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protocols::task_operations::pHVariantTaskOperation Class Reference

During repacking, allow interchangeability of protonated and deprotonated variants. More...

#include <pHVariantTaskOperation.hh>

Inheritance diagram for protocols::task_operations::pHVariantTaskOperation:
Inheritance graph
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Public Member Functions

 pHVariantTaskOperation ()
 
 pHVariantTaskOperation (pHVariantTaskOperation const &src)
 
 ~pHVariantTaskOperation () override
 
core::pack::task::operation::TaskOperationOP clone () const override
 Create another task operation of the type matching the most-derived version of the class. More...
 
void parse_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Configure from a RosettaScripts XML tag. More...
 
void apply (core::pose::Pose const &pose, core::pack::task::PackerTask &task) const override
 A TaskOp that enables sampling of protonation variants during repacking. The ionizable sidechains considered are ASP, GLU, LYS, TYR, and HIS. All other posiitons are restricted to repacking. The -pH_mode commandline option is still currently required to initially read the variants into the database. 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 Does this task_operation indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)?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 std::string keyname ()
 Return the name used to construct this TaskOperation from an XML file. More...
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 Describe the format of XML file used to initialize this TaskOperation. More...
 

Private Attributes

core::select::residue_selector::ResidueSelectorOP select_asp_
 
core::select::residue_selector::ResidueSelectorOP select_glu_
 
core::select::residue_selector::ResidueSelectorOP select_tyr_
 
core::select::residue_selector::ResidueSelectorOP select_lys_
 
core::select::residue_selector::ResidueSelectorOP select_his_
 

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

During repacking, allow interchangeability of protonated and deprotonated variants.

Constructor & Destructor Documentation

protocols::task_operations::pHVariantTaskOperation::pHVariantTaskOperation ( )

Referenced by clone().

protocols::task_operations::pHVariantTaskOperation::pHVariantTaskOperation ( pHVariantTaskOperation const &  src)
protocols::task_operations::pHVariantTaskOperation::~pHVariantTaskOperation ( )
override

Member Function Documentation

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

A TaskOp that enables sampling of protonation variants during repacking. The ionizable sidechains considered are ASP, GLU, LYS, TYR, and HIS. All other posiitons are restricted to repacking. The -pH_mode commandline option is still currently required to initially read the variants into the database.

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

References core::pack::task::PackerTask::nonconst_residue_task(), core::pack::task::ResidueLevelTask::restrict_restypes(), core::pack::task::ResidueLevelTask::restrict_to_repacking(), select_asp_, select_glu_, select_his_, select_lys_, select_tyr_, and core::pose::Pose::size().

TaskOperationOP protocols::task_operations::pHVariantTaskOperation::clone ( ) const
overridevirtual

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

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

References pHVariantTaskOperation().

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

Return the name used to construct this TaskOperation from an XML file.

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

void protocols::task_operations::pHVariantTaskOperation::parse_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &   
)
overridevirtual

Configure from a RosettaScripts XML tag.

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

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

Describe the format of XML file used to initialize this TaskOperation.

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

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

Member Data Documentation

core::select::residue_selector::ResidueSelectorOP protocols::task_operations::pHVariantTaskOperation::select_asp_
private

Referenced by apply().

core::select::residue_selector::ResidueSelectorOP protocols::task_operations::pHVariantTaskOperation::select_glu_
private

Referenced by apply().

core::select::residue_selector::ResidueSelectorOP protocols::task_operations::pHVariantTaskOperation::select_his_
private

Referenced by apply().

core::select::residue_selector::ResidueSelectorOP protocols::task_operations::pHVariantTaskOperation::select_lys_
private

Referenced by apply().

core::select::residue_selector::ResidueSelectorOP protocols::task_operations::pHVariantTaskOperation::select_tyr_
private

Referenced by apply().


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