protocols::stepwise::modeler::options::StepWiseProteinModelerOptions Class Reference

#include <StepWiseProteinModelerOptions.hh>

Public Member Functions
	StepWiseProteinModelerOptions ()
	StepWiseProteinModelerOptions (StepWiseProteinModelerOptions const &src)
	copy constructor More...
	~StepWiseProteinModelerOptions ()
StepWiseProteinModelerOptionsOP	clone () const
	clone the options More...
StepWiseProteinModelerOptions &	operator= (StepWiseProteinModelerOptions const &src)
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_mapfile_activated (bool const &setting)
bool	mapfile_activated () 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 (Size const &setting)
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_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 (Real const &setting)
Real	centroid_score_diff_cut () const
void	set_centroid_weights (std::string const &setting)
std::string	centroid_weights () const
void	set_nstruct_centroid (Size const &setting)
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
void	set_use_packer_instead_of_rotamer_trials (bool const &setting)
bool	use_packer_instead_of_rotamer_trials () const
void	set_min_type (std::string const &setting)
std::string	min_type () const
void	set_min_tolerance (Real const &setting)
Real	min_tolerance () 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< Size > const &setting)
utility::vector1< Size >	bridge_res () const

Protected Member Functions
void	initialize_variables ()

Private Attributes
bool	global_optimize_
bool	mapfile_activated_
bool	sample_beta_
bool	move_jumps_between_chains_
bool	disable_sampling_of_loop_takeoff_
bool	cart_min_
Size	n_sample_
bool	filter_native_big_bins_
bool	allow_virtual_side_chains_
bool	prepack_
bool	centroid_output_
bool	centroid_screen_
Real	centroid_score_diff_cut_
std::string	centroid_weights_
Size	nstruct_centroid_
bool	ghost_loops_
bool	ccd_close_
bool	cluster_by_all_atom_rmsd_
std::string	pack_weights_
bool	use_packer_instead_of_rotamer_trials_
std::string	min_type_
Real	min_tolerance_
bool	expand_loop_takeoff_
bool	skip_coord_constraints_
utility::vector1< std::string >	frag_files_
utility::vector1< Size >	bridge_res_

Constructor & Destructor Documentation

protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::StepWiseProteinModelerOptions

(

)

Referenced by clone().

protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::StepWiseProteinModelerOptions

(

StepWiseProteinModelerOptions const &

src

)

copy constructor

protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::~StepWiseProteinModelerOptions

(

)

Member Function Documentation

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

StepWiseProteinModelerOptionsOP protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::clone

(

)

const

clone the options

References StepWiseProteinModelerOptions().

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

(

)

References basic::options::OptionKeys::stepwise::protein::allow_virtual_side_chains, allow_virtual_side_chains_, bridge_res_, basic::options::OptionKeys::stepwise::protein::cart_min, cart_min_, basic::options::OptionKeys::stepwise::protein::ccd_close, ccd_close_, basic::options::OptionKeys::stepwise::protein::centroid_output, centroid_output_, basic::options::OptionKeys::stepwise::protein::centroid_score_diff_cut, centroid_score_diff_cut_, basic::options::OptionKeys::stepwise::protein::centroid_screen, centroid_screen_, basic::options::OptionKeys::stepwise::protein::centroid_weights, centroid_weights_, basic::options::OptionKeys::stepwise::protein::cluster_by_all_atom_rmsd, cluster_by_all_atom_rmsd_, basic::options::OptionKeys::stepwise::protein::disable_sampling_of_loop_takeoff, disable_sampling_of_loop_takeoff_, basic::options::OptionKeys::stepwise::protein::expand_loop_takeoff, expand_loop_takeoff_, basic::options::OptionKeys::stepwise::protein::filter_native_big_bins, filter_native_big_bins_, frag_files_, basic::options::OptionKeys::stepwise::protein::ghost_loops, ghost_loops_, basic::options::OptionKeys::stepwise::protein::global_optimize, global_optimize_, edensity::mapfile, mapfile_activated_, basic::options::OptionKeys::stepwise::protein::min_tolerance, min_tolerance_, basic::options::OptionKeys::stepwise::protein::min_type, min_type_, basic::options::OptionKeys::stepwise::protein::move_jumps_between_chains, move_jumps_between_chains_, basic::options::OptionKeys::stepwise::protein::n_sample, n_sample_, basic::options::OptionKeys::stepwise::protein::nstruct_centroid, nstruct_centroid_, option, score::pack_weights, basic::options::OptionKeys::score::pack_weights, pack_weights_, prepack_, basic::options::OptionKeys::stepwise::protein::protein_prepack, basic::options::OptionKeys::stepwise::protein::sample_beta, sample_beta_, skip_coord_constraints_, basic::options::OptionKeys::stepwise::protein::use_packer_instead_of_rotamer_trials, use_packer_instead_of_rotamer_trials_, and user.

Referenced by protocols::stepwise::modeler::options::StepWiseModelerOptions::initialize_from_command_line().

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

protected

References allow_virtual_side_chains_, 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_, ghost_loops_, global_optimize_, mapfile_activated_, min_tolerance_, min_type_, move_jumps_between_chains_, n_sample_, nstruct_centroid_, pack_weights_, prepack_, sample_beta_, skip_coord_constraints_, and use_packer_instead_of_rotamer_trials_.

Referenced by protocols::stepwise::modeler::options::StepWiseModelerOptions::initialize_variables().

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

inline

Real protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::min_tolerance ( ) const

inline

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

inline

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

inline

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

inline

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

inline

StepWiseProteinModelerOptions & protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::operator=

(

StepWiseProteinModelerOptions const &

src

)

References 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_, mapfile_activated_, min_tolerance_, min_type_, move_jumps_between_chains_, n_sample_, nstruct_centroid_, pack_weights_, prepack_, sample_beta_, skip_coord_constraints_, and use_packer_instead_of_rotamer_trials_.

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

inline

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

inlinevirtual

Initialize from the recursive "tag" structure.

Implements basic::resource_manager::ResourceOptions.

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

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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.

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

inline

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.

Implements basic::resource_manager::ResourceOptions.

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

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

inline

Member Data Documentation

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

private

Referenced by initialize_from_command_line(), initialize_variables(), and operator=().

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

private

Referenced by initialize_from_command_line(), and operator=().

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

private

Referenced by initialize_from_command_line(), initialize_variables(), and operator=().

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

private

Referenced by initialize_from_command_line(), initialize_variables(), and operator=().

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

private

Referenced by initialize_from_command_line(), initialize_variables(), and operator=().

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

private

Referenced by initialize_from_command_line(), initialize_variables(), and operator=().

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

private

Referenced by initialize_from_command_line(), initialize_variables(), and operator=().

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

private

Referenced by initialize_from_command_line(), initialize_variables(), and operator=().

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

private

Referenced by initialize_from_command_line(), initialize_variables(), and operator=().

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

private

Referenced by initialize_from_command_line(), initialize_variables(), and operator=().

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

private

Referenced by initialize_from_command_line(), initialize_variables(), and operator=().

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

private

Referenced by initialize_from_command_line(), initialize_variables(), and operator=().

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

private

Referenced by initialize_from_command_line(), and operator=().

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

private

Referenced by initialize_from_command_line(), initialize_variables(), and operator=().

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

private

Referenced by initialize_from_command_line(), initialize_variables(), and operator=().

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::mapfile_activated_

private

Referenced by initialize_from_command_line(), initialize_variables(), and operator=().

Real protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::min_tolerance_

private

Referenced by initialize_from_command_line(), initialize_variables(), and operator=().

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

private

Referenced by initialize_from_command_line(), initialize_variables(), and operator=().

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

private

Referenced by initialize_from_command_line(), initialize_variables(), and operator=().

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

private

Referenced by initialize_from_command_line(), initialize_variables(), and operator=().

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

private

Referenced by initialize_from_command_line(), initialize_variables(), and operator=().

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

private

Referenced by initialize_from_command_line(), initialize_variables(), and operator=().

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

private

Referenced by initialize_from_command_line(), initialize_variables(), and operator=().

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

private

Referenced by initialize_from_command_line(), initialize_variables(), and operator=().

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

private

Referenced by initialize_from_command_line(), initialize_variables(), and operator=().

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::use_packer_instead_of_rotamer_trials_

private

Referenced by initialize_from_command_line(), initialize_variables(), and operator=().

---

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