Rosetta  2021.16
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Types | Public Member Functions | Protected 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]

Public Types

typedef std::string String
 
typedef core::Size Size
 
typedef core::Real Real
 
typedef utility::vector1
< core::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=nullptr)
 value constructor More...
 
 StrandPairingSet (String const &spairstring, SS_Info2_COP const ssinfo, utility::vector1< String > const &abego)
 value constructor More...
 
 ~StrandPairingSet () override
 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...
 
core::Size size () const
 return num of strand_pairing More...
 
bool finalized () const
 
core::Size num_strands () const
 return all strand pairings More...
 
StrandPairings const & strand_pairings () const
 return all strand pairings More...
 
StrandPairingOP strand_pairing (core::Size const s) const
 return one of the strand_pairings given a number More...
 
StrandPairingOP strand_pairing (core::Size const s1, core::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 (core::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...
 

Protected Member Functions

void initialize_by_sspair_string (String const &spairstring, SS_Info2_COP const ssinfo)
 
void initialize_by_sspair_string_and_abego (String const &spairstring, SS_Info2_COP const ssinfo, utility::vector1< String > const &abego)
 

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...
 
core::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< core::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

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 = nullptr 
)

value constructor

References finalize(), and initialize_by_sspair_string().

protocols::fldsgn::topology::StrandPairingSet::StrandPairingSet ( String const &  spairstring,
SS_Info2_COP const  ssinfo,
utility::vector1< String > const &  abego 
)

value constructor

References finalize(), and initialize_by_sspair_string_and_abego().

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

default destructor

destructor

Member Function Documentation

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

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
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::initialize_by_sspair_string ( String const &  spairstring,
SS_Info2_COP const  ssinfo 
)
protected
void protocols::fldsgn::topology::StrandPairingSet::initialize_by_sspair_string_and_abego ( String const &  spairstring,
SS_Info2_COP const  ssinfo,
utility::vector1< String > const &  abego 
)
protected
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::compute(), drop_strand_pairs(), and protocols::fldsgn::topology::operator<<().

StrandPairingSet::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(), strand_pairing(), and strand_pairings_.

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

core::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)
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 make_strand_neighbor_two().

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

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

core::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: