written by flo, feb 2011 class that can apply a resfile to a pose that had its length changed at some point in a protocol. A LengthEventCollector must be set in the pose's observer cache for this to work properly More...

#include <TaskOperations.hh>

Inheritance diagram for core::pack::task::operation::ReadResfileAndObeyLengthEvents:

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Collaboration diagram for core::pack::task::operation::ReadResfileAndObeyLengthEvents:

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Public Types
typedef ReadResfile	parent

Public Types inherited from core::pack::task::operation::ReadResfile
typedef TaskOperation	parent

Public Types inherited from core::pack::task::operation::TaskOperation
typedef utility::tag::TagPtr	TagPtr

typedef pose::Pose	Pose

Public Member Functions
	ReadResfileAndObeyLengthEvents ()
	BEGIN ReadResfileAndObeyLengthEvents. More...

	ReadResfileAndObeyLengthEvents (std::string const &)

	~ReadResfileAndObeyLengthEvents ()

virtual TaskOperationOP	clone () const
	Create another task operation of the type matching the most-derived version of the class. More...

void	apply (pose::Pose const &pose, PackerTask &ptask) const

virtual void	parse_tag (TagPtr)
	Used to parse an xml-like tag to load parameters and properties. More...

std::list< ResfileCommandCOP > const &	resfile_commands (Size const resfile_seqpos, ResfileContents const &contents, PackerTask const &ptask) const

Public Member Functions inherited from core::pack::task::operation::ReadResfile
	ReadResfile ()
	BEGIN ReadResfile. More...

	ReadResfile (std::string const &)

virtual	~ReadResfile ()

void	filename (std::string const &filename)

void	default_filename ()
	queries options system for resfile name More...

std::string const &	filename () const

virtual void	parse_def (utility::lua::LuaObject const &def)

Public Member Functions inherited from core::pack::task::operation::TaskOperation
virtual	~TaskOperation ()

Private Attributes
bool	apply_default_commands_to_inserts_

Detailed Description

written by flo, feb 2011 class that can apply a resfile to a pose that had its length changed at some point in a protocol. A LengthEventCollector must be set in the pose's observer cache for this to work properly

Definition at line 305 of file TaskOperations.hh.

Member Typedef Documentation

typedef ReadResfile core::pack::task::operation::ReadResfileAndObeyLengthEvents::parent

Definition at line 309 of file TaskOperations.hh.

Constructor & Destructor Documentation

core::pack::task::operation::ReadResfileAndObeyLengthEvents::ReadResfileAndObeyLengthEvents ( )

BEGIN ReadResfileAndObeyLengthEvents.

Definition at line 618 of file TaskOperations.cc.

Referenced by clone().

core::pack::task::operation::ReadResfileAndObeyLengthEvents::ReadResfileAndObeyLengthEvents ( std::string const & filename)

Definition at line 623 of file TaskOperations.cc.

core::pack::task::operation::ReadResfileAndObeyLengthEvents::~ReadResfileAndObeyLengthEvents ( )

Definition at line 628 of file TaskOperations.cc.

Member Function Documentation

void core::pack::task::operation::ReadResfileAndObeyLengthEvents::apply	(	pose::Pose const &	pose,
		PackerTask &	ptask
	)		const

virtual

IMPORTANT: only use this if any length changes are not reflected in the pose's pdb info, such as seems to be the case after vlb not quite certain on the ideal approach yet. it's prolly best to parse the resfile, and then apply the ResfileCommands to the remapped residues. this necessitates getting the ResfileContents. the code under 2. here is some duplication of ResfileReader::parse_resfile/parse_resfile_string, ideally this and ResfileReader should be refactored a bit

Reimplemented from core::pack::task::operation::ReadResfile.

Definition at line 649 of file TaskOperations.cc.

References core::pack::task::operation::ReadResfile::apply(), apply_default_commands_to_inserts_, core::id::combine_sequence_mappings(), core::pack::task::operation::ReadResfile::filename(), core::pose::datacache::CacheableObserverType::LENGTH_EVENT_COLLECTOR, core::pose::Pose::observer_cache(), resfile_commands(), and core::pack::task::PackerTask::total_residue().

Referenced by protocols::enzdes::DetectProteinLigandInterface::apply().

TaskOperationOP core::pack::task::operation::ReadResfileAndObeyLengthEvents::clone ( ) const

virtual

Create another task operation of the type matching the most-derived version of the class.

Reimplemented from core::pack::task::operation::ReadResfile.

Definition at line 635 of file TaskOperations.cc.

References ReadResfileAndObeyLengthEvents().

void core::pack::task::operation::ReadResfileAndObeyLengthEvents::parse_tag ( TagPtr tag)

virtual

Used to parse an xml-like tag to load parameters and properties.

Reimplemented from core::pack::task::operation::ReadResfile.

Definition at line 700 of file TaskOperations.cc.

References apply_default_commands_to_inserts_, and core::pack::task::operation::ReadResfile::parse_tag().

std::list< ResfileCommandCOP > const & core::pack::task::operation::ReadResfileAndObeyLengthEvents::resfile_commands	(	core::Size const	resfile_seqpos,
		ResfileContents const &	contents,
		PackerTask const &	ptask
	)		const

note: this function will return default commands for resfile_seqpos == 0

Definition at line 710 of file TaskOperations.cc.

References core::pack::task::ResfileContents::commands_for_residue(), core::pack::task::ResfileContents::default_commands(), core::pack::task::ResfileContents::specialized_commands_exist_for_residue(), and core::pack::task::PackerTask::total_residue().

Referenced by apply().

Member Data Documentation

bool core::pack::task::operation::ReadResfileAndObeyLengthEvents::apply_default_commands_to_inserts_

private

Definition at line 330 of file TaskOperations.hh.

Referenced by apply(), and parse_tag().

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

src/core/pack/task/operation/TaskOperations.hh
src/core/pack/task/operation/TaskOperations.cc

Public Types

Public Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation