#include <StrandPairing.hh>

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

Collaboration diagram for protocols::fldsgn::topology::StrandPairingSet:

Public Types
typedef std::string	String

typedef core::Size	Size

typedef utility::vector1< 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=NULL)
	value constructor More...

	StrandPairingSet (StrandPairingSet const &s)
	copy constructor More...

virtual	~StrandPairingSet ()
	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...

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

bool	finalized () const

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

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

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

StrandPairingOP	strand_pairing (Size const s1, 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 (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...

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...

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< 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::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< Size > protocols::fldsgn::topology::StrandPairingSet::VecSize

Constructor & Destructor Documentation

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

default constructor

Referenced by clone().

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 = `NULL`
	)

value constructor

References finalize(), and push_back().

protocols::fldsgn::topology::StrandPairingSet::StrandPairingSet ( StrandPairingSet const & s)

copy constructor

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

virtual

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 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

References StrandPairingSet().

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 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 )

References empty_, finalize(), map_strand_pairings_, num_strands_, protocols::fldsgn::topology::DimerPairing::orient(), protocols::fldsgn::topology::DimerPairing::res1(), protocols::fldsgn::topology::DimerPairing::res2(), protocols::fldsgn::topology::DimerPairing::sign1(), protocols::fldsgn::topology::DimerPairing::sign2(), protocols::fldsgn::topology::SS_Info2::strand(), protocols::fldsgn::topology::SS_Info2::strand_id(), strand_pairings_, and protocols::fldsgn::topology::SS_Info2::strands().

Referenced by 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::apply(), drop_strand_pairs(), name_wo_rgstr(), and protocols::fldsgn::topology::operator<<().

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(), name(), and strand_pairings_.

StrandPairingSet::VecSize const & protocols::fldsgn::topology::StrandPairingSet::neighbor_strands ( 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().

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(), and StrandPairingSet().

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 protocols::fldsgn::filters::SheetTopologyFilter::apply(), and make_strand_neighbor_two().

StrandPairingOP protocols::fldsgn::topology::StrandPairingSet::strand_pairing ( 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::filters::SheetTopologyFilter::apply(), protocols::fldsgn::topology::BetaAlphaBetaMotif::calc_geometry(), protocols::fldsgn::topology::SheetSet::initialize(), and make_strand_neighbor_two().

StrandPairingOP protocols::fldsgn::topology::StrandPairingSet::strand_pairing	(	Size const	s1,
		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::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< Size, VecSize > protocols::fldsgn::topology::StrandPairingSet::neighbor_strands_

mutableprivate

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

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

Private Member Functions

Private Attributes

Friends

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation