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:

[legend]

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::TagCOP	TagCOP

typedef basic::datacache::DataMap	DataMap

typedef pose::Pose	Pose

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

	ReadResfileAndObeyLengthEvents (std::string const &)

	~ReadResfileAndObeyLengthEvents () override

TaskOperationOP	clone () const override
	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 override

void	parse_tag (TagCOP, DataMap &) override
	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 (utility::options::OptionCollection const &options)

	ReadResfile (std::string const &filename)

	ReadResfile (ReadResfile const &src)
	Copy constructor. More...

	~ReadResfile () override

void	set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector_in)
	Set the residue selector. More...

core::select::residue_selector::ResidueSelectorCOP	residue_selector () const
	Get the residue selector, if one exists. (Const-access owning pointer). More...

void	filename (std::string const &filename)

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

std::string const &	filename () const

void	cache_resfile ()
	Read in the resfile and store it, so that it doesn't have to be read over and over again at apply time. More...

void	set_cached_resfile (std::string const &file_contents)
	Allows code to provide resfile contents, so that this TaskOperation doesn't directly have to handle file i/o. Handly on large systems (e.g. Blue Gene), where one might only want the master process to read a file. More...

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

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static std::string	keyname ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static Public Member Functions inherited from core::pack::task::operation::ReadResfile
static std::string	keyname ()

static utility::tag::AttributeList	xml_schema_attributes ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static void	list_options_read (utility::options::OptionKeyList &options)

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

Member Typedef Documentation

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

Constructor & Destructor Documentation

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

BEGIN ReadResfileAndObeyLengthEvents.

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

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

overridedefault

Member Function Documentation

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

overridevirtual

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.

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::LENGTH_EVENT_COLLECTOR, core::pose::Pose::observer_cache(), resfile_commands(), core::pack::task::PackerTask::total_residue(), and core::pack::task::operation::TR().

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

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

overridevirtual

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

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

std::string core::pack::task::operation::ReadResfileAndObeyLengthEvents::keyname ( )

static

Referenced by core::pack::task::operation::ReadResfileAndObeyLengthEventsCreator::keyname(), and provide_xml_schema().

void core::pack::task::operation::ReadResfileAndObeyLengthEvents::parse_tag	(	TagCOP	tag,
		DataMap &
	)

overridevirtual

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

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

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

void core::pack::task::operation::ReadResfileAndObeyLengthEvents::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References keyname(), core::pack::task::operation::task_op_schema_w_attributes(), and core::pack::task::operation::ReadResfile::xml_schema_attributes().

Referenced by core::pack::task::operation::ReadResfileAndObeyLengthEventsCreator::provide_xml_schema().

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

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

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

Static Public Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation