#include <DesignAroundOperation.hh>

Inheritance diagram for protocols::task_operations::DesignAroundOperation:

[legend]

Public Types
typedef RestrictOperationsBase	parent

Public Types inherited from protocols::task_operations::RestrictOperationsBase
typedef core::pack::task::operation::TaskOperation	TaskOperation

typedef core::pack::task::operation::TaskOperationOP	TaskOperationOP

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
	DesignAroundOperation ()

void	design_shell (core::Real const radius)

core::Real	design_shell () const

void	include_residue (core::Size const resid)

	~DesignAroundOperation () override

TaskOperationOP	clone () const override
	Create another task operation of the type matching the most-derived version of the class. More...

void	apply (core::pose::Pose const &, core::pack::task::PackerTask &) const override
	restricts to repacking all residues outside of design_shell_ around each residue More...

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

void	repack_shell (core::Real const repack_shell)

core::Real	repack_shell () const

void	allow_design (bool const a)

bool	allow_design () const

void	resnums_allow_design (bool const a)

bool	resnums_allow_design () const

std::set< core::Size >	get_designable_residues () const

Public Member Functions inherited from protocols::task_operations::RestrictOperationsBase
	RestrictOperationsBase ()

	~RestrictOperationsBase () override

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 ()

Private Attributes
core::Real	design_shell_

core::Real	repack_shell_

bool	allow_design_

bool	resnums_allow_design_

std::set< core::Size >	resid_

std::string	string_resnums_

Additional Inherited Members
Protected Member Functions inherited from protocols::task_operations::RestrictOperationsBase
void	run_calculator (core::pose::Pose const &pose, std::string const &calculator, std::string const &calculation, utility::vector1_bool &residues) const
	this is the only real function - it takes a calculator name and calculation, and a PackerTask-compatible vector, and flips booleans in the vector according to the calculator More...

Member Typedef Documentation

◆ parent

typedef RestrictOperationsBase protocols::task_operations::DesignAroundOperation::parent

Constructor & Destructor Documentation

◆ DesignAroundOperation()

protocols::task_operations::DesignAroundOperation::DesignAroundOperation ( )

References resid_.

◆ ~DesignAroundOperation()

protocols::task_operations::DesignAroundOperation::~DesignAroundOperation ( )

overridedefault

Member Function Documentation

◆ allow_design() [1/2]

bool protocols::task_operations::DesignAroundOperation::allow_design ( ) const

inline

References allow_design_.

Referenced by apply(), and parse_tag().

◆ allow_design() [2/2]

void protocols::task_operations::DesignAroundOperation::allow_design ( bool const a )

inline

References core::pose::motif::a(), and allow_design_.

◆ apply()

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

overridevirtual

restricts to repacking all residues outside of design_shell_ around each residue

Implements protocols::task_operations::RestrictOperationsBase.

References allow_design(), core::pack::task::operation::OperateOnCertainResidues::apply(), design_shell(), core::kinematics::distance(), core::pose::get_resnum_list(), core::conformation::Residue::nbr_atom(), core::pack::task::operation::OperateOnCertainResidues::op(), repack_shell(), resid_, core::pose::Pose::residue(), core::pack::task::operation::OperateOnCertainResidues::residue_indices(), resnums_allow_design(), core::pose::Pose::size(), string_resnums_, and core::conformation::Residue::xyz().

Referenced by protocols::splice::DesignInterfacesOperation::apply(), protocols::splice::FindEndpointsOperation::apply(), protocols::task_operations::ProteinInterfaceDesignOperation::apply(), and protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::apply().

◆ clone()

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

overridevirtual

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

Implements protocols::task_operations::RestrictOperationsBase.

◆ design_shell() [1/2]

core::Real protocols::task_operations::DesignAroundOperation::design_shell ( ) const

inline

References design_shell_.

Referenced by apply(), parse_tag(), and repack_shell().

◆ design_shell() [2/2]

void protocols::task_operations::DesignAroundOperation::design_shell ( core::Real const radius )

References design_shell_, repack_shell(), and repack_shell_.

Referenced by protocols::splice::DesignInterfacesOperation::apply(), protocols::splice::FindEndpointsOperation::apply(), protocols::task_operations::ProteinInterfaceDesignOperation::apply(), and protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::apply().

◆ get_designable_residues()

std::set< core::Size > protocols::task_operations::DesignAroundOperation::get_designable_residues ( ) const

inline

References resid_.

◆ include_residue()

void protocols::task_operations::DesignAroundOperation::include_residue ( core::Size const resid )

References resid_.

Referenced by protocols::splice::DesignInterfacesOperation::apply(), protocols::splice::FindEndpointsOperation::apply(), protocols::task_operations::ProteinInterfaceDesignOperation::apply(), and protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::apply().

◆ keyname()

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

inlinestatic

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

◆ parse_tag()

void protocols::task_operations::DesignAroundOperation::parse_tag	(	TagCOP	tag,
		DataMap &
	)

overridevirtual

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

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

References allow_design(), design_shell(), repack_shell(), resnums_allow_design(), string_resnums_, and protocols::task_operations::TR().

◆ provide_xml_schema()

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

static

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

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

◆ repack_shell() [1/2]

core::Real protocols::task_operations::DesignAroundOperation::repack_shell ( ) const

inline

References repack_shell_.

Referenced by apply(), design_shell(), parse_tag(), and repack_shell().

◆ repack_shell() [2/2]

void protocols::task_operations::DesignAroundOperation::repack_shell ( core::Real const repack_shell )

inline

References design_shell(), design_shell_, repack_shell(), and repack_shell_.

Referenced by protocols::splice::DesignInterfacesOperation::apply(), protocols::splice::FindEndpointsOperation::apply(), and protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::apply().

◆ resnums_allow_design() [1/2]

bool protocols::task_operations::DesignAroundOperation::resnums_allow_design ( ) const

inline

References resnums_allow_design_.

Referenced by apply(), and parse_tag().

◆ resnums_allow_design() [2/2]

void protocols::task_operations::DesignAroundOperation::resnums_allow_design ( bool const a )

inline

References core::pose::motif::a(), and resnums_allow_design_.

Member Data Documentation

◆ allow_design_

bool protocols::task_operations::DesignAroundOperation::allow_design_

private

Referenced by allow_design().

◆ design_shell_

core::Real protocols::task_operations::DesignAroundOperation::design_shell_

private

Referenced by design_shell(), and repack_shell().

◆ repack_shell_

core::Real protocols::task_operations::DesignAroundOperation::repack_shell_

private

Referenced by design_shell(), and repack_shell().

◆ resid_

std::set< core::Size > protocols::task_operations::DesignAroundOperation::resid_

private

Referenced by apply(), DesignAroundOperation(), get_designable_residues(), and include_residue().

◆ resnums_allow_design_

bool protocols::task_operations::DesignAroundOperation::resnums_allow_design_

private

Referenced by resnums_allow_design().

◆ string_resnums_

std::string protocols::task_operations::DesignAroundOperation::string_resnums_

private

Referenced by apply(), and parse_tag().

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

src/protocols/task_operations/DesignAroundOperation.hh
src/protocols/task_operations/DesignAroundOperation.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ parent

Constructor & Destructor Documentation

◆ DesignAroundOperation()

◆ ~DesignAroundOperation()

Member Function Documentation

◆ allow_design() [1/2]

◆ allow_design() [2/2]

◆ apply()

◆ clone()

◆ design_shell() [1/2]

◆ design_shell() [2/2]

◆ get_designable_residues()

◆ include_residue()

◆ keyname()

◆ parse_tag()

◆ provide_xml_schema()

◆ repack_shell() [1/2]

◆ repack_shell() [2/2]

◆ resnums_allow_design() [1/2]

◆ resnums_allow_design() [2/2]

Member Data Documentation

◆ allow_design_

◆ design_shell_

◆ repack_shell_

◆ resid_

◆ resnums_allow_design_

◆ string_resnums_