#include <Template.hh>

Public Types
typedef utility::vector1 < core::scoring::constraints::AtomPairConstraintOP >	AtomPairConstraintList

typedef utility::vector1 < core::scoring::constraints::Obsolet_NamedAtomPairConstraintOP >	NamedAtomPairConstraintList

Public Member Functions
virtual	~Template ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...

	Template (std::string const &name, core::pose::PoseCOP, core::sequence::DerivedSequenceMapping const &mapping)

	Template (std::string const &name, core::pose::PoseCOP, std::string const &map_file, int offset, core::Real score)

Size	steal_frags (core::fragment::FrameList const &target_frames, core::fragment::FragSet &accumulator, Size ncopies=1) const
	good for continuous fragments: no torsions from insertions are mapped More...

void	map_pairings2template (core::scoring::dssp::PairingList const &in, core::scoring::dssp::PairingList &out) const

void	map_pairings2target (core::scoring::dssp::PairingList const &in, core::scoring::dssp::PairingList &out) const

void	map2target (core::fragment::FrameList const &template_frames, core::fragment::FrameList &target_frames) const

void	map2target (core::fragment::FrameList &) const

void	map2template (core::fragment::FrameList const &target_frames, core::fragment::FrameList &template_frames) const

void	map2template (core::fragment::FrameList &) const

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

void	map2target (NamedAtomPairConstraintList const &, NamedAtomPairConstraintList &) const

void	map2template (NamedAtomPairConstraintList const &, NamedAtomPairConstraintList &) const

void	cull_violators (NamedAtomPairConstraintList const &target_list, NamedAtomPairConstraintList &culled_list) const

void	read_constraints (std::string const &cst_file)

bool	has_constraints () const

core::scoring::dssp::StrandPairingSet const &	strand_pairings () const

NamedAtomPairConstraintList const &	constraints () const

std::string const &	name () const

core::Real	external_score () const

std::string	query_sequence () const

core::Real	topology_score () const

void	topology_score (core::Real setting)

bool	is_good () const

Static Public Member Functions
static void	register_options ()

Private Member Functions
bool	map_pairing (core::scoring::dssp::Pairing const &, core::scoring::dssp::Pairing &, core::sequence::DerivedSequenceMapping const &map) const

void	_read_constraints (std::string const &cst_file) const

Member Typedef Documentation

typedef utility::vector1< core::scoring::constraints::AtomPairConstraintOP > protocols::abinitio::Template::AtomPairConstraintList

typedef utility::vector1< core::scoring::constraints::Obsolet_NamedAtomPairConstraintOP > protocols::abinitio::Template::NamedAtomPairConstraintList

Constructor & Destructor Documentation

protocols::abinitio::Template::~Template ( )

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

protocols::abinitio::Template::Template	(	std::string const &	name,
		core::pose::PoseCOP	pose,
		core::sequence::DerivedSequenceMapping const &	mapping
	)

References good_, mapping_, pose_, reverse_mapping_, and tr.

protocols::abinitio::Template::Template	(	std::string const &	name,
		core::pose::PoseCOP	pose,
		std::string const &	map_file,
		int	offset,
		core::Real	score
	)

References core::scoring::dssp::StrandPairingSet::get_beta_pairs(), good_, map_pairings2target(), mapping_, templates::max_align_pos, max_align_pos, templates::min_align_pos, min_align_pos, option, out, pose_, reverse_mapping_, seq, core::sequence::DerivedSequenceMapping::seq2(), core::sequence::DerivedSequenceMapping::start_seq2(), strand_pairings(), strand_pairings_, tr, and user.

Member Function Documentation

void protocols::abinitio::Template::_read_constraints ( std::string const & cst_file ) const

private

References cstset_, utility::pointer::owning_ptr< T >::get(), core::scoring::constraints::ConstraintSet::get_all_constraints(), core::scoring::constraints::ConstraintIO::get_instance(), pose_, core::scoring::constraints::ConstraintIO::read_constraints(), and tr.

Referenced by constraints().

NamedAtomPairConstraintList const& protocols::abinitio::Template::constraints ( ) const

inline

References _read_constraints(), cstfile_, and cstset_.

Referenced by protocols::abinitio::Templates::add_target_constraints().

void protocols::abinitio::Template::cull_violators	(	NamedAtomPairConstraintList const &	target_list,
		NamedAtomPairConstraintList &	culled_list
	)		const

References cst, mapping_, pose_, and tr.

core::Real protocols::abinitio::Template::external_score ( ) const

inline

References score_.

bool protocols::abinitio::Template::has_constraints ( ) const

inline

References cstfile_.

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

inline

References good_.

void protocols::abinitio::Template::map2target	(	core::fragment::FrameList const &	template_frames,
		core::fragment::FrameList &	target_frames
	)		const

Referenced by protocols::abinitio::Templates::add_target_constraints(), pick_large_frags(), and steal_frags().

void protocols::abinitio::Template::map2target ( core::fragment::FrameList & ) const

void protocols::abinitio::Template::map2target	(	NamedAtomPairConstraintList const &	template_list,
		NamedAtomPairConstraintList &	target_list
	)		const

References reverse_mapping_, and tr.

void protocols::abinitio::Template::map2template	(	core::fragment::FrameList const &	target_frames,
		core::fragment::FrameList &	template_frames
	)		const

Referenced by steal_frags().

void protocols::abinitio::Template::map2template ( core::fragment::FrameList & ) const

void protocols::abinitio::Template::map2template	(	NamedAtomPairConstraintList const &	target_list,
		NamedAtomPairConstraintList &	template_list
	)		const

References mapping_, and tr.

bool protocols::abinitio::Template::map_pairing	(	core::scoring::dssp::Pairing const &	in,
		core::scoring::dssp::Pairing &	out,
		core::sequence::DerivedSequenceMapping const &	map
	)		const

private

References core::scoring::dssp::Pairing::Orientation(), core::scoring::dssp::Pairing::Pleating(), core::scoring::dssp::Pairing::Pos1(), and core::scoring::dssp::Pairing::Pos2().

Referenced by map_pairings2target(), and map_pairings2template().

void protocols::abinitio::Template::map_pairings2target	(	core::scoring::dssp::PairingList const &	in,
		core::scoring::dssp::PairingList &	out
	)		const

References map_pairing(), reverse_mapping_, and tr.

Referenced by protocols::abinitio::PairingStatistics::compute(), and Template().

void protocols::abinitio::Template::map_pairings2template	(	core::scoring::dssp::PairingList const &	in,
		core::scoring::dssp::PairingList &	out
	)		const

References map_pairing(), and mapping_.

std::string const& protocols::abinitio::Template::name ( ) const

inline

References name_.

Referenced by protocols::abinitio::PairingStatistics::compute(), pick_large_frags(), and steal_frags().

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

References map2target(), templates::max_shrink, max_shrink, templates::min_frag_size, templates::min_padding, min_padding, name(), nres, option, pose_, reverse_mapping_, templates::shrink_pos_step, shrink_step, templates::shrink_step, size(), and tr.

std::string protocols::abinitio::Template::query_sequence ( ) const

inline

References mapping_, and core::sequence::DerivedSequenceMapping::seq1().

void protocols::abinitio::Template::read_constraints ( std::string const & cst_file )

References cstfile_.

void protocols::abinitio::Template::register_options ( )

static

References utility::options::OptionCollection::add_relevant(), templates::max_align_pos, templates::max_shrink, templates::min_align_pos, templates::min_frag_size, templates::min_padding, option, templates::shrink_pos_step, and templates::shrink_step.

Size protocols::abinitio::Template::steal_frags	(	core::fragment::FrameList const &	target_frames,
		core::fragment::FragSet &	accumulator,
		Size	ncopies = `1`
	)		const

good for continuous fragments: no torsions from insertions are mapped

References map2target(), map2template(), name(), pose_, protocols::analysis::total, and tr.

core::scoring::dssp::StrandPairingSet const& protocols::abinitio::Template::strand_pairings ( ) const

inline

References strand_pairings_.

Referenced by protocols::abinitio::PairingStatistics::compute(), and Template().

core::Real protocols::abinitio::Template::topology_score ( ) const

inline

References topol_score_.

void protocols::abinitio::Template::topology_score ( core::Real setting )

inline

References topol_score_.

Member Data Documentation

std::string protocols::abinitio::Template::cstfile_

private

Referenced by constraints(), has_constraints(), and read_constraints().

NamedAtomPairConstraintList protocols::abinitio::Template::cstset_

mutableprivate

Referenced by _read_constraints(), and constraints().

bool protocols::abinitio::Template::good_

private

Referenced by is_good(), and Template().

core::sequence::DerivedSequenceMapping protocols::abinitio::Template::mapping_

private

Referenced by cull_violators(), map2template(), map_pairings2template(), query_sequence(), and Template().

std::string protocols::abinitio::Template::name_

private

Referenced by name().

core::pose::PoseCOP protocols::abinitio::Template::pose_

private

Referenced by _read_constraints(), cull_violators(), pick_large_frags(), steal_frags(), and Template().

core::sequence::DerivedSequenceMapping protocols::abinitio::Template::reverse_mapping_

private

Referenced by map2target(), map_pairings2target(), pick_large_frags(), and Template().

core::Real protocols::abinitio::Template::score_

private

Referenced by external_score().

core::scoring::dssp::StrandPairingSetOP protocols::abinitio::Template::strand_pairings_

private

Referenced by strand_pairings(), and Template().

core::Real protocols::abinitio::Template::topol_score_

private

Referenced by topology_score().

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

src/protocols/abinitio/Template.hh
src/protocols/abinitio/Template.cc

Private Attributes
core::sequence::DerivedSequenceMapping	mapping_

core::sequence::DerivedSequenceMapping	reverse_mapping_

core::pose::PoseCOP	pose_

std::string	name_

core::Real	score_

core::Real	topol_score_

NamedAtomPairConstraintList	cstset_

core::scoring::dssp::StrandPairingSetOP	strand_pairings_

std::string	cstfile_

bool	good_

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation