_fragment_insertion(), and set_exhaustive_fragment_insertion().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::filter_chain_closure_ = true

private

Referenced by filter_chain_closure(), and set_filter_chain_closure().

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::filter_chain_closure_distance_ = 6.0

private

Referenced by filter_chain_closure_distance(), and set_filter_chain_closure_distance().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::filter_chain_closure_halfway_ = true

private

Referenced by filter_chain_closure_halfway(), and set_filter_chain_closure_halfway().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::filter_lores_base_pairs_ = false

private

Referenced by filter_lores_base_pairs(), and set_filter_lores_base_pairs().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::filter_lores_base_pairs_early_ = false

private

Referenced by filter_lores_base_pairs_early(), and set_filter_lores_base_pairs_early().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::filter_vdw_ = false

private

Referenced by filter_vdw(), and set_filter_vdw().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::fixed_stems_ = false

private

Referenced by fixed_stems(), and set_fixed_stems().

Size core::import_pose::options::RNA_FragmentMonteCarloOptions::frag_size_ = 0

private

Referenced by frag_size(), and set_frag_size().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::ft_close_chains_ = true

private

Referenced by ft_close_chains(), and set_ft_close_chains().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::gradual_constraints_ = true

private

Referenced by gradual_constraints(), and set_gradual_constraints().

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::grid_vdw_weight_ = 1.0

private

Referenced by grid_vdw_weight(), and set_grid_vdw_weight().

utility::vector1< utility::vector1< Size > > core::import_pose::options::RNA_FragmentMonteCarloOptions::helical_substruct_res_

private

Referenced by helical_substruct_res(), and set_helical_substruct_res().

utility::vector1< std::string > core::import_pose::options::RNA_FragmentMonteCarloOptions::helical_substructs_

private

Referenced by helical_substructs(), and set_helical_substructs().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::ignore_secstruct_ = false

private

Referenced by ignore_secstruct(), and set_ignore_secstruct().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::initial_structures_provided_ = false

private

Referenced by initial_structures_provided(), and set_initial_structures_provided().

utility::vector1< core::Size > core::import_pose::options::RNA_FragmentMonteCarloOptions::input_res_

private

Referenced by input_res(), and set_input_res().

utility::vector1< core::Size > core::import_pose::options::RNA_FragmentMonteCarloOptions::input_res_initialize_

private

Referenced by input_res_initialize(), and set_input_res_initialize().

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::jump_change_frequency_ = 0.1

private

Referenced by jump_change_frequency(), and set_jump_change_frequency().

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::jump_histogram_binwidth_ = 0.0

private

Referenced by jump_histogram_binwidth(), and set_jump_histogram_binwidth().

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::jump_histogram_binwidth_rotvector_ = 0.0

private

Referenced by jump_histogram_binwidth_rotvector(), and set_jump_histogram_binwidth_rotvector().

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::jump_histogram_boxsize_ = 0.0

private

Referenced by jump_histogram_boxsize(), and set_jump_histogram_boxsize().

std::string core::import_pose::options::RNA_FragmentMonteCarloOptions::jump_library_file_ = ""

private

Referenced by jump_library_file(), and set_jump_library_file().

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::linear_chainbreak_weight_ = -1

private

Referenced by linear_chainbreak_weight(), and set_linear_chainbreak_weight().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::minimize_structure_ = false

private

Referenced by minimize_structure(), and set_minimize_structure().

Size core::import_pose::options::RNA_FragmentMonteCarloOptions::monte_carlo_cycles_ = 0

private

Referenced by monte_carlo_cycles(), and set_monte_carlo_cycles().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::new_fold_tree_initializer_ = false

private

Referenced by new_fold_tree_initializer(), and set_new_fold_tree_initializer().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::output_filters_ = false

private

Referenced by output_filters(), and set_output_filters().

std::string core::import_pose::options::RNA_FragmentMonteCarloOptions::output_histogram_file_ = ""

private

Referenced by output_histogram_file(), and set_output_histogram_file().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::output_jump_chainbreak_ = false

private

Referenced by output_jump_chainbreak(), and set_output_jump_chainbreak().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::output_jump_o3p_to_o5p_ = false

private

Referenced by output_jump_o3p_to_o5p(), and set_output_jump_o3p_to_o5p().

std::string core::import_pose::options::RNA_FragmentMonteCarloOptions::output_jump_reference_RT_string_ = ""

private

Referenced by output_jump_reference_RT_string(), and set_output_jump_reference_RT_string().

utility::vector1< core::Size > core::import_pose::options::RNA_FragmentMonteCarloOptions::output_jump_res_ = utility::vector1< core::Size >( 0 )

private

Referenced by output_jump_res(), and set_output_jump_res().

core::Vector core::import_pose::options::RNA_FragmentMonteCarloOptions::output_jump_target_xyz_ = core::Vector( 0 )

private

Referenced by output_jump_target_xyz(), and set_output_jump_target_xyz().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::output_lores_silent_file_ = false

private

Referenced by output_lores_silent_file(), and set_output_lores_silent_file().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::output_rotation_vector_ = false

private

Referenced by output_rotation_vector(), and set_output_rotation_vector().

std::string core::import_pose::options::RNA_FragmentMonteCarloOptions::output_score_file_ = ""

private

Referenced by output_score_file(), and set_output_score_file().

Size core::import_pose::options::RNA_FragmentMonteCarloOptions::output_score_frequency_ = 0

private

Referenced by output_score_frequency(), and set_output_score_frequency().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::override_refine_pose_rounds_ = false

private

Referenced by override_refine_pose_rounds(), and set_override_refine_pose_rounds().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::ramp_rnp_vdw_ = false

private

Referenced by ramp_rnp_vdw(), and set_ramp_rnp_vdw().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::randomize_init_rnp_ = true

private

Referenced by randomize_init_rnp(), and set_randomize_init_rnp().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::refine_native_get_good_FT_ = false

private

Referenced by refine_native_get_good_FT(), and set_refine_native_get_good_FT().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::refine_pose_ = false

private

Referenced by refine_pose(), and set_refine_pose().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::relax_structure_ = false

private

Referenced by relax_structure(), and set_relax_structure().

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::rmsd_screen_ = 0

private

Referenced by rmsd_screen(), and set_rmsd_screen().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::rna_protein_docking_ = false

private

Referenced by rna_protein_docking(), and set_rna_protein_docking().

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::rna_protein_docking_freq_ = 0.4

private

Referenced by rna_protein_docking_freq(), and set_rna_protein_docking_freq().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::rna_protein_docking_legacy_ = false

private

Referenced by rna_protein_docking_legacy(), and set_rna_protein_docking_legacy().

core::Size core::import_pose::options::RNA_FragmentMonteCarloOptions::rnp_high_res_cycles_ = 10

private

Referenced by rnp_high_res_cycles(), and set_rnp_high_res_cycles().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::rnp_high_res_relax_ = true

private

Referenced by rnp_high_res_relax(), and set_rnp_high_res_relax().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::rnp_min_first_ = false

private

Referenced by rnp_min_first(), and set_rnp_min_first().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::rnp_pack_first_ = false

private

Referenced by rnp_pack_first(), and set_rnp_pack_first().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::rnp_ramp_rep_ = false

private

Referenced by rnp_ramp_rep(), and set_rnp_ramp_rep().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::root_at_first_rigid_body_ = false

private

Referenced by root_at_first_rigid_body(), and set_root_at_first_rigid_body().

Size core::import_pose::options::RNA_FragmentMonteCarloOptions::rounds_ = 10

private

Referenced by rounds(), and set_rounds().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::save_jump_histogram_ = false

private

Referenced by save_jump_histogram(), and set_save_jump_histogram().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::save_times_ = false

private

Referenced by save_times(), and set_save_times().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::simple_rmsd_cutoff_relax_ = false

private

Referenced by set_simple_rmsd_cutoff_relax(), and simple_rmsd_cutoff_relax().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::small_docking_moves_ = false

private

Referenced by set_small_docking_moves(), and small_docking_moves().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::staged_constraints_ = false

private

Referenced by set_staged_constraints(), and staged_constraints().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::superimpose_over_all_ = false

private

Referenced by set_superimpose_over_all(), and superimpose_over_all().

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::suppress_bp_constraint_ = 1.0

private

Referenced by set_suppress_bp_constraint(), and suppress_bp_constraint().

Size core::import_pose::options::RNA_FragmentMonteCarloOptions::symm_hack_arity_ = 1

private

Referenced by set_symm_hack_arity(), and symm_hack_arity().

core::Real core::import_pose::options::RNA_FragmentMonteCarloOptions::temperature_ = 2.0

private

Referenced by set_temperature(), and temperature().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::titrate_stack_bonus_ = true

private

Referenced by set_titrate_stack_bonus(), and titrate_stack_bonus().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::use_chem_shift_data_ = false

private

Referenced by set_use_chem_shift_data(), and use_chem_shift_data().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::user_defined_cycles_ = false

private

Referenced by set_user_defined_cycles(), and user_defined_cycles().

bool core::import_pose::options::RNA_FragmentMonteCarloOptions::vdw_rep_screen_include_sidechains_ = false

private

Referenced by set_vdw_rep_screen_include_sidechains(), and vdw_rep_screen_include_sidechains().

utility::vector1< std::string > core::import_pose::options::RNA_FragmentMonteCarloOptions::VDW_rep_screen_info_

private

Referenced by set_VDW_rep_screen_info(), and VDW_rep_screen_info().

---

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

• src/core/import_pose/options/RNA_FragmentMonteCarloOptions.hh
• src/core/import_pose/options/RNA_FragmentMonteCarloOptions.cc