protocols::jumping::ResiduePairJumpSetup Class Reference

#include <ResiduePairJumpSetup.hh>

Inheritance diagram for protocols::jumping::ResiduePairJumpSetup:

Collaboration 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
	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_

Detailed Description

Definition at line 48 of file ResiduePairJumpSetup.hh.

Member Typedef Documentation

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

Definition at line 65 of file ResiduePairJumpSetup.hh.

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

Definition at line 66 of file ResiduePairJumpSetup.hh.

Constructor & Destructor Documentation

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

inline

Definition at line 70 of file ResiduePairJumpSetup.hh.

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

inline

Definition at line 75 of file ResiduePairJumpSetup.hh.

Member Function Documentation

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

inline

Definition at line 81 of file ResiduePairJumpSetup.hh.

References jumps_.

Referenced by add_jump().

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

inline

Definition at line 86 of file ResiduePairJumpSetup.hh.

References add_jump().

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

inline

Definition at line 91 of file ResiduePairJumpSetup.hh.

References add_jump().

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

inline

Definition at line 96 of file ResiduePairJumpSetup.hh.

References ResiduePairJumps_.

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

inline

Definition at line 117 of file ResiduePairJumpSetup.hh.

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.

Definition at line 133 of file ResiduePairJumpSetup.hh.

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

inline

Definition at line 145 of file ResiduePairJumpSetup.hh.

References jumps_.

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

virtual

Implements protocols::jumping::BaseJumpSetup.

Definition at line 203 of file ResiduePairJumpSetup.cc.

References core::sequence::end.

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

inline

Definition at line 122 of file ResiduePairJumpSetup.hh.

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.

Definition at line 166 of file ResiduePairJumpSetup.cc.

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)

Definition at line 68 of file ResiduePairJumpSetup.cc.

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

Definition at line 107 of file ResiduePairJumpSetup.hh.

References root_.

Referenced by set_root().

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

inline

Definition at line 101 of file ResiduePairJumpSetup.hh.

References root(), root_, and total_residue_.

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

inline

Definition at line 112 of file ResiduePairJumpSetup.hh.

References jumps_.

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

inline

Definition at line 142 of file ResiduePairJumpSetup.hh.

References total_residue_.

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

inlinevirtual

Implements protocols::jumping::BaseJumpSetup.

Definition at line 59 of file ResiduePairJumpSetup.hh.

Member Data Documentation

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

private

Definition at line 150 of file ResiduePairJumpSetup.hh.

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

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

private

Definition at line 153 of file ResiduePairJumpSetup.hh.

Referenced by add_residue_pair_jump().

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

private

Definition at line 152 of file ResiduePairJumpSetup.hh.

Referenced by root(), and set_root().

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

private

Definition at line 151 of file ResiduePairJumpSetup.hh.

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