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- builtins.object
-
- BB_Pos
- BetaAlphaBetaMotif
- BetaAlphaBetaMotifSet
- DimerPairing
- HSSTriplet
- HSSTripletSet
- HelixPairing
- HelixPairingSet
- SS_Base
-
- Helix
- Loop
- Strand
- Sheet
- SheetFoldType
- SheetFoldTypeManager
- SheetSet
- StrandPairing
- StrandPairingSet
- rosetta.basic.datacache.CacheableData(builtins.object)
-
- SS_Info2
- rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t(builtins.object)
-
- DimerPairings
class BB_Pos(builtins.object) |
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///////////////////////////////////////////////////////////////////////////////////////////////////
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Methods defined here:
- C(...) from builtins.PyCapsule
- C(self : rosetta.protocols.fldsgn.topology.BB_Pos, i : int) -> rosetta.numeric.xyzVector_double_t
accessor for C's coordinate on residue i, requires take_coordinates_from_pose have been recently called.
- CA(...) from builtins.PyCapsule
- CA(self : rosetta.protocols.fldsgn.topology.BB_Pos, i : int) -> rosetta.numeric.xyzVector_double_t
accessor for CA's coordinate on residue i, requires take_coordinates_from_pose have been recently called.
- CB(...) from builtins.PyCapsule
- CB(self : rosetta.protocols.fldsgn.topology.BB_Pos, i : int) -> rosetta.numeric.xyzVector_double_t
accessor for CB's coordinate on residue i, requires take_coordinates_from_pose have been recently called.
- N(...) from builtins.PyCapsule
- N(self : rosetta.protocols.fldsgn.topology.BB_Pos, i : int) -> rosetta.numeric.xyzVector_double_t
accessor for N's coordinate on residue i, requires take_coordinates_from_pose have been recently called.
- O(...) from builtins.PyCapsule
- O(self : rosetta.protocols.fldsgn.topology.BB_Pos, i : int) -> rosetta.numeric.xyzVector_double_t
accessor for O's coordinate on residue i, requires take_coordinates_from_pose have been recently called.
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.protocols.fldsgn.topology.BB_Pos) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.fldsgn.topology.BB_Pos, : rosetta.protocols.fldsgn.topology.BB_Pos) -> rosetta.protocols.fldsgn.topology.BB_Pos
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.fldsgn.topology.BB_Pos) -> NoneType
- resize(...) from builtins.PyCapsule
- resize(self : rosetta.protocols.fldsgn.topology.BB_Pos, nres : int) -> NoneType
- size(...) from builtins.PyCapsule
- size(rosetta.protocols.fldsgn.topology.BB_Pos) -> int
@
- take_coordinates_from_pose(...) from builtins.PyCapsule
- take_coordinates_from_pose(self : rosetta.protocols.fldsgn.topology.BB_Pos, pose : rosetta.core.pose.Pose) -> NoneType
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class BetaAlphaBetaMotif(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) -> NoneType
2. __init__(self : rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif, strand1 : int, strand2 : int, helix : int, cross_over : int) -> NoneType
3. __init__(self : rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif, s : rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif, : rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) -> rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif
- calc_geometry(...) from builtins.PyCapsule
- calc_geometry(self : rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif, ssinfo : rosetta.protocols.fldsgn.topology.SS_Info2, sheet_set : protocols::fldsgn::topology::SheetSet) -> NoneType
- calc_inout(...) from builtins.PyCapsule
- calc_inout(self : rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif, ssinfo : rosetta.protocols.fldsgn.topology.SS_Info2, resi : int) -> int
- cross_over(...) from builtins.PyCapsule
- cross_over(rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) -> int
- helix(...) from builtins.PyCapsule
- helix(rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) -> int
- helix_cycle(...) from builtins.PyCapsule
- helix_cycle(rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) -> rosetta.utility.vector1_unsigned_long
- helix_cycle_as_string(...) from builtins.PyCapsule
- helix_cycle_as_string(rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) -> str
- hs1_dist(...) from builtins.PyCapsule
- hs1_dist(rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) -> float
- hs2_dist(...) from builtins.PyCapsule
- hs2_dist(rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) -> float
- hs_angle(...) from builtins.PyCapsule
- hs_angle(rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) -> float
- hsheet_dist(...) from builtins.PyCapsule
- hsheet_dist(rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) -> float
- hsheet_elev_angle(...) from builtins.PyCapsule
- hsheet_elev_angle(rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) -> float
- is_lefthanded(...) from builtins.PyCapsule
- is_lefthanded(rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) -> bool
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) -> str
- strand1(...) from builtins.PyCapsule
- strand1(rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) -> int
- strand2(...) from builtins.PyCapsule
- strand2(rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) -> int
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class BetaAlphaBetaMotifSet(builtins.object) |
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/////////////////////////////////////////////////////////////////////////////////////////////////
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet) -> NoneType
2. __init__(self : rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet, bab_motifs : rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_BetaAlphaBetaMotif_t) -> NoneType
3. __init__(self : rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet, ssinfo : rosetta.protocols.fldsgn.topology.SS_Info2, sheet_set : protocols::fldsgn::topology::SheetSet) -> NoneType
4. __init__(self : rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet, s : rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet, : rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet) -> rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet
- bab_motif(...) from builtins.PyCapsule
- bab_motif(self : rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet, i : int) -> rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif
- bab_motifs(...) from builtins.PyCapsule
- bab_motifs(rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet) -> rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_BetaAlphaBetaMotif_t
- calc_geometry(...) from builtins.PyCapsule
- calc_geometry(self : rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet, ssinfo : rosetta.protocols.fldsgn.topology.SS_Info2, sheet_set : protocols::fldsgn::topology::SheetSet) -> NoneType
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet) -> NoneType
- push_back(...) from builtins.PyCapsule
- push_back(self : rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet, bop : rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) -> NoneType
- set_babmotifs(...) from builtins.PyCapsule
- set_babmotifs(self : rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet, ssinfo : rosetta.protocols.fldsgn.topology.SS_Info2, sheet_set : protocols::fldsgn::topology::SheetSet) -> NoneType
- size(...) from builtins.PyCapsule
- size(rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet) -> int
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class DimerPairing(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(self : rosetta.protocols.fldsgn.topology.DimerPairing, res1 : int, res2 : int, dist : float, phi : float, theta : float, sigma : float, dp : float, sign1 : int, sign2 : int, score : float) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.fldsgn.topology.DimerPairing) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.fldsgn.topology.DimerPairing, : rosetta.protocols.fldsgn.topology.DimerPairing) -> rosetta.protocols.fldsgn.topology.DimerPairing
- dist(...) from builtins.PyCapsule
- dist(rosetta.protocols.fldsgn.topology.DimerPairing) -> float
- dp(...) from builtins.PyCapsule
- dp(rosetta.protocols.fldsgn.topology.DimerPairing) -> float
- is_parallel(...) from builtins.PyCapsule
- is_parallel(self : rosetta.protocols.fldsgn.topology.DimerPairing, phi : float, theta : float) -> bool
- orient(...) from builtins.PyCapsule
- orient(rosetta.protocols.fldsgn.topology.DimerPairing) -> str
- phi(...) from builtins.PyCapsule
- phi(rosetta.protocols.fldsgn.topology.DimerPairing) -> float
- res1(...) from builtins.PyCapsule
- res1(rosetta.protocols.fldsgn.topology.DimerPairing) -> int
- res2(...) from builtins.PyCapsule
- res2(rosetta.protocols.fldsgn.topology.DimerPairing) -> int
- score(...) from builtins.PyCapsule
- score(rosetta.protocols.fldsgn.topology.DimerPairing) -> float
- sigma(...) from builtins.PyCapsule
- sigma(rosetta.protocols.fldsgn.topology.DimerPairing) -> float
- sign1(...) from builtins.PyCapsule
- sign1(rosetta.protocols.fldsgn.topology.DimerPairing) -> int
- sign2(...) from builtins.PyCapsule
- sign2(rosetta.protocols.fldsgn.topology.DimerPairing) -> int
- theta(...) from builtins.PyCapsule
- theta(rosetta.protocols.fldsgn.topology.DimerPairing) -> float
- valid(...) from builtins.PyCapsule
- valid(*args, **kwargs)
Overloaded function.
1. valid(rosetta.protocols.fldsgn.topology.DimerPairing) -> bool
2. valid(self : rosetta.protocols.fldsgn.topology.DimerPairing, v : bool) -> NoneType
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class DimerPairings(rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t) |
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- Method resolution order:
- DimerPairings
- rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.protocols.fldsgn.topology.DimerPairings) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.fldsgn.topology.DimerPairings) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.fldsgn.topology.DimerPairings, : rosetta.protocols.fldsgn.topology.DimerPairings) -> rosetta.protocols.fldsgn.topology.DimerPairings
- finalize(...) from builtins.PyCapsule
- finalize(self : rosetta.protocols.fldsgn.topology.DimerPairings, ss_info : rosetta.protocols.fldsgn.topology.SS_Info2) -> NoneType
Methods inherited from rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t:
- __bool__(...) from builtins.PyCapsule
- __bool__(rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t) -> bool
Check whether the list is nonempty
- __contains__(...) from builtins.PyCapsule
- __contains__(rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t, protocols::fldsgn::topology::DimerPairing) -> bool
return true if item in the container
- __eq__(...) from builtins.PyCapsule
- __eq__(rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t, rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t) -> bool
- __getitem__(...) from builtins.PyCapsule
- __getitem__(rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t, int) -> protocols::fldsgn::topology::DimerPairing
- __iter__(...) from builtins.PyCapsule
- __iter__(rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t) -> iterator
- __len__(...) from builtins.PyCapsule
- __len__(rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t) -> int
- __ne__(...) from builtins.PyCapsule
- __ne__(rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t, rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t) -> bool
- __repr__(...) from builtins.PyCapsule
- __repr__(rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t) -> str
- __setitem__(...) from builtins.PyCapsule
- __setitem__(rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t, int, protocols::fldsgn::topology::DimerPairing) -> NoneType
- append(...) from builtins.PyCapsule
- append(rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t, protocols::fldsgn::topology::DimerPairing) -> NoneType
adds an element to the end
- back(...) from builtins.PyCapsule
- back(rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t) -> protocols::fldsgn::topology::DimerPairing
access the last element
- capacity(...) from builtins.PyCapsule
- capacity(std::vector<std::shared_ptr<protocols::fldsgn::topology::DimerPairing>, std::allocator<std::shared_ptr<protocols::fldsgn::topology::DimerPairing> > >) -> int
returns the number of elements that can be held in currently allocated storage
- clear(...) from builtins.PyCapsule
- clear(std::vector<std::shared_ptr<protocols::fldsgn::topology::DimerPairing>, std::allocator<std::shared_ptr<protocols::fldsgn::topology::DimerPairing> > >) -> NoneType
clears the contents
- count(...) from builtins.PyCapsule
- count(rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t, protocols::fldsgn::topology::DimerPairing) -> int
counts the elements that are equal to value
- erase(...) from builtins.PyCapsule
- erase(rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t, int) -> NoneType
erases element at index
- extend = _vector_extend_func(vec, othervec)
- # Vector compatibility: Adding 'extend' to all utility.vector* functions
- front(...) from builtins.PyCapsule
- front(rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t) -> protocols::fldsgn::topology::DimerPairing
access the first element
- l(...) from builtins.PyCapsule
- l(rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t) -> int
lower index
- max_size(...) from builtins.PyCapsule
- max_size(std::vector<std::shared_ptr<protocols::fldsgn::topology::DimerPairing>, std::allocator<std::shared_ptr<protocols::fldsgn::topology::DimerPairing> > >) -> int
returns the maximum possible number of elements
- pop(...) from builtins.PyCapsule
- pop(*args, **kwargs)
Overloaded function.
1. pop(rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t) -> protocols::fldsgn::topology::DimerPairing
remove and return last item
2. pop(rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t, int) -> protocols::fldsgn::topology::DimerPairing
remove and return item at index
- remove(...) from builtins.PyCapsule
- remove(rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t, protocols::fldsgn::topology::DimerPairing) -> NoneType
Remove the first item from the list whose value is x. It is an error if there is no such item.
- reserve(...) from builtins.PyCapsule
- reserve(std::vector<std::shared_ptr<protocols::fldsgn::topology::DimerPairing>, std::allocator<std::shared_ptr<protocols::fldsgn::topology::DimerPairing> > >, int) -> NoneType
reserves storage
- resize(...) from builtins.PyCapsule
- resize(rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t, int) -> NoneType
changes the number of elements stored
- shrink_to_fit(...) from builtins.PyCapsule
- shrink_to_fit(std::vector<std::shared_ptr<protocols::fldsgn::topology::DimerPairing>, std::allocator<std::shared_ptr<protocols::fldsgn::topology::DimerPairing> > >) -> NoneType
reduces memory usage by freeing unused memory
- u(...) from builtins.PyCapsule
- u(rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t) -> int
upper index
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class HSSTriplet(builtins.object) |
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Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(self : rosetta.protocols.fldsgn.topology.HSSTriplet, rval : rosetta.protocols.fldsgn.topology.HSSTriplet) -> bool
operator ==
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.fldsgn.topology.HSSTriplet) -> NoneType
2. __init__(self : rosetta.protocols.fldsgn.topology.HSSTriplet, h : int, s1 : int, s2 : int) -> NoneType
3. __init__(self : rosetta.protocols.fldsgn.topology.HSSTriplet, hss : str) -> NoneType
4. __init__(self : rosetta.protocols.fldsgn.topology.HSSTriplet, hss : rosetta.protocols.fldsgn.topology.HSSTriplet) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.fldsgn.topology.HSSTriplet) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.fldsgn.topology.HSSTriplet, : rosetta.protocols.fldsgn.topology.HSSTriplet) -> rosetta.protocols.fldsgn.topology.HSSTriplet
- calc_geometry(...) from builtins.PyCapsule
- calc_geometry(self : rosetta.protocols.fldsgn.topology.HSSTriplet, ssinfo : protocols::fldsgn::topology::SS_Info2) -> NoneType
- geometry_is_initialized(...) from builtins.PyCapsule
- geometry_is_initialized(rosetta.protocols.fldsgn.topology.HSSTriplet) -> bool
geometry is initialized or not
- helix(...) from builtins.PyCapsule
- helix(rosetta.protocols.fldsgn.topology.HSSTriplet) -> int
- hs1_dist(...) from builtins.PyCapsule
- hs1_dist(rosetta.protocols.fldsgn.topology.HSSTriplet) -> float
distance between mid helix and midpoint of 1st strand
- hs1_orient(...) from builtins.PyCapsule
- hs1_orient(rosetta.protocols.fldsgn.topology.HSSTriplet) -> str
orientation between helix and 1st strand
- hs2_dist(...) from builtins.PyCapsule
- hs2_dist(rosetta.protocols.fldsgn.topology.HSSTriplet) -> float
distance between mid helix and midpoint of 2nd strand
- hs2_orient(...) from builtins.PyCapsule
- hs2_orient(rosetta.protocols.fldsgn.topology.HSSTriplet) -> str
orientation between helix and 2nd strand
- hs_angle(...) from builtins.PyCapsule
- hs_angle(rosetta.protocols.fldsgn.topology.HSSTriplet) -> float
return distance between sheet ( defined by the 2 strands ) and helix
- hsheet_dist(...) from builtins.PyCapsule
- hsheet_dist(rosetta.protocols.fldsgn.topology.HSSTriplet) -> float
reutrn distance between sheet ( defined by the 2 strands ) and helix
- left_handed(...) from builtins.PyCapsule
- left_handed(rosetta.protocols.fldsgn.topology.HSSTriplet) -> bool
hsstriplet is left handed or not
- ss_dist(...) from builtins.PyCapsule
- ss_dist(rosetta.protocols.fldsgn.topology.HSSTriplet) -> float
distance between midpoints of strands
- ss_orient(...) from builtins.PyCapsule
- ss_orient(rosetta.protocols.fldsgn.topology.HSSTriplet) -> str
orientation between strands
- strand1(...) from builtins.PyCapsule
- strand1(rosetta.protocols.fldsgn.topology.HSSTriplet) -> int
- strand2(...) from builtins.PyCapsule
- strand2(rosetta.protocols.fldsgn.topology.HSSTriplet) -> int
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class HSSTripletSet(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.fldsgn.topology.HSSTripletSet) -> NoneType
2. __init__(self : rosetta.protocols.fldsgn.topology.HSSTripletSet, s : rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_HSSTriplet_t) -> NoneType
3. __init__(self : rosetta.protocols.fldsgn.topology.HSSTripletSet, s : str) -> NoneType
4. __init__(self : rosetta.protocols.fldsgn.topology.HSSTripletSet, s : rosetta.protocols.fldsgn.topology.HSSTripletSet) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.fldsgn.topology.HSSTripletSet) -> str
- add_hsstriplets(...) from builtins.PyCapsule
- add_hsstriplets(self : rosetta.protocols.fldsgn.topology.HSSTripletSet, s : rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_HSSTriplet_t) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.fldsgn.topology.HSSTripletSet, : rosetta.protocols.fldsgn.topology.HSSTripletSet) -> rosetta.protocols.fldsgn.topology.HSSTripletSet
- begin(...) from builtins.PyCapsule
- begin(*args, **kwargs)
Overloaded function.
1. begin(rosetta.protocols.fldsgn.topology.HSSTripletSet) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::fldsgn::topology::HSSTriplet>*, std::vector<std::shared_ptr<protocols::fldsgn::topology::HSSTriplet>, std::allocator<std::shared_ptr<protocols::fldsgn::topology::HSSTriplet> > > >
return an interator that points to the first HSSTripletOP
2. begin(rosetta.protocols.fldsgn.topology.HSSTripletSet) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::fldsgn::topology::HSSTriplet> const*, std::vector<std::shared_ptr<protocols::fldsgn::topology::HSSTriplet>, std::allocator<std::shared_ptr<protocols::fldsgn::topology::HSSTriplet> > > >
return an const interator that points to the first HSSTripletOP
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.fldsgn.topology.HSSTripletSet) -> NoneType
- end(...) from builtins.PyCapsule
- end(*args, **kwargs)
Overloaded function.
1. end(rosetta.protocols.fldsgn.topology.HSSTripletSet) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::fldsgn::topology::HSSTriplet>*, std::vector<std::shared_ptr<protocols::fldsgn::topology::HSSTriplet>, std::allocator<std::shared_ptr<protocols::fldsgn::topology::HSSTriplet> > > >
return an interator that points beyond the last HSSTripletOP
2. end(rosetta.protocols.fldsgn.topology.HSSTripletSet) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::fldsgn::topology::HSSTriplet> const*, std::vector<std::shared_ptr<protocols::fldsgn::topology::HSSTriplet>, std::allocator<std::shared_ptr<protocols::fldsgn::topology::HSSTriplet> > > >
return an const interator that points beyond the last HSSTripletOP
- hss_triplet(...) from builtins.PyCapsule
- hss_triplet(self : rosetta.protocols.fldsgn.topology.HSSTripletSet, helix : int) -> rosetta.protocols.fldsgn.topology.HSSTriplet
- hss_triplets(...) from builtins.PyCapsule
- hss_triplets(rosetta.protocols.fldsgn.topology.HSSTripletSet) -> rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_HSSTriplet_t
- push_back(...) from builtins.PyCapsule
- push_back(self : rosetta.protocols.fldsgn.topology.HSSTripletSet, hssop : rosetta.protocols.fldsgn.topology.HSSTriplet) -> NoneType
- size(...) from builtins.PyCapsule
- size(rosetta.protocols.fldsgn.topology.HSSTripletSet) -> int
return the size of vector of hss_triplets_
|
class Helix(SS_Base) |
| |
///////////////////////////////////////////////////////////////////////////////////////////////////
|
| |
- Method resolution order:
- Helix
- SS_Base
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.fldsgn.topology.Helix) -> NoneType
2. __init__(self : rosetta.protocols.fldsgn.topology.Helix, begin : int, end : int) -> NoneType
3. __init__(self : rosetta.protocols.fldsgn.topology.Helix, s : rosetta.protocols.fldsgn.topology.Helix) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.fldsgn.topology.Helix) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.fldsgn.topology.Helix, : rosetta.protocols.fldsgn.topology.Helix) -> rosetta.protocols.fldsgn.topology.Helix
- bend(...) from builtins.PyCapsule
- bend(rosetta.protocols.fldsgn.topology.Helix) -> float
- calc_geometry(...) from builtins.PyCapsule
- calc_geometry(self : rosetta.protocols.fldsgn.topology.Helix, bbpos : rosetta.protocols.fldsgn.topology.BB_Pos) -> NoneType
calc geometry of helix
Methods inherited from SS_Base:
- Cend_orient(...) from builtins.PyCapsule
- Cend_orient(rosetta.protocols.fldsgn.topology.SS_Base) -> rosetta.numeric.xyzVector_double_t
- Cend_pos(...) from builtins.PyCapsule
- Cend_pos(rosetta.protocols.fldsgn.topology.SS_Base) -> rosetta.numeric.xyzVector_double_t
- Nend_orient(...) from builtins.PyCapsule
- Nend_orient(rosetta.protocols.fldsgn.topology.SS_Base) -> rosetta.numeric.xyzVector_double_t
- Nend_pos(...) from builtins.PyCapsule
- Nend_pos(rosetta.protocols.fldsgn.topology.SS_Base) -> rosetta.numeric.xyzVector_double_t
- begin(...) from builtins.PyCapsule
- begin(rosetta.protocols.fldsgn.topology.SS_Base) -> int
- end(...) from builtins.PyCapsule
- end(rosetta.protocols.fldsgn.topology.SS_Base) -> int
- is_geometry_initialized(...) from builtins.PyCapsule
- is_geometry_initialized(rosetta.protocols.fldsgn.topology.SS_Base) -> bool
- length(...) from builtins.PyCapsule
- length(rosetta.protocols.fldsgn.topology.SS_Base) -> int
- mid_pos(...) from builtins.PyCapsule
- mid_pos(rosetta.protocols.fldsgn.topology.SS_Base) -> rosetta.numeric.xyzVector_double_t
- orient(...) from builtins.PyCapsule
- orient(rosetta.protocols.fldsgn.topology.SS_Base) -> rosetta.numeric.xyzVector_double_t
|
class HelixPairing(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.fldsgn.topology.HelixPairing) -> NoneType
2. __init__(self : rosetta.protocols.fldsgn.topology.HelixPairing, h1 : int, h2 : int, o : str) -> NoneType
3. __init__(self : rosetta.protocols.fldsgn.topology.HelixPairing, hp : str) -> NoneType
4. __init__(self : rosetta.protocols.fldsgn.topology.HelixPairing, hp : rosetta.protocols.fldsgn.topology.HelixPairing) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.fldsgn.topology.HelixPairing) -> str
- align_angle(...) from builtins.PyCapsule
- align_angle(rosetta.protocols.fldsgn.topology.HelixPairing) -> float
helix angle projected on sheet helices belongs to
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.fldsgn.topology.HelixPairing, : rosetta.protocols.fldsgn.topology.HelixPairing) -> rosetta.protocols.fldsgn.topology.HelixPairing
- calc_geometry(...) from builtins.PyCapsule
- calc_geometry(self : rosetta.protocols.fldsgn.topology.HelixPairing, ss_info : protocols::fldsgn::topology::SS_Info2) -> NoneType
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.fldsgn.topology.HelixPairing) -> rosetta.protocols.fldsgn.topology.HelixPairing
clone this object
- cross_angle(...) from builtins.PyCapsule
- cross_angle(rosetta.protocols.fldsgn.topology.HelixPairing) -> float
- dist(...) from builtins.PyCapsule
- dist(rosetta.protocols.fldsgn.topology.HelixPairing) -> float
- h1(...) from builtins.PyCapsule
- h1(rosetta.protocols.fldsgn.topology.HelixPairing) -> int
the strand number of the 1st strand in strand pairing
- h2(...) from builtins.PyCapsule
- h2(rosetta.protocols.fldsgn.topology.HelixPairing) -> int
the strand number of the 2nd strand in strand pairing
- initialize(...) from builtins.PyCapsule
- initialize(rosetta.protocols.fldsgn.topology.HelixPairing) -> NoneType
- is_parallel(...) from builtins.PyCapsule
- is_parallel(rosetta.protocols.fldsgn.topology.HelixPairing) -> bool
is parallel
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.fldsgn.topology.HelixPairing) -> str
HelixPairing is descripbed as s1()-s2().orient()
For example, 2-3.A means 2nd and 3rd helices make anti-parallel helix_pairing
- orient(...) from builtins.PyCapsule
- orient(rosetta.protocols.fldsgn.topology.HelixPairing) -> str
orientation, parallel or anti-parallel, of helix pairing
|
class HelixPairingSet(builtins.object) |
| |
/////////////////////////////////////////////////////////////////////////////////////////////////////////
|
| |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.fldsgn.topology.HelixPairingSet) -> NoneType
2. __init__(self : rosetta.protocols.fldsgn.topology.HelixPairingSet, helix_pairings : rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_HelixPairing_t) -> NoneType
3. __init__(self : rosetta.protocols.fldsgn.topology.HelixPairingSet, helix_pairings : str) -> NoneType
4. __init__(self : rosetta.protocols.fldsgn.topology.HelixPairingSet, s : rosetta.protocols.fldsgn.topology.HelixPairingSet) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.fldsgn.topology.HelixPairingSet) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.fldsgn.topology.HelixPairingSet, : rosetta.protocols.fldsgn.topology.HelixPairingSet) -> rosetta.protocols.fldsgn.topology.HelixPairingSet
- calc_geometry(...) from builtins.PyCapsule
- calc_geometry(self : rosetta.protocols.fldsgn.topology.HelixPairingSet, ss_info : protocols::fldsgn::topology::SS_Info2) -> NoneType
calc geomtry of helix pairing
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.fldsgn.topology.HelixPairingSet) -> NoneType
clear data of this HelixPairingSet
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.fldsgn.topology.HelixPairingSet) -> rosetta.protocols.fldsgn.topology.HelixPairingSet
clone this object
- helix_pairing(...) from builtins.PyCapsule
- helix_pairing(*args, **kwargs)
Overloaded function.
1. helix_pairing(self : rosetta.protocols.fldsgn.topology.HelixPairingSet, s : int) -> rosetta.protocols.fldsgn.topology.HelixPairing
return one of the strand_pairings given a number
2. helix_pairing(self : rosetta.protocols.fldsgn.topology.HelixPairingSet, h1 : int, h2 : int) -> rosetta.protocols.fldsgn.topology.HelixPairing
return the pointer of the helix pairing, given the two helix numbers of h1, and h2
if h1 and h2 does not make pairing, return 0
- helix_pairings(...) from builtins.PyCapsule
- helix_pairings(rosetta.protocols.fldsgn.topology.HelixPairingSet) -> rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_HelixPairing_t
return all helix pairings
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.fldsgn.topology.HelixPairingSet) -> str
the name of HelixPairingSet is expressed by the combination of helix pairings
- push_back(...) from builtins.PyCapsule
- push_back(self : rosetta.protocols.fldsgn.topology.HelixPairingSet, hop : rosetta.protocols.fldsgn.topology.HelixPairing) -> NoneType
add HelixPairingOP to StrandPairingSet
- size(...) from builtins.PyCapsule
- size(rosetta.protocols.fldsgn.topology.HelixPairingSet) -> int
return the size of helix_pairings_
|
class Loop(SS_Base) |
| |
///////////////////////////////////////////////////////////////////////////////////////////////////
|
| |
- Method resolution order:
- Loop
- SS_Base
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.fldsgn.topology.Loop) -> NoneType
2. __init__(rosetta.protocols.fldsgn.topology.Loop, int, int) -> NoneType
doc
3. __init__(self : rosetta.protocols.fldsgn.topology.Loop, begin : int, end : int, type : str) -> NoneType
4. __init__(self : rosetta.protocols.fldsgn.topology.Loop, s : rosetta.protocols.fldsgn.topology.Loop) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.fldsgn.topology.Loop) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.fldsgn.topology.Loop, : rosetta.protocols.fldsgn.topology.Loop) -> rosetta.protocols.fldsgn.topology.Loop
- type(...) from builtins.PyCapsule
- type(rosetta.protocols.fldsgn.topology.Loop) -> str
Data descriptors defined here:
- type_
Methods inherited from SS_Base:
- Cend_orient(...) from builtins.PyCapsule
- Cend_orient(rosetta.protocols.fldsgn.topology.SS_Base) -> rosetta.numeric.xyzVector_double_t
- Cend_pos(...) from builtins.PyCapsule
- Cend_pos(rosetta.protocols.fldsgn.topology.SS_Base) -> rosetta.numeric.xyzVector_double_t
- Nend_orient(...) from builtins.PyCapsule
- Nend_orient(rosetta.protocols.fldsgn.topology.SS_Base) -> rosetta.numeric.xyzVector_double_t
- Nend_pos(...) from builtins.PyCapsule
- Nend_pos(rosetta.protocols.fldsgn.topology.SS_Base) -> rosetta.numeric.xyzVector_double_t
- begin(...) from builtins.PyCapsule
- begin(rosetta.protocols.fldsgn.topology.SS_Base) -> int
- end(...) from builtins.PyCapsule
- end(rosetta.protocols.fldsgn.topology.SS_Base) -> int
- is_geometry_initialized(...) from builtins.PyCapsule
- is_geometry_initialized(rosetta.protocols.fldsgn.topology.SS_Base) -> bool
- length(...) from builtins.PyCapsule
- length(rosetta.protocols.fldsgn.topology.SS_Base) -> int
- mid_pos(...) from builtins.PyCapsule
- mid_pos(rosetta.protocols.fldsgn.topology.SS_Base) -> rosetta.numeric.xyzVector_double_t
- orient(...) from builtins.PyCapsule
- orient(rosetta.protocols.fldsgn.topology.SS_Base) -> rosetta.numeric.xyzVector_double_t
|
class SS_Info2(rosetta.basic.datacache.CacheableData) |
| |
///////////////////////////////////////////////////////////////////////////////////////////////////
|
| |
- Method resolution order:
- SS_Info2
- rosetta.basic.datacache.CacheableData
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, secstruct : str) -> NoneType
3. __init__(handle, rosetta.core.pose.Pose) -> NoneType
doc
4. __init__(self : handle, pose : rosetta.core.pose.Pose, secstruct : str) -> NoneType
5. __init__(handle, rosetta.protocols.fldsgn.topology.SS_Info2) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.fldsgn.topology.SS_Info2) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.fldsgn.topology.SS_Info2, : rosetta.protocols.fldsgn.topology.SS_Info2) -> rosetta.protocols.fldsgn.topology.SS_Info2
- bb_pos(...) from builtins.PyCapsule
- bb_pos(rosetta.protocols.fldsgn.topology.SS_Info2) -> rosetta.protocols.fldsgn.topology.BB_Pos
get xyz-coordinates of backbone structure
- bbpos_is_set(...) from builtins.PyCapsule
- bbpos_is_set(rosetta.protocols.fldsgn.topology.SS_Info2) -> bool
get flag for telling whether bb_pos_ was initiliazed by pose or not
- clear_data(...) from builtins.PyCapsule
- clear_data(rosetta.protocols.fldsgn.topology.SS_Info2) -> NoneType
clear data
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.fldsgn.topology.SS_Info2) -> rosetta.basic.datacache.CacheableData
make clone
- helices(...) from builtins.PyCapsule
- helices(rosetta.protocols.fldsgn.topology.SS_Info2) -> rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_Helix_t
return helices
- helix(...) from builtins.PyCapsule
- helix(self : rosetta.protocols.fldsgn.topology.SS_Info2, ih : int) -> rosetta.protocols.fldsgn.topology.Helix
return owning pointer of helix given an index of helices
- helix_id(...) from builtins.PyCapsule
- helix_id(self : rosetta.protocols.fldsgn.topology.SS_Info2, nres : int) -> int
return helix index in helices given a residue number
- initialize(...) from builtins.PyCapsule
- initialize(*args, **kwargs)
Overloaded function.
1. initialize(self : rosetta.protocols.fldsgn.topology.SS_Info2, secstruct : str) -> NoneType
initialize parameters of this class
2. initialize(self : rosetta.protocols.fldsgn.topology.SS_Info2, pose : rosetta.core.pose.Pose) -> NoneType
initialize parameters of this class
3. initialize(self : rosetta.protocols.fldsgn.topology.SS_Info2, pose : rosetta.core.pose.Pose, secstruct : str) -> NoneType
initialize parameters of this class
- loop(...) from builtins.PyCapsule
- loop(self : rosetta.protocols.fldsgn.topology.SS_Info2, il : int) -> rosetta.protocols.fldsgn.topology.Loop
return owning pointer of loop given an index of loops
- loop_id(...) from builtins.PyCapsule
- loop_id(self : rosetta.protocols.fldsgn.topology.SS_Info2, nres : int) -> int
return loop index in loops given a residue number
- loops(...) from builtins.PyCapsule
- loops(rosetta.protocols.fldsgn.topology.SS_Info2) -> rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_Loop_t
return loops
- secstruct(...) from builtins.PyCapsule
- secstruct(*args, **kwargs)
Overloaded function.
1. secstruct(rosetta.protocols.fldsgn.topology.SS_Info2) -> str
string of secondary structure elements
2. secstruct(self : rosetta.protocols.fldsgn.topology.SS_Info2, ii : int) -> str
- set_SSorient(...) from builtins.PyCapsule
- set_SSorient(*args, **kwargs)
Overloaded function.
1. set_SSorient(self : rosetta.protocols.fldsgn.topology.SS_Info2, pose : rosetta.core.pose.Pose) -> NoneType
set orientation vector of secondary structures given a pose
2. set_SSorient(rosetta.protocols.fldsgn.topology.SS_Info2) -> NoneType
set orientation vector of secondary structures given a pose which is defined in the constructor
- ss_element_id(...) from builtins.PyCapsule
- ss_element_id(self : rosetta.protocols.fldsgn.topology.SS_Info2, nres : int) -> int
return the index of secondary structure element given a residue number
- strand(...) from builtins.PyCapsule
- strand(self : rosetta.protocols.fldsgn.topology.SS_Info2, is : int) -> rosetta.protocols.fldsgn.topology.Strand
return owning pointer of strand given an index of strands
- strand_id(...) from builtins.PyCapsule
- strand_id(self : rosetta.protocols.fldsgn.topology.SS_Info2, nres : int) -> int
return strand index in strands given a residue number
- strands(...) from builtins.PyCapsule
- strands(rosetta.protocols.fldsgn.topology.SS_Info2) -> rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_Strand_t
return strands
Methods inherited from rosetta.basic.datacache.CacheableData:
- get_self_ptr(...) from builtins.PyCapsule
- get_self_ptr(*args, **kwargs)
Overloaded function.
1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData
self pointers
2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData
- get_self_weak_ptr(...) from builtins.PyCapsule
- get_self_weak_ptr(*args, **kwargs)
Overloaded function.
1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t
2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t
|
class Sheet(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.fldsgn.topology.Sheet) -> NoneType
2. __init__(self : rosetta.protocols.fldsgn.topology.Sheet, order_strands : rosetta.utility.vector1_unsigned_long, orient_strands : rosetta.utility.vector1_int, is_barrel : bool) -> NoneType
3. __init__(self : rosetta.protocols.fldsgn.topology.Sheet, s : rosetta.protocols.fldsgn.topology.Sheet) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.fldsgn.topology.Sheet) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.fldsgn.topology.Sheet, : rosetta.protocols.fldsgn.topology.Sheet) -> rosetta.protocols.fldsgn.topology.Sheet
- ca_cb_orient(...) from builtins.PyCapsule
- ca_cb_orient(self : rosetta.protocols.fldsgn.topology.Sheet, s : int) -> int
- ca_cb_orients(...) from builtins.PyCapsule
- ca_cb_orients(rosetta.protocols.fldsgn.topology.Sheet) -> rosetta.utility.vector1_int
- calc_geometry(...) from builtins.PyCapsule
- calc_geometry(self : rosetta.protocols.fldsgn.topology.Sheet, ssinfo : rosetta.protocols.fldsgn.topology.SS_Info2) -> NoneType
calc geometry of sheet, sheet_plane_, sheet_center_, ca_cb_orients_
- calc_sasa_bothsides(...) from builtins.PyCapsule
- calc_sasa_bothsides(*args, **kwargs)
Overloaded function.
1. calc_sasa_bothsides(self : rosetta.protocols.fldsgn.topology.Sheet, pose : rosetta.core.pose.Pose, ssinfo : rosetta.protocols.fldsgn.topology.SS_Info2) -> rosetta.utility.vector1_double
calc surface areas only with beta-sheet
2. calc_sasa_bothsides(self : rosetta.protocols.fldsgn.topology.Sheet, pose : rosetta.core.pose.Pose, ssinfo : rosetta.protocols.fldsgn.topology.SS_Info2, pore_radius : float) -> rosetta.utility.vector1_double
calc surface areas only with beta-sheet
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.fldsgn.topology.Sheet) -> rosetta.protocols.fldsgn.topology.Sheet
clone this object
- initialize(...) from builtins.PyCapsule
- initialize(rosetta.protocols.fldsgn.topology.Sheet) -> NoneType
intialize this class
- is_barrel(...) from builtins.PyCapsule
- is_barrel(rosetta.protocols.fldsgn.topology.Sheet) -> bool
is this barrel ?
- is_member(...) from builtins.PyCapsule
- is_member(self : rosetta.protocols.fldsgn.topology.Sheet, s : int) -> bool
- num_strands(...) from builtins.PyCapsule
- num_strands(rosetta.protocols.fldsgn.topology.Sheet) -> int
the number strands inclued in
- order_strand(...) from builtins.PyCapsule
- order_strand(self : rosetta.protocols.fldsgn.topology.Sheet, s : int) -> int
- order_strands(...) from builtins.PyCapsule
- order_strands(rosetta.protocols.fldsgn.topology.Sheet) -> rosetta.utility.vector1_unsigned_long
- orient_strand(...) from builtins.PyCapsule
- orient_strand(self : rosetta.protocols.fldsgn.topology.Sheet, s : int) -> int
- orient_strands(...) from builtins.PyCapsule
- orient_strands(rosetta.protocols.fldsgn.topology.Sheet) -> rosetta.utility.vector1_int
- strand_order(...) from builtins.PyCapsule
- strand_order(self : rosetta.protocols.fldsgn.topology.Sheet, s : int) -> int
- which_side(...) from builtins.PyCapsule
- which_side(self : rosetta.protocols.fldsgn.topology.Sheet, vec : rosetta.numeric.xyzVector_double_t) -> int
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class SheetFoldType(builtins.object) |
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Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(rosetta.protocols.fldsgn.topology.SheetFoldType, rosetta.protocols.fldsgn.topology.SheetFoldType) -> bool
- __hash__(...) from builtins.PyCapsule
- __hash__(rosetta.protocols.fldsgn.topology.SheetFoldType) -> int
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.fldsgn.topology.SheetFoldType, int) -> NoneType
2. __init__(rosetta.protocols.fldsgn.topology.SheetFoldType, int) -> NoneType
- __int__(...) from builtins.PyCapsule
- __int__(rosetta.protocols.fldsgn.topology.SheetFoldType) -> int
- __ne__(...) from builtins.PyCapsule
- __ne__(rosetta.protocols.fldsgn.topology.SheetFoldType, rosetta.protocols.fldsgn.topology.SheetFoldType) -> bool
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __repr__(...) from builtins.PyCapsule
- __repr__(rosetta.protocols.fldsgn.topology.SheetFoldType) -> str
Data and other attributes defined here:
- BAB_CFr = SheetFoldType.BAB_CFr
- BABx1 = SheetFoldType.BABx1
- BABx2 = SheetFoldType.BABx2
- BABx3 = SheetFoldType.BABx3
- BEFr = SheetFoldType.BEFr
- BFr = SheetFoldType.BFr
- CDFr = SheetFoldType.CDFr
- CFr = SheetFoldType.CFr
- DFr = SheetFoldType.DFr
- DFr_BAB = SheetFoldType.DFr_BAB
- DFr_HPN = SheetFoldType.DFr_HPN
- EFr = SheetFoldType.EFr
- Fd_like = SheetFoldType.Fd_like
- Flavodoxin = SheetFoldType.Flavodoxin
- HPN_CFr = SheetFoldType.HPN_CFr
- NO_STRANDS = SheetFoldType.NO_STRANDS
- PG_like = SheetFoldType.PG_like
- Ploop2x3 = SheetFoldType.Ploop2x3
- Ploop3x3 = SheetFoldType.Ploop3x3
- RFd_like = SheetFoldType.RFd_like
- RNAseH = SheetFoldType.RNAseH
- RosI = SheetFoldType.RosI
- RosO = SheetFoldType.RosO
- Rsmn2x2 = SheetFoldType.Rsmn2x2
- Rsmn3x3 = SheetFoldType.Rsmn3x3
- Rsmn3x3_Half = SheetFoldType.Rsmn3x3_Half
- Thio = SheetFoldType.Thio
- Thioredoxin = SheetFoldType.Thioredoxin
- Top7 = SheetFoldType.Top7
- UNFOLD = SheetFoldType.UNFOLD
- UNKNOWN = SheetFoldType.n_fold_types
- n_fold_types = SheetFoldType.n_fold_types
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class SheetSet(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.fldsgn.topology.SheetSet) -> NoneType
2. __init__(self : rosetta.protocols.fldsgn.topology.SheetSet, sheets : rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_Sheet_t) -> NoneType
3. __init__(self : rosetta.protocols.fldsgn.topology.SheetSet, ssinfo : rosetta.protocols.fldsgn.topology.SS_Info2, spairset : rosetta.protocols.fldsgn.topology.StrandPairingSet) -> NoneType
4. __init__(self : rosetta.protocols.fldsgn.topology.SheetSet, s : rosetta.protocols.fldsgn.topology.SheetSet) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.fldsgn.topology.SheetSet) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.fldsgn.topology.SheetSet, : rosetta.protocols.fldsgn.topology.SheetSet) -> rosetta.protocols.fldsgn.topology.SheetSet
- calc_geometry(...) from builtins.PyCapsule
- calc_geometry(self : rosetta.protocols.fldsgn.topology.SheetSet, ssinfo : rosetta.protocols.fldsgn.topology.SS_Info2) -> NoneType
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.fldsgn.topology.SheetSet) -> NoneType
- initialize(...) from builtins.PyCapsule
- initialize(self : rosetta.protocols.fldsgn.topology.SheetSet, ssinfo : rosetta.protocols.fldsgn.topology.SS_Info2, spairset : rosetta.protocols.fldsgn.topology.StrandPairingSet) -> NoneType
- num_sheets(...) from builtins.PyCapsule
- num_sheets(rosetta.protocols.fldsgn.topology.SheetSet) -> int
return number of sheets
- push_back(...) from builtins.PyCapsule
- push_back(self : rosetta.protocols.fldsgn.topology.SheetSet, sop : rosetta.protocols.fldsgn.topology.Sheet) -> NoneType
- sheet(...) from builtins.PyCapsule
- sheet(self : rosetta.protocols.fldsgn.topology.SheetSet, s : int) -> rosetta.protocols.fldsgn.topology.Sheet
- sheets(...) from builtins.PyCapsule
- sheets(rosetta.protocols.fldsgn.topology.SheetSet) -> rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_Sheet_t
- size(...) from builtins.PyCapsule
- size(rosetta.protocols.fldsgn.topology.SheetSet) -> int
return number of sheets
- spairset(...) from builtins.PyCapsule
- spairset(rosetta.protocols.fldsgn.topology.SheetSet) -> rosetta.protocols.fldsgn.topology.StrandPairingSet
return strand pairing set
- which_sheet(...) from builtins.PyCapsule
- which_sheet(self : rosetta.protocols.fldsgn.topology.SheetSet, s : int) -> int
return the id of sheet that a given strand belongs to.
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class StrandPairing(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.fldsgn.topology.StrandPairing) -> NoneType
2. __init__(self : rosetta.protocols.fldsgn.topology.StrandPairing, s1 : int, s2 : int, b1 : int, b2 : int, p : int, rs : float, o : str) -> NoneType
3. __init__(self : rosetta.protocols.fldsgn.topology.StrandPairing, s1 : int, s2 : int, rs : float, o : str) -> NoneType
4. __init__(self : rosetta.protocols.fldsgn.topology.StrandPairing, spair : str) -> NoneType
5. __init__(self : rosetta.protocols.fldsgn.topology.StrandPairing, : rosetta.protocols.fldsgn.topology.StrandPairing) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.fldsgn.topology.StrandPairing) -> str
- add_pair(...) from builtins.PyCapsule
- add_pair(self : rosetta.protocols.fldsgn.topology.StrandPairing, r1 : int, r2 : int, orient : str, rgstr : float) -> bool
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.fldsgn.topology.StrandPairing, : rosetta.protocols.fldsgn.topology.StrandPairing) -> rosetta.protocols.fldsgn.topology.StrandPairing
- begin1(...) from builtins.PyCapsule
- begin1(rosetta.protocols.fldsgn.topology.StrandPairing) -> int
the residue number of the beginning of 1st strand
- begin2(...) from builtins.PyCapsule
- begin2(rosetta.protocols.fldsgn.topology.StrandPairing) -> int
the residue number of the beginning of 2nd strand
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.fldsgn.topology.StrandPairing) -> rosetta.protocols.fldsgn.topology.StrandPairing
clone this object
- elongate(...) from builtins.PyCapsule
- elongate(self : rosetta.protocols.fldsgn.topology.StrandPairing, r1 : int, r2 : int, p1 : int, p2 : int) -> bool
elongate strand pairings
- end1(...) from builtins.PyCapsule
- end1(rosetta.protocols.fldsgn.topology.StrandPairing) -> int
the residue number of the end of 1st strand
- end2(...) from builtins.PyCapsule
- end2(rosetta.protocols.fldsgn.topology.StrandPairing) -> int
the residue number of the end of 2nd strand
- has_bulge(...) from builtins.PyCapsule
- has_bulge(rosetta.protocols.fldsgn.topology.StrandPairing) -> bool
whether the strand pairing have bulge or not
- has_paired_residue(...) from builtins.PyCapsule
- has_paired_residue(self : rosetta.protocols.fldsgn.topology.StrandPairing, res : int) -> bool
return residue pairing
- is_bulge(...) from builtins.PyCapsule
- is_bulge(self : rosetta.protocols.fldsgn.topology.StrandPairing, resid : int) -> bool
whethe the given residue number is a bulge
- is_member(...) from builtins.PyCapsule
- is_member(self : rosetta.protocols.fldsgn.topology.StrandPairing, res : int) -> bool
whether input residue is included in this StrandPairinge or not
- is_parallel(...) from builtins.PyCapsule
- is_parallel(rosetta.protocols.fldsgn.topology.StrandPairing) -> bool
is parallel
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.fldsgn.topology.StrandPairing) -> str
StrandPairing is descripbed as s1()-s2().orient().rgstr_shift()
For example, 2-3.A.1 means 2nd and 3rd strands make anti-parallel strand_pairing with register shift 1
- orient(...) from builtins.PyCapsule
- orient(rosetta.protocols.fldsgn.topology.StrandPairing) -> str
orientation, parallel or anti-parallel, of strand pairing
- pleats1(...) from builtins.PyCapsule
- pleats1(rosetta.protocols.fldsgn.topology.StrandPairing) -> rosetta.utility.vector1_unsigned_long
the pleating at the begining of strand_pairing
- pleats2(...) from builtins.PyCapsule
- pleats2(rosetta.protocols.fldsgn.topology.StrandPairing) -> rosetta.utility.vector1_unsigned_long
the pleating at the end of strand_pairing
- redefine_begin_end(...) from builtins.PyCapsule
- redefine_begin_end(self : rosetta.protocols.fldsgn.topology.StrandPairing, ss_info : protocols::fldsgn::topology::SS_Info2, abego : rosetta.utility.vector1_std_string) -> NoneType
reset begin1_, begin2_, and end1_, end2_ based on ssinfo
abego is used for obtaining bulge information if it is non-empty
- residue_pair(...) from builtins.PyCapsule
- residue_pair(self : rosetta.protocols.fldsgn.topology.StrandPairing, res : int) -> int
residue pair
- rgstr_shift(...) from builtins.PyCapsule
- rgstr_shift(rosetta.protocols.fldsgn.topology.StrandPairing) -> float
the number of register shift between the strands
- s1(...) from builtins.PyCapsule
- s1(rosetta.protocols.fldsgn.topology.StrandPairing) -> int
the strand number of the 1st strand in strand pairing
- s2(...) from builtins.PyCapsule
- s2(rosetta.protocols.fldsgn.topology.StrandPairing) -> int
the strand number of the 2nd strand in strand pairing
- size1(...) from builtins.PyCapsule
- size1(rosetta.protocols.fldsgn.topology.StrandPairing) -> int
the length of 1st strand
- size2(...) from builtins.PyCapsule
- size2(rosetta.protocols.fldsgn.topology.StrandPairing) -> int
the length of 2nd strand
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class StrandPairingSet(builtins.object) |
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/////////////////////////////////////////////////////////////////////////////////////////////////////////
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.fldsgn.topology.StrandPairingSet) -> NoneType
2. __init__(self : rosetta.protocols.fldsgn.topology.StrandPairingSet, strand_pairings : rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_StrandPairing_t) -> NoneType
3. __init__(self : rosetta.protocols.fldsgn.topology.StrandPairingSet, ssinfo : protocols::fldsgn::topology::SS_Info2, dimer_pairs : protocols::fldsgn::topology::DimerPairings) -> NoneType
4. __init__(rosetta.protocols.fldsgn.topology.StrandPairingSet, str) -> NoneType
doc
5. __init__(self : rosetta.protocols.fldsgn.topology.StrandPairingSet, spairstring : str, ssinfo : protocols::fldsgn::topology::SS_Info2) -> NoneType
6. __init__(self : rosetta.protocols.fldsgn.topology.StrandPairingSet, spairstring : str, ssinfo : protocols::fldsgn::topology::SS_Info2, abego : rosetta.utility.vector1_std_string) -> NoneType
7. __init__(self : rosetta.protocols.fldsgn.topology.StrandPairingSet, s : rosetta.protocols.fldsgn.topology.StrandPairingSet) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.protocols.fldsgn.topology.StrandPairingSet) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.fldsgn.topology.StrandPairingSet, : rosetta.protocols.fldsgn.topology.StrandPairingSet) -> rosetta.protocols.fldsgn.topology.StrandPairingSet
- begin(...) from builtins.PyCapsule
- begin(rosetta.protocols.fldsgn.topology.StrandPairingSet) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::fldsgn::topology::StrandPairing> const*, std::vector<std::shared_ptr<protocols::fldsgn::topology::StrandPairing>, std::allocator<std::shared_ptr<protocols::fldsgn::topology::StrandPairing> > > >
return begin of iterator of strand_pairings_
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.fldsgn.topology.StrandPairingSet) -> NoneType
clear data of this StrandPairingSet
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.fldsgn.topology.StrandPairingSet) -> rosetta.protocols.fldsgn.topology.StrandPairingSet
clone this object
- drop_strand_pairs(...) from builtins.PyCapsule
- drop_strand_pairs(self : rosetta.protocols.fldsgn.topology.StrandPairingSet, drop_spairs : rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_StrandPairing_t) -> NoneType
remove a set of strand pairings from datay
- end(...) from builtins.PyCapsule
- end(rosetta.protocols.fldsgn.topology.StrandPairingSet) -> __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::fldsgn::topology::StrandPairing> const*, std::vector<std::shared_ptr<protocols::fldsgn::topology::StrandPairing>, std::allocator<std::shared_ptr<protocols::fldsgn::topology::StrandPairing> > > >
return end of iterator of strand_pairings_
- finalize(...) from builtins.PyCapsule
- finalize(rosetta.protocols.fldsgn.topology.StrandPairingSet) -> NoneType
finalize this and create_map_strand_pairings
- finalized(...) from builtins.PyCapsule
- finalized(rosetta.protocols.fldsgn.topology.StrandPairingSet) -> bool
- make_strand_neighbor_two(...) from builtins.PyCapsule
- make_strand_neighbor_two(rosetta.protocols.fldsgn.topology.StrandPairingSet) -> NoneType
make the number of strand pairing as two
- name(...) from builtins.PyCapsule
- name(rosetta.protocols.fldsgn.topology.StrandPairingSet) -> str
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
- name_wo_rgstr(...) from builtins.PyCapsule
- name_wo_rgstr(rosetta.protocols.fldsgn.topology.StrandPairingSet) -> str
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
- neighbor_strands(...) from builtins.PyCapsule
- neighbor_strands(self : rosetta.protocols.fldsgn.topology.StrandPairingSet, s : int) -> rosetta.utility.vector1_unsigned_long
return strand number of neighbor strands of a input strand
- num_strands(...) from builtins.PyCapsule
- num_strands(rosetta.protocols.fldsgn.topology.StrandPairingSet) -> int
return all strand pairings
- push_back(...) from builtins.PyCapsule
- push_back(self : rosetta.protocols.fldsgn.topology.StrandPairingSet, sop : rosetta.protocols.fldsgn.topology.StrandPairing) -> NoneType
add StrandPairingOP to StandPairingSet
- push_back_and_finalize(...) from builtins.PyCapsule
- push_back_and_finalize(self : rosetta.protocols.fldsgn.topology.StrandPairingSet, sop : rosetta.protocols.fldsgn.topology.StrandPairing) -> NoneType
add StrandPairingOP to StandPairingSet
- size(...) from builtins.PyCapsule
- size(rosetta.protocols.fldsgn.topology.StrandPairingSet) -> int
- strand_pairing(...) from builtins.PyCapsule
- strand_pairing(*args, **kwargs)
Overloaded function.
1. strand_pairing(self : rosetta.protocols.fldsgn.topology.StrandPairingSet, s : int) -> rosetta.protocols.fldsgn.topology.StrandPairing
return one of the strand_pairings given a number
2. strand_pairing(self : rosetta.protocols.fldsgn.topology.StrandPairingSet, s1 : int, s2 : int) -> rosetta.protocols.fldsgn.topology.StrandPairing
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
- strand_pairings(...) from builtins.PyCapsule
- strand_pairings(rosetta.protocols.fldsgn.topology.StrandPairingSet) -> rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_StrandPairing_t
return all strand pairings
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