protocols::jumping::JumpSelector Class Reference

#include <JumpSetup.hh>

Inheritance diagram for protocols::jumping::JumpSelector:

Classes
class	JumpWeightDef

Public Types
typedef utility::vector1< JumpWeightDef >	JumpList
typedef JumpList::const_iterator	const_iterator
typedef JumpList::iterator	iterator

Public Member Functions
std::string	type_name () const override
	JumpSelector ()
	JumpSelector (std::string const &ss)
	~JumpSelector () override
void	add_jump (JumpWeightDef const &jd)
void	add_jump (Interval const &jump, core::Real weight)
void	add_jump (core::Size js, core::Size je, core::Real weight)
core::Size	size () const
const_iterator	begin () const
const_iterator	end () const
void	read_file (std::string file)
Interval	select_random () const
JumpSample	create_jump_sample () const override
JumpSample	clean_jumps (JumpSample const &js) const override
	take from a given JumpSample only those Jumps, which could also have been created by create_jump_sample() More...
void	set_secstruct (std::string ss)
Public Member Functions inherited from protocols::jumping::BaseJumpSetup
	~BaseJumpSetup () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
virtual core::fragment::FragSetOP	generate_jump_frags (JumpSample const &, core::kinematics::MoveMap const &mm) const
	returns an ordered FragSet that is compatible with the JumpSample default: generate jumps from ss-library according to JumpSample More...

Private Attributes
std::string	secstruct_
core::pose::PoseCOP	native_pose_
JumpList	jumps_
core::Real	total_weight_
core::Size	min_loop_length_
core::Size	loop_extension_
core::Size	nr_jumps_min_
core::Size	nr_jumps_max_

Member Typedef Documentation

const_iterator

typedef JumpList::const_iterator protocols::jumping::JumpSelector::const_iterator

iterator

typedef JumpList::iterator protocols::jumping::JumpSelector::iterator

JumpList

typedef utility::vector1< JumpWeightDef > protocols::jumping::JumpSelector::JumpList

Constructor & Destructor Documentation

JumpSelector() [1/2]

protocols::jumping::JumpSelector::JumpSelector

(

)

JumpSelector() [2/2]

protocols::jumping::JumpSelector::JumpSelector

(

std::string const &

ss

)

~JumpSelector()

protocols::jumping::JumpSelector::~JumpSelector ( )

overridedefault

Member Function Documentation

add_jump() [1/3]

void protocols::jumping::JumpSelector::add_jump ( core::Size  js, core::Size  je, core::Real  weight  )

inline

References add_jump().

add_jump() [2/3]

void protocols::jumping::JumpSelector::add_jump ( Interval const &  jump, core::Real  weight  )

inline

References add_jump().

add_jump() [3/3]

void protocols::jumping::JumpSelector::add_jump ( JumpWeightDef const &  jd )

inline

References jumps_, total_weight_, and protocols::jumping::JumpSelector::JumpWeightDef::weight_.

Referenced by add_jump(), and read_file().

begin()

const_iterator protocols::jumping::JumpSelector::begin ( ) const

inline

References jumps_.

Referenced by select_random().

clean_jumps()

JumpSample protocols::jumping::JumpSelector::clean_jumps ( JumpSample const &  ) const

overridevirtual

take from a given JumpSample only those Jumps, which could also have been created by create_jump_sample()

Implements protocols::jumping::BaseJumpSetup.

References protocols::jumping::tr().

create_jump_sample()

JumpSample protocols::jumping::JumpSelector::create_jump_sample ( ) const

overridevirtual

Implements protocols::jumping::BaseJumpSetup.

References protocols::jumping::JumpSetup::add_jump(), protocols::jumping::dump_tags_(), protocols::jumping::Interval::end_, protocols::jumping::fill_tags_(), loop_extension_, protocols::mean_field::max(), protocols::mean_field::min(), min_loop_length_, nr_jumps_max_, nr_jumps_min_, core::scoring::rg, secstruct_, select_random(), protocols::jumping::Interval::start_, and protocols::jumping::tr().

end()

const_iterator protocols::jumping::JumpSelector::end ( ) const

inline

References jumps_.

Referenced by select_random().

read_file()

void protocols::jumping::JumpSelector::read_file

(

std::string

file

)

References add_jump(), protocols::jumping::Interval::end_, core::conformation::membrane::in, loop_extension_, min_loop_length_, nr_jumps_max_, nr_jumps_min_, protocols::jumping::Interval::start_, and protocols::jumping::tr().

select_random()

Interval protocols::jumping::JumpSelector::select_random

(

)

const

References begin(), end(), core::scoring::rg, and total_weight_.

Referenced by create_jump_sample().

set_secstruct()

void protocols::jumping::JumpSelector::set_secstruct ( std::string  ss )

inline

References secstruct_.

size()

core::Size protocols::jumping::JumpSelector::size ( ) const

inline

References jumps_.

type_name()

std::string protocols::jumping::JumpSelector::type_name ( ) const

inlineoverridevirtual

Implements protocols::jumping::BaseJumpSetup.

Member Data Documentation

jumps_

JumpList protocols::jumping::JumpSelector::jumps_

private

Referenced by add_jump(), begin(), end(), and size().

loop_extension_

core::Size protocols::jumping::JumpSelector::loop_extension_

private

Referenced by create_jump_sample(), and read_file().

min_loop_length_

core::Size protocols::jumping::JumpSelector::min_loop_length_

private

Referenced by create_jump_sample(), and read_file().

native_pose_

core::pose::PoseCOP protocols::jumping::JumpSelector::native_pose_

private

nr_jumps_max_

core::Size protocols::jumping::JumpSelector::nr_jumps_max_

private

Referenced by create_jump_sample(), and read_file().

nr_jumps_min_

core::Size protocols::jumping::JumpSelector::nr_jumps_min_

private

Referenced by create_jump_sample(), and read_file().

secstruct_

std::string protocols::jumping::JumpSelector::secstruct_

private

Referenced by create_jump_sample(), and set_secstruct().

total_weight_

core::Real protocols::jumping::JumpSelector::total_weight_

private

Referenced by add_jump(), and select_random().

---

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

• src/protocols/jumping/JumpSetup.hh
• src/protocols/jumping/JumpSetup.cc