core::pack::task::operation::ClashBasedRepackShell Class Reference

Create a shell of residues that can repack around a smaller group of residues being repacked or designed. More...

#include <ClashBasedRepackShell.hh>

Inheritance diagram for core::pack::task::operation::ClashBasedRepackShell:

Public Member Functions
	ClashBasedRepackShell ()
	Default constructor. More...
	ClashBasedRepackShell (ClashBasedRepackShell const &)=default
	Default copy constructor. More...
	~ClashBasedRepackShell () override=default
	Default destructor. More...
TaskOperationOP	clone () const override
	Return a shallow copy of this object. More...
void	apply (Pose const &pose, PackerTask &task) const override
	apply operations to PackerTask More...
void	parse_tag (utility::tag::TagCOP, basic::datacache::DataMap &) override
	Initialize from an XML tag. More...
core::pack::task::residue_selector::ClashBasedShellSelectorOP	selector () const
	Get the ResidueSelector used to define the repack shell. More...
void	selector (core::pack::task::residue_selector::ClashBasedShellSelectorOP)
	Set the ResidueSelector used to define the repack shell. 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)
	Define the expected XML options. More...
static std::string	keyname ()
	Return "ClashBasedRepackShell". More...

Private Attributes
core::pack::task::residue_selector::ClashBasedShellSelectorOP	shell_selector_ = nullptr

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

Create a shell of residues that can repack around a smaller group of residues being repacked or designed.

More specifically, this task operation disables repacking for (i.e. freezes) any position that isn't part of the aforementioned group or its shell. The most common use-case is to define a set of positions that you're interested in designing (i.e. with a resfile), and limit the rest of the protein to repacking (e.g. NATAA). Then you can apply the ClashBasedRepackShell to limit the repacking to only the positions that really interact with the design positions. This keeps the simulations efficient and prevents the final scores from being affected by random changes in packing far away from the region being designed.

This task operation is a very thin wrapper around ClashBasedShellSelector. You can access and configure the selector in question via the selector() method.

Constructor & Destructor Documentation

core::pack::task::operation::ClashBasedRepackShell::ClashBasedRepackShell

(

)

Default constructor.

core::pack::task::operation::ClashBasedRepackShell::ClashBasedRepackShell ( ClashBasedRepackShell const &  )

default

Default copy constructor.

core::pack::task::operation::ClashBasedRepackShell::~ClashBasedRepackShell ( )

overridedefault

Default destructor.

Member Function Documentation

void core::pack::task::operation::ClashBasedRepackShell::apply ( Pose const &  pose, PackerTask &  task  ) const

overridevirtual

apply operations to PackerTask

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

References core::pack::task::PackerTask::nonconst_residue_task(), core::pack::task::ResidueLevelTask::prevent_repacking(), shell_selector_, and core::pose::Pose::size().

TaskOperationOP core::pack::task::operation::ClashBasedRepackShell::clone ( ) const

overridevirtual

Return a shallow copy of this object.

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

string core::pack::task::operation::ClashBasedRepackShell::keyname ( )

static

Return "ClashBasedRepackShell".

Referenced by core::pack::task::operation::ClashBasedRepackShellCreator::keyname(), and provide_xml_schema().

void core::pack::task::operation::ClashBasedRepackShell::parse_tag ( utility::tag::TagCOP  tag, basic::datacache::DataMap &  datamap  )

overridevirtual

Initialize from an XML tag.

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

References shell_selector_.

void core::pack::task::operation::ClashBasedRepackShell::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

Define the expected XML options.

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

Referenced by core::pack::task::operation::ClashBasedRepackShellCreator::provide_xml_schema().

ClashBasedShellSelectorOP core::pack::task::operation::ClashBasedRepackShell::selector

(

)

const

Get the ResidueSelector used to define the repack shell.

References shell_selector_.

void core::pack::task::operation::ClashBasedRepackShell::selector

(

core::pack::task::residue_selector::ClashBasedShellSelectorOP

)

Set the ResidueSelector used to define the repack shell.

Member Data Documentation

core::pack::task::residue_selector::ClashBasedShellSelectorOP core::pack::task::operation::ClashBasedRepackShell::shell_selector_ = nullptr

private

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

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

• src/core/pack/task/operation/ClashBasedRepackShell.hh
• src/core/pack/task/operation/ClashBasedRepackShell.cc