protocols::splice::SampleRotamersFromPDB Class Reference

#include <SampleRotamersFromPDB.hh>

Inheritance diagram for protocols::splice::SampleRotamersFromPDB:

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

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

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

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

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

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

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

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

Constructor & Destructor Documentation

protocols::splice::SampleRotamersFromPDB::SampleRotamersFromPDB

(

)

default constructor

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

override

destructor

Member Function Documentation

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_.

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

overridevirtual

make clone

clone

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

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().

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

References protocols::splice::TR().

Referenced by combine_rot_dbs().

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

inlinestatic

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

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().

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().

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

inline

References SampleAtAlignedpositions_.

Referenced by apply(), and parse_tag().

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

inline

References SampleAtAlignedpositions_.

Member Data Documentation

bool protocols::splice::SampleRotamersFromPDB::add_rotamer_

private

Referenced by apply(), and parse_tag().

bool protocols::splice::SampleRotamersFromPDB::ccd_

private

Referenced by apply(), and parse_tag().

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

private

Referenced by apply(), and parse_tag().

bool protocols::splice::SampleRotamersFromPDB::debug_

private

Referenced by apply(), and parse_tag().

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

private

Referenced by combine_rot_dbs(), and parse_tag().

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

private

Referenced by parse_tag(), and SampleAtAlignedpositions().

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

private

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

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

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