#include <HelixPairing.hh>

Public Types
typedef std::string	String

typedef core::Size	Size

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

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

	HelixPairingSet (HelixPairings const &helix_pairings)
	value constructor More...

	HelixPairingSet (String const &helix_pairings)
	value constructor More...

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

virtual	~HelixPairingSet ()
	default destructor More...

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

void	push_back (HelixPairingOP const hop)
	add HelixPairingOP to StrandPairingSet More...

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

HelixPairingOP	helix_pairing (Size const s) const
	return one of the strand_pairings given a number More...

HelixPairingOP	helix_pairing (Size const h1, Size const h2)
	return the pointer of the helix pairing, given the two helix numbers of h1, and h2 if h1 and h2 does not make pairing, return 0 More...

HelixPairings const &	helix_pairings () const
	return all helix pairings More...

Size	size () const
	return the size of helix_pairings_ More...

void	calc_geometry (SS_Info2_COP ss_info)
	calc geomtry of helix pairing More...

String	name () const
	the name of HelixPairingSet is expressed by the combination of helix pairings More...

Private Member Functions
void	create_map_helix_pairings ()
	create map strand_pairings More...

Private Attributes
HelixPairings	helix_pairings_
	vector1 including owning pointers of HelixPairing More...

String	hpairset_name_
	the name of HelixPairingSet is expressed by the combination of helix pairings More...

Size	num_helices_
	the total number of strands included in HelixPairingSet More...

bool	initialize_map_helix_pairings_
	whether the map_helix_pairings_ is initialized or not More...

utility::vector1 < utility::vector1 < HelixPairingOP > >	map_helix_pairings_
	2D table of the pointer of helix pairing, which is sorted by the helix number More...

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

Member Typedef Documentation

typedef core::Size protocols::fldsgn::topology::HelixPairingSet::Size

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

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

Constructor & Destructor Documentation

protocols::fldsgn::topology::HelixPairingSet::HelixPairingSet ( )

default constructor

Referenced by clone().

protocols::fldsgn::topology::HelixPairingSet::HelixPairingSet ( HelixPairings const & helix_pairings )

value constructor

References helix_pairings_, hpairset_name_, and protocols::fldsgn::topology::HelixPairing::name().

protocols::fldsgn::topology::HelixPairingSet::HelixPairingSet ( String const & helix_pairings )

value constructor

References helix_pairings_, and utility::string_split().

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

copy constructor

protocols::fldsgn::topology::HelixPairingSet::~HelixPairingSet ( )

virtual

default destructor

destructor

Member Function Documentation

void protocols::fldsgn::topology::HelixPairingSet::calc_geometry ( SS_Info2_COP ss_info )

calc geomtry of helix pairing

calculate geomtry of helix parings

References helix_pairings_.

Referenced by protocols::fldsgn::filters::HelixPairingFilter::apply(), and protocols::fldsgn::filters::HelixPairingFilter::compute().

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

clear data of this HelixPairingSet

clear data of this HelixParingSet

References helix_pairings_, hpairset_name_, initialize_map_helix_pairings_, and map_helix_pairings_.

HelixPairingSetOP protocols::fldsgn::topology::HelixPairingSet::clone ( ) const

clone this object

References HelixPairingSet().

void protocols::fldsgn::topology::HelixPairingSet::create_map_helix_pairings ( )

private

create map strand_pairings

create 2D table of helix pairings

References protocols::fldsgn::topology::HelixPairing::h2(), helix_pairings_, initialize_map_helix_pairings_, map_helix_pairings_, and num_helices_.

Referenced by helix_pairing().

HelixPairingOP protocols::fldsgn::topology::HelixPairingSet::helix_pairing ( Size const s ) const

return one of the strand_pairings given a number

return one of the stand_pairings give a number

References helix_pairings_, and runtime_assert.

Referenced by protocols::fldsgn::filters::HelixPairingFilter::compute().

HelixPairingOP protocols::fldsgn::topology::HelixPairingSet::helix_pairing	(	Size const	h1,
		Size const	h2
	)

return the pointer of the helix pairing, given the two helix numbers of h1, and h2 if h1 and h2 does not make pairing, return 0

References create_map_helix_pairings(), protocols::antibody::h1, protocols::antibody::h2, initialize_map_helix_pairings_, map_helix_pairings_, and num_helices_.

HelixPairings const & protocols::fldsgn::topology::HelixPairingSet::helix_pairings ( ) const

return all helix pairings

References helix_pairings_.

Referenced by protocols::fldsgn::filters::HelixPairingFilter::apply(), protocols::fldsgn::filters::HelixPairingFilter::compute(), and protocols::fldsgn::topology::operator<<().

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

the name of HelixPairingSet is expressed by the combination of helix pairings

return hpairset_name_

References hpairset_name_.

Referenced by protocols::fldsgn::topology::operator<<().

void protocols::fldsgn::topology::HelixPairingSet::push_back ( HelixPairingOP const hop )

add HelixPairingOP to StrandPairingSet

add HelixPairingOP to StandPairingSet

References helix_pairings_, hpairset_name_, and initialize_map_helix_pairings_.

Size protocols::fldsgn::topology::HelixPairingSet::size ( ) const

return the size of helix_pairings_

References helix_pairings_.

Friends And Related Function Documentation

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

friend

return strand pairing

Member Data Documentation

HelixPairings protocols::fldsgn::topology::HelixPairingSet::helix_pairings_

private

vector1 including owning pointers of HelixPairing

Referenced by calc_geometry(), clear(), create_map_helix_pairings(), helix_pairing(), helix_pairings(), HelixPairingSet(), push_back(), and size().

String protocols::fldsgn::topology::HelixPairingSet::hpairset_name_

private

the name of HelixPairingSet is expressed by the combination of helix pairings

Referenced by clear(), HelixPairingSet(), name(), and push_back().

bool protocols::fldsgn::topology::HelixPairingSet::initialize_map_helix_pairings_

private

whether the map_helix_pairings_ is initialized or not

Referenced by clear(), create_map_helix_pairings(), helix_pairing(), and push_back().

utility::vector1< utility::vector1< HelixPairingOP > > protocols::fldsgn::topology::HelixPairingSet::map_helix_pairings_

private

2D table of the pointer of helix pairing, which is sorted by the helix number

Referenced by clear(), create_map_helix_pairings(), and helix_pairing().

Size protocols::fldsgn::topology::HelixPairingSet::num_helices_

private

the total number of strands included in HelixPairingSet

Referenced by create_map_helix_pairings(), and helix_pairing().

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

src/protocols/fldsgn/topology/HelixPairing.hh
src/protocols/fldsgn/topology/HelixPairing.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