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:

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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 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 ()
	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
	)

References set_motif(), and set_residue_selector().

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

Configure from a RosettaScripts XML tag.

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

References core::select::residue_selector::parse_residue_selector(), set_motif(), and set_residue_selector().

void protocols::task_operations::SequenceMotifTaskOperation::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

Describe the format of XML file used to initialize this TaskOperation.

References core::select::residue_selector::attributes_for_parse_residue_selector(), core::sequence::get_design_sequence_motif_syntax(), keyname(), and core::pack::task::operation::task_op_schema_w_attributes().

Referenced by protocols::task_operations::SequenceMotifTaskOperationCreator::provide_xml_schema().

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.