#include <RNA_DeNovoProtocolOptions.hh>

Inheritance diagram for core::import_pose::options::RNA_DeNovoProtocolOptions:

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 ( )

References core::import_pose::options::RNA_FragmentMonteCarloOptions::initialize_from_options(), and initialize_from_options().

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

Referenced by initialize_from_command_line().

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

References core::import_pose::options::RNA_FragmentMonteCarloOptions::list_attributes().

Referenced by protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::provide_xml_schema().

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

static

References core::import_pose::dump_stems(), and core::import_pose::options::RNA_FragmentMonteCarloOptions::list_options_read().

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

References lores_scorefxn_.

Referenced by initialize_from_options(), and initialize_from_tag().

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

Referenced by binary_rna_output(), and set_binary_rna_output().

bool core::import_pose::options::RNA_DeNovoProtocolOptions::cst_gap_

private

Referenced by cst_gap(), initialize_from_options(), and set_cst_gap().

bool core::import_pose::options::RNA_DeNovoProtocolOptions::dump_stems_

private

Referenced by dump_stems(), initialize_from_options(), and set_dump_stems().

std::string core::import_pose::options::RNA_DeNovoProtocolOptions::lores_scorefxn_

private

Referenced by lores_scorefxn(), and set_lores_scorefxn().

Size core::import_pose::options::RNA_DeNovoProtocolOptions::nstruct_

private

Referenced by initialize_from_options(), nstruct(), and set_nstruct().

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

Referenced by initialize_from_options(), set_silent_file(), and silent_file().

bool core::import_pose::options::RNA_DeNovoProtocolOptions::use_legacy_setup_

private

Referenced by initialize_from_options(), set_use_legacy_setup(), and use_legacy_setup().

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

src/core/import_pose/options/RNA_DeNovoProtocolOptions.hh
src/core/import_pose/options/RNA_DeNovoProtocolOptions.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation