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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:
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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 bool task_operation_provides_citation_info () const
 Does this task operation provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool task_operation_is_unpublished () const
 Does this task_operation indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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
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
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
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().


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