protocols::toolbox::task_operations::DesignAroundOperation Class Reference

#include <DesignAroundOperation.hh>

Inheritance diagram for protocols::toolbox::task_operations::DesignAroundOperation:

Collaboration diagram for protocols::toolbox::task_operations::DesignAroundOperation:

Public Types
typedef RestrictOperationsBase	parent
Public Types inherited from protocols::toolbox::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::TagPtr	TagPtr
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)
virtual	~DesignAroundOperation ()
virtual TaskOperationOP	clone () const
	Create another task operation of the type matching the most-derived version of the class. More...
virtual void	apply (core::pose::Pose const &, core::pack::task::PackerTask &) const
	restricts to repacking all residues outside of design_shell_ around each residue More...
virtual void	parse_tag (TagPtr)
	Used to parse an xml-like tag to load parameters and properties. More...
virtual void	parse_def (utility::lua::LuaObject const &def)
void	repack_shell (core::Real const repack_shell)
core::Real	repack_shell () const
void	allow_design (bool const a)
bool	allow_design () const
Public Member Functions inherited from protocols::toolbox::task_operations::RestrictOperationsBase
	RestrictOperationsBase ()
virtual	~RestrictOperationsBase ()
Public Member Functions inherited from core::pack::task::operation::TaskOperation
virtual	~TaskOperation ()

Private Attributes
core::Real	design_shell_
core::Real	repack_shell_
bool	allow_design_
std::set< core::Size >	resid_
std::string	string_resnums_

Additional Inherited Members
Protected Member Functions inherited from protocols::toolbox::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...

Detailed Description

this class is a TaskOperation to prevent repacking of residues not near an interface.

Member Typedef Documentation

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

Constructor & Destructor Documentation

protocols::toolbox::task_operations::DesignAroundOperation::DesignAroundOperation

(

)

References resid_.

Referenced by clone().

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

virtual

Member Function Documentation

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

inline

References allow_design_.

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

inline

References allow_design_.

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

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

virtual

restricts to repacking all residues outside of design_shell_ around each residue

Implements protocols::toolbox::task_operations::RestrictOperationsBase.

References allow_design(), 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(), string_resnums_, core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

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

virtual

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

Implements protocols::toolbox::task_operations::RestrictOperationsBase.

References DesignAroundOperation().

void protocols::toolbox::task_operations::DesignAroundOperation::design_shell

(

core::Real const

radius)

References design_shell_, repack_shell(), and repack_shell_.

Referenced by protocols::simple_moves::ForceDisulfidesMover::apply(), protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::apply(), protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation::apply(), protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::apply(), protocols::protein_interface_design::movers::Splice::apply(), protocols::simple_filters::RotamerBoltzmannWeight::compute_Boltzmann_weight(), protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator::init_task(), and protocols::protein_interface_design::filters::FilterScanFilter::single_substitution().

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

inline

References design_shell_.

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

void protocols::toolbox::task_operations::DesignAroundOperation::include_residue

(

core::Size const

resid)

References resid_.

Referenced by protocols::protein_interface_design::movers::Splice::apply().

void protocols::toolbox::task_operations::DesignAroundOperation::parse_def ( utility::lua::LuaObject const &  def)

virtual

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

References allow_design(), design_shell(), core::sequence::end, repack_shell(), string_resnums_, and protocols::TR().

void protocols::toolbox::task_operations::DesignAroundOperation::parse_tag ( TagPtr  tag)

virtual

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(), string_resnums_, and protocols::TR().

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

inline

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

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

inline

References repack_shell_.

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

Member Data Documentation

bool protocols::toolbox::task_operations::DesignAroundOperation::allow_design_

private

Referenced by allow_design().

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

private

Referenced by design_shell(), and repack_shell().

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

private

Referenced by design_shell(), and repack_shell().

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

private

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

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

private

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

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

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