Base class for SRFD classes Instances of SRFD classes contain information on specific dofs in a single residue or a jump connected to a residue The classes' apply method will now how to implement the specified dofs in the give pose at the given residue position. More...

#include <SingleResidueFragData.hh>

Inheritance diagram for core::fragment::SingleResidueFragData:

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Collaboration diagram for core::fragment::SingleResidueFragData:

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List of all members.

Public Member Functions
	SingleResidueFragData (char sequence)
	SingleResidueFragData ()
virtual SingleResidueFragDataOP	clone () const =0
virtual SingleResidueFragDataOP	create () const =0
	create a new instance of this object
virtual bool	apply (pose::Pose &, Size seq_pos) const =0
	insert fragment_data into pose at position seq_pos
virtual bool	apply (kinematics::MoveMap const &movemap, pose::Pose &pose, Size const seqpos) const =0
	insert fragment_data into pose at position seq_pos for dofs that are allowed to move in the movemap
virtual bool	apply_ss (std::string &, Size seq_pos) const =0
	insert fragment_data sec-struct into ss-string at position seq_pos
virtual bool	steal (pose::Pose const &, Size seq_pos)=0
	insert fragment_data into pose at position seq_pos
virtual bool	apply (pose::Pose &, Size const intra_frame_pos, Frame const &) const
	insert fragment_data into pose at position given by Frame.seqpos( intra_frame_pos );
virtual bool	apply (kinematics::MoveMap const &movemap, pose::Pose &pose, Size const intra_frame_pos, Frame const &frame) const
	insert fragment_data into pose at position given by Frame.seqpos( intra_frame_pos ) for dofs that are allowed to move in the MoveMap
virtual bool	apply_ss (std::string &, Size intra_frame_pos, Frame const &) const
	insert fragment_data sec-struct into ss-string at position seq_pos
virtual bool	steal (pose::Pose const &, Size intra_frame_pos, Frame const &)
	insert fragment_data into pose at position seq_pos
virtual bool	is_compatible (SingleResidueFragData const &) const =0
	check weather SRFD applies to same dofs and is of same type
virtual bool	is_applicable (kinematics::MoveMap const &, Size intra_frame_pos, Frame const &) const
	check weather dofs can be moved
virtual bool	is_applicable (kinematics::MoveMap const &, Size pos) const =0
	check whether dofs can be moved
void	set_sequence (char const sequence)
char	sequence () const
virtual char	secstruct () const
virtual void	show (std::ostream &out) const
virtual void	read_data (std::istream &)
	Default implementation: noop.
virtual std::string	type () const
Static Public Member Functions
static std::string	_static_type_name ()
Protected Attributes
char	sequence_

Detailed Description

Base class for SRFD classes Instances of SRFD classes contain information on specific dofs in a single residue or a jump connected to a residue The classes' apply method will now how to implement the specified dofs in the give pose at the given residue position.

TODO: change SRFD interface such that apply is called like this apply( pose, inframe_pos (1..length), Frame const& ) jumpFrags can then ask the Frame for their upstream residue and check that if they are at position 1 that they do nothgin... can have basic implementation that translates this apply into the old apply

Constructor & Destructor Documentation

core::fragment::SingleResidueFragData::SingleResidueFragData ( char sequence ) [inline]

core::fragment::SingleResidueFragData::SingleResidueFragData ( ) [inline]

Member Function Documentation

std::string core::fragment::SingleResidueFragData::_static_type_name ( ) [static]

Reimplemented in core::fragment::BBTorsionAndAnglesSRFD, core::fragment::BBTorsionSRFD, core::fragment::UpJumpSRFD, core::fragment::DownJumpSRFD, and core::fragment::SecstructSRFD.

virtual bool core::fragment::SingleResidueFragData::apply	(	pose::Pose &	,
		Size	seq_pos
	)		const `[pure virtual]`

insert fragment_data into pose at position seq_pos

Implemented in core::fragment::BBTorsionAndAnglesSRFD, core::fragment::BBTorsionSRFD, core::fragment::UpJumpSRFD, core::fragment::DownJumpSRFD, and core::fragment::SecstructSRFD.

Referenced by apply().

bool core::fragment::SingleResidueFragData::apply	(	kinematics::MoveMap const &	movemap,
		pose::Pose &	pose,
		Size const	intra_frame_pos,
		Frame const &	frame
	)		const `[virtual]`

insert fragment_data into pose at position given by Frame.seqpos( intra_frame_pos ) for dofs that are allowed to move in the MoveMap

Reimplemented in core::fragment::UpJumpSRFD, and core::fragment::DownJumpSRFD.

References apply(), and core::fragment::Frame::seqpos().

virtual bool core::fragment::SingleResidueFragData::apply	(	kinematics::MoveMap const &	movemap,
		pose::Pose &	pose,
		Size const	seqpos
	)		const `[pure virtual]`

insert fragment_data into pose at position seq_pos for dofs that are allowed to move in the movemap

Returns:: True if operation succeeds, False otherwise.

Implemented in core::fragment::BBTorsionAndAnglesSRFD, core::fragment::BBTorsionSRFD, core::fragment::IndependentBBTorsionSRFD, core::fragment::UpJumpSRFD, core::fragment::DownJumpSRFD, and core::fragment::SecstructSRFD.

bool core::fragment::SingleResidueFragData::apply	(	pose::Pose &	pose,
		Size const	intra_frame_pos,
		Frame const &	frame
	)		const `[virtual]`

insert fragment_data into pose at position given by Frame.seqpos( intra_frame_pos );

Reimplemented in core::fragment::UpJumpSRFD, and core::fragment::DownJumpSRFD.

References apply(), and core::fragment::Frame::seqpos().

bool core::fragment::SingleResidueFragData::apply_ss	(	std::string &	ss,
		Size	intra_frame_pos,
		Frame const &	frame
	)		const `[virtual]`

insert fragment_data sec-struct into ss-string at position seq_pos

Reimplemented in core::fragment::UpJumpSRFD, and core::fragment::DownJumpSRFD.

References apply_ss(), and core::fragment::Frame::seqpos().

virtual bool core::fragment::SingleResidueFragData::apply_ss	(	std::string &	,
		Size	seq_pos
	)		const `[pure virtual]`

insert fragment_data sec-struct into ss-string at position seq_pos

Implemented in core::fragment::UpJumpSRFD, core::fragment::DownJumpSRFD, and core::fragment::SecstructSRFD.

Referenced by apply_ss().

virtual SingleResidueFragDataOP core::fragment::SingleResidueFragData::clone ( ) const [pure virtual]

Implemented in core::fragment::BBTorsionAndAnglesSRFD, core::fragment::BBTorsionSRFD, core::fragment::IndependentBBTorsionSRFD, core::fragment::UpJumpSRFD, core::fragment::DownJumpSRFD, and core::fragment::SecstructSRFD.

virtual SingleResidueFragDataOP core::fragment::SingleResidueFragData::create ( ) const [pure virtual]

create a new instance of this object

Implemented in core::fragment::BBTorsionAndAnglesSRFD, core::fragment::BBTorsionSRFD, core::fragment::IndependentBBTorsionSRFD, core::fragment::UpJumpSRFD, core::fragment::DownJumpSRFD, and core::fragment::SecstructSRFD.

bool core::fragment::SingleResidueFragData::is_applicable	(	kinematics::MoveMap const &	mm,
		Size	intra_frame_pos,
		Frame const &	frame
	)		const `[virtual]`

check weather dofs can be moved

Reimplemented in core::fragment::DownJumpSRFD.

References core::fragment::Frame::seqpos().

virtual bool core::fragment::SingleResidueFragData::is_applicable	(	kinematics::MoveMap const &	,
		Size	pos
	)		const `[pure virtual]`

check whether dofs can be moved

Implemented in core::fragment::BBTorsionAndAnglesSRFD, core::fragment::BBTorsionSRFD, core::fragment::IndependentBBTorsionSRFD, core::fragment::UpJumpSRFD, core::fragment::DownJumpSRFD, and core::fragment::SecstructSRFD.

virtual bool core::fragment::SingleResidueFragData::is_compatible ( SingleResidueFragData const & ) const [pure virtual]

check weather SRFD applies to same dofs and is of same type

Implemented in core::fragment::BBTorsionAndAnglesSRFD, core::fragment::BBTorsionSRFD, core::fragment::UpJumpSRFD, core::fragment::DownJumpSRFD, and core::fragment::SecstructSRFD.

void core::fragment::SingleResidueFragData::read_data ( std::istream & ) [virtual]

Default implementation: noop.

Reimplemented in core::fragment::BBTorsionSRFD, and core::fragment::SecstructSRFD.

Referenced by core::fragment::operator>>().

virtual char core::fragment::SingleResidueFragData::secstruct ( ) const [inline, virtual]

Reimplemented in core::fragment::SecstructSRFD.

char core::fragment::SingleResidueFragData::sequence ( ) const [inline]

References sequence_.

Referenced by set_sequence().

void core::fragment::SingleResidueFragData::set_sequence ( char const sequence ) [inline]

References sequence(), and sequence_.

Referenced by protocols::frag_picker::VallResidue::bbtorsion_srfd().

void core::fragment::SingleResidueFragData::show ( std::ostream & out ) const [virtual]

Reimplemented in core::fragment::BBTorsionAndAnglesSRFD, core::fragment::BBTorsionSRFD, core::fragment::DownJumpSRFD, and core::fragment::SecstructSRFD.

References type().

Referenced by core::fragment::operator<<().

bool core::fragment::SingleResidueFragData::steal	(	pose::Pose const &	pose,
		Size	seq_pos
	)		`[pure virtual]`

insert fragment_data into pose at position seq_pos

Implemented in core::fragment::BBTorsionAndAnglesSRFD, core::fragment::BBTorsionSRFD, core::fragment::UpJumpSRFD, core::fragment::DownJumpSRFD, and core::fragment::SecstructSRFD.

References core::conformation::Residue::aa(), core::chemical::oneletter_code_from_aa(), core::pose::Pose::residue(), and sequence_.

Referenced by steal().

bool core::fragment::SingleResidueFragData::steal	(	pose::Pose const &	pose,
		Size	intra_frame_pos,
		Frame const &	frame
	)		`[virtual]`

insert fragment_data into pose at position seq_pos

Reimplemented in core::fragment::UpJumpSRFD, and core::fragment::DownJumpSRFD.

References core::fragment::Frame::seqpos(), and steal().

std::string core::fragment::SingleResidueFragData::type ( ) const [virtual]

Reimplemented in core::fragment::BBTorsionAndAnglesSRFD, core::fragment::BBTorsionSRFD, core::fragment::UpJumpSRFD, core::fragment::DownJumpSRFD, and core::fragment::SecstructSRFD.

Referenced by show().

Member Data Documentation

char core::fragment::SingleResidueFragData::sequence_ [protected]

Referenced by sequence(), set_sequence(), and steal().

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

src/core/fragment/SingleResidueFragData.hh
src/core/fragment/SingleResidueFragData.cc

Public Member Functions

Static Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation