protocols::jumping::ResiduePairJumpSetup Class Reference

#include <ResiduePairJumpSetup.hh>

Inheritance diagram for protocols::jumping::ResiduePairJumpSetup:

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 override
	ResiduePairJumpSetup ()
	ResiduePairJumpSetup (core::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 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...
core::fragment::FragSetOP	generate_jump_frags (JumpSample const &, core::kinematics::MoveMap const &mm) const override
	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
	~BaseJumpSetup () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. More...

Private Attributes
utility::vector1< JumpDef >	jumps_
core::Size	total_residue_
core::Size	root_
utility::vector1< ResiduePairJumpOP >	ResiduePairJumps_

Member Typedef Documentation

const_iterator

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

iterator

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

Constructor & Destructor Documentation

ResiduePairJumpSetup() [1/2]

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

inline

ResiduePairJumpSetup() [2/2]

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

inline

Member Function Documentation

add_jump() [1/3]

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

inline

References add_jump().

add_jump() [2/3]

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

inline

References add_jump().

add_jump() [3/3]

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

inline

References jumps_.

Referenced by add_jump().

add_residue_pair_jump()

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

inline

References ResiduePairJumps_.

begin()

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

inline

References jumps_.

clean_jumps()

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

inlineoverridevirtual

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

Implements protocols::jumping::BaseJumpSetup.

clear()

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

inline

References jumps_.

create_jump_sample()

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

overridevirtual

Implements protocols::jumping::BaseJumpSetup.

References core::sequence::end.

end()

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

inline

References jumps_.

generate_jump_frags()

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

overridevirtual

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().

read_file()

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::conformation::membrane::in, protocols::jumping::Interval::start_, and protocols::jumping::tr().

root()

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

inline

References root_.

Referenced by set_root().

set_root()

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

inline

References root(), root_, and total_residue_.

size()

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

inline

References jumps_.

total_residue()

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

inline

References total_residue_.

type_name()

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

inlineoverridevirtual

Implements protocols::jumping::BaseJumpSetup.

Member Data Documentation

jumps_

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

private

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

ResiduePairJumps_

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

private

Referenced by add_residue_pair_jump().

root_

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

private

Referenced by root(), and set_root().

total_residue_

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

private

Referenced by set_root(), and total_residue().

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

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