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core::pack::task::operation::ReadResfileAndObeyLengthEvents Class Reference

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:
Inheritance graph
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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::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 bool task_operation_provides_citation_info () const
 Does this task operation provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool task_operation_is_unpublished () const
 Does this task_operation indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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

Constructor & Destructor Documentation

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

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: