core::membrane::io::EmbedSearchParamsOptions Class Reference

Embedding Search Param Options. More...

#include <EmbedSearchParamsOptions.hh>

Public Member Functions
	EmbedSearchParamsOptions ()
	Constructor. More...
virtual	~EmbedSearchParamsOptions ()
	Destructor. More...
virtual void	parse_my_tag (utility::tag::TagCOP tag)
	Parse .xml file for embedding opts. More...
virtual std::string	type () const
	Return Options Class Type - Embedding Search Parameters. More...
bool	normal_search ()
	Setters and Getters for Options. More...
void	set_normal_search (bool setting)
core::Real	normal_start_angle ()
	Normal Start Angle. More...
void	set_normal_start_angle (core::Real setting)
core::Real	normal_max_angle ()
	Normal Max Angle. More...
void	set_normal_max_angle (core::Real setting)
core::Real	normal_delta_angle ()
	Normal Delta Angle. More...
void	set_normal_delta_angle (core::Real setting)
bool	center_search ()
	Center Search. More...
void	set_center_max_delta (bool setting)
core::Real	center_max_delta ()
	Center Max Delta. More...
void	set_center_max_delta (core::Real setting)
core::Size	center_mag ()
	Center Magnitude. More...
void	set_center_mag (core::Size setting)
core::Size	normal_mag ()
	Normal Mag. More...
void	set_normal_mag (core::Size setting)
core::Size	normal_cycles ()
	Normal Cycles. More...
void	set_normal_cycles (core::Size setting)
	EmbedSearchParamsOptions ()
	Constructor. More...
virtual	~EmbedSearchParamsOptions ()
	Destructor. More...
virtual void	parse_my_tag (utility::tag::TagCOP tag)
	Parse .xml file for embedding opts. More...
virtual std::string	type () const
	Return Options Class Type - Embedding Search Parameters. More...
bool	normal_search () const
	Setters and Getters for Options. More...
void	set_normal_search (bool setting)
core::Real	normal_start_angle () const
	Normal Start Angle. More...
void	set_normal_start_angle (core::Real setting)
core::Real	normal_max_angle () const
	Normal Max Angle. More...
void	set_normal_max_angle (core::Real setting)
core::Real	normal_delta_angle () const
	Normal Delta Angle. More...
void	set_normal_delta_angle (core::Real setting)
bool	center_search () const
	Center Search. More...
void	set_center_search (bool setting)
core::Real	center_max_delta () const
	Center Max Delta. More...
void	set_center_max_delta (core::Real setting)
core::Size	center_mag () const
	Center Magnitude. More...
void	set_center_mag (core::Size setting)
core::Size	normal_mag () const
	Normal Mag. More...
void	set_normal_mag (core::Size setting)
core::Size	normal_cycles () const
	Normal Cycles. More...
void	set_normal_cycles (core::Size setting)
bool	penalties () const
	Getter/Setter pair for penalties. More...
void	set_penalties (bool setting)
bool	no_interpolate_mpair () const
	Getter/Setter pair for interpolating mpair term. More...
void	set_no_interpolate_mpair (bool setting)

Private Attributes
bool	normal_search_
core::Real	normal_delta_angle_
core::Real	normal_start_angle_
core::Real	normal_max_angle_
bool	center_search_
core::Real	center_max_delta_
core::Size	center_mag_
core::Size	normal_mag_
core::Size	normal_cycles_
bool	penalties_
bool	no_interpolate_mpair_

Detailed Description

Embedding Search Param Options.

Specify options for searching and scoring membrane protein embeddings

Constructor & Destructor Documentation

core::membrane::io::EmbedSearchParamsOptions::EmbedSearchParamsOptions

(

)

Constructor.

core::membrane::io::EmbedSearchParamsOptions::~EmbedSearchParamsOptions ( )

virtual

Destructor.

core::membrane::io::EmbedSearchParamsOptions::EmbedSearchParamsOptions

(

)

Constructor.

virtual core::membrane::io::EmbedSearchParamsOptions::~EmbedSearchParamsOptions ( )

virtual

Destructor.

Member Function Documentation

core::Size core::membrane::io::EmbedSearchParamsOptions::center_mag

(

)

Center Magnitude.

Referenced by core::membrane::io::EmbedSearchParamsIO::get_embed_params_from_file().

core::Size core::membrane::io::EmbedSearchParamsOptions::center_mag

(

)

const

Center Magnitude.

Getter/Setter Pair for Center Mag.

Param Type: abs(int) Precodnition setting >=0

References center_mag_.

core::Real core::membrane::io::EmbedSearchParamsOptions::center_max_delta

(

)

Center Max Delta.

Center Max Delta for Search

Referenced by core::membrane::io::EmbedSearchParamsIO::get_embed_params_from_file().

core::Real core::membrane::io::EmbedSearchParamsOptions::center_max_delta

(

)

const

Center Max Delta.

Getter/Setter Pair for Center max delta.

Center Max Delta for Search

Param Type: abs(int) Precodnition 0 <= setting

References center_max_delta_.

bool core::membrane::io::EmbedSearchParamsOptions::center_search

(

)

Center Search.

Search for Center

Referenced by core::membrane::io::EmbedSearchParamsIO::get_embed_params_from_file().

bool core::membrane::io::EmbedSearchParamsOptions::center_search

(

)

const

Center Search.

Getter/Setter Pair for center search.

Search for Center

Param Type: Boolean

References center_search_.

bool core::membrane::io::EmbedSearchParamsOptions::no_interpolate_mpair

(

)

const

Getter/Setter pair for interpolating mpair term.

Param Type: bool

References no_interpolate_mpair_.

Referenced by core::membrane::io::EmbedSearchParamsIO::get_embed_params_from_file().

core::Size core::membrane::io::EmbedSearchParamsOptions::normal_cycles

(

)

Normal Cycles.

Max Cycles allowed in normal search

Referenced by core::membrane::io::EmbedSearchParamsIO::get_embed_params_from_file().

core::Size core::membrane::io::EmbedSearchParamsOptions::normal_cycles

(

)

const

Normal Cycles.

Getter/Setter Pair for Normal Cycles.

Max Cycles allowed in normal search

Param Type: abs(int) Precodnition setting >=0

References normal_cycles_.

core::Real core::membrane::io::EmbedSearchParamsOptions::normal_delta_angle

(

)

Normal Delta Angle.

Set allowed delta value for normal search (also bound on search)

Referenced by core::membrane::io::EmbedSearchParamsIO::get_embed_params_from_file().

core::Real core::membrane::io::EmbedSearchParamsOptions::normal_delta_angle

(

)

const

Normal Delta Angle.

Getter/Setter Pair for Normal delta Angle.

Set allowed delta value for normal search (also bound on search)

Param Type: abs(int) Precodnition 0 <= setting && setting <= 360

References normal_delta_angle_.

core::Size core::membrane::io::EmbedSearchParamsOptions::normal_mag

(

)

Normal Mag.

Referenced by core::membrane::io::EmbedSearchParamsIO::get_embed_params_from_file().

core::Size core::membrane::io::EmbedSearchParamsOptions::normal_mag

(

)

const

Normal Mag.

Getter/Setter Pair for Normal Mag.

Param Type: abs(int) Precodnition setting >=0

References normal_mag_.

core::Real core::membrane::io::EmbedSearchParamsOptions::normal_max_angle

(

)

Normal Max Angle.

Set max normal search angle (upper bound)

Referenced by core::membrane::io::EmbedSearchParamsIO::get_embed_params_from_file().

core::Real core::membrane::io::EmbedSearchParamsOptions::normal_max_angle

(

)

const

Normal Max Angle.

Getter/Setter Pair for Normal Max Angle.

Set max normal search angle (upper bound)

Param Type: abs(int) Precodnition 0 <= setting && setting <= 360

References normal_max_angle_.

bool core::membrane::io::EmbedSearchParamsOptions::normal_search

(

)

Setters and Getters for Options.

Normal Search

Search for membrane protein embedding normal

Referenced by core::membrane::io::EmbedSearchParamsIO::get_embed_params_from_file().

bool core::membrane::io::EmbedSearchParamsOptions::normal_search

(

)

const

Setters and Getters for Options.

Getter/Setter Pair for normal search.

Normal Search

Search for membrane protein embedding normal

Param Type: Boolean

References normal_search_.

core::Real core::membrane::io::EmbedSearchParamsOptions::normal_start_angle

(

)

Normal Start Angle.

Search for membrane protein embedding start angle

Referenced by core::membrane::io::EmbedSearchParamsIO::get_embed_params_from_file().

core::Real core::membrane::io::EmbedSearchParamsOptions::normal_start_angle

(

)

const

Normal Start Angle.

Getter/Setter Pair for Normal Start Angle.

Search for membrane protein embedding start angle

Param Type: abs(int) Preconditions: 0 <= setting && setting <= 360

References normal_start_angle_.

void core::membrane::io::EmbedSearchParamsOptions::parse_my_tag ( utility::tag::TagCOP  tag )

virtual

Parse .xml file for embedding opts.

Implements basic::resource_manager::ResourceOptions.

References set_center_mag(), set_center_max_delta(), set_center_search(), set_no_interpolate_mpair(), set_normal_cycles(), set_normal_delta_angle(), set_normal_mag(), set_normal_max_angle(), set_normal_search(), set_normal_start_angle(), and set_penalties().

virtual void core::membrane::io::EmbedSearchParamsOptions::parse_my_tag ( utility::tag::TagCOP  tag )

virtual

Parse .xml file for embedding opts.

Implements basic::resource_manager::ResourceOptions.

bool core::membrane::io::EmbedSearchParamsOptions::penalties

(

)

const

Getter/Setter pair for penalties.

Param tyupe: bool

References penalties_.

Referenced by core::membrane::io::EmbedSearchParamsIO::get_embed_params_from_file().

void core::membrane::io::EmbedSearchParamsOptions::set_center_mag

(

core::Size

setting

)

References center_mag_.

Referenced by parse_my_tag().

void core::membrane::io::EmbedSearchParamsOptions::set_center_mag

(

core::Size

setting

)

void core::membrane::io::EmbedSearchParamsOptions::set_center_max_delta

(

bool

setting

)

Referenced by parse_my_tag().

void core::membrane::io::EmbedSearchParamsOptions::set_center_max_delta

(

core::Real

setting

)

References center_max_delta_.

void core::membrane::io::EmbedSearchParamsOptions::set_center_max_delta

(

core::Real

setting

)

void core::membrane::io::EmbedSearchParamsOptions::set_center_search

(

bool

setting

)

References center_search_.

Referenced by parse_my_tag().

void core::membrane::io::EmbedSearchParamsOptions::set_no_interpolate_mpair

(

bool

setting

)

References no_interpolate_mpair_.

Referenced by parse_my_tag().

void core::membrane::io::EmbedSearchParamsOptions::set_normal_cycles

(

core::Size

setting

)

References normal_cycles_.

Referenced by parse_my_tag().

void core::membrane::io::EmbedSearchParamsOptions::set_normal_cycles

(

core::Size

setting

)

void core::membrane::io::EmbedSearchParamsOptions::set_normal_delta_angle

(

core::Real

setting

)

References normal_delta_angle_.

Referenced by parse_my_tag().

void core::membrane::io::EmbedSearchParamsOptions::set_normal_delta_angle

(

core::Real

setting

)

void core::membrane::io::EmbedSearchParamsOptions::set_normal_mag

(

core::Size

setting

)

References normal_mag_.

Referenced by parse_my_tag().

void core::membrane::io::EmbedSearchParamsOptions::set_normal_mag

(

core::Size

setting

)

void core::membrane::io::EmbedSearchParamsOptions::set_normal_max_angle

(

core::Real

setting

)

References normal_max_angle_.

Referenced by parse_my_tag().

void core::membrane::io::EmbedSearchParamsOptions::set_normal_max_angle

(

core::Real

setting

)

void core::membrane::io::EmbedSearchParamsOptions::set_normal_search

(

bool

setting

)

References normal_search_.

Referenced by parse_my_tag().

void core::membrane::io::EmbedSearchParamsOptions::set_normal_search

(

bool

setting

)

void core::membrane::io::EmbedSearchParamsOptions::set_normal_start_angle

(

core::Real

setting

)

References normal_start_angle_.

Referenced by parse_my_tag().

void core::membrane::io::EmbedSearchParamsOptions::set_normal_start_angle

(

core::Real

setting

)

void core::membrane::io::EmbedSearchParamsOptions::set_penalties

(

bool

setting

)

References penalties_.

Referenced by parse_my_tag().

std::string core::membrane::io::EmbedSearchParamsOptions::type ( ) const

virtual

Return Options Class Type - Embedding Search Parameters.

Implements basic::resource_manager::ResourceOptions.

virtual std::string core::membrane::io::EmbedSearchParamsOptions::type ( ) const

virtual

Return Options Class Type - Embedding Search Parameters.

Implements basic::resource_manager::ResourceOptions.

Member Data Documentation

core::Size core::membrane::io::EmbedSearchParamsOptions::center_mag_

private

Referenced by center_mag(), and set_center_mag().

core::Real core::membrane::io::EmbedSearchParamsOptions::center_max_delta_

private

Referenced by center_max_delta(), and set_center_max_delta().

bool core::membrane::io::EmbedSearchParamsOptions::center_search_

private

Referenced by center_search(), and set_center_search().

bool core::membrane::io::EmbedSearchParamsOptions::no_interpolate_mpair_

private

Referenced by no_interpolate_mpair(), and set_no_interpolate_mpair().

core::Size core::membrane::io::EmbedSearchParamsOptions::normal_cycles_

private

Referenced by normal_cycles(), and set_normal_cycles().

core::Real core::membrane::io::EmbedSearchParamsOptions::normal_delta_angle_

private

Referenced by normal_delta_angle(), and set_normal_delta_angle().

core::Size core::membrane::io::EmbedSearchParamsOptions::normal_mag_

private

Referenced by normal_mag(), and set_normal_mag().

core::Real core::membrane::io::EmbedSearchParamsOptions::normal_max_angle_

private

Referenced by normal_max_angle(), and set_normal_max_angle().

bool core::membrane::io::EmbedSearchParamsOptions::normal_search_

private

Referenced by normal_search(), and set_normal_search().

core::Real core::membrane::io::EmbedSearchParamsOptions::normal_start_angle_

private

Referenced by normal_start_angle(), and set_normal_start_angle().

bool core::membrane::io::EmbedSearchParamsOptions::penalties_

private

Referenced by penalties(), and set_penalties().

---

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

• symlinks/rosetta/src/core/membrane/io/EmbedSearchParamOptions.hh
• symlinks/rosetta/src/core/membrane/io/EmbedSearchParamsOptions.hh
• symlinks/rosetta/src/core/membrane/io/EmbedSearchParamsOptions.cc