#include <ConsensusLoopDesignOperation.hh>

Inheritance diagram for protocols::denovo_design::task_operations::ConsensusLoopDesignOperation:

Public Types
typedef std::string	AAs

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
	ConsensusLoopDesignOperation ()
	default constructor More...

	~ConsensusLoopDesignOperation () override
	destructor More...

core::pack::task::operation::TaskOperationOP	clone () const override
	make clone More...

void	apply (core::pose::Pose const &pose, core::pack::task::PackerTask &task) const override
	apply More...

virtual std::string	get_name () const
	Returns the name of the class. More...

void	set_secstruct (std::string const &secstruct)
	Sets the secondary structure to be used for selection of loops. If a residue selector is set, this is ignored. More...

void	set_residue_selector (core::select::residue_selector::ResidueSelector const &selector_val)
	Sets residue selector. If set, only selected residues will be operated upon. (default = select by secondary structure type L) More...

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

AAFrequencies const &	aa_frequencies (LoopInfo const &info, core::Size const resid) const

AAs	forbidden_aas (AAFrequencies const &frequencies) const

void	disallow_aas (core::pack::task::PackerTask &task, LoopInfo const &info) const

LoopInfoVec	get_loop_info (core::pose::Pose const &pose) const

LoopInfoVec	loop_info_from_subset (core::pose::Pose const &pose, std::string const &ss, core::select::residue_selector::ResidueSubset const &subset) const

void	set_include_adjacent_residues (bool const include_res)
	if true, residues adjacent to loops will be restricted. Otherwise, just the loop. (default=false) More...

void	set_secstruct_from_blueprint (std::string const &bp_file)
	Reads/parses a blueprint file and calls set_secstruct() on the resulting secondary structure. Length of blueprint file must match the length of the input pose. More...

void	set_enrichment_threshold (core::Real const threshold)

void	set_use_dssp (bool const use_dssp)

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	class_name ()

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

Private Member Functions
std::string	get_secstruct (core::pose::Pose const &pose) const
	Gets secondary structure to be used for determining what is surrounding the loops. More...

core::select::residue_selector::ResidueSelectorCOP	residue_selector (std::string const &secstruct) const
	Returns a residue selector to be used to choose loops. More...

AAs	compute_aas_after_disallowing (AAs const &aas, core::pack::task::ResidueLevelTask const &task) const

AAs	compute_best_allowed_aas (AAFrequencies const &aa_freqs, core::pack::task::ResidueLevelTask const &task) const

Private Attributes
std::string	secstruct_

bool	include_adjacent_residues_

bool	use_dssp_

core::Real	enrichment_threshold_

core::select::residue_selector::ResidueSelectorCOP	selector_

Member Typedef Documentation

typedef std::string protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::AAs

Constructor & Destructor Documentation

protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::ConsensusLoopDesignOperation ( )

default constructor

protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::~ConsensusLoopDesignOperation ( )

overridedefault

destructor

Member Function Documentation

AAFrequencies const & protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::aa_frequencies	(	LoopInfo const &	info,
		core::Size const	resid
	)		const

References protocols::denovo_design::task_operations::LoopInfo::abego, protocols::denovo_design::task_operations::ConsensusLoopDatabase::frequencies(), and protocols::denovo_design::task_operations::LoopInfo::ss_around.

Referenced by disallow_aas().

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

overridevirtual

apply

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

References disallow_aas(), get_loop_info(), core::pack::task::PackerTask::show(), and protocols::TR().

std::string protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::class_name ( )

static

Referenced by get_loop_info(), get_name(), protocols::denovo_design::task_operations::ConsensusLoopDesignOperationCreator::keyname(), and provide_xml_schema().

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

overridevirtual

make clone

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

ConsensusLoopDesignOperation::AAs protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::compute_aas_after_disallowing	(	AAs const &	aas,
		core::pack::task::ResidueLevelTask const &	task
	)		const

private

References core::pack::task::ResidueLevelTask::allowed_residue_types_begin(), core::pack::task::ResidueLevelTask::allowed_residue_types_end(), and protocols::hybridization::t.

Referenced by disallow_aas().

ConsensusLoopDesignOperation::AAs protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::compute_best_allowed_aas	(	AAFrequencies const &	aa_freqs,
		core::pack::task::ResidueLevelTask const &	task
	)		const

private

References core::pack::task::ResidueLevelTask::allowed_residue_types_begin(), core::pack::task::ResidueLevelTask::allowed_residue_types_end(), protocols::denovo_design::task_operations::AAFrequencies::frequency(), protocols::denovo_design::task_operations::AAFrequencies::has_frequency(), protocols::hybridization::t, and protocols::TR().

Referenced by disallow_aas().

void protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::disallow_aas	(	core::pack::task::PackerTask &	task,
		LoopInfo const &	info
	)		const

References aa_frequencies(), protocols::denovo_design::task_operations::LoopInfo::abego, compute_aas_after_disallowing(), compute_best_allowed_aas(), enrichment_threshold_, forbidden_aas(), include_adjacent_residues_, protocols::denovo_design::task_operations::make_aa_bitmap_from_allowed_aas(), protocols::denovo_design::task_operations::make_aa_bitmap_from_forbidden_aas(), core::pack::task::PackerTask::nonconst_residue_task(), core::pack::task::PackerTask::residue_task(), core::pack::task::ResidueLevelTask::restrict_absent_canonical_aas(), protocols::denovo_design::task_operations::LoopInfo::ss_around, protocols::loops::start, protocols::denovo_design::task_operations::LoopInfo::startres, protocols::loops::stop, core::pack::task::PackerTask::total_residue(), and protocols::TR().

Referenced by apply().

ConsensusLoopDesignOperation::AAs protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::forbidden_aas ( AAFrequencies const & frequencies ) const

References enrichment_threshold_.

Referenced by disallow_aas().

LoopInfoVec protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::get_loop_info ( core::pose::Pose const & pose ) const

References class_name(), get_secstruct(), loop_info_from_subset(), residue_selector(), and core::pose::Pose::size().

Referenced by apply().

std::string protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::get_name ( ) const

virtual

Returns the name of the class.

References class_name().

std::string protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::get_secstruct ( core::pose::Pose const & pose ) const

private

Gets secondary structure to be used for determining what is surrounding the loops.

Parameters

[in] pose input pose

Returns

Secondary structure string according to the following rules:

If secstruct_ is set, return that.
If use_dssp_ is set, return string computed from DSSP.
return pose.secstruct()

References protocols::simple_filters::dssp(), core::scoring::dssp::Dssp::get_dssp_secstruct(), core::pose::Pose::secstruct(), secstruct_, protocols::TR(), and use_dssp_.

Referenced by get_loop_info().

LoopInfoVec protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::loop_info_from_subset	(	core::pose::Pose const &	pose,
		std::string const &	ss,
		core::select::residue_selector::ResidueSubset const &	subset
	)		const

References protocols::denovo_design::task_operations::LoopInfo::abego, core::scoring::abego, protocols::denovo_design::task_operations::SurroundingSS::after, protocols::denovo_design::task_operations::SurroundingSS::before, core::sequence::get_abego(), protocols::denovo_design::task_operations::LoopInfo::ss_around, and protocols::denovo_design::task_operations::LoopInfo::startres.

Referenced by get_loop_info().

void protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::parse_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &
	)

overridevirtual

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

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

References enrichment_threshold_, include_adjacent_residues_, core::select::residue_selector::parse_residue_selector(), secstruct_, set_enrichment_threshold(), set_include_adjacent_residues(), set_residue_selector(), set_secstruct(), set_secstruct_from_blueprint(), set_use_dssp(), and use_dssp_.

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

static

References class_name(), and core::pack::task::operation::task_op_schema_w_attributes().

Referenced by protocols::denovo_design::task_operations::ConsensusLoopDesignOperationCreator::provide_xml_schema().

core::select::residue_selector::ResidueSelectorCOP protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::residue_selector ( std::string const & secstruct ) const

private

Returns a residue selector to be used to choose loops.

Parameters

[in] secstruct Secondary structure to be used, if default selector is used

If selector_ is provided, simply return that. If not, create a default secondary structure selector using the given secstruct

References selector_.

Referenced by get_loop_info().

void protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::set_enrichment_threshold ( core::Real const threshold )

References enrichment_threshold_.

Referenced by parse_tag().

void protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::set_include_adjacent_residues ( bool const include_res )

if true, residues adjacent to loops will be restricted. Otherwise, just the loop. (default=false)

References include_adjacent_residues_.

Referenced by parse_tag().

void protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::set_residue_selector ( core::select::residue_selector::ResidueSelector const & selector_val )

Sets residue selector. If set, only selected residues will be operated upon. (default = select by secondary structure type L)

Parameters

[in] selector_val Residue selector to be used. Cloned by this function and set as selector_

References core::select::residue_selector::ResidueSelector::clone(), and selector_.

Referenced by parse_tag().

void protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::set_secstruct ( std::string const & secstruct )

Sets the secondary structure to be used for selection of loops. If a residue selector is set, this is ignored.

Parameters

[in] secstruct Secondary structure to be used. Must match pose length

References secstruct_.

Referenced by parse_tag(), and set_secstruct_from_blueprint().

void protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::set_secstruct_from_blueprint ( std::string const & bp_file )

Reads/parses a blueprint file and calls set_secstruct() on the resulting secondary structure. Length of blueprint file must match the length of the input pose.

References protocols::parser::BluePrint::secstruct(), and set_secstruct().

Referenced by parse_tag().

void protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::set_use_dssp ( bool const use_dssp )

inline

References use_dssp_.

Referenced by parse_tag().

Member Data Documentation

core::Real protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::enrichment_threshold_

private

Referenced by disallow_aas(), forbidden_aas(), parse_tag(), and set_enrichment_threshold().

bool protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::include_adjacent_residues_

private

Referenced by disallow_aas(), parse_tag(), and set_include_adjacent_residues().

std::string protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::secstruct_

private

Referenced by get_secstruct(), parse_tag(), and set_secstruct().

core::select::residue_selector::ResidueSelectorCOP protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::selector_

private

Referenced by residue_selector(), and set_residue_selector().

bool protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::use_dssp_

private

Referenced by get_secstruct(), parse_tag(), and set_use_dssp().

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

src/protocols/denovo_design/task_operations/ConsensusLoopDesignOperation.hh
src/protocols/denovo_design/task_operations/ConsensusLoopDesignOperation.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation