A TaskOperation that sets the allowed amino acids of designable residues to the native amino acid's conservative mutations. More...

#include <ConservativeDesignOperation.hh>

Inheritance diagram for protocols::task_operations::ConservativeDesignOperation:

[legend]

Public Member Functions
	ConservativeDesignOperation ()
	Default constructor. Will use native aa from apply (Changes each pack if tf is passed). More...

	ConservativeDesignOperation (std::string data_source)
	Constructor with setting of data source. More...

	~ConservativeDesignOperation () override

	ConservativeDesignOperation (ConservativeDesignOperation const &src)

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	parse_tag (utility::tag::TagCOP, basic::datacache::DataMap &) override
	Used to parse an xml-like tag to load parameters and properties. More...

void	limit_to_positions (utility::vector1< core::Size > const &positions)
	Limit to a subset of residue positions, already set to designable. More...

void	include_residue (core::Size resnum)

void	clear_positions ()
	Clear any set positions. More...

void	include_native_aa (bool setting)
	Include native amino acid in the allowed_aas list. Default true. More...

void	use_pose_sequence_as_native (core::pose::Pose const &pose)
	Will use native residues from the this pose to determine conserved aa. More...

void	set_native_sequence (std::string const &seq)

void	set_data_source (std::string const &data_source)
	Set the source of the data used to define what is conservative. Options are: chothia_76 and the Blosum matrices from 30 to 100; designated as blosum30, 62, etc. Default is blosum62. The higher the number, the more conservative the set of mutations (numbers are sequence identity cutoffs) More...

ConservativeDesignOperation &	operator= (ConservativeDesignOperation const &rhs)

core::pack::task::operation::TaskOperationOP	clone () const override
	Create another task operation of the type matching the most-derived version of the class. 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 void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static std::string	keyname ()

Protected Member Functions
bool	skip_resid (core::Size resid, core::pack::task::PackerTask const &task, std::string const &seq) const

Private Member Functions
void	load_data_from_db ()

void	init_for_equal_operator_and_copy_constructor (ConservativeDesignOperation &lhs, ConservativeDesignOperation const &rhs)

void	set_defaults ()

Private Attributes
utility::vector1 < utility::vector1< bool > >	conserved_mutations_

utility::vector1< core::Size >	positions_

core::select::residue_selector::ResidueSelectorCOP	residue_selector_

bool	include_native_aa_

std::string	pose_sequence_

std::string	data_source_

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 TaskOperation that sets the allowed amino acids of designable residues to the native amino acid's conservative mutations.

Default is to act on all designable residues. Use limit_to_positions to limit this. Default is to replace the allowed_aas with these conservative mutations. Data is loaded from database/sequence/resinfo.db.

Constructor & Destructor Documentation

protocols::task_operations::ConservativeDesignOperation::ConservativeDesignOperation ( )

Default constructor. Will use native aa from apply (Changes each pack if tf is passed).

References set_data_source(), and set_defaults().

protocols::task_operations::ConservativeDesignOperation::ConservativeDesignOperation ( std::string data_source )

Constructor with setting of data source.

References set_data_source(), and set_defaults().

protocols::task_operations::ConservativeDesignOperation::~ConservativeDesignOperation ( )

overridedefault

protocols::task_operations::ConservativeDesignOperation::ConservativeDesignOperation ( ConservativeDesignOperation const & src )

References init_for_equal_operator_and_copy_constructor().

Member Function Documentation

void protocols::task_operations::ConservativeDesignOperation::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 core::chemical::aa_from_oneletter_code(), conserved_mutations_, include_native_aa_, core::pack::task::PackerTask::nonconst_residue_task(), pose_sequence_, positions_, residue_selector_, core::pack::task::ResidueLevelTask::restrict_absent_canonical_aas(), core::pose::Pose::sequence(), core::pose::Pose::size(), and skip_resid().

void protocols::task_operations::ConservativeDesignOperation::clear_positions ( )

Clear any set positions.

References positions_.

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

overridevirtual

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

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

void protocols::task_operations::ConservativeDesignOperation::include_native_aa ( bool setting )

inline

Include native amino acid in the allowed_aas list. Default true.

References include_native_aa_.

Referenced by parse_tag().

void protocols::task_operations::ConservativeDesignOperation::include_residue ( core::Size resnum )

References positions_.

void protocols::task_operations::ConservativeDesignOperation::init_for_equal_operator_and_copy_constructor	(	ConservativeDesignOperation &	lhs,
		ConservativeDesignOperation const &	rhs
	)

private

References conserved_mutations_, data_source_, include_native_aa_, pose_sequence_, and positions_.

Referenced by ConservativeDesignOperation(), and operator=().

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

inlinestatic

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

void protocols::task_operations::ConservativeDesignOperation::limit_to_positions ( utility::vector1< core::Size > const & positions )

Limit to a subset of residue positions, already set to designable.

References positions_.

void protocols::task_operations::ConservativeDesignOperation::load_data_from_db ( )

private

References core::chemical::aa_from_oneletter_code(), conserved_mutations_, data_source_, and protocols::task_operations::TR().

Referenced by set_data_source().

ConservativeDesignOperation & protocols::task_operations::ConservativeDesignOperation::operator= ( ConservativeDesignOperation const & rhs )

References init_for_equal_operator_and_copy_constructor().

void protocols::task_operations::ConservativeDesignOperation::parse_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	datamap
	)

overridevirtual

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

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

References protocols::pack_daemon::error_message, core::select::residue_selector::get_residue_selector(), include_native_aa(), residue_selector_, and set_data_source().

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

static

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

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

void protocols::task_operations::ConservativeDesignOperation::set_data_source ( std::string const & data_source )

Set the source of the data used to define what is conservative. Options are: chothia_76 and the Blosum matrices from 30 to 100; designated as blosum30, 62, etc. Default is blosum62. The higher the number, the more conservative the set of mutations (numbers are sequence identity cutoffs)

References data_source_, and load_data_from_db().

Referenced by ConservativeDesignOperation(), and parse_tag().

void protocols::task_operations::ConservativeDesignOperation::set_defaults ( )

private

References conserved_mutations_, data_source_, include_native_aa_, and pose_sequence_.

Referenced by ConservativeDesignOperation().

void protocols::task_operations::ConservativeDesignOperation::set_native_sequence ( std::string const & seq )

inline

References pose_sequence_.

Referenced by use_pose_sequence_as_native().

bool protocols::task_operations::ConservativeDesignOperation::skip_resid	(	core::Size	resid,
		core::pack::task::PackerTask const &	task,
		std::string const &	seq
	)		const

protected

References core::pack::task::PackerTask::being_designed(), core::chemical::oneletter_code_specifies_aa(), positions_, core::id::to_string(), and protocols::task_operations::TR().

Referenced by apply().

void protocols::task_operations::ConservativeDesignOperation::use_pose_sequence_as_native ( core::pose::Pose const & pose )

Will use native residues from the this pose to determine conserved aa.

References core::pose::Pose::sequence(), and set_native_sequence().

Member Data Documentation

utility::vector1< utility::vector1<bool> > protocols::task_operations::ConservativeDesignOperation::conserved_mutations_

private

Referenced by apply(), init_for_equal_operator_and_copy_constructor(), load_data_from_db(), and set_defaults().

std::string protocols::task_operations::ConservativeDesignOperation::data_source_

private

Referenced by init_for_equal_operator_and_copy_constructor(), load_data_from_db(), set_data_source(), and set_defaults().

bool protocols::task_operations::ConservativeDesignOperation::include_native_aa_

private

Referenced by apply(), include_native_aa(), init_for_equal_operator_and_copy_constructor(), and set_defaults().

std::string protocols::task_operations::ConservativeDesignOperation::pose_sequence_

private

Referenced by apply(), init_for_equal_operator_and_copy_constructor(), set_defaults(), and set_native_sequence().

utility::vector1< core::Size > protocols::task_operations::ConservativeDesignOperation::positions_

private

Referenced by apply(), clear_positions(), include_residue(), init_for_equal_operator_and_copy_constructor(), limit_to_positions(), and skip_resid().

core::select::residue_selector::ResidueSelectorCOP protocols::task_operations::ConservativeDesignOperation::residue_selector_

private

Referenced by apply(), and parse_tag().

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

src/protocols/task_operations/ConservativeDesignOperation.hh
src/protocols/task_operations/ConservativeDesignOperation.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation