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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
 
struct  TripletID
 

Typedefs

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

Enumerations

enum  SheetFoldType : char {
  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< core::Size, Real >::const_iterator a, std::map< core::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 &os, TripletID const &id)
 
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::set< core::Sizecompute_bulges (core::Size const strand_begin, core::Size const strand_end, utility::vector1< String > const &abego)
 
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...
 
core::Real calc_strand_helix_angle (core::pose::Pose const &pose, protocols::fldsgn::topology::SS_Info2_COP const ssinfo, core::Size const strand_id1, core::Size const strand_id2, core::Size const helix_id, std::string const &geom_type)
 

Typedef Documentation

typedef utility::pointer::shared_ptr< BetaAlphaBetaMotif const > protocols::fldsgn::topology::BetaAlphaBetaMotifCOP
typedef utility::pointer::shared_ptr< DimerPairing const > protocols::fldsgn::topology::DimerPairingCOP
typedef utility::pointer::shared_ptr< DimerPairing > protocols::fldsgn::topology::DimerPairingOP
typedef utility::vector1< HelixOP > protocols::fldsgn::topology::Helices
typedef utility::pointer::shared_ptr< Helix const > protocols::fldsgn::topology::HelixCOP
typedef utility::pointer::shared_ptr< Helix > protocols::fldsgn::topology::HelixOP
typedef utility::pointer::shared_ptr< HelixPairing const > protocols::fldsgn::topology::HelixPairingCOP
typedef utility::pointer::shared_ptr< HelixPairing > protocols::fldsgn::topology::HelixPairingOP
typedef utility::pointer::shared_ptr< HelixPairingSet const > protocols::fldsgn::topology::HelixPairingSetCOP
typedef utility::pointer::shared_ptr< HelixPairingSet > protocols::fldsgn::topology::HelixPairingSetOP
typedef HSSTriplets::const_iterator protocols::fldsgn::topology::HSSConstIterator
typedef HSSTriplets::iterator protocols::fldsgn::topology::HSSIterator
typedef utility::pointer::shared_ptr< HSSTriplet const > protocols::fldsgn::topology::HSSTripletCOP
typedef utility::pointer::shared_ptr< HSSTriplet > protocols::fldsgn::topology::HSSTripletOP
typedef utility::pointer::shared_ptr< HSSTripletSet const > protocols::fldsgn::topology::HSSTripletSetCOP
typedef utility::pointer::shared_ptr< HSSTripletSet > protocols::fldsgn::topology::HSSTripletSetOP
typedef utility::pointer::shared_ptr< Loop const > protocols::fldsgn::topology::LoopCOP
typedef utility::pointer::shared_ptr< Loop > protocols::fldsgn::topology::LoopOP
typedef utility::vector1< LoopOP > protocols::fldsgn::topology::Loops
typedef utility::pointer::shared_ptr< Sheet const > protocols::fldsgn::topology::SheetCOP
typedef utility::pointer::shared_ptr< Sheet > protocols::fldsgn::topology::SheetOP
typedef utility::vector1< SheetOP > protocols::fldsgn::topology::Sheets
typedef utility::pointer::shared_ptr< SheetSet const > protocols::fldsgn::topology::SheetSetCOP
typedef utility::pointer::shared_ptr< SheetSet > protocols::fldsgn::topology::SheetSetOP
typedef utility::pointer::shared_ptr< SS_Base const > protocols::fldsgn::topology::SS_BaseCOP
typedef utility::pointer::shared_ptr< SS_Base > protocols::fldsgn::topology::SS_BaseOP
typedef utility::pointer::shared_ptr< SS_Info2 const > protocols::fldsgn::topology::SS_Info2_COP
typedef utility::pointer::shared_ptr< SS_Info2 > protocols::fldsgn::topology::SS_Info2_OP
typedef utility::pointer::shared_ptr< Strand const > protocols::fldsgn::topology::StrandCOP
typedef utility::pointer::shared_ptr< Strand > protocols::fldsgn::topology::StrandOP
typedef utility::pointer::shared_ptr< StrandPairing const > protocols::fldsgn::topology::StrandPairingCOP
typedef utility::pointer::shared_ptr< StrandPairing > protocols::fldsgn::topology::StrandPairingOP
typedef utility::pointer::shared_ptr< StrandPairingSet const > protocols::fldsgn::topology::StrandPairingSetCOP
typedef utility::pointer::shared_ptr< StrandPairingSet > protocols::fldsgn::topology::StrandPairingSetOP
typedef utility::vector1< StrandOP > protocols::fldsgn::topology::Strands

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 
)
core::Real protocols::fldsgn::topology::calc_strand_helix_angle ( core::pose::Pose const &  pose,
protocols::fldsgn::topology::SS_Info2_COP const  ssinfo,
core::Size const  strand_id1,
core::Size const  strand_id2,
core::Size const  helix_id,
std::string const &  geom_type 
)
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< core::Size, Real >::const_iterator  a,
std::map< core::Size, Real >::const_iterator  b 
)
std::set< core::Size > protocols::fldsgn::topology::compute_bulges ( core::Size const  strand_begin,
core::Size const  strand_end,
utility::vector1< String > const &  abego 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  os,
TripletID const &  id 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const DimerPairing &  dp 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const HSSTriplet &  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 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 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const StrandPairing &  sp 
)
std::ostream& protocols::fldsgn::topology::operator<< ( std::ostream &  out,
const Helix &  hx 
)
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 
)
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 
)