#include <HelixPairing.hh>

Inheritance diagram for protocols::fldsgn::topology::HelixPairingSet:

Collaboration diagram for protocols::fldsgn::topology::HelixPairingSet:

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...

Detailed Description

Definition at line 147 of file HelixPairing.hh.

Member Typedef Documentation

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

Definition at line 152 of file HelixPairing.hh.

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

Definition at line 153 of file HelixPairing.hh.

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

Definition at line 151 of file HelixPairing.hh.

Constructor & Destructor Documentation

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

default constructor

Definition at line 206 of file HelixPairing.cc.

Referenced by clone().

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

value constructor

Definition at line 229 of file HelixPairing.cc.

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

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

value constructor

Definition at line 213 of file HelixPairing.cc.

References helix_pairings_.

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

copy constructor

Definition at line 247 of file HelixPairing.cc.

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

virtual

default destructor

destructor

Definition at line 257 of file HelixPairing.cc.

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

Definition at line 348 of file HelixPairing.cc.

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

Definition at line 294 of file HelixPairing.cc.

References helix_pairings_, hpairset_name_, initialize_map_helix_pairings_, and map_helix_pairings_.

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

clone this object

Definition at line 261 of file HelixPairing.cc.

References HelixPairingSet().

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

private

create map strand_pairings

create 2D table of helix pairings

Definition at line 357 of file HelixPairing.cc.

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

Definition at line 304 of file HelixPairing.cc.

References helix_pairings_.

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

Definition at line 312 of file HelixPairing.cc.

References create_map_helix_pairings(), protocols::antibody2::h1, protocols::antibody2::h2, initialize_map_helix_pairings_, map_helix_pairings_, and num_helices_.

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

return all helix pairings

Definition at line 327 of file HelixPairing.cc.

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_

Definition at line 341 of file HelixPairing.cc.

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

Definition at line 281 of file HelixPairing.cc.

References helix_pairings_, hpairset_name_, and initialize_map_helix_pairings_.

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

return the size of helix_pairings_

Definition at line 334 of file HelixPairing.cc.

References helix_pairings_.

Friends And Related Function Documentation

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

friend

return strand pairing

Definition at line 267 of file HelixPairing.cc.

Member Data Documentation

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

private

vector1 including owning pointers of HelixPairing

Definition at line 229 of file HelixPairing.hh.

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

Definition at line 232 of file HelixPairing.hh.

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

Definition at line 238 of file HelixPairing.hh.

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

Definition at line 241 of file HelixPairing.hh.

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

Definition at line 235 of file HelixPairing.hh.

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

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation