Rosetta 3.4
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protocols::fldsgn::topology Namespace Reference

Classes

class  BB_Pos
class  BetaAlphaBetaMotif
class  BetaAlphaBetaMotifSet
class  DimerPairing
class  DimerPairings
class  HelixPairing
class  HelixPairingSet
class  HSSTriplet
class  HSSTripletSet
class  Sheet
class  SheetSet
class  SheetFoldTypeManager
class  SS_Base
class  Strand
class  Helix
class  Loop
class  SS_Info2
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.
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
std::ostream & operator<< (std::ostream &out, const HelixPairingSet &s)
 return helix pairing
std::ostream & operator<< (std::ostream &out, const HSSTriplet &s)
 IO Operator.
std::ostream & operator<< (std::ostream &out, const HSSTripletSet &s)
 IO Operator.
std::ostream & operator<< (std::ostream &out, const Sheet &s)
 return strand pairing
std::ostream & operator<< (std::ostream &out, const SheetSet &s)
 return strand pairing
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
std::ostream & operator<< (std::ostream &out, const StrandPairingSet &s)
 output detail of strand pairing set
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
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.
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
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

Typedef Documentation

typedef HSSTriplets::const_iterator protocols::fldsgn::topology::HSSConstIterator
typedef HSSTriplets::iterator protocols::fldsgn::topology::HSSIterator

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 
)

check kink of helix, return number of loosen hydrogen

References core::scoring::Energies::data(), core::pose::Pose::energies(), and core::scoring::EnergiesCacheableDataType::HBOND_SET.

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 DimerPairing &  dp 
)
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 HelixPairingSet &  s 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const SS_Info2 &  ssinfo 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const Loop &  lp 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const Helix &  hx 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const Strand &  st 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const SheetSet &  s 
)
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 StrandPairing &  sp 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const HSSTriplet &  s 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const HelixPairing &  hp 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const DimerPairings &  dps 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const HSSTripletSet &  s 
)
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::sort_by_length ( protocols::fldsgn::topology::StrandPairingCOP const  a,
protocols::fldsgn::topology::StrandPairingCOP const  b 
)
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