protocols::abinitio::Template Class Reference

#include <Template.hh>

Inheritance diagram for protocols::abinitio::Template:

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

Public Member Functions
	~Template () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. 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)
core::Size	steal_frags (core::fragment::FrameList const &target_frames, core::fragment::FragSet &accumulator, core::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
core::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

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_

Member Typedef Documentation

AtomPairConstraintList

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

NamedAtomPairConstraintList

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

Constructor & Destructor Documentation

~Template()

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

overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

Template() [1/2]

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

References good_, mapping_, pose_, core::id::SequenceMapping::reverse(), reverse_mapping_, and tr().

Template() [2/2]

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_, name(), core::conformation::membrane::out, pose_, core::id::SequenceMapping::reverse(), reverse_mapping_, core::sequence::DerivedSequenceMapping::seq2(), core::id::SequenceMapping::set_offset(), core::sequence::simple_mapping_from_file(), core::id::SequenceMapping::size1(), core::sequence::DerivedSequenceMapping::start_seq2(), strand_pairings(), strand_pairings_, and tr().

Member Function Documentation

_read_constraints()

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

private

References cstset_, pose_, and tr().

Referenced by constraints().

constraints()

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

inline

References _read_constraints(), cstfile_, and cstset_.

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

cull_violators()

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

References mapping_, pose_, and tr().

external_score()

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

inline

References score_.

has_constraints()

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

inline

References cstfile_.

is_good()

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

inline

References good_.

map2target() [1/3]

void protocols::abinitio::Template::map2target

(

core::fragment::FrameList &

frames

)

const

References reverse_mapping_, protocols::loops::start, and tr().

map2target() [2/3]

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

References reverse_mapping_.

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

map2target() [3/3]

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

References reverse_mapping_, and tr().

map2template() [1/3]

void protocols::abinitio::Template::map2template

(

core::fragment::FrameList &

frames

)

const

References mapping_, and tr().

map2template() [2/3]

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

References mapping_.

Referenced by steal_frags().

map2template() [3/3]

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

References mapping_, and tr().

map_pairing()

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::conformation::membrane::in, and core::conformation::membrane::out.

Referenced by map_pairings2target(), and map_pairings2template().

map_pairings2target()

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

References core::conformation::membrane::in, map_pairing(), core::conformation::membrane::out, reverse_mapping_, and tr().

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

map_pairings2template()

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

References core::conformation::membrane::in, map_pairing(), mapping_, and core::conformation::membrane::out.

name()

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

inline

References name_.

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

pick_large_frags()

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

References core::fragment::FragSet::add(), map2target(), protocols::mean_field::max(), protocols::mean_field::min(), name(), pose_, reverse_mapping_, core::id::SequenceMapping::size1(), and tr().

query_sequence()

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

inline

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

read_constraints()

void protocols::abinitio::Template::read_constraints

(

std::string const &

cst_file

)

References cstfile_.

register_options()

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

static

steal_frags()

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

good for continuous fragments: no torsions from insertions are mapped

References core::fragment::FragSet::add(), map2target(), map2template(), name(), pose_, protocols::analysis::total, and tr().

strand_pairings()

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

inline

References strand_pairings_.

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

topology_score() [1/2]

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

inline

References topol_score_.

topology_score() [2/2]

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

inline

References topol_score_.

Member Data Documentation

cstfile_

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

private

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

cstset_

NamedAtomPairConstraintList protocols::abinitio::Template::cstset_

mutableprivate

Referenced by _read_constraints(), and constraints().

good_

bool protocols::abinitio::Template::good_

private

Referenced by is_good(), and Template().

mapping_

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

private

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

name_

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

private

Referenced by name().

pose_

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

private

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

reverse_mapping_

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

private

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

score_

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

private

Referenced by external_score().

strand_pairings_

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

private

Referenced by strand_pairings(), and Template().

topol_score_

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