Rosetta 3.5
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Types | Public Member Functions | Private Member Functions | Private Attributes | Friends | List of all members
protocols::fldsgn::topology::StrandPairingSet Class Reference

#include <StrandPairing.hh>

Inheritance diagram for protocols::fldsgn::topology::StrandPairingSet:
Inheritance graph
[legend]
Collaboration diagram for protocols::fldsgn::topology::StrandPairingSet:
Collaboration graph
[legend]

Public Types

typedef std::string String
 
typedef core::Size Size
 
typedef utility::vector1< SizeVecSize
 
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, VecSizeneighbor_strands_
 
StrandPairingOP empty_
 

Friends

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

Member Typedef Documentation

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 ( )
bool protocols::fldsgn::topology::StrandPairingSet::finalized ( ) const
inline
void protocols::fldsgn::topology::StrandPairingSet::initialize_by_dimer_pairs ( SS_Info2 const &  ssinfo,
DimerPairings const &  dimer_pairs 
)
private
void protocols::fldsgn::topology::StrandPairingSet::make_strand_neighbor_two ( )
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
StrandPairingOP protocols::fldsgn::topology::StrandPairingSet::strand_pairing ( Size const  s) const
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

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
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
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

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