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protocols::task_operations::SequenceMotifTaskOperation Class Reference

A TaskOp that takes a regex-like pattern and turns it into a set of design residues. The string should identify what to do for each position. More...

#include <SequenceMotifTaskOperation.hh>

Inheritance diagram for protocols::task_operations::SequenceMotifTaskOperation:
Inheritance graph
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Public Member Functions

 SequenceMotifTaskOperation ()
 
 SequenceMotifTaskOperation (core::select::residue_selector::ResidueSelectorCOP selector, std::string const &motif)
 
 SequenceMotifTaskOperation (SequenceMotifTaskOperation const &src)
 
 ~SequenceMotifTaskOperation () override
 
core::pack::task::operation::TaskOperationOP clone () const override
 Create another task operation of the type matching the most-derived version of the class. More...
 
void parse_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Configure from a RosettaScripts XML tag. More...
 
void apply (core::pose::Pose const &pose, core::pack::task::PackerTask &task) const override
 Change a packer task in some way. The input pose is the one to which the input task will be later applied. More...
 
void set_motif (std::string const &motif)
 Set a string that tells this operation how to design. More...
 
void set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector)
 
- 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 Does this task_operation indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)?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 ()
 Return the name used to construct this TaskOperation from an XML file. More...
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 Describe the format of XML file used to initialize this TaskOperation. More...
 

Private Member Functions

void setup_commands ()
 Setup our private list of commands. THis saves a lot of time instead of needing to do this at every apply. More...
 

Private Attributes

core::select::residue_selector::ResidueSelectorCOP selector_ = nullptr
 
std::string motif_ = ""
 
utility::vector1
< utility::vector1
< core::pack::task::ResfileCommandOP > > 
commands_
 

Additional Inherited Members

- Public Types inherited from core::pack::task::operation::TaskOperation
typedef utility::tag::TagCOP TagCOP
 
typedef basic::datacache::DataMap DataMap
 
typedef pose::Pose Pose
 

Detailed Description

A TaskOp that takes a regex-like pattern and turns it into a set of design residues. The string should identify what to do for each position.

See the MOTIF option for a description of the syntax used to define a motif.

Constructor & Destructor Documentation

protocols::task_operations::SequenceMotifTaskOperation::SequenceMotifTaskOperation ( )
protocols::task_operations::SequenceMotifTaskOperation::SequenceMotifTaskOperation ( core::select::residue_selector::ResidueSelectorCOP  selector,
std::string const &  motif 
)
protocols::task_operations::SequenceMotifTaskOperation::SequenceMotifTaskOperation ( SequenceMotifTaskOperation const &  src)

References motif_, selector_, and setup_commands().

protocols::task_operations::SequenceMotifTaskOperation::~SequenceMotifTaskOperation ( )
override

Member Function Documentation

void protocols::task_operations::SequenceMotifTaskOperation::apply ( core::pose::Pose const &  ,
core::pack::task::PackerTask  
) const
overridevirtual

Change a packer task in some way. The input pose is the one to which the input task will be later applied.

Implements core::pack::task::operation::TaskOperation.

References commands_, motif_, core::select::residue_selector::selection_positions(), selector_, core::id::to_string(), and protocols::task_operations::TR().

core::pack::task::operation::TaskOperationOP protocols::task_operations::SequenceMotifTaskOperation::clone ( ) const
overridevirtual

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

Implements core::pack::task::operation::TaskOperation.

std::string protocols::task_operations::SequenceMotifTaskOperation::keyname ( )
static

Return the name used to construct this TaskOperation from an XML file.

Referenced by protocols::task_operations::SequenceMotifTaskOperationCreator::keyname(), and provide_xml_schema().

void protocols::task_operations::SequenceMotifTaskOperation::parse_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::task_operations::SequenceMotifTaskOperation::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::task_operations::SequenceMotifTaskOperation::set_motif ( std::string const &  motif)

Set a string that tells this operation how to design.

This is slightly similar to a regex, but not quite. We are not matching a sequence, we are designing in a motif regardless of the current sequence, anywhere in a protein.

  • Each letter corresponds to a position. Using [ ] indicates a more complicated expression for that position.
  • An X indicates it can be anything, and that we are designing here.
  • An AA Letter, like V, indicates that that position will be designed to a V.
  • A - charactor indicates that that position stays with whatever it is currently. We essentially skip this position.
  • An expression like: [^PAV] indicates that we will design anything except Proline, Alanine, and Valine
  • An expression like: [NTS] indicates that that position can be Asparigine, Threonine, or Serine and only of these will be enabled during the design.
  • RESFILE commands are accepted as well. Resfile commands need a % in front of the whole set. FOr example [POLAR] is totally cool.

EXAMPLE: Glycosylation N-Linked motif design: N[^P][ST]

References motif_, and setup_commands().

Referenced by parse_tag(), and SequenceMotifTaskOperation().

void protocols::task_operations::SequenceMotifTaskOperation::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP  selector)

References selector_.

Referenced by parse_tag(), and SequenceMotifTaskOperation().

void protocols::task_operations::SequenceMotifTaskOperation::setup_commands ( )
private

Setup our private list of commands. THis saves a lot of time instead of needing to do this at every apply.

References commands_, core::pack::task::get_resfile_commands(), and motif_.

Referenced by SequenceMotifTaskOperation(), and set_motif().

Member Data Documentation

utility::vector1< utility::vector1< core::pack::task::ResfileCommandOP > > protocols::task_operations::SequenceMotifTaskOperation::commands_
private

Referenced by apply(), and setup_commands().

std::string protocols::task_operations::SequenceMotifTaskOperation::motif_ = ""
private
core::select::residue_selector::ResidueSelectorCOP protocols::task_operations::SequenceMotifTaskOperation::selector_ = nullptr
private

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