#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...

Detailed Description

Definition at line 199 of file StrandPairing.hh.

Member Typedef Documentation

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

Definition at line 208 of file StrandPairing.hh.

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

Definition at line 209 of file StrandPairing.hh.

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

Definition at line 204 of file StrandPairing.hh.

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

Definition at line 206 of file StrandPairing.hh.

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

Definition at line 207 of file StrandPairing.hh.

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

Definition at line 203 of file StrandPairing.hh.

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

Definition at line 205 of file StrandPairing.hh.

Constructor & Destructor Documentation

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

default constructor

Definition at line 420 of file StrandPairing.cc.

Referenced by clone().

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

value constructor

Definition at line 429 of file StrandPairing.cc.

References finalize().

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

value constructor

Definition at line 465 of file StrandPairing.cc.

References initialize_by_dimer_pairs().

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

value constructor

Definition at line 441 of file StrandPairing.cc.

References finalize(), and push_back().

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

copy constructor

Definition at line 476 of file StrandPairing.cc.

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

virtual

default destructor

destructor

Definition at line 489 of file StrandPairing.cc.

Member Function Documentation

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

inline

return begin of iterator of strand_pairings_

Definition at line 257 of file StrandPairing.hh.

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

Definition at line 535 of file StrandPairing.cc.

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

Definition at line 494 of file StrandPairing.cc.

References StrandPairingSet().

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

remove a set of strand pairings from datay

Definition at line 697 of file StrandPairing.cc.

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_

Definition at line 260 of file StrandPairing.hh.

References strand_pairings_.

Referenced by make_strand_neighbor_two().

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

finalize this and create_map_strand_pairings

Definition at line 632 of file StrandPairing.cc.

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

Definition at line 269 of file StrandPairing.hh.

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 )

Definition at line 767 of file StrandPairing.cc.

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

Definition at line 726 of file StrandPairing.cc.

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_

Definition at line 555 of file StrandPairing.cc.

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

Definition at line 604 of file StrandPairing.cc.

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

Definition at line 593 of file StrandPairing.cc.

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

Definition at line 272 of file StrandPairing.hh.

References num_strands_.

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

add StrandPairingOP to StandPairingSet

Definition at line 517 of file StrandPairing.cc.

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

Definition at line 526 of file StrandPairing.cc.

References finalize(), and strand_pairings_.

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

return num of strand_pairing

Definition at line 546 of file StrandPairing.cc.

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

Definition at line 572 of file StrandPairing.cc.

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

Definition at line 581 of file StrandPairing.cc.

References empty_, finalized_, map_strand_pairings_, and num_strands_.

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

return all strand pairings

Definition at line 564 of file StrandPairing.cc.

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

Definition at line 501 of file StrandPairing.cc.

Member Data Documentation

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

private

Definition at line 342 of file StrandPairing.hh.

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

Definition at line 333 of file StrandPairing.hh.

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

Definition at line 336 of file StrandPairing.hh.

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

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

mutableprivate

Definition at line 339 of file StrandPairing.hh.

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

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

private

the total number of strands included in StrandPairingSet

Definition at line 330 of file StrandPairing.hh.

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

Definition at line 327 of file StrandPairing.hh.

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

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

private

vector1 including owning pointers of StrandPairing

Definition at line 323 of file StrandPairing.hh.

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

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation