Rosetta: protocols::splice::SampleRotamersFromPDB Class Reference

Rosetta

#include <SampleRotamersFromPDB.hh>

Inheritance diagram for protocols::splice::SampleRotamersFromPDB:

Inheritance graph

[legend]

Public Types
typedef core::Real	Real

typedef core::pose::Pose	Pose

typedef core::pack::task::PackerTask	PackerTask

typedef core::pack::task::operation::TaskOperation	TaskOperation

typedef core::pack::task::operation::TaskOperationOP	TaskOperationOP

typedef TaskOperation	parent

typedef utility::tag::TagCOP	TagCOP

Public Types inherited from core::pack::task::operation::TaskOperation
typedef utility::tag::TagCOP	TagCOP

typedef basic::datacache::DataMap	DataMap

typedef pose::Pose	Pose

Public Member Functions
	SampleRotamersFromPDB ()
	default constructor More...

	~SampleRotamersFromPDB () override
	destructor More...

TaskOperationOP	clone () const override
	make clone More...

void	apply (Pose const &pose, PackerTask &task) const override
	apply More...

utility::vector1< core::Size >	SampleAtAlignedpositions () const

void	SampleAtAlignedpositions (utility::vector1< core::Size > const s)

void	parse_tag (TagCOP tag, DataMap &) override
	Used to parse an xml-like tag to load parameters and properties. More...

rot_matrix	combine_rot_dbs (core::pose::Pose const &pose) const

void	concatenate_rot_matrix (rot_matrix &a, rot_matrix const &b) const

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)

static std::string	keyname ()

Private Attributes
bool	add_rotamer_

utility::vector1< core::Size >	SampleAtAlignedpositions_

bool	debug_

bool	ccd_

std::string	db_fname_

std::map< std::string, RotLibdbOP >	ROTdb_segments_

utility::vector1< std::string >	segment_names_ordered_

Member Typedef Documentation

◆ PackerTask

typedef core::pack::task::PackerTask protocols::splice::SampleRotamersFromPDB::PackerTask

◆ parent

typedef TaskOperation protocols::splice::SampleRotamersFromPDB::parent

◆ Pose

typedef core::pose::Pose protocols::splice::SampleRotamersFromPDB::Pose

◆ Real

typedef core::Real protocols::splice::SampleRotamersFromPDB::Real

◆ TagCOP

typedef utility::tag::TagCOP protocols::splice::SampleRotamersFromPDB::TagCOP

◆ TaskOperation

typedef core::pack::task::operation::TaskOperation protocols::splice::SampleRotamersFromPDB::TaskOperation

◆ TaskOperationOP

typedef core::pack::task::operation::TaskOperationOP protocols::splice::SampleRotamersFromPDB::TaskOperationOP

Constructor & Destructor Documentation

◆ SampleRotamersFromPDB()

protocols::splice::SampleRotamersFromPDB::SampleRotamersFromPDB ( )

default constructor

◆ ~SampleRotamersFromPDB()

protocols::splice::SampleRotamersFromPDB::~SampleRotamersFromPDB ( )

override

destructor

Member Function Documentation

◆ apply()

void protocols::splice::SampleRotamersFromPDB::apply	(	Pose const &	pose,
		PackerTask &	task
	)		const

overridevirtual

apply

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

References add_rotamer_, core::pack::task::PackerTask::append_rotamerset_operation(), ccd_, combine_rot_dbs(), db_fname_, debug_, SampleAtAlignedpositions(), and segment_names_ordered_.

◆ clone()

core::pack::task::operation::TaskOperationOP protocols::splice::SampleRotamersFromPDB::clone ( ) const

overridevirtual

make clone

clone

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

◆ combine_rot_dbs()

rot_matrix protocols::splice::SampleRotamersFromPDB::combine_rot_dbs ( core::pose::Pose const & pose ) const

References core::conformation::Conformation::chain_end(), concatenate_rot_matrix(), core::pose::Pose::conformation(), protocols::splice::RotLibdb::fill_rotamer_matrix_from_db_file(), protocols::splice::load_pdb_segments_from_pose_comments(), ROTdb_segments_, segment_names_ordered_, and protocols::splice::TR().

Referenced by apply().

◆ concatenate_rot_matrix()

void protocols::splice::SampleRotamersFromPDB::concatenate_rot_matrix	(	rot_matrix &	a,
		rot_matrix const &	b
	)		const

References core::pose::motif::a(), protocols::match::upstream::b, and protocols::splice::TR().

Referenced by combine_rot_dbs().

◆ keyname()

static std::string protocols::splice::SampleRotamersFromPDB::keyname ( )

inlinestatic

Referenced by protocols::splice::SampleRotamersFromPDBCreator::keyname(), and provide_xml_schema().

◆ parse_tag()

void protocols::splice::SampleRotamersFromPDB::parse_tag	(	TagCOP	tag,
		DataMap &
	)

overridevirtual

Used to parse an xml-like tag to load parameters and properties.

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

References add_rotamer_, ccd_, db_fname_, debug_, protocols::jd2::get_current_jobs_starting_pose(), ROTdb_segments_, SampleAtAlignedpositions(), SampleAtAlignedpositions_, segment_names_ordered_, and protocols::splice::TR().

◆ provide_xml_schema()

void protocols::splice::SampleRotamersFromPDB::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::pack::task::operation::complex_type_name_for_task_op(), keyname(), protocols::splice::Srfp_complex_type_name_for_subsubtag(), and protocols::splice::Srfp_complex_type_name_for_subtag().

Referenced by protocols::splice::SampleRotamersFromPDBCreator::provide_xml_schema().

◆ SampleAtAlignedpositions() [1/2]

utility::vector1< core::Size > protocols::splice::SampleRotamersFromPDB::SampleAtAlignedpositions ( ) const

inline

References SampleAtAlignedpositions_.

Referenced by apply(), and parse_tag().

◆ SampleAtAlignedpositions() [2/2]

void protocols::splice::SampleRotamersFromPDB::SampleAtAlignedpositions ( utility::vector1< core::Size > const s )

inline

References SampleAtAlignedpositions_.

Member Data Documentation

◆ add_rotamer_

bool protocols::splice::SampleRotamersFromPDB::add_rotamer_

private

Referenced by apply(), and parse_tag().

◆ ccd_

bool protocols::splice::SampleRotamersFromPDB::ccd_

private

Referenced by apply(), and parse_tag().

◆ db_fname_

std::string protocols::splice::SampleRotamersFromPDB::db_fname_

private

Referenced by apply(), and parse_tag().

◆ debug_

bool protocols::splice::SampleRotamersFromPDB::debug_

private

Referenced by apply(), and parse_tag().

◆ ROTdb_segments_

std::map< std::string, RotLibdbOP > protocols::splice::SampleRotamersFromPDB::ROTdb_segments_

private

Referenced by combine_rot_dbs(), and parse_tag().

◆ SampleAtAlignedpositions_

utility::vector1< core::Size > protocols::splice::SampleRotamersFromPDB::SampleAtAlignedpositions_

private

Referenced by parse_tag(), and SampleAtAlignedpositions().

◆ segment_names_ordered_

utility::vector1< std::string > protocols::splice::SampleRotamersFromPDB::segment_names_ordered_

private

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

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

src/protocols/splice/SampleRotamersFromPDB.hh
src/protocols/splice/SampleRotamersFromPDB.cc