#include <StrandPairing.hh>

Inheritance diagram for protocols::fldsgn::topology::StrandPairingSet:

Public Types
typedef std::string	String

typedef core::Size	Size

typedef core::Real	Real

typedef utility::vector1 < core::Size >	VecSize

typedef protocols::fldsgn::topology::SS_Info2	SS_Info2

typedef protocols::fldsgn::topology::SS_Info2_COP	SS_Info2_COP

typedef protocols::fldsgn::topology::DimerPairing	DimerPairing

typedef protocols::fldsgn::topology::DimerPairings	DimerPairings

Public Member Functions
	StrandPairingSet ()
	default constructor More...

	StrandPairingSet (StrandPairings const &strand_pairings)
	value constructor More...

	StrandPairingSet (SS_Info2 const &ssinfo, DimerPairings const &dimer_pairs)
	value constructor More...

	StrandPairingSet (String const &spairstring, SS_Info2_COP const ssinfo=nullptr)
	value constructor More...

	StrandPairingSet (String const &spairstring, SS_Info2_COP const ssinfo, utility::vector1< String > const &abego)
	value constructor More...

	~StrandPairingSet () override
	default destructor More...

StrandPairingSetOP	clone () const
	clone this object More...

void	push_back (StrandPairingOP const sop)
	add StrandPairingOP to StandPairingSet More...

void	push_back_and_finalize (StrandPairingOP const sop)
	add StrandPairingOP to StandPairingSet More...

void	clear ()
	clear data of this StrandPairingSet More...

StrandPairings::const_iterator	begin ()
	return begin of iterator of strand_pairings_ More...

StrandPairings::const_iterator	end ()
	return end of iterator of strand_pairings_ More...

core::Size	size () const
	return num of strand_pairing More...

bool	finalized () const

core::Size	num_strands () const
	return all strand pairings More...

StrandPairings const &	strand_pairings () const
	return all strand pairings More...

StrandPairingOP	strand_pairing (core::Size const s) const
	return one of the strand_pairings given a number More...

StrandPairingOP	strand_pairing (core::Size const s1, core::Size const s2) const
	return the pointer of the strand pairing, given the two strand numbers of s1, and s2 if s1 and s2 does not make pairing, return 0 More...

VecSize const &	neighbor_strands (core::Size const s) const
	return strand number of neighbor strands of a input strand More...

String	name () const
	the name of StrandPairingSet is expressed by the combination of strand pairings For example, 2kl8 of ferredoxin-like fold is described as 1-3.A.0;2-3.A.0;1-4.A.0 More...

String	name_wo_rgstr () const
	the name of StrandPairingSet without register shift For example, 2kl8 of ferredoxin-like fold is described as 1-3.A;2-3.A;1-4.A More...

void	make_strand_neighbor_two ()
	make the number of strand pairing as two More...

void	drop_strand_pairs (StrandPairings const &drop_spairs)
	remove a set of strand pairings from datay More...

void	finalize ()
	finalize this and create_map_strand_pairings More...

Protected Member Functions
void	initialize_by_sspair_string (String const &spairstring, SS_Info2_COP const ssinfo)

void	initialize_by_sspair_string_and_abego (String const &spairstring, SS_Info2_COP const ssinfo, utility::vector1< String > const &abego)

Private Member Functions
void	initialize_by_dimer_pairs (SS_Info2 const &ssinfo, DimerPairings const &dimer_pairs)
	initialize StrandPairingSet based on dimer_pairs ( under developed ) More...

Private Attributes
StrandPairings	strand_pairings_
	vector1 including owning pointers of StrandPairing More...

String	spairset_name_
	the name of StrandPairingSet is expressed by the combination of strand pairings For example, 2kl8 of ferredoxin-like fold is given as 1-3.A.0;2-3.A.0;1-4.A.0 More...

core::Size	num_strands_
	the total number of strands included in StrandPairingSet More...

bool	finalized_
	whether the map_strand_pairings_ is initialized or not More...

utility::vector1 < utility::vector1 < StrandPairingOP > >	map_strand_pairings_
	2D table of the pointers of strand pairings, which are sorted by the strand number More...

std::map< core::Size, VecSize >	neighbor_strands_

StrandPairingOP	empty_

Friends
std::ostream &	operator<< (std::ostream &out, const StrandPairingSet &s)
	return strand pairing More...

Member Typedef Documentation

typedef protocols::fldsgn::topology::DimerPairing protocols::fldsgn::topology::StrandPairingSet::DimerPairing

typedef protocols::fldsgn::topology::DimerPairings protocols::fldsgn::topology::StrandPairingSet::DimerPairings

typedef core::Real protocols::fldsgn::topology::StrandPairingSet::Real

typedef core::Size protocols::fldsgn::topology::StrandPairingSet::Size

typedef protocols::fldsgn::topology::SS_Info2 protocols::fldsgn::topology::StrandPairingSet::SS_Info2

typedef protocols::fldsgn::topology::SS_Info2_COP protocols::fldsgn::topology::StrandPairingSet::SS_Info2_COP

typedef std::string protocols::fldsgn::topology::StrandPairingSet::String

typedef utility::vector1< core::Size > protocols::fldsgn::topology::StrandPairingSet::VecSize

Constructor & Destructor Documentation

protocols::fldsgn::topology::StrandPairingSet::StrandPairingSet ( )

default constructor

protocols::fldsgn::topology::StrandPairingSet::StrandPairingSet ( StrandPairings const & strand_pairings )

value constructor

References finalize().

protocols::fldsgn::topology::StrandPairingSet::StrandPairingSet	(	SS_Info2 const &	ssinfo,
		DimerPairings const &	dimer_pairs
	)

value constructor

References initialize_by_dimer_pairs().

protocols::fldsgn::topology::StrandPairingSet::StrandPairingSet	(	String const &	spairstring,
		SS_Info2_COP const	ssinfo = `nullptr`
	)

value constructor

References finalize(), and initialize_by_sspair_string().

protocols::fldsgn::topology::StrandPairingSet::StrandPairingSet	(	String const &	spairstring,
		SS_Info2_COP const	ssinfo,
		utility::vector1< String > const &	abego
	)

value constructor

References finalize(), and initialize_by_sspair_string_and_abego().

protocols::fldsgn::topology::StrandPairingSet::~StrandPairingSet ( )

overridedefault

default destructor

destructor

Member Function Documentation

StrandPairings::const_iterator protocols::fldsgn::topology::StrandPairingSet::begin ( )

inline

return begin of iterator of strand_pairings_

References strand_pairings_.

Referenced by protocols::fldsgn::filters::SheetTopologyFilter::compute(), protocols::fldsgn::filters::SheetTopologyFilter::compute_residue_pairings(), protocols::fldsgn::filters::find_pairing_idx(), and make_strand_neighbor_two().

void protocols::fldsgn::topology::StrandPairingSet::clear ( )

clear data of this StrandPairingSet

clear data of this StrandParingSet

References finalized_, map_strand_pairings_, neighbor_strands_, spairset_name_, and strand_pairings_.

Referenced by drop_strand_pairs().

StrandPairingSetOP protocols::fldsgn::topology::StrandPairingSet::clone ( ) const

clone this object

void protocols::fldsgn::topology::StrandPairingSet::drop_strand_pairs ( StrandPairings const & drop_spairs )

remove a set of strand pairings from datay

References clear(), finalize(), name(), and strand_pairings_.

Referenced by make_strand_neighbor_two().

StrandPairings::const_iterator protocols::fldsgn::topology::StrandPairingSet::end ( )

inline

return end of iterator of strand_pairings_

References strand_pairings_.

Referenced by protocols::fldsgn::filters::SheetTopologyFilter::compute(), protocols::fldsgn::filters::SheetTopologyFilter::compute_residue_pairings(), protocols::fldsgn::filters::find_pairing_idx(), and make_strand_neighbor_two().

void protocols::fldsgn::topology::StrandPairingSet::finalize ( )

finalize this and create_map_strand_pairings

References empty_, finalized_, map_strand_pairings_, protocols::fldsgn::topology::StrandPairing::name(), neighbor_strands_, num_strands_, protocols::fldsgn::topology::pointer_sorter(), protocols::fldsgn::topology::StrandPairing::s2(), spairset_name_, and strand_pairings_.

Referenced by protocols::fldsgn::topology::calc_strand_pairing_set(), drop_strand_pairs(), initialize_by_dimer_pairs(), make_strand_neighbor_two(), push_back_and_finalize(), and StrandPairingSet().

bool protocols::fldsgn::topology::StrandPairingSet::finalized ( ) const

inline

References finalized_.

Referenced by protocols::fldsgn::topology::SheetSet::initialize().

void protocols::fldsgn::topology::StrandPairingSet::initialize_by_dimer_pairs	(	SS_Info2 const &	ssinfo,
		DimerPairings const &	dimer_pairs
	)

private

initialize StrandPairingSet based on dimer_pairs ( under developed )

Referenced by StrandPairingSet().

void protocols::fldsgn::topology::StrandPairingSet::initialize_by_sspair_string	(	String const &	spairstring,
		SS_Info2_COP const	ssinfo
	)

protected

References initialize_by_sspair_string_and_abego().

Referenced by StrandPairingSet().

void protocols::fldsgn::topology::StrandPairingSet::initialize_by_sspair_string_and_abego	(	String const &	spairstring,
		SS_Info2_COP const	ssinfo,
		utility::vector1< String > const &	abego
	)

protected

References push_back().

Referenced by initialize_by_sspair_string(), and StrandPairingSet().

void protocols::fldsgn::topology::StrandPairingSet::make_strand_neighbor_two ( )

make the number of strand pairing as two

References begin(), drop_strand_pairs(), end(), finalize(), finalized_, neighbor_strands(), num_strands_, size(), protocols::fldsgn::topology::sort_by_length(), and strand_pairing().

Referenced by protocols::fldsgn::topology::SheetSet::initialize().

String protocols::fldsgn::topology::StrandPairingSet::name ( ) const

the name of StrandPairingSet is expressed by the combination of strand pairings For example, 2kl8 of ferredoxin-like fold is described as 1-3.A.0;2-3.A.0;1-4.A.0

return spairset_name_

References finalized_, and spairset_name_.

Referenced by protocols::fldsgn::filters::SheetTopologyFilter::compute(), drop_strand_pairs(), and protocols::fldsgn::topology::operator<<().

StrandPairingSet::String protocols::fldsgn::topology::StrandPairingSet::name_wo_rgstr ( ) const

the name of StrandPairingSet without register shift For example, 2kl8 of ferredoxin-like fold is described as 1-3.A;2-3.A;1-4.A

References protocols::fldsgn::topology::StrandPairing::name(), strand_pairing(), and strand_pairings_.

StrandPairingSet::VecSize const & protocols::fldsgn::topology::StrandPairingSet::neighbor_strands ( core::Size const s ) const

return strand number of neighbor strands of a input strand

References finalized_, neighbor_strands_, and num_strands_.

Referenced by protocols::fldsgn::topology::SheetSet::initialize(), and make_strand_neighbor_two().

core::Size protocols::fldsgn::topology::StrandPairingSet::num_strands ( ) const

inline

return all strand pairings

References num_strands_.

void protocols::fldsgn::topology::StrandPairingSet::push_back ( StrandPairingOP const sop )

add StrandPairingOP to StandPairingSet

References finalized_, and strand_pairings_.

Referenced by protocols::fldsgn::topology::calc_strand_pairing_set(), initialize_by_sspair_string_and_abego(), and protocols::fldsgn::filters::SheetTopologyFilter::replace_register_shifts().

void protocols::fldsgn::topology::StrandPairingSet::push_back_and_finalize ( StrandPairingOP const sop )

add StrandPairingOP to StandPairingSet

References finalize(), and strand_pairings_.

core::Size protocols::fldsgn::topology::StrandPairingSet::size ( ) const

return num of strand_pairing

References strand_pairings_.

Referenced by make_strand_neighbor_two().

StrandPairingOP protocols::fldsgn::topology::StrandPairingSet::strand_pairing ( core::Size const s ) const

return one of the strand_pairings given a number

return one of the stand_pairings given a number

References strand_pairings_.

Referenced by protocols::fldsgn::topology::BetaAlphaBetaMotif::calc_geometry(), protocols::denovo_design::components::calc_paired_residues(), protocols::fldsgn::filters::SheetTopologyFilter::compute(), protocols::fldsgn::topology::SheetSet::initialize(), protocols::denovo_design::components::make_lengths_str(), make_strand_neighbor_two(), and name_wo_rgstr().

StrandPairingOP protocols::fldsgn::topology::StrandPairingSet::strand_pairing	(	core::Size const	s1,
		core::Size const	s2
	)		const

return the pointer of the strand pairing, given the two strand numbers of s1, and s2 if s1 and s2 does not make pairing, return 0

References empty_, finalized_, map_strand_pairings_, and num_strands_.

StrandPairings const & protocols::fldsgn::topology::StrandPairingSet::strand_pairings ( ) const

return all strand pairings

References strand_pairings_.

Referenced by protocols::denovo_design::components::SheetDB::add_sheets_from_spairs(), protocols::fldsgn::SheetConstraintGenerator::apply(), protocols::fldsgn::topology::SheetSet::initialize(), and protocols::fldsgn::topology::operator<<().

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	out,
		const StrandPairingSet &	s
	)

friend

return strand pairing

Member Data Documentation

StrandPairingOP protocols::fldsgn::topology::StrandPairingSet::empty_

private

Referenced by finalize(), initialize_by_dimer_pairs(), and strand_pairing().

bool protocols::fldsgn::topology::StrandPairingSet::finalized_

private

whether the map_strand_pairings_ is initialized or not

Referenced by clear(), finalize(), finalized(), make_strand_neighbor_two(), name(), neighbor_strands(), push_back(), and strand_pairing().

utility::vector1< utility::vector1< StrandPairingOP > > protocols::fldsgn::topology::StrandPairingSet::map_strand_pairings_

private

2D table of the pointers of strand pairings, which are sorted by the strand number

Referenced by clear(), finalize(), initialize_by_dimer_pairs(), and strand_pairing().

std::map< core::Size, VecSize > protocols::fldsgn::topology::StrandPairingSet::neighbor_strands_

mutableprivate

Referenced by clear(), finalize(), and neighbor_strands().

core::Size protocols::fldsgn::topology::StrandPairingSet::num_strands_

private

the total number of strands included in StrandPairingSet

Referenced by finalize(), initialize_by_dimer_pairs(), make_strand_neighbor_two(), neighbor_strands(), num_strands(), and strand_pairing().

String protocols::fldsgn::topology::StrandPairingSet::spairset_name_

private

the name of StrandPairingSet is expressed by the combination of strand pairings For example, 2kl8 of ferredoxin-like fold is given as 1-3.A.0;2-3.A.0;1-4.A.0

Referenced by clear(), finalize(), and name().

StrandPairings protocols::fldsgn::topology::StrandPairingSet::strand_pairings_

private

vector1 including owning pointers of StrandPairing

Referenced by begin(), clear(), drop_strand_pairs(), end(), finalize(), initialize_by_dimer_pairs(), name_wo_rgstr(), push_back(), push_back_and_finalize(), size(), strand_pairing(), and strand_pairings().

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

src/protocols/fldsgn/topology/StrandPairing.hh
src/protocols/fldsgn/topology/StrandPairing.cc

Public Types

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Friends

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation