#include <Templates.hh>

Inheritance diagram for protocols::abinitio::Templates:

Collaboration diagram for protocols::abinitio::Templates:

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::FragDataOP frag_type, Size min_nr_frags, Size ncopies=1) const

Size	pick_frags (core::fragment::FragSet &, core::fragment::FragDataOP 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_

Detailed Description

Definition at line 60 of file Templates.hh.

Member Typedef Documentation

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

Definition at line 65 of file Templates.hh.

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

Definition at line 66 of file Templates.hh.

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

Definition at line 62 of file Templates.hh.

Constructor & Destructor Documentation

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

Definition at line 154 of file Templates.cc.

References protocols::abinitio::StructureStore::add(), cull_list_, fragpick_list_, good_, protocols::abinitio::StructureStore::has(), helixjump_pick_list_, native_, scored_fragpick_list(), strand_stats_, target_sequence_, templates_, and tr().

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

virtual

Definition at line 150 of file Templates.cc.

Member Function Documentation

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

private

Definition at line 290 of file Templates.cc.

References 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

Definition at line 469 of file Templates.cc.

References protocols::abinitio::Template::constraints(), cull_list_, get_cst_list(), protocols::abinitio::Template::map2target(), and tr().

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

inline

Definition at line 99 of file Templates.hh.

References templates_.

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

TemplateJumpSetupOP protocols::abinitio::Templates::create_jump_def ( core::fragment::SecondaryStructureCOP ss_def = NULL) const

Definition at line 449 of file Templates.cc.

References pick_frags(), read_pairings(), strand_stats_, target_total_residue(), and tr().

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

inline

Definition at line 103 of file Templates.hh.

References templates_.

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

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

private

Definition at line 242 of file Templates.cc.

References _get_scored_list(), and templates_.

Referenced by add_target_constraints().

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

inline

Definition at line 118 of file Templates.hh.

References templates_.

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

inline

Definition at line 79 of file Templates.hh.

References pairings_.

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

inline

Definition at line 114 of file Templates.hh.

References templates_.

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

inline

Definition at line 107 of file Templates.hh.

References helixjump_pick_list_.

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

inline

Definition at line 127 of file Templates.hh.

References good_.

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

inline

Definition at line 83 of file Templates.hh.

References pairings_.

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

Referenced by create_jump_def().

Size protocols::abinitio::Templates::pick_frags	(	core::fragment::FragSet &	,
		core::fragment::FragDataOP	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