Rosetta 3.5: core::fragment::FragData Class Reference

#include <FragData.hh>

Inheritance diagram for core::fragment::FragData:

Inheritance graph

Collaboration diagram for core::fragment::FragData:

Collaboration graph

Public Member Functions
	FragData ()

	FragData (SingleResidueFragDataOP, core::Size n)

virtual	~FragData ()

virtual FragDataOP	clone () const

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 &)

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

FragDataOP	generate_sub_fragment (Size start, Size stop)

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

Protected Member Functions
	FragData (Size nr_res)

Private Types
typedef utility::vector1 < SingleResidueFragDataOP >	SRFD_List

Private Attributes
SRFD_List	data_

bool	valid_

Real	score_

Detailed Description

Definition at line 47 of file FragData.hh.

Member Typedef Documentation

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

private

Definition at line 48 of file FragData.hh.

Constructor & Destructor Documentation

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

inline

Definition at line 51 of file FragData.hh.

Referenced by clone(), and generate_sub_fragment().

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

Definition at line 67 of file FragData.cc.

References data_.

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

inlinevirtual

Definition at line 58 of file FragData.hh.

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

inlineprotected

Definition at line 176 of file FragData.hh.

Member Function Documentation

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

inline

Definition at line 129 of file FragData.hh.

References data_.

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

virtual

Definition at line 82 of file FragData.cc.

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

Referenced by protocols::antibody::CDRH3Modeler::antibody_modeling_insert_ter(), protocols::antibody2::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

Definition at line 109 of file FragData.cc.

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

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

virtual

Definition at line 126 of file FragData.cc.

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

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

virtual

Definition at line 97 of file FragData.cc.

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

Definition at line 139 of file FragData.cc.

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.

Definition at line 156 of file FragData.hh.

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

virtual

Reimplemented in core::fragment::AnnotatedFragData.

Definition at line 74 of file FragData.cc.

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

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

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

Definition at line 203 of file FragData.cc.

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

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

inline

Definition at line 133 of file FragData.hh.

References data_.

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

virtual

Definition at line 152 of file FragData.cc.

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

Definition at line 162 of file FragData.cc.

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

Definition at line 214 of file FragData.cc.

References data_, and size().

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

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

inline

Definition at line 86 of file FragData.hh.

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.

Definition at line 151 of file FragData.hh.

Referenced by show().

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

inlinevirtual

Reimplemented in core::fragment::AnnotatedFragData.

Definition at line 161 of file FragData.hh.

Referenced by show().

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

inline

Returns the score for this fragment.

Definition at line 171 of file FragData.hh.

References score_.

Referenced by set_score().

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

inline

Definition at line 94 of file FragData.hh.

References data_.

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

inline

Definition at line 102 of file FragData.hh.

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

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

inline

Definition at line 98 of file FragData.hh.

References data_, and sequence().

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

inline

Definition at line 110 of file FragData.hh.

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

Referenced by sequence().

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

inline

Definition at line 122 of file FragData.hh.

References data_.

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

inline

Set a score value for this fragment.

Definition at line 166 of file FragData.hh.

References score(), and score_.

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

inline

Definition at line 118 of file FragData.hh.

References data_.

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

inline

Definition at line 146 of file FragData.hh.

References valid_.

Referenced by steal().

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

virtual

Definition at line 238 of file FragData.cc.

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

Definition at line 223 of file FragData.cc.

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

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

virtual

Definition at line 251 of file FragData.cc.

References data_.

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

inline

Definition at line 90 of file FragData.hh.

References data_.

Referenced by apply(), clone(), 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

Definition at line 176 of file FragData.cc.

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

Referenced by steal().

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

virtual

Definition at line 188 of file FragData.cc.

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

Member Data Documentation

SRFD_List core::fragment::FragData::data_

private

Definition at line 176 of file FragData.hh.

Referenced by add_residue(), apply(), apply_ss(), clone(), FragData(), 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

Definition at line 184 of file FragData.hh.

Referenced by score(), and set_score().

bool core::fragment::FragData::valid_

private

Definition at line 182 of file FragData.hh.

Referenced by 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