Package rosetta :: Package protocols :: Package fldsgn :: Package topology :: Module _protocols_fldsgn_topology_

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Module _protocols_fldsgn_topology_

Classes

[hide private]

BB_Pos
///////////////////////////////////////////////////////////////////////////////////////////////////

BB_PosAP

BB_PosCAP

BetaAlphaBetaMotif
protocols/fldsgn/topology/BetaAlphaBetaMotif.hh:38

BetaAlphaBetaMotifAP

BetaAlphaBetaMotifCAP

BetaAlphaBetaMotifSet
/////////////////////////////////////////////////////////////////////////////////////////////////

BetaAlphaBetaMotifSetAP

BetaAlphaBetaMotifSetCAP

DimerPairing
protocols/fldsgn/topology/DimerPairing.hh:28

DimerPairingAP

DimerPairingCAP

DimerPairings
protocols/fldsgn/topology/DimerPairing.hh:162

DimerPairingsAP

DimerPairingsCAP

HSSTriplet
protocols/fldsgn/topology/HSSTriplet.hh:33

HSSTripletAP

HSSTripletCAP

HSSTripletSet
protocols/fldsgn/topology/HSSTriplet.hh:220

HSSTripletSetAP

HSSTripletSetCAP

Helix
///////////////////////////////////////////////////////////////////////////////////////////////////

HelixAP

HelixCAP

HelixPairing
protocols/fldsgn/topology/HelixPairing.hh:35

HelixPairingAP

HelixPairingCAP

HelixPairingSet
/////////////////////////////////////////////////////////////////////////////////////////////////////////

HelixPairingSetAP

HelixPairingSetCAP

Loop
///////////////////////////////////////////////////////////////////////////////////////////////////

LoopAP

LoopCAP

SS_Base
protocols/fldsgn/topology/SS_Info2.hh:40

SS_BaseAP

SS_BaseCAP

SS_Info2
///////////////////////////////////////////////////////////////////////////////////////////////////

SS_Info2AP

SS_Info2CAP

Sheet
protocols/fldsgn/topology/Sheet.hh:40

SheetAP

SheetCAP

SheetFoldType
List of topologies determined by strand pairings

SheetFoldTypeManager
/////////////////////////////////////////////////////////////////////////////////////////////////////////

SheetFoldTypeManagerAP

SheetFoldTypeManagerCAP

SheetSet
protocols/fldsgn/topology/Sheet.hh:160

SheetSetAP

SheetSetCAP

Strand
///////////////////////////////////////////////////////////////////////////////////////////////////

StrandAP

StrandCAP

StrandPairing
protocols/fldsgn/topology/StrandPairing.hh:37

StrandPairingAP

StrandPairingCAP

StrandPairingSet
/////////////////////////////////////////////////////////////////////////////////////////////////////////

StrandPairingSetAP

StrandPairingSetCAP

__CPP_SS_Info2__

Functions

[hide private]

calc_delta_sasa(...)
calc_delta_sasa( (Pose)pose, (object)intervals, (float)pore_radius) -> float : calc delta sasa, when a molecule is splited to 2parts.

calc_strand_pairing_set(...)
calc_strand_pairing_set( (Pose)pose, (__CPP_SS_Info2__)ssinfo [, (int)minimum_pair_length=1]) -> StrandPairingSet : convert StrandParingSet of dssp to fldsgn::topology::StrandPairingSet

check_internal_hbonds(...)
check_internal_hbonds( (Pose)pose, (int)begin, (int)end) -> object : protocols/fldsgn/topology/util.hh:63

check_kink_helix(...)
check_kink_helix( (Pose)pose, (int)begin, (int)end) -> int : check kink of helix, return number of loosen hydrogen

Variables

[hide private]

BAB_CFr = rosetta.protocols.fldsgn.topology._protocols_fldsgn_...

BABx1 = rosetta.protocols.fldsgn.topology._protocols_fldsgn_to...

BABx2 = rosetta.protocols.fldsgn.topology._protocols_fldsgn_to...

BABx3 = rosetta.protocols.fldsgn.topology._protocols_fldsgn_to...

BEFr = rosetta.protocols.fldsgn.topology._protocols_fldsgn_top...

BFr = rosetta.protocols.fldsgn.topology._protocols_fldsgn_topo...

CDFr = rosetta.protocols.fldsgn.topology._protocols_fldsgn_top...

CFr = rosetta.protocols.fldsgn.topology._protocols_fldsgn_topo...

DFr = rosetta.protocols.fldsgn.topology._protocols_fldsgn_topo...

DFr_BAB = rosetta.protocols.fldsgn.topology._protocols_fldsgn_...

DFr_HPN = rosetta.protocols.fldsgn.topology._protocols_fldsgn_...

EFr = rosetta.protocols.fldsgn.topology._protocols_fldsgn_topo...

Fd_like = rosetta.protocols.fldsgn.topology._protocols_fldsgn_...

Flavodoxin = rosetta.protocols.fldsgn.topology._protocols_flds...

HPN_CFr = rosetta.protocols.fldsgn.topology._protocols_fldsgn_...

NO_STRANDS = rosetta.protocols.fldsgn.topology._protocols_flds...

PG_like = rosetta.protocols.fldsgn.topology._protocols_fldsgn_...

Ploop2x3 = rosetta.protocols.fldsgn.topology._protocols_fldsgn...

Ploop3x3 = rosetta.protocols.fldsgn.topology._protocols_fldsgn...

RFd_like = rosetta.protocols.fldsgn.topology._protocols_fldsgn...

RNAseH = rosetta.protocols.fldsgn.topology._protocols_fldsgn_t...

RosI = rosetta.protocols.fldsgn.topology._protocols_fldsgn_top...

RosO = rosetta.protocols.fldsgn.topology._protocols_fldsgn_top...

Rsmn2x2 = rosetta.protocols.fldsgn.topology._protocols_fldsgn_...

Rsmn3x3 = rosetta.protocols.fldsgn.topology._protocols_fldsgn_...

Rsmn3x3_Half = rosetta.protocols.fldsgn.topology._protocols_fl...

Thio = rosetta.protocols.fldsgn.topology._protocols_fldsgn_top...

Thioredoxin = rosetta.protocols.fldsgn.topology._protocols_fld...

Top7 = rosetta.protocols.fldsgn.topology._protocols_fldsgn_top...

UNFOLD = rosetta.protocols.fldsgn.topology._protocols_fldsgn_t...

UNKNOWN = rosetta.protocols.fldsgn.topology._protocols_fldsgn_...

__package__ = None

n_fold_types = rosetta.protocols.fldsgn.topology._protocols_fl...

Function Details

[hide private]

calc_delta_sasa(...)


calc_delta_sasa( (Pose)pose, (object)intervals, (float)pore_radius) -> float :
    calc delta sasa, when a molecule is splited to 2parts.
    

    C++ signature :
        double calc_delta_sasa(core::pose::Pose,utility::vector1<protocols::forge::build::Interval, std::allocator<protocols::forge::build::Interval> >,double)

calc_strand_pairing_set(...)


calc_strand_pairing_set( (Pose)pose, (__CPP_SS_Info2__)ssinfo [, (int)minimum_pair_length=1]) -> StrandPairingSet :
    convert StrandParingSet of dssp to fldsgn::topology::StrandPairingSet
    

    C++ signature :
        protocols::fldsgn::topology::StrandPairingSet calc_strand_pairing_set(core::pose::Pose,boost::shared_ptr<protocols::fldsgn::topology::SS_Info2 const> [,unsigned long=1])

check_internal_hbonds(...)


check_internal_hbonds( (Pose)pose, (int)begin, (int)end) -> object :
    protocols/fldsgn/topology/util.hh:63

    C++ signature :
        utility::vector1<core::scoring::hbonds::HBond, std::allocator<core::scoring::hbonds::HBond> > check_internal_hbonds(core::pose::Pose,unsigned long,unsigned long)

check_kink_helix(...)


check_kink_helix( (Pose)pose, (int)begin, (int)end) -> int :
    check kink of helix, return number of loosen hydrogen
    

    C++ signature :
        unsigned long check_kink_helix(core::pose::Pose,unsigned long,unsigned long)

Variables Details

[hide private]

BAB_CFr

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.BAB_CFr

BABx1

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.BABx1

BABx2

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.BABx2

BABx3

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.BABx3

BEFr

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.BEFr

BFr

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.BFr

CDFr

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.CDFr

CFr

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.CFr

DFr

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.DFr

DFr_BAB

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.DFr_BAB

DFr_HPN

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.DFr_HPN

EFr

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.EFr

Fd_like

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.Fd_like

Flavodoxin

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.Flavodoxin

HPN_CFr

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.HPN_CFr

NO_STRANDS

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.NO_STRANDS

PG_like

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.PG_like

Ploop2x3

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.Ploop2x3

Ploop3x3

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.Ploop3x3

RFd_like

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.RFd_like

RNAseH

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.RNAseH

RosI

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.RosI

RosO

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.RosO

Rsmn2x2

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.Rsmn2x2

Rsmn3x3

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.Rsmn3x3

Rsmn3x3_Half

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.Rsmn3x3_Half

Thio

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.Thio

Thioredoxin

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.Thioredoxin

Top7

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.Top7

UNFOLD

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.UNFOLD

UNKNOWN

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.UNKNOWN

n_fold_types

Value:

rosetta.protocols.fldsgn.topology._protocols_fldsgn_topology_.SheetFol
dType.n_fold_types