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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Collaboration 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 (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...

virtual	~GuardedLoopsFromFile ()
	virtual dstor More...

GuardedLoopsFromFile const &	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...

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

Private Attributes
bool	in_charge_

bool	pose_has_resolved_loop_indices_

bool	rely_on_loopfile_indices_

LoopsFileData	loops_file_data_

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.

Definition at line 190 of file LoopsFileIO.hh.

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

Definition at line 284 of file LoopsFileIO.cc.

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

Definition at line 292 of file LoopsFileIO.cc.

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

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

construct from a LoopsOP

Definition at line 301 of file LoopsFileIO.cc.

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

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

construct from a LoopsOP

Definition at line 310 of file LoopsFileIO.cc.

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

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.

Definition at line 320 of file LoopsFileIO.cc.

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.

Definition at line 331 of file LoopsFileIO.cc.

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

virtual

virtual dstor

Definition at line 340 of file LoopsFileIO.cc.

Member Function Documentation

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

set to "in charge" state.

Definition at line 358 of file LoopsFileIO.cc.

References in_charge_.

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

get "in charge" state.

Definition at line 363 of file LoopsFileIO.cc.

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".

Definition at line 389 of file LoopsFileIO.cc.

References in_charge_, loops_, and pose_has_resolved_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".

Definition at line 398 of file LoopsFileIO.cc.

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.

Definition at line 407 of file LoopsFileIO.cc.

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

Definition at line 428 of file LoopsFileIO.cc.

References in_charge_, loops_file_data_, pose_has_resolved_loop_indices_, and rely_on_loopfile_indices_.

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

read access to the LoopsFileData

Definition at line 438 of file LoopsFileIO.cc.

References loops_file_data_.

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

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

Definition at line 343 of file LoopsFileIO.cc.

References in_charge_, loops_, loops_file_data_, pose_has_resolved_loop_indices_, and rely_on_loopfile_indices_.

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.

Definition at line 367 of file LoopsFileIO.cc.

References in_charge_, loops_file_data_, pose_has_resolved_loop_indices_, rely_on_loopfile_indices_, and protocols::loops::LoopsFileData::resolve_loops().

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.

Definition at line 379 of file LoopsFileIO.cc.

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.

Definition at line 417 of file LoopsFileIO.cc.