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:

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	Does this task_operation indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)?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().

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

• src/protocols/task_operations/pHVariantTaskOperation.hh
• src/protocols/task_operations/pHVariantTaskOperation.cc