protocols::jumping::JumpSelector Class Reference

#include <JumpSetup.hh>

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
	JumpSelector ()
	JumpSelector (std::string ss)
	~JumpSelector ()
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
JumpSample	clean_jumps (JumpSample const &js) const
	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
virtual	~BaseJumpSetup ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. 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

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

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

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

Constructor & Destructor Documentation

protocols::jumping::JumpSelector::JumpSelector

(

)

protocols::jumping::JumpSelector::JumpSelector

(

std::string

ss

)

protocols::jumping::JumpSelector::~JumpSelector

(

)

Member Function Documentation

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().

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

inline

References add_jump().

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

inline

References add_jump().

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

inline

References jumps_.

Referenced by select_random().

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

inlinevirtual

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

Implements protocols::jumping::BaseJumpSetup.

References hh_tr.

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

virtual

Implements protocols::jumping::BaseJumpSetup.

References protocols::jumping::JumpSetup::add_jump(), protocols::jumping::dump_tags_(), protocols::jumping::Interval::end_, protocols::jumping::fill_tags_(), j, loop_extension_, min_loop_length_, nr_jumps_max_, nr_jumps_min_, nres, protocols::jumping::RG, runtime_assert, secstruct_, select_random(), protocols::jumping::Interval::start_, tags, protocols::jumping::tr, and numeric::random::RandomGenerator::uniform().

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

inline

References jumps_.

Referenced by select_random().

void protocols::jumping::JumpSelector::read_file

(

std::string

file

)

References add_jump(), protocols::jumping::Interval::end_, getline(), in, loop_extension_, min_loop_length_, nr_jumps_max_, nr_jumps_min_, protocols::jumping::Interval::start_, tag, protocols::jumping::tr, utility_exit_with_message, and weight.

Interval protocols::jumping::JumpSelector::select_random

(

)

const

References begin(), end(), protocols::jumping::RG, runtime_assert, total_weight_, and numeric::random::RandomGenerator::uniform().

Referenced by create_jump_sample().

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

inline

References secstruct_.

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

inline

References jumps_.

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

inlinevirtual

Implements protocols::jumping::BaseJumpSetup.

Member Data Documentation

JumpList protocols::jumping::JumpSelector::jumps_

private

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

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

private

Referenced by create_jump_sample(), and read_file().

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

private

Referenced by create_jump_sample(), and read_file().

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

private

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

private

Referenced by create_jump_sample(), and read_file().

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

private

Referenced by create_jump_sample(), and read_file().

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

private

Referenced by create_jump_sample(), and set_secstruct().

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:

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