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Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
core::import_pose::options::RNA_FragmentMonteCarloOptions Class Reference

#include <RNA_FragmentMonteCarloOptions.hh>

Inheritance diagram for core::import_pose::options::RNA_FragmentMonteCarloOptions:
Inheritance graph
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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::Sizeoutput_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::Sizeallowed_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< Sizedock_chunks_res_
 
utility::vector1< std::string > chunk_initialization_pdb_files_
 
utility::vector1< std::string > chunk_silent_files_
 
utility::vector1< core::Sizeinput_res_
 
utility::vector1< core::Sizeinput_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

◆ RNA_FragmentMonteCarloOptions()

core::import_pose::options::RNA_FragmentMonteCarloOptions::RNA_FragmentMonteCarloOptions ( )

Member Function Documentation

◆ align_pdb()

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

References align_pdb_.

◆ all_rna_fragments_file()

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

◆ allow_bulge()

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

References allow_bulge_.

◆ allow_consecutive_bulges()

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

◆ allow_fragment_moves_in_bps()

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

◆ allowed_bulge_res()

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

References allowed_bulge_res_.

◆ autofilter()

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

References autofilter_.

◆ autofilter_score_quantile()

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

◆ bps_moves()

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

References bps_moves_.

◆ center_jumps_in_single_stranded()

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

◆ chainbreak_weight()

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

References chainbreak_weight_.

◆ chunk_initialization_pdb_files()

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

◆ chunk_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().

◆ chunk_silent_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().

◆ clone()

RNA_FragmentMonteCarloOptionsOP core::import_pose::options::RNA_FragmentMonteCarloOptions::clone ( ) const

clone the options

◆ close_loops()

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

◆ close_loops_after_each_move()

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

◆ convert_protein_centroid()

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

◆ disallow_bps_at_extra_min_res()

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

◆ disallow_realign()

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

References disallow_realign_.

◆ dock_chunks()

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

References dock_chunks_.

Referenced by set_dock_chunks().

◆ dock_chunks_res()

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

References dock_chunks_res_.

◆ dock_each_chunk()

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

References dock_each_chunk_.

◆ dock_each_chunk_per_chain()

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

◆ dock_into_density_legacy()

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

◆ docking()

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

References docking_.

◆ docking_move_size()

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

References docking_move_size_.

◆ exhaustive_fragment_insertion()

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

◆ filter_chain_closure()

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

References filter_chain_closure_.

◆ filter_chain_closure_distance()

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

◆ filter_chain_closure_halfway()

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

◆ filter_lores_base_pairs()

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

◆ filter_lores_base_pairs_early()

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

◆ filter_vdw()

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

References filter_vdw_.

◆ fixed_stems()

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

References fixed_stems_.

◆ frag_size()

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

References frag_size_.

◆ ft_close_chains()

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

References ft_close_chains_.

◆ gradual_constraints()

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

References gradual_constraints_.

◆ grid_vdw_weight()

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

References grid_vdw_weight_.

◆ helical_substruct_res()

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

◆ helical_substructs()

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

References helical_substructs_.

◆ ignore_secstruct()

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

References ignore_secstruct_.

◆ initial_structures_provided()

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

◆ initialize_for_farna_optimizer()

void core::import_pose::options::RNA_FragmentMonteCarloOptions::initialize_for_farna_optimizer ( core::Size const &  cycles)

◆ initialize_from_command_line()

void core::import_pose::options::RNA_FragmentMonteCarloOptions::initialize_from_command_line ( )

◆ initialize_from_options()

void core::import_pose::options::RNA_FragmentMonteCarloOptions::initialize_from_options ( utility::options::OptionCollection const &  opts)

◆ initialize_from_tag()

void core::import_pose::options::RNA_FragmentMonteCarloOptions::initialize_from_tag ( utility::tag::TagCOP const &  tag)

◆ input_res()

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().

◆ input_res_initialize()

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

References input_res_initialize_.

◆ jump_change_frequency()

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

◆ jump_histogram_binwidth()

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

◆ jump_histogram_binwidth_rotvector()

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

◆ jump_histogram_boxsize()

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

◆ jump_library_file()

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

◆ linear_chainbreak_weight()

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

◆ list_attributes()

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

◆ list_options_read()

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

◆ minimize_structure()

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

References minimize_structure_.

◆ monte_carlo_cycles()

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

References monte_carlo_cycles_.

◆ new_fold_tree_initializer()

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

◆ output_filters()

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

References output_filters_.

◆ output_histogram_file()

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

◆ output_jump_chainbreak()

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

◆ output_jump_o3p_to_o5p()

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

◆ output_jump_reference_RT_string()

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

◆ output_jump_res()

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().

◆ output_jump_target_xyz()

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

◆ output_lores_silent_file()

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

◆ output_rotation_vector()

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

◆ output_score_file()

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

References output_score_file_.

◆ output_score_frequency()

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

◆ override_refine_pose_rounds()

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

◆ parse_my_tag()

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.

◆ ramp_rnp_vdw()

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

References ramp_rnp_vdw_.

◆ randomize_init_rnp()

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

References randomize_init_rnp_.

◆ refine_native_get_good_FT()

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

◆ refine_pose()

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

References refine_pose_.

◆ relax_structure()

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

References relax_structure_.

◆ rmsd_screen()

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

References rmsd_screen_.

◆ rna_protein_docking()

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

References rna_protein_docking_.

◆ rna_protein_docking_freq()

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

◆ rna_protein_docking_legacy()

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

◆ rnp_high_res_cycles()

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

References rnp_high_res_cycles_.

◆ rnp_high_res_relax()

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

References rnp_high_res_relax_.

◆ rnp_min_first()

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

References rnp_min_first_.

◆ rnp_pack_first()

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

References rnp_pack_first_.

◆ rnp_ramp_rep()

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

References rnp_ramp_rep_.

◆ root_at_first_rigid_body()

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

◆ rounds()

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

References rounds_.

◆ save_jump_histogram()

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

References save_jump_histogram_.

◆ save_times()

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

References save_times_.

◆ set_align_pdb()

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

References align_pdb_.

◆ set_all_rna_fragments_file()

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

◆ set_allow_bulge()

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

References allow_bulge_.

◆ set_allow_consecutive_bulges()

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

◆ set_allow_fragment_moves_in_bps()

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

◆ set_allowed_bulge_res()

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

References allowed_bulge_res_.

◆ set_autofilter()

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

References autofilter_.

◆ set_autofilter_score_quantile()

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

◆ set_bps_moves()

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

References bps_moves_.

◆ set_center_jumps_in_single_stranded()

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

◆ set_chainbreak_weight()

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

References chainbreak_weight_.

◆ set_chunk_initialization_pdb_files()

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

◆ set_chunk_pdb_files()

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

◆ set_chunk_silent_files()

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

◆ set_close_loops()

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

References close_loops_.

◆ set_close_loops_after_each_move()

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

◆ set_convert_protein_centroid()

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

◆ set_disallow_bps_at_extra_min_res()

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

◆ set_disallow_realign()

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

References disallow_realign_.

◆ set_dock_chunks()

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

References dock_chunks(), and dock_chunks_.

◆ set_dock_chunks_res()

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

References dock_chunks_res_.

◆ set_dock_each_chunk()

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

References dock_each_chunk_.

◆ set_dock_each_chunk_per_chain()

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

◆ set_dock_into_density_legacy()

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

◆ set_docking()

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

References docking_.

◆ set_docking_move_size()

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

References docking_move_size_.

◆ set_exhaustive_fragment_insertion()

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

◆ set_filter_chain_closure()

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

References filter_chain_closure_.

◆ set_filter_chain_closure_distance()

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

◆ set_filter_chain_closure_halfway()

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

◆ set_filter_lores_base_pairs()

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

◆ set_filter_lores_base_pairs_early()

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

◆ set_filter_vdw()

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

References filter_vdw_.

◆ set_fixed_stems()

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

References fixed_stems_.

◆ set_frag_size()

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

References frag_size_.

◆ set_ft_close_chains()

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

References ft_close_chains_.

◆ set_gradual_constraints()

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

References gradual_constraints_.

◆ set_grid_vdw_weight()

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

References grid_vdw_weight_.

◆ set_helical_substruct_res()

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

◆ set_helical_substructs()

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

References helical_substructs_.

◆ set_ignore_secstruct()

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

References ignore_secstruct_.

◆ set_initial_structures_provided()

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

◆ set_input_res()

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

◆ set_input_res_initialize()

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

◆ set_jump_change_frequency()

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

◆ set_jump_histogram_binwidth()

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

◆ set_jump_histogram_binwidth_rotvector()

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

◆ set_jump_histogram_boxsize()

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

◆ set_jump_library_file()

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

References jump_library_file_.

◆ set_linear_chainbreak_weight()

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

◆ set_minimize_structure()

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

References minimize_structure_.

◆ set_monte_carlo_cycles()

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

References monte_carlo_cycles_.

◆ set_new_fold_tree_initializer()

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

◆ set_output_filters()

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

References output_filters_.

◆ set_output_histogram_file()

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

◆ set_output_jump_chainbreak()

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

◆ set_output_jump_o3p_to_o5p()

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

◆ set_output_jump_reference_RT_string()

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

◆ set_output_jump_res()

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

◆ set_output_jump_target_xyz()

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

◆ set_output_lores_silent_file()

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

◆ set_output_rotation_vector()

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

◆ set_output_score_file()

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

References output_score_file_.

◆ set_output_score_frequency()

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

◆ set_override_refine_pose_rounds()

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

◆ set_ramp_rnp_vdw()

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

References ramp_rnp_vdw_.

◆ set_randomize_init_rnp()

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

References randomize_init_rnp_.

◆ set_refine_native_get_good_FT()

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

◆ set_refine_pose()

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

References refine_pose_.

◆ set_relax_structure()

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

References relax_structure_.

◆ set_rmsd_screen()

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

References rmsd_screen_.

◆ set_rna_protein_docking()

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

References rna_protein_docking_.

◆ set_rna_protein_docking_freq()

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

◆ set_rna_protein_docking_legacy()

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

◆ set_rnp_high_res_cycles()

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

References rnp_high_res_cycles_.

◆ set_rnp_high_res_relax()

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

References rnp_high_res_relax_.

◆ set_rnp_min_first()

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

References rnp_min_first_.

◆ set_rnp_pack_first()

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

References rnp_pack_first_.

◆ set_rnp_ramp_rep()

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

References rnp_ramp_rep_.

◆ set_root_at_first_rigid_body()

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

◆ set_rounds()

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

References rounds_.

◆ set_save_jump_histogram()

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

References save_jump_histogram_.

◆ set_save_times()

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

References save_times_.

◆ set_simple_rmsd_cutoff_relax()

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

◆ set_small_docking_moves()

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

References small_docking_moves_.

◆ set_staged_constraints()

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

References staged_constraints_.

◆ set_superimpose_over_all()

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

References superimpose_over_all_.

◆ set_suppress_bp_constraint()

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

◆ set_symm_hack_arity()

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

References symm_hack_arity_.

◆ set_temperature()

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

References temperature_.

◆ set_titrate_stack_bonus()

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

References titrate_stack_bonus_.

◆ set_use_chem_shift_data()

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

References use_chem_shift_data_.

◆ set_user_defined_cycles()

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

References user_defined_cycles_.

◆ set_vall_torsions_file()

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

◆ set_vdw_rep_screen_include_sidechains()

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

◆ set_VDW_rep_screen_info()

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

References VDW_rep_screen_info_.

◆ simple_rmsd_cutoff_relax()

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

◆ small_docking_moves()

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

References small_docking_moves_.

◆ staged_constraints()

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

References staged_constraints_.

◆ superimpose_over_all()

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

References superimpose_over_all_.

◆ suppress_bp_constraint()

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

◆ symm_hack_arity()

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

References symm_hack_arity_.

◆ temperature()

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

References temperature_.

◆ titrate_stack_bonus()

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

References titrate_stack_bonus_.

◆ type()

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.

◆ use_chem_shift_data()

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

References use_chem_shift_data_.

◆ user_defined_cycles()

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

References user_defined_cycles_.

◆ vall_torsions_file()

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

◆ vdw_rep_screen_include_sidechains()

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

◆ VDW_rep_screen_info()

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

References VDW_rep_screen_info_.

Member Data Documentation

◆ align_pdb_

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

Referenced by align_pdb(), and set_align_pdb().

◆ all_rna_fragments_file_

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

◆ allow_bulge_

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

Referenced by allow_bulge(), and set_allow_bulge().

◆ allow_consecutive_bulges_

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

◆ allow_fragment_moves_in_bps_

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

◆ allowed_bulge_res_

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

◆ autofilter_

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

Referenced by autofilter(), and set_autofilter().

◆ autofilter_score_quantile_

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

◆ bps_moves_

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

Referenced by bps_moves(), and set_bps_moves().

◆ center_jumps_in_single_stranded_

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

◆ chainbreak_weight_

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

◆ chunk_initialization_pdb_files_

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

◆ chunk_pdb_files_

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

◆ chunk_silent_files_

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

◆ close_loops_

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

Referenced by close_loops(), and set_close_loops().

◆ close_loops_after_each_move_

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

◆ convert_protein_centroid_

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

◆ disallow_bps_at_extra_min_res_

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

◆ disallow_realign_

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

◆ dock_chunks_

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

Referenced by dock_chunks(), and set_dock_chunks().

◆ dock_chunks_res_

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

◆ dock_each_chunk_

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

◆ dock_each_chunk_per_chain_

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

◆ dock_into_density_legacy_

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

◆ docking_

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

Referenced by docking(), and set_docking().

◆ docking_move_size_

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

◆ exhaustive_fragment_insertion_

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

◆ filter_chain_closure_

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

◆ filter_chain_closure_distance_

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

◆ filter_chain_closure_halfway_

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

◆ filter_lores_base_pairs_

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

◆ filter_lores_base_pairs_early_

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

◆ filter_vdw_

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

Referenced by filter_vdw(), and set_filter_vdw().

◆ fixed_stems_

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

Referenced by fixed_stems(), and set_fixed_stems().

◆ frag_size_

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

Referenced by frag_size(), and set_frag_size().

◆ ft_close_chains_

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

◆ gradual_constraints_

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

◆ grid_vdw_weight_

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

◆ helical_substruct_res_

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

◆ helical_substructs_

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

◆ ignore_secstruct_

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

◆ initial_structures_provided_

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

◆ input_res_

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

Referenced by input_res(), and set_input_res().

◆ input_res_initialize_

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

◆ jump_change_frequency_

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

◆ jump_histogram_binwidth_

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

◆ jump_histogram_binwidth_rotvector_

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

◆ jump_histogram_boxsize_

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

◆ jump_library_file_

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

◆ linear_chainbreak_weight_

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

◆ minimize_structure_

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

◆ monte_carlo_cycles_

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

◆ new_fold_tree_initializer_

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

◆ output_filters_

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

◆ output_histogram_file_

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

◆ output_jump_chainbreak_

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

◆ output_jump_o3p_to_o5p_

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

◆ output_jump_reference_RT_string_

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

◆ output_jump_res_

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

◆ output_jump_target_xyz_

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

◆ output_lores_silent_file_

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

◆ output_rotation_vector_

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

◆ output_score_file_

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

◆ output_score_frequency_

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

◆ override_refine_pose_rounds_

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

◆ ramp_rnp_vdw_

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

Referenced by ramp_rnp_vdw(), and set_ramp_rnp_vdw().

◆ randomize_init_rnp_

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

◆ refine_native_get_good_FT_

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

◆ refine_pose_

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

Referenced by refine_pose(), and set_refine_pose().

◆ relax_structure_

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

◆ rmsd_screen_

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

Referenced by rmsd_screen(), and set_rmsd_screen().

◆ rna_protein_docking_

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

◆ rna_protein_docking_freq_

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

◆ rna_protein_docking_legacy_

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

◆ rnp_high_res_cycles_

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

◆ rnp_high_res_relax_

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

◆ rnp_min_first_

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

Referenced by rnp_min_first(), and set_rnp_min_first().

◆ rnp_pack_first_

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

◆ rnp_ramp_rep_

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

Referenced by rnp_ramp_rep(), and set_rnp_ramp_rep().

◆ root_at_first_rigid_body_

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

◆ rounds_

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

Referenced by rounds(), and set_rounds().

◆ save_jump_histogram_

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

◆ save_times_

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

Referenced by save_times(), and set_save_times().

◆ simple_rmsd_cutoff_relax_

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

◆ small_docking_moves_

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

◆ staged_constraints_

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

◆ superimpose_over_all_

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

◆ suppress_bp_constraint_

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

◆ symm_hack_arity_

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

◆ temperature_

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

Referenced by set_temperature(), and temperature().

◆ titrate_stack_bonus_

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

◆ use_chem_shift_data_

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

◆ user_defined_cycles_

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

◆ vdw_rep_screen_include_sidechains_

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

◆ VDW_rep_screen_info_

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

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