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core::import_pose::options::RNA_DeNovoProtocolOptions Class Reference

#include <RNA_DeNovoProtocolOptions.hh>

Inheritance diagram for core::import_pose::options::RNA_DeNovoProtocolOptions:
Inheritance graph
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Public Member Functions

 RNA_DeNovoProtocolOptions ()
 
RNA_DeNovoProtocolOptionsOP clone () const
 clone the options More...
 
void parse_my_tag (utility::tag::TagCOP) override
 Initialize from the recursive "tag" structure. More...
 
std::string type () const override
 The class name (its type) for a particular instance. This function allows for better error message delivery. More...
 
void set_nstruct (core::Size const setting)
 
core::Size nstruct () const
 
void set_lores_scorefxn (std::string const &setting)
 
std::string lores_scorefxn () const
 
void set_align_output (bool const setting)
 
bool align_output () const
 
void set_binary_rna_output (bool const setting)
 
bool binary_rna_output () const
 
void set_use_legacy_setup (bool const setting)
 
bool use_legacy_setup () const
 
void set_cst_gap (bool const setting)
 
bool cst_gap () const
 
void set_overwrite (bool const setting)
 
bool overwrite () const
 
void set_silent_file (std::string const &setting)
 
std::string silent_file () const
 
void set_dump_stems (bool const setting)
 
bool dump_stems () const
 
void initialize_from_command_line ()
 
void initialize_from_options (utility::options::OptionCollection const &opts)
 
void initialize_from_tag (utility::tag::TagCOP const &tag)
 
- Public Member Functions inherited from core::import_pose::options::RNA_FragmentMonteCarloOptions
 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_FragmentMonteCarloOptions
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 nstruct_
 
std::string lores_scorefxn_
 
std::string silent_file_
 
bool align_output_
 
bool overwrite_
 
bool binary_rna_output_
 
bool use_legacy_setup_
 
bool cst_gap_
 
bool dump_stems_
 

Constructor & Destructor Documentation

core::import_pose::options::RNA_DeNovoProtocolOptions::RNA_DeNovoProtocolOptions ( )

Member Function Documentation

bool core::import_pose::options::RNA_DeNovoProtocolOptions::align_output ( ) const
inline

References align_output_.

bool core::import_pose::options::RNA_DeNovoProtocolOptions::binary_rna_output ( ) const
inline

References binary_rna_output_.

RNA_DeNovoProtocolOptionsOP core::import_pose::options::RNA_DeNovoProtocolOptions::clone ( ) const

clone the options

bool core::import_pose::options::RNA_DeNovoProtocolOptions::cst_gap ( ) const
inline

References cst_gap_.

bool core::import_pose::options::RNA_DeNovoProtocolOptions::dump_stems ( ) const
inline

References dump_stems_.

void core::import_pose::options::RNA_DeNovoProtocolOptions::initialize_from_command_line ( )
void core::import_pose::options::RNA_DeNovoProtocolOptions::initialize_from_options ( utility::options::OptionCollection const &  opts)
void core::import_pose::options::RNA_DeNovoProtocolOptions::initialize_from_tag ( utility::tag::TagCOP const &  tag)

I don't really want the RosettaScripts interface to support some of the "archaic" options that are kind of RosettaScripts antipatterns, like managing input and output mid protocol... so I just won't.

References core::import_pose::options::RNA_FragmentMonteCarloOptions::initialize_from_tag(), set_cst_gap(), and set_lores_scorefxn().

void core::import_pose::options::RNA_DeNovoProtocolOptions::list_attributes ( utility::tag::AttributeList &  attlist)
static
void core::import_pose::options::RNA_DeNovoProtocolOptions::list_options_read ( utility::options::OptionKeyList &  opts)
static
std::string core::import_pose::options::RNA_DeNovoProtocolOptions::lores_scorefxn ( ) const
inline

References lores_scorefxn_.

core::Size core::import_pose::options::RNA_DeNovoProtocolOptions::nstruct ( ) const
inline

References nstruct_.

bool core::import_pose::options::RNA_DeNovoProtocolOptions::overwrite ( ) const
inline

References overwrite_.

void core::import_pose::options::RNA_DeNovoProtocolOptions::parse_my_tag ( utility::tag::TagCOP  )
inlineoverridevirtual

Initialize from the recursive "tag" structure.

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

void core::import_pose::options::RNA_DeNovoProtocolOptions::set_align_output ( bool const  setting)
inline

References align_output_.

Referenced by initialize_from_options().

void core::import_pose::options::RNA_DeNovoProtocolOptions::set_binary_rna_output ( bool const  setting)
inline

References binary_rna_output_.

Referenced by initialize_from_options().

void core::import_pose::options::RNA_DeNovoProtocolOptions::set_cst_gap ( bool const  setting)
inline

References cst_gap_.

Referenced by initialize_from_tag().

void core::import_pose::options::RNA_DeNovoProtocolOptions::set_dump_stems ( bool const  setting)
inline

References dump_stems_.

void core::import_pose::options::RNA_DeNovoProtocolOptions::set_lores_scorefxn ( std::string const &  setting)
inline
void core::import_pose::options::RNA_DeNovoProtocolOptions::set_nstruct ( core::Size const  setting)
inline

References nstruct_.

void core::import_pose::options::RNA_DeNovoProtocolOptions::set_overwrite ( bool const  setting)
inline

References overwrite_.

Referenced by initialize_from_options().

void core::import_pose::options::RNA_DeNovoProtocolOptions::set_silent_file ( std::string const &  setting)
inline

References silent_file_.

void core::import_pose::options::RNA_DeNovoProtocolOptions::set_use_legacy_setup ( bool const  setting)
inline

References use_legacy_setup_.

std::string core::import_pose::options::RNA_DeNovoProtocolOptions::silent_file ( ) const
inline

References silent_file_.

std::string core::import_pose::options::RNA_DeNovoProtocolOptions::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_DeNovoProtocolOptions::use_legacy_setup ( ) const
inline

References use_legacy_setup_.

Member Data Documentation

bool core::import_pose::options::RNA_DeNovoProtocolOptions::align_output_
private

Referenced by align_output(), and set_align_output().

bool core::import_pose::options::RNA_DeNovoProtocolOptions::binary_rna_output_
private
bool core::import_pose::options::RNA_DeNovoProtocolOptions::cst_gap_
private
bool core::import_pose::options::RNA_DeNovoProtocolOptions::dump_stems_
private
std::string core::import_pose::options::RNA_DeNovoProtocolOptions::lores_scorefxn_
private
Size core::import_pose::options::RNA_DeNovoProtocolOptions::nstruct_
private
bool core::import_pose::options::RNA_DeNovoProtocolOptions::overwrite_
private

Referenced by overwrite(), and set_overwrite().

std::string core::import_pose::options::RNA_DeNovoProtocolOptions::silent_file_
private
bool core::import_pose::options::RNA_DeNovoProtocolOptions::use_legacy_setup_
private

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