protocols::loophash::BackboneDB Class Reference

#include <BackboneDB.hh>

Public Member Functions
	BackboneDB ()
core::Real	angle (core::Size index, core::Size offset) const
void	add_pose (const core::pose::Pose &pose, core::Size nres, core::Size &offset, protocols::frag_picker::VallChunkOP chunk=nullptr)
void	get_protein (core::Size index, BBData &protein) const
void	get_extra_data (core::Size index, BBExtraData &extra) const
void	add_protein (BBData new_protein)
void	add_extra_data (BBExtraData extra)
void	get_backbone_segment (const core::Size index, const core::Size offset, const core::Size len, BackboneSegment &bs) const
core::Size	size () const
core::Size	extra_size () const
void	write_db (std::string filename) const
void	read_db (std::string filename, bool load_extra, core::Size num_partitions, core::Size assigned_num, std::pair< core::Size, core::Size > &loop_range, std::map< core::Size, bool > &homolog_index)
void	read_db (std::string filename, bool load_extra)
void	read_legacydb (std::string filename)
void	read_homologs ()
core::Size	get_mem_foot_print () const

Private Attributes
std::vector< BBData >	data_
std::vector< BBExtraData >	extra_data_
bool	extra_
std::map< std::string, bool >	homologs_
	Homology map, contains all homologs. More...

Constructor & Destructor Documentation

BackboneDB()

protocols::loophash::BackboneDB::BackboneDB ( )

inline

References extra_.

Member Function Documentation

add_extra_data()

void protocols::loophash::BackboneDB::add_extra_data

(

BBExtraData

extra

)

Referenced by protocols::loophash::LoopHashLibrary::merge_bbdb().

add_pose()

void protocols::loophash::BackboneDB::add_pose	(	const core::pose::Pose &	pose,
		core::Size	nres,
		core::Size &	offset,
		protocols::frag_picker::VallChunkOP	chunk = nullptr
	)

References protocols::loophash::BBData::angles, protocols::loophash::BBData::extra_key, core::pose::get_score_line_string(), core::pose::Pose::omega(), protocols::loophash::BBExtraData::pdb_id, core::pose::Pose::phi(), core::pose::Pose::psi(), protocols::loophash::RealAngleToShort(), core::pose::Pose::sequence(), and protocols::loophash::BBExtraData::sequence.

Referenced by protocols::loophash::LoopHashLibrary::extract_data_from_pose(), protocols::loophash::LoopHashLibrary::test_loop_sample(), and protocols::loophash::LoopHashLibrary::test_saving_library().

add_protein()

void protocols::loophash::BackboneDB::add_protein

(

BBData

new_protein

)

Referenced by protocols::loophash::LoopHashLibrary::merge_bbdb().

angle()

core::Real protocols::loophash::BackboneDB::angle	(	core::Size	index,
		core::Size	offset
	)		const

References core::scoring::packstat::old::angles, and protocols::loophash::ShortToRealAngle().

extra_size()

core::Size protocols::loophash::BackboneDB::extra_size ( ) const

inline

References extra_data_.

Referenced by protocols::loophash::LoopHashLibrary::merge_bbdb().

get_backbone_segment()

void protocols::loophash::BackboneDB::get_backbone_segment	(	const core::Size	index,
		const core::Size	offset,
		const core::Size	len,
		BackboneSegment &	bs
	)		const

References core::scoring::packstat::old::angles, core::scoring::omega, and protocols::loophash::ShortToRealAngle().

Referenced by protocols::loophash::LoopHashLibrary::apply_random(), protocols::sic_dock::dump_loophash_linkers(), protocols::loophash::LoopHashLibrary::get_all(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::loophash::LoopHashLibrary::merge(), protocols::loophash::LoopHashLibrary::test_loop_sample(), and protocols::loophash::LoopHashLibrary::test_saving_library().

get_extra_data()

void protocols::loophash::BackboneDB::get_extra_data	(	core::Size	index,
		BBExtraData &	extra
	)		const

Referenced by protocols::loophash::LoopHashLibrary::merge_bbdb().

get_mem_foot_print()

core::Size protocols::loophash::BackboneDB::get_mem_foot_print ( ) const

inline

References data_.

Referenced by protocols::loophash::LoopHashLibrary::mem_foot_print().

get_protein()

void protocols::loophash::BackboneDB::get_protein	(	core::Size	index,
		BBData &	protein
	)		const

References protocols::loophash::BBData::angles, and protocols::loophash::BBData::extra_key.

Referenced by protocols::loophash::LoopHashLibrary::merge_bbdb().

read_db() [1/2]

void protocols::loophash::BackboneDB::read_db ( std::string  filename, bool  load_extra  )

inline

References protocols::abinitio::filename(), protocols::sic_dock::range(), and read_db().

read_db() [2/2]

void protocols::loophash::BackboneDB::read_db	(	std::string	filename,
		bool	load_extra,
		core::Size	num_partitions,
		core::Size	assigned_num,
		std::pair< core::Size, core::Size > &	loop_range,
		std::map< core::Size, bool > &	homolog_index
	)

References protocols::loophash::BBData::angles, core::sequence::end, protocols::loophash::BBData::extra_key, protocols::abinitio::filename(), protocols::loophash::BBExtraData::pdb_id, protocols::loophash::BBExtraData::rotamer_id, protocols::loophash::BBExtraData::sequence, and core::pose::TR().

Referenced by protocols::loophash::LoopHashLibrary::load_db(), protocols::loophash::LoopHashLibrary::load_mergeddb(), and read_db().

read_homologs()

void protocols::loophash::BackboneDB::read_homologs

(

)

References protocols::sparta::split(), and core::pose::TR().

read_legacydb()

void protocols::loophash::BackboneDB::read_legacydb

(

std::string

filename

)

References protocols::abinitio::filename(), and core::pose::TR().

size()

core::Size protocols::loophash::BackboneDB::size ( ) const

inline

References data_.

Referenced by protocols::loophash::LoopHashLibrary::merge_bbdb().

write_db()

void protocols::loophash::BackboneDB::write_db

(

std::string

filename

)

const

References protocols::abinitio::filename().

Referenced by protocols::loophash::LoopHashLibrary::save_db().

Member Data Documentation

data_

std::vector< BBData > protocols::loophash::BackboneDB::data_

private

Referenced by get_mem_foot_print(), and size().

extra_

bool protocols::loophash::BackboneDB::extra_

private

Referenced by BackboneDB().

extra_data_

std::vector< BBExtraData > protocols::loophash::BackboneDB::extra_data_

private

Referenced by extra_size().

homologs_

std::map< std::string, bool > protocols::loophash::BackboneDB::homologs_

private

Homology map, contains all homologs.

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

• src/protocols/loophash/BackboneDB.hh
• src/protocols/loophash/BackboneDB.cc