#include <FragData.hh>

Inheritance diagram for core::fragment::FragData:

Public Member Functions
	FragData ()

	FragData (SingleResidueFragDataOP, core::Size n)

	~FragData () override=default

virtual FragDataOP	clone () const

FragDataCOP	get_self_ptr () const
	self pointers More...

FragDataOP	get_self_ptr ()

virtual Size	apply (kinematics::MoveMap const &, pose::Pose &, Size start, Size end) const

virtual Size	apply (kinematics::MoveMap const &, pose::Pose &, Frame const &) const

virtual Size	apply (pose::Pose &, Frame const &) const

virtual Size	apply (pose::Pose &, Size start, Size end) const

virtual Size	apply_ss (kinematics::MoveMap const &, std::string &ss, Frame const &) const

virtual Size	is_applicable (kinematics::MoveMap const &, Size start, Size end) const

virtual Size	is_applicable (kinematics::MoveMap const &, Frame const &) const

virtual bool	steal (pose::Pose const &, Size start, Size end)

virtual bool	steal (pose::Pose const &, Frame const &)

virtual void	copy (FragData const &frag_data)

bool	is_compatible (FragData const &frag_data) const

bool	is_valid () const

Size	size () const

char	secstruct (Size const pos) const

char	sequence (Size const pos) const

std::string	secstruct () const

std::string	sequence () const

void	set_sequence (Size const pos, char const setting)

void	set_residue (Size pos, SingleResidueFragDataOP res)

void	add_residue (SingleResidueFragDataOP res)

SingleResidueFragDataCOP	get_residue (core::Size pos) const

virtual FragDataOP	generate_sub_fragment (Size start, Size stop) const

virtual void	show (std::ostream &out) const

virtual void	show (std::ostream &out, Frame const &) const

virtual void	show_classic (std::ostream &out) const

void	set_valid (bool setting=true)

virtual std::string	pdbid () const
	Returns the PDB identifier if it has been specified, "no_pdb" otherwise. More...

virtual char	chain () const
	Returns the chain if it has been specified, '_' otherwise. More...

virtual Size	pdbpos () const

void	set_score (Real score)
	Set a score value for this fragment. More...

Real	score () const
	Returns the score for this fragment. More...

Protected Member Functions
	FragData (Size nr_res)

Protected Attributes
SRFD_List	data_

Private Types
typedef utility::vector1 < SingleResidueFragDataOP >	SRFD_List

Private Attributes
bool	valid_

Real	score_

Member Typedef Documentation

typedef utility::vector1< SingleResidueFragDataOP > core::fragment::FragData::SRFD_List

private

Constructor & Destructor Documentation

core::fragment::FragData::FragData ( )

inline

Referenced by clone().

core::fragment::FragData::FragData	(	SingleResidueFragDataOP	SRFD,
		core::Size	n
	)

References data_.

core::fragment::FragData::~FragData ( )

overridedefault

core::fragment::FragData::FragData ( Size nr_res )

inlineprotected

Member Function Documentation

void core::fragment::FragData::add_residue ( SingleResidueFragDataOP res )

inline

References data_.

Size core::fragment::FragData::apply	(	kinematics::MoveMap const &	mm,
		pose::Pose &	pose,
		Size	start,
		Size	end
	)		const

virtual

References data_, is_valid(), core::pose::Pose::size(), and protocols::loops::start.

Referenced by protocols::antibody_legacy::CDRH3Modeler::antibody_modeling_insert_ter(), protocols::antibody::H3CterInsert::apply(), apply(), core::fragment::Frame::apply(), protocols::simple_moves::SymmetricFragmentMover::apply_fragment(), protocols::simple_moves::GunnCost::compute_gunn(), and core::fragment::Frame::fragment_as_pose().

Size core::fragment::FragData::apply	(	kinematics::MoveMap const &	mm,
		pose::Pose &	pose,
		Frame const &	frame
	)		const

virtual

References apply(), data_, core::fragment::Frame::end(), core::fragment::Frame::is_continuous(), is_valid(), core::fragment::Frame::length(), core::fragment::Frame::seqpos(), size(), core::pose::Pose::size(), and core::fragment::Frame::start().

Size core::fragment::FragData::apply	(	pose::Pose &	pose,
		Frame const &	frame
	)		const

virtual

References data_, is_valid(), core::fragment::Frame::length(), core::fragment::Frame::seqpos(), size(), and core::pose::Pose::size().

Size core::fragment::FragData::apply	(	pose::Pose &	pose,
		Size	start,
		Size	end
	)		const

virtual

References data_, is_valid(), and protocols::loops::start.

Size core::fragment::FragData::apply_ss	(	kinematics::MoveMap const &	mm,
		std::string &	ss,
		Frame const &	frame
	)		const

virtual

References data_, and is_valid().

Referenced by core::fragment::Frame::apply_ss().

virtual char core::fragment::FragData::chain ( ) const

inlinevirtual

Returns the chain if it has been specified, '_' otherwise.

Reimplemented in core::fragment::AnnotatedFragData.

Referenced by core::fragment::AnnotatedFragData::copy().

FragDataOP core::fragment::FragData::clone ( ) const

virtual

Reimplemented in core::fragment::AnnotatedFragData.

References data_, FragData(), and size().

Referenced by core::fragment::AnnotatedFragData::clone().

void core::fragment::FragData::copy ( FragData const & frag_data )

virtual

Reimplemented in core::fragment::AnnotatedFragData.

References data_, score_, and valid_.

Referenced by core::fragment::AnnotatedFragData::copy().

FragDataOP core::fragment::FragData::generate_sub_fragment	(	Size	start,
		Size	stop
	)		const

virtual

Reimplemented in core::fragment::AnnotatedFragData.

References data_, size(), and protocols::loops::stop.

SingleResidueFragDataCOP core::fragment::FragData::get_residue ( core::Size pos ) const

inline

References data_.

FragDataCOP core::fragment::FragData::get_self_ptr ( ) const

inline

self pointers

FragDataOP core::fragment::FragData::get_self_ptr ( )

inline

Size core::fragment::FragData::is_applicable	(	kinematics::MoveMap const &	mm,
		Size	start,
		Size	end
	)		const

virtual

References data_, and core::sequence::end.

Referenced by is_applicable(), and core::fragment::Frame::is_applicable().

Size core::fragment::FragData::is_applicable	(	kinematics::MoveMap const &	mm,
		Frame const &	frame
	)		const

virtual

References data_, core::fragment::Frame::end(), is_applicable(), core::fragment::Frame::is_continuous(), core::fragment::Frame::length(), size(), and core::fragment::Frame::start().

bool core::fragment::FragData::is_compatible ( FragData const & frag_data ) const

References data_, and size().

Referenced by core::fragment::Frame::is_mergeable().

bool core::fragment::FragData::is_valid ( ) const

inline

References valid_.

Referenced by apply(), apply_ss(), core::fragment::FragID::is_valid(), core::fragment::Frame::is_valid(), and show().

virtual std::string core::fragment::FragData::pdbid ( ) const

inlinevirtual

Returns the PDB identifier if it has been specified, "no_pdb" otherwise.

Reimplemented in core::fragment::AnnotatedFragData.

Referenced by core::fragment::AnnotatedFragData::copy(), protocols::fold_from_loops::utils::Nub::fix_fragment(), and show().

virtual Size core::fragment::FragData::pdbpos ( ) const

inlinevirtual

Reimplemented in core::fragment::AnnotatedFragData.

Referenced by core::fragment::AnnotatedFragData::copy(), and show().

Real core::fragment::FragData::score ( ) const

inline

Returns the score for this fragment.

References score_.

Referenced by set_score().

char core::fragment::FragData::secstruct ( Size const pos ) const

inline

References data_.

Referenced by protocols::loop_grower::LoopGrower::single_grow().

std::string core::fragment::FragData::secstruct ( ) const

inline

References size(), and protocols::kinmatch::str().

char core::fragment::FragData::sequence ( Size const pos ) const

inline

References data_, and sequence().

std::string core::fragment::FragData::sequence ( ) const

inline

References size(), and protocols::kinmatch::str().

Referenced by sequence().

void core::fragment::FragData::set_residue	(	Size	pos,
		SingleResidueFragDataOP	res
	)

inline

References data_.

void core::fragment::FragData::set_score ( Real score )

inline

Set a score value for this fragment.

References score(), and score_.

void core::fragment::FragData::set_sequence	(	Size const	pos,
		char const	setting
	)

inline

References data_.

void core::fragment::FragData::set_valid ( bool setting = true )

inline

References valid_.

Referenced by steal().

void core::fragment::FragData::show ( std::ostream & out ) const

virtual

References data_, is_valid(), pdbid(), and pdbpos().

Referenced by core::fragment::operator<<(), core::fragment::Frame::show_classic(), and core::fragment::Frame::show_fragments().

void core::fragment::FragData::show	(	std::ostream &	out,
		Frame const &	frame
	)		const

virtual

References data_, is_valid(), pdbid(), pdbpos(), and core::fragment::Frame::seqpos().

void core::fragment::FragData::show_classic ( std::ostream & out ) const

virtual

References data_.

Size core::fragment::FragData::size ( ) const

inline

References data_.

Referenced by apply(), clone(), generate_sub_fragment(), core::fragment::AnnotatedFragData::generate_sub_fragment(), is_applicable(), is_compatible(), secstruct(), sequence(), and steal().

bool core::fragment::FragData::steal	(	pose::Pose const &	pose,
		Size	start,
		Size	end
	)

virtual

References data_, core::sequence::end, set_valid(), and core::pose::Pose::size().

Referenced by steal().

bool core::fragment::FragData::steal	(	pose::Pose const &	pose,
		Frame const &	frame
	)

virtual

References data_, core::fragment::Frame::end(), core::fragment::Frame::is_continuous(), core::fragment::Frame::length(), core::fragment::Frame::seqpos(), set_valid(), size(), core::pose::Pose::size(), core::fragment::Frame::start(), and steal().

Member Data Documentation

SRFD_List core::fragment::FragData::data_

protected

Referenced by add_residue(), apply(), apply_ss(), clone(), copy(), FragData(), generate_sub_fragment(), core::fragment::AnnotatedFragData::generate_sub_fragment(), get_residue(), is_applicable(), is_compatible(), secstruct(), sequence(), set_residue(), set_sequence(), show(), show_classic(), size(), and steal().

Real core::fragment::FragData::score_

private

Referenced by copy(), score(), and set_score().

bool core::fragment::FragData::valid_

private

Referenced by copy(), is_valid(), and set_valid().

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

src/core/fragment/FragData.hh
src/core/fragment/FragData.cc

Public Member Functions

Protected Member Functions

Protected Attributes

Private Types

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation