#include <StepWiseProteinModelerOptions.hh>

Inheritance diagram for protocols::stepwise::modeler::options::StepWiseProteinModelerOptions:

Public Member Functions
	StepWiseProteinModelerOptions ()

StepWiseProteinModelerOptionsOP	clone () const
	clone the options More...

virtual void	show (std::ostream &) const
	Describe this instance to a given output stream. More...

virtual void	parse_my_tag (utility::tag::TagCOP)
	Initialize from the recursive "tag" structure. More...

virtual std::string	type () const
	The class name (its type) for a particular ResourceOptions instance. This function allows for better error message delivery. More...

void	initialize_from_command_line ()

void	set_global_optimize (bool const &setting)

bool	global_optimize () const

void	set_sample_beta (bool const &setting)

bool	sample_beta () const

void	set_move_jumps_between_chains (bool const &setting)

bool	move_jumps_between_chains () const

void	set_disable_sampling_of_loop_takeoff (bool const &setting)

bool	disable_sampling_of_loop_takeoff () const

void	set_cart_min (bool const &setting)

bool	cart_min () const

void	set_n_sample (core::Size const &setting)

core::Size	n_sample () const

void	set_filter_native_big_bins (bool const &setting)

bool	filter_native_big_bins () const

void	set_allow_virtual_side_chains (bool const &setting)

bool	allow_virtual_side_chains () const

void	set_prepack (bool const &setting)

bool	prepack () const

void	set_pack_protein_side_chains (bool const &setting)

bool	pack_protein_side_chains () const

void	set_centroid_output (bool const &setting)

bool	centroid_output () const

void	set_centroid_screen (bool const &setting)

bool	centroid_screen () const

void	set_centroid_score_diff_cut (core::Real const &setting)

core::Real	centroid_score_diff_cut () const

void	set_centroid_weights (std::string const &setting)

std::string	centroid_weights () const

void	set_nstruct_centroid (core::Size const &setting)

core::Size	nstruct_centroid () const

void	set_ghost_loops (bool const &setting)

bool	ghost_loops () const

void	set_ccd_close (bool const &setting)

bool	ccd_close () const

void	set_cluster_by_all_atom_rmsd (bool const &setting)

bool	cluster_by_all_atom_rmsd () const

void	set_pack_weights (std::string const &setting)

std::string	pack_weights () const

bool const &	expand_loop_takeoff () const

void	set_expand_loop_takeoff (bool const &setting)

bool const &	skip_coord_constraints () const

void	set_skip_coord_constraints (bool const &setting)

void	set_frag_files (utility::vector1< std::string > const &setting)

utility::vector1< std::string >	frag_files () const

void	set_bridge_res (utility::vector1< core::Size > const &setting)

utility::vector1< core::Size >	bridge_res () const

Protected Member Functions
void	initialize_variables ()

Private Attributes
bool	global_optimize_

bool	sample_beta_

bool	move_jumps_between_chains_

bool	disable_sampling_of_loop_takeoff_

bool	cart_min_

core::Size	n_sample_

bool	filter_native_big_bins_

bool	allow_virtual_side_chains_

bool	prepack_

bool	pack_protein_side_chains_

bool	centroid_output_

bool	centroid_screen_

core::Real	centroid_score_diff_cut_

std::string	centroid_weights_

core::Size	nstruct_centroid_

bool	ghost_loops_

bool	ccd_close_

bool	cluster_by_all_atom_rmsd_

std::string	pack_weights_

bool	expand_loop_takeoff_

bool	skip_coord_constraints_

utility::vector1< std::string >	frag_files_

utility::vector1< core::Size >	bridge_res_

Constructor & Destructor Documentation

◆ StepWiseProteinModelerOptions()

protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::StepWiseProteinModelerOptions ( )

Member Function Documentation

◆ allow_virtual_side_chains()

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::allow_virtual_side_chains ( ) const

inline

References allow_virtual_side_chains_.

◆ bridge_res()

utility::vector1< core::Size > protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::bridge_res ( ) const

inline

References bridge_res_.

◆ cart_min()

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::cart_min ( ) const

inline

References cart_min_.

◆ ccd_close()

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::ccd_close ( ) const

inline

References ccd_close_.

◆ centroid_output()

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_output ( ) const

inline

References centroid_output_.

◆ centroid_score_diff_cut()

core::Real protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_score_diff_cut ( ) const

inline

References centroid_score_diff_cut_.

◆ centroid_screen()

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_screen ( ) const

inline

References centroid_screen_.

◆ centroid_weights()

std::string protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_weights ( ) const

inline

References centroid_weights_.

◆ clone()

StepWiseProteinModelerOptionsOP protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::clone ( ) const

clone the options

◆ cluster_by_all_atom_rmsd()

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::cluster_by_all_atom_rmsd ( ) const

inline

References cluster_by_all_atom_rmsd_.

◆ disable_sampling_of_loop_takeoff()

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::disable_sampling_of_loop_takeoff ( ) const

inline

References disable_sampling_of_loop_takeoff_.

◆ expand_loop_takeoff()

bool const& protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::expand_loop_takeoff ( ) const

inline

References expand_loop_takeoff_.

◆ filter_native_big_bins()

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::filter_native_big_bins ( ) const

inline

References filter_native_big_bins_.

◆ frag_files()

utility::vector1< std::string > protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::frag_files ( ) const

inline

References frag_files_.

◆ ghost_loops()

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::ghost_loops ( ) const

inline

References ghost_loops_.

◆ global_optimize()

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::global_optimize ( ) const

inline

References global_optimize_.

◆ initialize_from_command_line()

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::initialize_from_command_line ( )

◆ initialize_variables()

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::initialize_variables ( )

protected

◆ move_jumps_between_chains()

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::move_jumps_between_chains ( ) const

inline

References move_jumps_between_chains_.

◆ n_sample()

core::Size protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::n_sample ( ) const

inline

References n_sample_.

◆ nstruct_centroid()

core::Size protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::nstruct_centroid ( ) const

inline

References nstruct_centroid_.

◆ pack_protein_side_chains()

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::pack_protein_side_chains ( ) const

inline

References pack_protein_side_chains_.

◆ pack_weights()

std::string protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::pack_weights ( ) const

inline

References pack_weights_.

◆ parse_my_tag()

virtual void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::parse_my_tag ( utility::tag::TagCOP )

inlinevirtual

Initialize from the recursive "tag" structure.

Reimplemented in protocols::stepwise::modeler::options::StepWiseModelerOptions.

◆ prepack()

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::prepack ( ) const

inline

References prepack_.

◆ sample_beta()

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::sample_beta ( ) const

inline

References sample_beta_.

◆ set_allow_virtual_side_chains()

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_allow_virtual_side_chains ( bool const & setting )

inline

References allow_virtual_side_chains_.

◆ set_bridge_res()

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_bridge_res ( utility::vector1< core::Size > const & setting )

inline

References bridge_res_.

◆ set_cart_min()

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_cart_min ( bool const & setting )

inline

References cart_min_.

◆ set_ccd_close()

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_ccd_close ( bool const & setting )

inline

References ccd_close_.

◆ set_centroid_output()

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_centroid_output ( bool const & setting )

inline

References centroid_output_.

◆ set_centroid_score_diff_cut()

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_centroid_score_diff_cut ( core::Real const & setting )

inline

References centroid_score_diff_cut_.

◆ set_centroid_screen()

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_centroid_screen ( bool const & setting )

inline

References centroid_screen_.

◆ set_centroid_weights()

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_centroid_weights ( std::string const & setting )

inline

References centroid_weights_.

◆ set_cluster_by_all_atom_rmsd()

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_cluster_by_all_atom_rmsd ( bool const & setting )

inline

References cluster_by_all_atom_rmsd_.

◆ set_disable_sampling_of_loop_takeoff()

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_disable_sampling_of_loop_takeoff ( bool const & setting )

inline

References disable_sampling_of_loop_takeoff_.

◆ set_expand_loop_takeoff()

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_expand_loop_takeoff ( bool const & setting )

inline

References expand_loop_takeoff_.

◆ set_filter_native_big_bins()

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_filter_native_big_bins ( bool const & setting )

inline

References filter_native_big_bins_.

◆ set_frag_files()

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_frag_files ( utility::vector1< std::string > const & setting )

inline

References frag_files_.

◆ set_ghost_loops()

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_ghost_loops ( bool const & setting )

inline

References ghost_loops_.

◆ set_global_optimize()

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_global_optimize ( bool const & setting )

inline

References global_optimize_.

◆ set_move_jumps_between_chains()

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_move_jumps_between_chains ( bool const & setting )

inline

References move_jumps_between_chains_.

◆ set_n_sample()

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_n_sample ( core::Size const & setting )

inline

References n_sample_.

◆ set_nstruct_centroid()

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_nstruct_centroid ( core::Size const & setting )

inline

References nstruct_centroid_.

◆ set_pack_protein_side_chains()

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_pack_protein_side_chains ( bool const & setting )

inline

References pack_protein_side_chains_.

◆ set_pack_weights()

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_pack_weights ( std::string const & setting )

inline

References pack_weights_.

◆ set_prepack()

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_prepack ( bool const & setting )

inline

References prepack_.

◆ set_sample_beta()

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_sample_beta ( bool const & setting )

inline

References sample_beta_.

◆ set_skip_coord_constraints()

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_skip_coord_constraints ( bool const & setting )

inline

References skip_coord_constraints_.

◆ show()

virtual void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::show ( std::ostream & ) const

inlinevirtual

Describe this instance to a given output stream.

Reimplemented in protocols::stepwise::modeler::options::StepWiseModelerOptions.

◆ skip_coord_constraints()

bool const& protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::skip_coord_constraints ( ) const

inline

References skip_coord_constraints_.

◆ type()

virtual std::string protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::type ( ) const

inlinevirtual

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

Reimplemented in protocols::stepwise::modeler::options::StepWiseModelerOptions.

Member Data Documentation

◆ allow_virtual_side_chains_

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::allow_virtual_side_chains_

private

Referenced by allow_virtual_side_chains(), and set_allow_virtual_side_chains().

◆ bridge_res_

utility::vector1< core::Size > protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::bridge_res_

private

Referenced by bridge_res(), and set_bridge_res().

◆ cart_min_

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::cart_min_

private

Referenced by cart_min(), and set_cart_min().

◆ ccd_close_

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::ccd_close_

private

Referenced by ccd_close(), and set_ccd_close().

◆ centroid_output_

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_output_

private

Referenced by centroid_output(), and set_centroid_output().

◆ centroid_score_diff_cut_

core::Real protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_score_diff_cut_

private

Referenced by centroid_score_diff_cut(), and set_centroid_score_diff_cut().

◆ centroid_screen_

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_screen_

private

Referenced by centroid_screen(), and set_centroid_screen().

◆ centroid_weights_

std::string protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_weights_

private

Referenced by centroid_weights(), and set_centroid_weights().

◆ cluster_by_all_atom_rmsd_

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::cluster_by_all_atom_rmsd_

private

Referenced by cluster_by_all_atom_rmsd(), and set_cluster_by_all_atom_rmsd().

◆ disable_sampling_of_loop_takeoff_

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::disable_sampling_of_loop_takeoff_

private

Referenced by disable_sampling_of_loop_takeoff(), and set_disable_sampling_of_loop_takeoff().

◆ expand_loop_takeoff_

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::expand_loop_takeoff_

private

Referenced by expand_loop_takeoff(), and set_expand_loop_takeoff().

◆ filter_native_big_bins_

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::filter_native_big_bins_

private

Referenced by filter_native_big_bins(), and set_filter_native_big_bins().

◆ frag_files_

utility::vector1< std::string > protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::frag_files_

private

Referenced by frag_files(), and set_frag_files().

◆ ghost_loops_

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::ghost_loops_

private

Referenced by ghost_loops(), and set_ghost_loops().

◆ global_optimize_

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::global_optimize_

private

Referenced by global_optimize(), and set_global_optimize().

◆ move_jumps_between_chains_

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::move_jumps_between_chains_

private

Referenced by move_jumps_between_chains(), and set_move_jumps_between_chains().

◆ n_sample_

core::Size protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::n_sample_

private

Referenced by n_sample(), and set_n_sample().

◆ nstruct_centroid_

core::Size protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::nstruct_centroid_

private

Referenced by nstruct_centroid(), and set_nstruct_centroid().

◆ pack_protein_side_chains_

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::pack_protein_side_chains_

private

Referenced by pack_protein_side_chains(), and set_pack_protein_side_chains().

◆ pack_weights_

std::string protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::pack_weights_

private

Referenced by pack_weights(), and set_pack_weights().

◆ prepack_

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::prepack_

private

Referenced by prepack(), and set_prepack().

◆ sample_beta_

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::sample_beta_

private

Referenced by sample_beta(), and set_sample_beta().

◆ skip_coord_constraints_

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::skip_coord_constraints_

private

Referenced by set_skip_coord_constraints(), and skip_coord_constraints().

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

src/protocols/stepwise/modeler/options/StepWiseProteinModelerOptions.hh
src/protocols/stepwise/modeler/options/StepWiseProteinModelerOptions.cc

Public Member Functions

Protected Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ StepWiseProteinModelerOptions()

Member Function Documentation

◆ allow_virtual_side_chains()

◆ bridge_res()

◆ cart_min()

◆ ccd_close()

◆ centroid_output()

◆ centroid_score_diff_cut()

◆ centroid_screen()

◆ centroid_weights()

◆ clone()

◆ cluster_by_all_atom_rmsd()

◆ disable_sampling_of_loop_takeoff()

◆ expand_loop_takeoff()

◆ filter_native_big_bins()

◆ frag_files()

◆ ghost_loops()

◆ global_optimize()

◆ initialize_from_command_line()

◆ initialize_variables()

◆ move_jumps_between_chains()

◆ n_sample()

◆ nstruct_centroid()

◆ pack_protein_side_chains()

◆ pack_weights()

◆ parse_my_tag()

◆ prepack()

◆ sample_beta()

◆ set_allow_virtual_side_chains()

◆ set_bridge_res()

◆ set_cart_min()

◆ set_ccd_close()

◆ set_centroid_output()

◆ set_centroid_score_diff_cut()

◆ set_centroid_screen()

◆ set_centroid_weights()

◆ set_cluster_by_all_atom_rmsd()

◆ set_disable_sampling_of_loop_takeoff()

◆ set_expand_loop_takeoff()

◆ set_filter_native_big_bins()

◆ set_frag_files()

◆ set_ghost_loops()

◆ set_global_optimize()

◆ set_move_jumps_between_chains()

◆ set_n_sample()

◆ set_nstruct_centroid()

◆ set_pack_protein_side_chains()

◆ set_pack_weights()

◆ set_prepack()

◆ set_sample_beta()

◆ set_skip_coord_constraints()

◆ show()

◆ skip_coord_constraints()

◆ type()

Member Data Documentation

◆ allow_virtual_side_chains_

◆ bridge_res_

◆ cart_min_

◆ ccd_close_

◆ centroid_output_

◆ centroid_score_diff_cut_

◆ centroid_screen_

◆ centroid_weights_

◆ cluster_by_all_atom_rmsd_

◆ disable_sampling_of_loop_takeoff_

◆ expand_loop_takeoff_

◆ filter_native_big_bins_

◆ frag_files_

◆ ghost_loops_

◆ global_optimize_

◆ move_jumps_between_chains_

◆ n_sample_

◆ nstruct_centroid_

◆ pack_protein_side_chains_

◆ pack_weights_

◆ prepack_