Rosetta Protocols  2014.35
Classes | Typedefs | Enumerations | Functions
protocols::fldsgn::topology Namespace Reference

Classes

class  BB_Pos
 
class  BetaAlphaBetaMotif
 
class  BetaAlphaBetaMotifSet
 
class  DimerPairing
 
class  DimerPairings
 
class  Helix
 
class  HelixPairing
 
class  HelixPairingSet
 
class  HSSTriplet
 
class  HSSTripletSet
 
class  Loop
 
class  Sheet
 
class  SheetFoldTypeManager
 
class  SheetSet
 
class  SS_Base
 
class  SS_Info2
 
class  Strand
 
class  StrandPairing
 
class  StrandPairingSet
 

Typedefs

typedef
utility::pointer::owning_ptr
< BetaAlphaBetaMotif
BetaAlphaBetaMotifOP
 
typedef
utility::pointer::owning_ptr
< BetaAlphaBetaMotif const > 
BetaAlphaBetaMotifCOP
 
typedef utility::vector1
< BetaAlphaBetaMotifOP
BetaAlphaBetaMotifs
 
typedef
utility::pointer::owning_ptr
< BetaAlphaBetaMotifSet
BetaAlphaBetaMotifSetOP
 
typedef
utility::pointer::owning_ptr
< BetaAlphaBetaMotifSet const > 
BetaAlphaBetaMotifSetCOP
 
typedef
utility::pointer::owning_ptr
< DimerPairing
DimerPairingOP
 
typedef
utility::pointer::owning_ptr
< DimerPairing const > 
DimerPairingCOP
 
typedef
utility::pointer::owning_ptr
< HelixPairing
HelixPairingOP
 
typedef
utility::pointer::owning_ptr
< HelixPairingSet
HelixPairingSetOP
 
typedef
utility::pointer::owning_ptr
< HelixPairing const > 
HelixPairingCOP
 
typedef
utility::pointer::owning_ptr
< HelixPairingSet const > 
HelixPairingSetCOP
 
typedef utility::vector1
< HelixPairingOP
HelixPairings
 
typedef
utility::pointer::owning_ptr
< HSSTriplet
HSSTripletOP
 
typedef
utility::pointer::owning_ptr
< HSSTripletSet
HSSTripletSetOP
 
typedef
utility::pointer::owning_ptr
< HSSTriplet const > 
HSSTripletCOP
 
typedef
utility::pointer::owning_ptr
< HSSTripletSet const > 
HSSTripletSetCOP
 
typedef utility::vector1
< HSSTripletOP
HSSTriplets
 
typedef HSSTriplets::const_iterator HSSConstIterator
 
typedef HSSTriplets::iterator HSSIterator
 
typedef
utility::pointer::owning_ptr
< Sheet
SheetOP
 
typedef
utility::pointer::owning_ptr
< Sheet const > 
SheetCOP
 
typedef utility::vector1< SheetOPSheets
 
typedef
utility::pointer::owning_ptr
< SheetSet
SheetSetOP
 
typedef
utility::pointer::owning_ptr
< SheetSet const > 
SheetSetCOP
 
typedef utility::vector1
< SheetFoldType
SheetFoldTypes
 
typedef
utility::pointer::owning_ptr
< SS_Base
SS_BaseOP
 
typedef
utility::pointer::owning_ptr
< Helix
HelixOP
 
typedef
utility::pointer::owning_ptr
< Strand
StrandOP
 
typedef
utility::pointer::owning_ptr
< Loop
LoopOP
 
typedef
utility::pointer::owning_ptr
< SS_Base const > 
SS_BaseCOP
 
typedef
utility::pointer::owning_ptr
< Helix const > 
HelixCOP
 
typedef
utility::pointer::owning_ptr
< Strand const > 
StrandCOP
 
typedef
utility::pointer::owning_ptr
< Loop const > 
LoopCOP
 
typedef utility::vector1< HelixOPHelices
 
typedef utility::vector1
< StrandOP
Strands
 
typedef utility::vector1< LoopOPLoops
 
typedef
utility::pointer::owning_ptr
< SS_Info2
SS_Info2_OP
 
typedef
utility::pointer::owning_ptr
< SS_Info2 const > 
SS_Info2_COP
 
typedef
utility::pointer::owning_ptr
< StrandPairing
StrandPairingOP
 
typedef
utility::pointer::owning_ptr
< StrandPairingSet
StrandPairingSetOP
 
typedef
utility::pointer::owning_ptr
< StrandPairing const > 
StrandPairingCOP
 
typedef
utility::pointer::owning_ptr
< StrandPairingSet const > 
StrandPairingSetCOP
 
typedef utility::vector1
< StrandPairingOP
StrandPairings
 

Enumerations

enum  SheetFoldType {
  BABx1 = 1, RosI, RosO, BABx2,
  Thio, BFr, EFr, CFr,
  DFr, Rsmn2x2, Rsmn3x3_Half, BABx3,
  PG_like, Thioredoxin, BAB_CFr, DFr_BAB,
  BEFr, Fd_like, RFd_like, CDFr,
  HPN_CFr, DFr_HPN, Flavodoxin, Ploop2x3,
  RNAseH, Top7, Rsmn3x3, Ploop3x3,
  UNFOLD, NO_STRANDS, UNKNOWN, n_fold_types = UNKNOWN
}
 List of topologies determined by strand pairings. More...
 

Functions

std::ostream & operator<< (std::ostream &out, const BetaAlphaBetaMotif &s)
 IO operator. More...
 
bool compare (std::map< Size, Real >::const_iterator a, std::map< Size, Real >::const_iterator b)
 
std::ostream & operator<< (std::ostream &out, const BetaAlphaBetaMotifSet &s)
 
std::ostream & operator<< (std::ostream &out, const DimerPairing &dp)
 
bool pointer_sorter (DimerPairingCOP const a, DimerPairingCOP const b)
 
std::ostream & operator<< (std::ostream &out, const DimerPairings &dps)
 
std::ostream & operator<< (std::ostream &out, const HelixPairing &hp)
 return name More...
 
std::ostream & operator<< (std::ostream &out, const HelixPairingSet &s)
 return helix pairing More...
 
std::ostream & operator<< (std::ostream &out, const HSSTriplet &s)
 IO Operator. More...
 
std::ostream & operator<< (std::ostream &out, const HSSTripletSet &s)
 IO Operator. More...
 
std::ostream & operator<< (std::ostream &out, const Sheet &s)
 return strand pairing More...
 
std::ostream & operator<< (std::ostream &out, const SheetSet &s)
 return strand pairing More...
 
std::ostream & operator<< (std::ostream &out, const Strand &st)
 
std::ostream & operator<< (std::ostream &out, const Helix &hx)
 
std::ostream & operator<< (std::ostream &out, const Loop &lp)
 
std::ostream & operator<< (std::ostream &out, const SS_Info2 &ssinfo)
 
std::ostream & operator<< (std::ostream &out, const StrandPairing &sp)
 return name More...
 
std::ostream & operator<< (std::ostream &out, const StrandPairingSet &s)
 output detail of strand pairing set More...
 
bool pointer_sorter (StrandPairingCOP const a, StrandPairingCOP const b)
 
bool sort_by_length (protocols::fldsgn::topology::StrandPairingCOP const a, protocols::fldsgn::topology::StrandPairingCOP const b)
 
protocols::fldsgn::topology::StrandPairingSet calc_strand_pairing_set (core::pose::Pose const &pose, protocols::fldsgn::topology::SS_Info2_COP const ssinfo, core::Size minimum_pair_length)
 convert StrandParingSet of dssp to fldsgn::topology::StrandPairingSet More...
 
core::Real calc_delta_sasa (core::pose::Pose const &pose, utility::vector1< protocols::forge::build::Interval > intervals, Real const pore_radius)
 calc delta sasa, when a molecule is splited to 2parts. More...
 
core::Size check_kink_helix (core::pose::Pose const &pose, core::Size const begin, core::Size const end)
 check kink of helix, return number of loosen hydrogen More...
 
utility::vector1
< core::scoring::hbonds::HBond
check_internal_hbonds (core::pose::Pose const &pose, core::Size const begin, core::Size const end)
 check kink of helix, return number of loosen hydrogen More...
 

Typedef Documentation

Enumeration Type Documentation

List of topologies determined by strand pairings.

Enumerator
BABx1 
RosI 

3strands

RosO 
BABx2 
Thio 
BFr 
EFr 
CFr 
DFr 
Rsmn2x2 

4strands

Rsmn3x3_Half 

rossmann2x2

BABx3 

Half structure of Rossmann3x3.

PG_like 
Thioredoxin 
BAB_CFr 
DFr_BAB 
BEFr 
Fd_like 
RFd_like 

ferredoxin-like

CDFr 

reverse ferredoxin-like

HPN_CFr 
DFr_HPN 
Flavodoxin 

5strands

Ploop2x3 
RNAseH 

mixture

Top7 
Rsmn3x3 

6 strands

Ploop3x3 
UNFOLD 
NO_STRANDS 
UNKNOWN 
n_fold_types 

Function Documentation

core::Real protocols::fldsgn::topology::calc_delta_sasa ( core::pose::Pose const &  pose,
utility::vector1< protocols::forge::build::Interval intervals,
Real const  pore_radius 
)
protocols::fldsgn::topology::StrandPairingSet protocols::fldsgn::topology::calc_strand_pairing_set ( core::pose::Pose const &  pose,
protocols::fldsgn::topology::SS_Info2_COP const  ssinfo,
core::Size  minimum_pair_length 
)
utility::vector1< core::scoring::hbonds::HBond > protocols::fldsgn::topology::check_internal_hbonds ( core::pose::Pose const &  pose,
core::Size const  begin,
core::Size const  end 
)
core::Size protocols::fldsgn::topology::check_kink_helix ( core::pose::Pose const &  pose,
core::Size const  begin,
core::Size const  end 
)
bool protocols::fldsgn::topology::compare ( std::map< Size, Real >::const_iterator  a,
std::map< Size, Real >::const_iterator  b 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const HSSTriplet &  s 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const DimerPairing &  dp 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const Sheet &  s 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const BetaAlphaBetaMotif &  s 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const Strand &  st 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const HelixPairing &  hp 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const DimerPairings &  dps 
)

References I, and LJ.

std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const Helix &  hx 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const StrandPairing &  sp 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const Loop &  lp 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const HelixPairingSet &  s 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const HSSTripletSet &  s 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const SheetSet &  s 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const SS_Info2 &  ssinfo 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const StrandPairingSet &  s 
)

output detail of strand pairing set

return strand pairing

References protocols::fldsgn::topology::StrandPairingSet::name(), and protocols::fldsgn::topology::StrandPairingSet::strand_pairings().

std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const BetaAlphaBetaMotifSet &  s 
)
bool protocols::fldsgn::topology::pointer_sorter ( DimerPairingCOP const  a,
DimerPairingCOP const  b 
)
bool protocols::fldsgn::topology::pointer_sorter ( StrandPairingCOP const  a,
StrandPairingCOP const  b 
)
bool protocols::fldsgn::topology::sort_by_length ( protocols::fldsgn::topology::StrandPairingCOP const  a,
protocols::fldsgn::topology::StrandPairingCOP const  b 
)