protocols::abinitio::Templates Class Reference

#include <Templates.hh>

Public Types
typedef std::map< std::string, TemplateOP >	TemplateMap
typedef TemplateMap::const_iterator	const_iterator
typedef utility::vector1 < TemplateCOP >	TemplateList

Public Member Functions
	Templates (std::string const &config_file, core::pose::PoseCOP native=NULL)
virtual	~Templates ()
core::fragment::FragSetOP	pick_frags (core::fragment::FragSetOP, core::fragment::FragDataCOP frag_type, Size min_nr_frags, Size ncopies=1) const
Size	pick_frags (core::fragment::FragSet &, core::fragment::FragDataCOP frag_type, Size ncopies=1) const
void	read_pairings (std::string const &filename, core::scoring::dssp::PairingsList &) const
TemplateJumpSetupOP	create_jump_def (core::fragment::SecondaryStructureCOP=NULL) const
bool	has_pairings () const
core::scoring::dssp::PairingsList const &	pairings () const
std::string const &	target_sequence () const
std::string &	target_sequence ()
core::Size	target_total_residue () const
const_iterator	begin () const
const_iterator	end () const
TemplateList const &	helixjump_picks () const
void	add_target_constraints (core::scoring::constraints::ConstraintSetOP, core::pose::Pose const &) const
bool	has_template (std::string const &ModelID) const
Template const &	get_template (std::string const &ModelID) const
bool	is_good () const
Size	pick_large_frags (core::fragment::FragSet &frag_set, core::fragment::SingleResidueFragDataOP frag_type, core::Size ncopies=1) const
void	set_native (core::pose::PoseCOP native)
PairingStatistics const &	strand_pairing_stats ()

Static Public Member Functions
static void	register_options ()

Private Member Functions
void	get_cst_list (TemplateList &cst_list, TemplateList &cull_list) const
void	scored_fragpick_list (TemplateList &frag_pick_list) const
void	_get_scored_list (TemplateList &cst_list, core::Size topN, core::Real wTopol, core::Real wExtern) const

Private Attributes
bool	good_
TemplateMap	templates_
core::scoring::dssp::PairingsList	pairings_
std::string	target_sequence_
PairingStatisticsCOP	strand_stats_
core::pose::PoseCOP	native_
TemplateList	cull_list_
TemplateList	fragpick_list_
TemplateList	helixjump_pick_list_

Member Typedef Documentation

typedef TemplateMap::const_iterator protocols::abinitio::Templates::const_iterator

typedef utility::vector1< TemplateCOP > protocols::abinitio::Templates::TemplateList

typedef std::map< std::string, TemplateOP > protocols::abinitio::Templates::TemplateMap

Constructor & Destructor Documentation

protocols::abinitio::Templates::Templates	(	std::string const &	config_file,
		core::pose::PoseCOP	native = NULL
	)

References protocols::abinitio::StructureStore::add(), cst_file, cull_list_, fragpick_list_, getline(), good_, protocols::abinitio::StructureStore::has(), helixjump_pick_list_, in, native_, option, pdb, templates::prefix, prefix, score, scored_fragpick_list(), strand_stats_, tag, target_sequence_, templates_, templates::fragsteal::topN, tr, user, and utility_exit_with_message.

protocols::abinitio::Templates::~Templates ( )

virtual

Member Function Documentation

void protocols::abinitio::Templates::_get_scored_list ( TemplateList &  cst_list, core::Size  topN, core::Real  wTopol, core::Real  wExtern  ) const

private

References score, and templates_.

Referenced by get_cst_list(), and scored_fragpick_list().

void protocols::abinitio::Templates::add_target_constraints	(	core::scoring::constraints::ConstraintSetOP	cstset,
		core::pose::Pose const &	pose
	)		const

References core::scoring::constraints::ConstraintSet::add_constraints(), protocols::abinitio::Template::constraints(), cst, cull_list_, get_cst_list(), protocols::abinitio::Template::map2target(), templates::no_culling, option, and tr.

const_iterator protocols::abinitio::Templates::begin ( ) const

inline

References templates_.

Referenced by protocols::abinitio::PairingStatistics::compute().

TemplateJumpSetupOP protocols::abinitio::Templates::create_jump_def

(

core::fragment::SecondaryStructureCOP

ss_def = NULL

)

const

References helix_pairings, templates::helix_pairings, option, pick_frags(), read_pairings(), strand_stats_, target_total_residue(), tr, and user.

const_iterator protocols::abinitio::Templates::end ( ) const

inline

References templates_.

Referenced by protocols::abinitio::PairingStatistics::compute().

void protocols::abinitio::Templates::get_cst_list ( TemplateList &  cst_list, TemplateList &  cull_list  ) const

private

References _get_scored_list(), option, templates_, templates::cst::topN, user, templates::cst::wExtern, wExtern, wTopol, and templates::cst::wTopol.

Referenced by add_target_constraints().

Template const& protocols::abinitio::Templates::get_template ( std::string const &  ModelID ) const

inline

References templates_, and utility_exit_with_message.

bool protocols::abinitio::Templates::has_pairings ( ) const

inline

References pairings_.

bool protocols::abinitio::Templates::has_template ( std::string const &  ModelID ) const

inline

References templates_.

TemplateList const& protocols::abinitio::Templates::helixjump_picks ( ) const

inline

References helixjump_pick_list_.

bool protocols::abinitio::Templates::is_good ( ) const

inline

References good_.

core::scoring::dssp::PairingsList const& protocols::abinitio::Templates::pairings ( ) const

inline

References pairings_.

FragSetOP protocols::abinitio::Templates::pick_frags	(	core::fragment::FragSetOP	frag_set,
		core::fragment::FragDataCOP	frag_type,
		Size	min_nr_frags,
		Size	ncopies = 1
	)		const

References core::fragment::FragSet::empty_clone(), target_total_residue(), protocols::analysis::total, and tr.

Referenced by create_jump_def().

Size protocols::abinitio::Templates::pick_frags	(	core::fragment::FragSet &	,
		core::fragment::FragDataCOP	frag_type,
		Size	ncopies = 1
	)		const

Size protocols::abinitio::Templates::pick_large_frags	(	core::fragment::FragSet &	frag_set,
		core::fragment::SingleResidueFragDataOP	frag_type,
		core::Size	ncopies = 1
	)		const

References fragpick_list_, protocols::analysis::total, and tr.

void protocols::abinitio::Templates::read_pairings	(	std::string const &	filename,
		core::scoring::dssp::PairingsList &	pairings
	)		const

References in, pairings_, pdb, protocols::jumping::read_pairing_list(), templates_, tr, and utility_exit_with_message.

Referenced by create_jump_def().

void protocols::abinitio::Templates::register_options ( )

static

References utility::options::OptionCollection::add_relevant(), templates::helix_pairings, templates::no_culling, option, templates::prefix, protocols::evaluation::register_options(), templates::fragsteal::topN, templates::cst::topN, templates::cst::wExtern, templates::fragsteal::wExtern, templates::fragsteal::wTopol, and templates::cst::wTopol.

void protocols::abinitio::Templates::scored_fragpick_list ( TemplateList &  frag_pick_list ) const

private

References _get_scored_list(), option, templates_, templates::fragsteal::topN, user, templates::fragsteal::wExtern, wExtern, wTopol, and templates::fragsteal::wTopol.

Referenced by Templates().

void protocols::abinitio::Templates::set_native

(

core::pose::PoseCOP

native

)

References native_.

PairingStatistics const& protocols::abinitio::Templates::strand_pairing_stats ( )

inline

References strand_stats_.

std::string const& protocols::abinitio::Templates::target_sequence ( ) const

inline

References target_sequence_.

Referenced by target_total_residue().

std::string& protocols::abinitio::Templates::target_sequence ( )

inline

References target_sequence_.

core::Size protocols::abinitio::Templates::target_total_residue ( ) const

inline

References target_sequence().

Referenced by create_jump_def(), and pick_frags().

Member Data Documentation

TemplateList protocols::abinitio::Templates::cull_list_

private

Referenced by add_target_constraints(), and Templates().

TemplateList protocols::abinitio::Templates::fragpick_list_

private

Referenced by pick_large_frags(), and Templates().

bool protocols::abinitio::Templates::good_

private

Referenced by is_good(), and Templates().

TemplateList protocols::abinitio::Templates::helixjump_pick_list_

private

Referenced by helixjump_picks(), and Templates().

core::pose::PoseCOP protocols::abinitio::Templates::native_

private

Referenced by set_native(), and Templates().

core::scoring::dssp::PairingsList protocols::abinitio::Templates::pairings_

private

Referenced by has_pairings(), pairings(), and read_pairings().

PairingStatisticsCOP protocols::abinitio::Templates::strand_stats_

private

Referenced by create_jump_def(), strand_pairing_stats(), and Templates().

std::string protocols::abinitio::Templates::target_sequence_

private

Referenced by target_sequence(), and Templates().

TemplateMap protocols::abinitio::Templates::templates_

private

Referenced by _get_scored_list(), begin(), end(), get_cst_list(), get_template(), has_template(), read_pairings(), scored_fragpick_list(), and Templates().

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

• src/protocols/abinitio/Templates.hh
• src/protocols/abinitio/Templates.cc