Rosetta 3.5: protocols::jumping::ResiduePairJumpSetup Class Reference

#include <ResiduePairJumpSetup.hh>

Inheritance diagram for protocols::jumping::ResiduePairJumpSetup:

Inheritance graph

Collaboration diagram for protocols::jumping::ResiduePairJumpSetup:

Collaboration graph

Classes
class	JumpDef

Public Types
typedef utility::vector1 < JumpDef >::const_iterator	const_iterator

typedef utility::vector1 < JumpDef >::iterator	iterator

Public Member Functions
std::string	type_name () const

	ResiduePairJumpSetup ()

	ResiduePairJumpSetup (Size total_residue)

void	add_jump (JumpDef const &jd)

void	add_jump (Interval const &jump, Interval const &cut_reg)

void	add_jump (core::Size js, core::Size je, core::Size crs, core::Size cre)

void	add_residue_pair_jump (ResiduePairJumpOP ptr)

void	set_root (core::Size root)

core::Size	root () const

core::Size	size () const

const_iterator	begin () const

const_iterator	end () const

void	read_file (std::string file)

JumpSample	create_jump_sample () const

virtual 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...

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...

core::Size	total_residue () const

void	clear ()

Public Member Functions inherited from protocols::jumping::BaseJumpSetup
virtual	~BaseJumpSetup ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...

Private Attributes
utility::vector1< JumpDef >	jumps_

core::Size	total_residue_

core::Size	root_

utility::vector1 < ResiduePairJumpOP >	ResiduePairJumps_

Member Typedef Documentation

typedef utility::vector1< JumpDef >::const_iterator protocols::jumping::ResiduePairJumpSetup::const_iterator

typedef utility::vector1< JumpDef >::iterator protocols::jumping::ResiduePairJumpSetup::iterator

Constructor & Destructor Documentation

protocols::jumping::ResiduePairJumpSetup::ResiduePairJumpSetup ( )

inline

protocols::jumping::ResiduePairJumpSetup::ResiduePairJumpSetup ( Size total_residue)

inline

Member Function Documentation

void protocols::jumping::ResiduePairJumpSetup::add_jump ( JumpDef const & jd)

inline

References jumps_.

Referenced by add_jump().

void protocols::jumping::ResiduePairJumpSetup::add_jump	(	Interval const &	jump,
		Interval const &	cut_reg
	)

inline

References add_jump().

void protocols::jumping::ResiduePairJumpSetup::add_jump	(	core::Size	js,
		core::Size	je,
		core::Size	crs,
		core::Size	cre
	)

inline

References add_jump().

void protocols::jumping::ResiduePairJumpSetup::add_residue_pair_jump ( ResiduePairJumpOP ptr)

inline

References ResiduePairJumps_.

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

inline

References jumps_.

virtual JumpSample protocols::jumping::ResiduePairJumpSetup::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.

void protocols::jumping::ResiduePairJumpSetup::clear ( )

inline

References jumps_.

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

virtual

Implements protocols::jumping::BaseJumpSetup.

References core::sequence::end.

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

inline

References jumps_.

FragSetOP protocols::jumping::ResiduePairJumpSetup::generate_jump_frags	(	JumpSample const &	jumps,
		core::kinematics::MoveMap const &	mm
	)		const

virtual

returns an ordered FragSet that is compatible with the JumpSample default: generate jumps from ss-library according to JumpSample

Reimplemented from protocols::jumping::BaseJumpSetup.

References core::sequence::end, core::kinematics::MoveMap::get_jump(), core::id::SequenceMapping::insert_aligned_residue(), protocols::jumping::JumpSample::jumps(), protocols::jumping::JumpSample::size(), and protocols::jumping::tr().

void protocols::jumping::ResiduePairJumpSetup::read_file ( std::string file)

References protocols::jumping::angleA, protocols::jumping::angleB, protocols::jumping::dihedralA, protocols::jumping::dihedralAB, protocols::jumping::dihedralB, protocols::jumping::disAB, protocols::jumping::Interval::end_, core::chemical::FA_STANDARD, core::chemical::ChemicalManager::get_instance(), protocols::jumping::Interval::start_, and protocols::jumping::tr().

core::Size protocols::jumping::ResiduePairJumpSetup::root ( ) const

inline

References root_.

Referenced by set_root().

void protocols::jumping::ResiduePairJumpSetup::set_root ( core::Size root)

inline

References root(), root_, and total_residue_.

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

inline

References jumps_.

core::Size protocols::jumping::ResiduePairJumpSetup::total_residue ( ) const

inline

References total_residue_.

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

inlinevirtual

Implements protocols::jumping::BaseJumpSetup.

Member Data Documentation

utility::vector1< JumpDef > protocols::jumping::ResiduePairJumpSetup::jumps_

private

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

utility::vector1<ResiduePairJumpOP> protocols::jumping::ResiduePairJumpSetup::ResiduePairJumps_

private

Referenced by add_residue_pair_jump().

core::Size protocols::jumping::ResiduePairJumpSetup::root_

private

Referenced by root(), and set_root().

core::Size protocols::jumping::ResiduePairJumpSetup::total_residue_

private

Referenced by set_root(), and total_residue().

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

src/protocols/jumping/ResiduePairJumpSetup.hh
src/protocols/jumping/ResiduePairJumpSetup.cc