This class ensures that the Loops object that is needed to run any of the various forms of loop modeling is correctly initialized from a Pose. If the residues specified from a loops file have not been resolved into the residue indices for a Pose, then this class will die with an assertion failure. More...

#include <LoopsFileIO.hh>

Inheritance diagram for protocols::loops::GuardedLoopsFromFile:

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Public Member Functions
	GuardedLoopsFromFile ()
	default ctor; sets the object in an "in charge" state. More...

	GuardedLoopsFromFile (LoopsFileData const &lfd)
	constructor from a loops-file-data object: sets this object in an "in charge" state. More...

	GuardedLoopsFromFile (loops_definers::LoopsDefinerOP ld)
	constructor from a loops-definer object: sets this object in an "in charge" state. More...

	GuardedLoopsFromFile (LoopsOP loops)
	constructor from loops pointer: sets this object in a "not in charge" state. More...

	GuardedLoopsFromFile (Loops const &loops)
	constructor from a loops object: set this object in an "in charge" state. More...

	GuardedLoopsFromFile (GuardedLoopsFromFile const &src)
	copy constructor; takes it's "in charge" state from src. More...

	GuardedLoopsFromFile (GuardedLoopsFromFile const &src, bool)
	copy constructor; takes it's "in charge" state from src. Set the copy as not-in-charge. More...

	~GuardedLoopsFromFile () override
	virtual dstor More...

GuardedLoopsFromFile &	operator= (GuardedLoopsFromFile const &rhs)
	assignment operator; takes it's "in charge" state from rhs More...

void	in_charge (bool setting)
	set to "in charge" state. More...

bool	in_charge () const
	get "in charge" state. More...

void	resolve_loop_indices (core::pose::Pose const &)
	Resolve the loop indices, and mark the state as resolved, so that calls to loops() will succeed. This function will re-resolve loop indices with a new pose, which may be important if the same loop_file_data_ is being applied to a pose which has different PDB indices. If I am not in charge, this is a no-op. More...

void	resolve_loop_indices_once (core::pose::Pose const &)

LoopsCOP	loops () const
	request the LoopsCOP pointer; asserts that the loop indices have been resolved or that "I am not in charge". More...

LoopsOP	loops ()
	request the LoopsOP pointer; asserts that the loop indices have been resolved or that "I am not in charge". More...

void	set_loops_pointer (LoopsOP setting)
	set the loops owning pointer object directly More...

void	loops (Loops const &setting)
	set the loops to copy the contents of settings into the existing Loops object More...

void	loops (LoopsFileData const &setting)
	set the LoopsFileData object directly More...

LoopsFileDataCOP	loops_file_data () const
	read access to the LoopsFileData More...

void	loops (loops_definers::LoopsDefinerOP const &setting)
	set the LoopsDefiner object directly More...

loops_definers::LoopsDefinerCOP	loops_definer () const
	read access to the LoopsFileData More...

Private Attributes
bool	in_charge_

bool	pose_has_resolved_loop_indices_

bool	rely_on_loopfile_indices_

LoopsFileDataOP	loops_file_data_

loops_definers::LoopsDefinerOP	loops_definer_

LoopsOP	loops_

Detailed Description

This class ensures that the Loops object that is needed to run any of the various forms of loop modeling is correctly initialized from a Pose. If the residues specified from a loops file have not been resolved into the residue indices for a Pose, then this class will die with an assertion failure.

Constructor & Destructor Documentation

protocols::loops::GuardedLoopsFromFile::GuardedLoopsFromFile ( )

default ctor; sets the object in an "in charge" state.

default constructor: set state to not expect a pose, but to return an empty Loops object

protocols::loops::GuardedLoopsFromFile::GuardedLoopsFromFile ( LoopsFileData const & lfd )

constructor from a loops-file-data object: sets this object in an "in charge" state.

construct from LoopsFileData: set state to expect a Pose

protocols::loops::GuardedLoopsFromFile::GuardedLoopsFromFile ( loops_definers::LoopsDefinerOP ld )

constructor from a loops-definer object: sets this object in an "in charge" state.

construct from LoopsFileData: set state to expect a Pose

protocols::loops::GuardedLoopsFromFile::GuardedLoopsFromFile ( LoopsOP loops )

constructor from loops pointer: sets this object in a "not in charge" state.

construct from a LoopsOP

protocols::loops::GuardedLoopsFromFile::GuardedLoopsFromFile ( Loops const & loops )

constructor from a loops object: set this object in an "in charge" state.

construct from a LoopsOP

protocols::loops::GuardedLoopsFromFile::GuardedLoopsFromFile ( GuardedLoopsFromFile const & src )

default

copy constructor; takes it's "in charge" state from src.

Shallow copy of the LoopsOP data so that it can be shared between multiple objects; take the "in_charge_" bit from the source in the event that this is a called as part of a clone.

protocols::loops::GuardedLoopsFromFile::GuardedLoopsFromFile	(	GuardedLoopsFromFile const &	src,
		bool
	)

copy constructor; takes it's "in charge" state from src. Set the copy as not-in-charge.

Shallow copy of the LoopsOP data so that it can be shared between multiple objects – also assume that the GuardedLoopsFromFile object is the one that is in charge.

References in_charge_.

protocols::loops::GuardedLoopsFromFile::~GuardedLoopsFromFile ( )

overridedefault

virtual dstor

Member Function Documentation

void protocols::loops::GuardedLoopsFromFile::in_charge ( bool setting )

set to "in charge" state.

References in_charge_.

bool protocols::loops::GuardedLoopsFromFile::in_charge ( ) const

get "in charge" state.

References in_charge_.

LoopsCOP protocols::loops::GuardedLoopsFromFile::loops ( ) const

request the LoopsCOP pointer; asserts that the loop indices have been resolved or that "I am not in charge".

References in_charge_, loops_, and pose_has_resolved_loop_indices_.

Referenced by resolve_loop_indices().

LoopsOP protocols::loops::GuardedLoopsFromFile::loops ( )

request the LoopsOP pointer; asserts that the loop indices have been resolved or that "I am not in charge".

References in_charge_, loops_, and pose_has_resolved_loop_indices_.

void protocols::loops::GuardedLoopsFromFile::loops ( Loops const & setting )

set the loops to copy the contents of settings into the existing Loops object

Deep copy into the loops data; this updates the single Loops object that is / can be shared among multiple objects.

References loops_, pose_has_resolved_loop_indices_, and rely_on_loopfile_indices_.

void protocols::loops::GuardedLoopsFromFile::loops ( LoopsFileData const & setting )

set the LoopsFileData object directly

References in_charge_, loops_file_data_, pose_has_resolved_loop_indices_, and rely_on_loopfile_indices_.

void protocols::loops::GuardedLoopsFromFile::loops ( loops_definers::LoopsDefinerOP const & setting )

set the LoopsDefiner object directly

set the LoopsFileData object directly

References in_charge_, loops_definer_, pose_has_resolved_loop_indices_, and rely_on_loopfile_indices_.

loops_definers::LoopsDefinerCOP protocols::loops::GuardedLoopsFromFile::loops_definer ( ) const

read access to the LoopsFileData

References loops_definer_.

LoopsFileDataCOP protocols::loops::GuardedLoopsFromFile::loops_file_data ( ) const

read access to the LoopsFileData

References loops_file_data_.

GuardedLoopsFromFile & protocols::loops::GuardedLoopsFromFile::operator= ( GuardedLoopsFromFile const & rhs )

default

assignment operator; takes it's "in charge" state from rhs

void protocols::loops::GuardedLoopsFromFile::resolve_loop_indices ( core::pose::Pose const & pose )

Resolve the loop indices, and mark the state as resolved, so that calls to loops() will succeed. This function will re-resolve loop indices with a new pose, which may be important if the same loop_file_data_ is being applied to a pose which has different PDB indices. If I am not in charge, this is a no-op.

This will re-resolve the loop indices with the input pose, even if they had been resolved in the past.

References in_charge_, loops(), loops_definer_, loops_file_data_, pose_has_resolved_loop_indices_, and rely_on_loopfile_indices_.

Referenced by resolve_loop_indices_once().

void protocols::loops::GuardedLoopsFromFile::resolve_loop_indices_once ( core::pose::Pose const & pose )

This will only resolve the loop indices once, so repeated calls to this will not alter the Loops object with (possibly) new loop indices.

References in_charge_, pose_has_resolved_loop_indices_, and resolve_loop_indices().

void protocols::loops::GuardedLoopsFromFile::set_loops_pointer ( LoopsOP setting )

set the loops owning pointer object directly

Shallow copy of the loops data.

References in_charge_, loops_, pose_has_resolved_loop_indices_, and rely_on_loopfile_indices_.