topology¶

Bindings for protocols::fldsgn::topology namespace

class pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos¶

Bases: pybind11_object

C(self: pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos, i: int) → pyrosetta.rosetta.numeric.xyzVector_double_t¶

accessor for C’s coordinate on residue i, requires take_coordinates_from_pose have been recently called.

C++: protocols::fldsgn::topology::BB_Pos::C(const unsigned long) const –> const class numeric::xyzVector<double> &

CA(self: pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos, i: int) → pyrosetta.rosetta.numeric.xyzVector_double_t¶

accessor for CA’s coordinate on residue i, requires take_coordinates_from_pose have been recently called.

C++: protocols::fldsgn::topology::BB_Pos::CA(const unsigned long) const –> const class numeric::xyzVector<double> &

CB(self: pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos, i: int) → pyrosetta.rosetta.numeric.xyzVector_double_t¶

accessor for CB’s coordinate on residue i, requires take_coordinates_from_pose have been recently called.

C++: protocols::fldsgn::topology::BB_Pos::CB(const unsigned long) const –> const class numeric::xyzVector<double> &

N(self: pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos, i: int) → pyrosetta.rosetta.numeric.xyzVector_double_t¶

accessor for N’s coordinate on residue i, requires take_coordinates_from_pose have been recently called.

C++: protocols::fldsgn::topology::BB_Pos::N(const unsigned long) const –> const class numeric::xyzVector<double> &

O(self: pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos, i: int) → pyrosetta.rosetta.numeric.xyzVector_double_t¶

accessor for O’s coordinate on residue i, requires take_coordinates_from_pose have been recently called.

C++: protocols::fldsgn::topology::BB_Pos::O(const unsigned long) const –> const class numeric::xyzVector<double> &

assign(self: pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos, : pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos) → pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos¶: C++: protocols::fldsgn::topology::BB_Pos::operator=(const class protocols::fldsgn::topology::BB_Pos &) –> class protocols::fldsgn::topology::BB_Pos &

clear(self: pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos) → None¶: C++: protocols::fldsgn::topology::BB_Pos::clear() –> void

resize(self: pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos, nres: int) → None¶: C++: protocols::fldsgn::topology::BB_Pos::resize(const unsigned long) –> void

size(self: pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos) → int¶

@

C++: protocols::fldsgn::topology::BB_Pos::size() const –> unsigned long

take_coordinates_from_pose(self: pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::fldsgn::topology::BB_Pos::take_coordinates_from_pose(const class core::pose::Pose &) –> void

class pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif, : pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) → pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif¶: C++: protocols::fldsgn::topology::BetaAlphaBetaMotif::operator=(const class protocols::fldsgn::topology::BetaAlphaBetaMotif &) –> class protocols::fldsgn::topology::BetaAlphaBetaMotif &

calc_geometry(self: pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif, ssinfo: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, sheet_set: protocols::fldsgn::topology::SheetSet) → None¶: C++: protocols::fldsgn::topology::BetaAlphaBetaMotif::calc_geometry(const class std::shared_ptr<const class protocols::fldsgn::topology::SS_Info2>, const class std::shared_ptr<const class protocols::fldsgn::topology::SheetSet>) –> void

calc_inout(self: pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif, ssinfo: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, resi: int) → int¶: C++: protocols::fldsgn::topology::BetaAlphaBetaMotif::calc_inout(const class std::shared_ptr<const class protocols::fldsgn::topology::SS_Info2>, const unsigned long) const –> unsigned long

cross_over(self: pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) → int¶: C++: protocols::fldsgn::topology::BetaAlphaBetaMotif::cross_over() const –> unsigned long

helix(self: pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) → int¶: C++: protocols::fldsgn::topology::BetaAlphaBetaMotif::helix() const –> unsigned long

helix_cycle(self: pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::fldsgn::topology::BetaAlphaBetaMotif::helix_cycle() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

helix_cycle_as_string(self: pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) → str¶: C++: protocols::fldsgn::topology::BetaAlphaBetaMotif::helix_cycle_as_string() const –> std::string

hs1_dist(self: pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) → float¶: C++: protocols::fldsgn::topology::BetaAlphaBetaMotif::hs1_dist() const –> double

hs2_dist(self: pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) → float¶: C++: protocols::fldsgn::topology::BetaAlphaBetaMotif::hs2_dist() const –> double

hs_angle(self: pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) → float¶: C++: protocols::fldsgn::topology::BetaAlphaBetaMotif::hs_angle() const –> double

hsheet_dist(self: pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) → float¶: C++: protocols::fldsgn::topology::BetaAlphaBetaMotif::hsheet_dist() const –> double

hsheet_elev_angle(self: pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) → float¶: C++: protocols::fldsgn::topology::BetaAlphaBetaMotif::hsheet_elev_angle() const –> double

is_lefthanded(self: pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) → bool¶: C++: protocols::fldsgn::topology::BetaAlphaBetaMotif::is_lefthanded() const –> bool

name(self: pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) → str¶: C++: protocols::fldsgn::topology::BetaAlphaBetaMotif::name() const –> std::string

strand1(self: pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) → int¶: C++: protocols::fldsgn::topology::BetaAlphaBetaMotif::strand1() const –> unsigned long

strand2(self: pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) → int¶: C++: protocols::fldsgn::topology::BetaAlphaBetaMotif::strand2() const –> unsigned long

class pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet, : pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet) → pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet¶: C++: protocols::fldsgn::topology::BetaAlphaBetaMotifSet::operator=(const class protocols::fldsgn::topology::BetaAlphaBetaMotifSet &) –> class protocols::fldsgn::topology::BetaAlphaBetaMotifSet &

bab_motif(self: pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet, i: int) → pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif¶: C++: protocols::fldsgn::topology::BetaAlphaBetaMotifSet::bab_motif(const unsigned long &) const –> class std::shared_ptr<class protocols::fldsgn::topology::BetaAlphaBetaMotif>

bab_motifs(self: pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_BetaAlphaBetaMotif_t¶: C++: protocols::fldsgn::topology::BetaAlphaBetaMotifSet::bab_motifs() const –> const class utility::vector1<class std::shared_ptr<class protocols::fldsgn::topology::BetaAlphaBetaMotif>, class std::allocator<class std::shared_ptr<class protocols::fldsgn::topology::BetaAlphaBetaMotif> > > &

calc_geometry(self: pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet, ssinfo: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, sheet_set: protocols::fldsgn::topology::SheetSet) → None¶: C++: protocols::fldsgn::topology::BetaAlphaBetaMotifSet::calc_geometry(const class std::shared_ptr<const class protocols::fldsgn::topology::SS_Info2>, const class std::shared_ptr<const class protocols::fldsgn::topology::SheetSet>) –> void

clear(self: pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet) → None¶: C++: protocols::fldsgn::topology::BetaAlphaBetaMotifSet::clear() –> void

push_back(self: pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet, bop: pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif) → None¶: C++: protocols::fldsgn::topology::BetaAlphaBetaMotifSet::push_back(const class std::shared_ptr<class protocols::fldsgn::topology::BetaAlphaBetaMotif>) –> void

set_babmotifs(self: pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet, ssinfo: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, sheet_set: protocols::fldsgn::topology::SheetSet) → None¶: C++: protocols::fldsgn::topology::BetaAlphaBetaMotifSet::set_babmotifs(const class std::shared_ptr<const class protocols::fldsgn::topology::SS_Info2>, const class std::shared_ptr<const class protocols::fldsgn::topology::SheetSet>) –> void

size(self: pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet) → int¶: C++: protocols::fldsgn::topology::BetaAlphaBetaMotifSet::size() const –> unsigned long

class pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing, : pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing) → pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing¶: C++: protocols::fldsgn::topology::DimerPairing::operator=(const class protocols::fldsgn::topology::DimerPairing &) –> class protocols::fldsgn::topology::DimerPairing &

dist(self: pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing) → float¶: C++: protocols::fldsgn::topology::DimerPairing::dist() const –> double

dp(self: pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing) → float¶: C++: protocols::fldsgn::topology::DimerPairing::dp() const –> double

is_parallel(self: pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing, phi: float, theta: float) → bool¶: C++: protocols::fldsgn::topology::DimerPairing::is_parallel(const double, const double) –> bool

orient(self: pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing) → str¶: C++: protocols::fldsgn::topology::DimerPairing::orient() const –> char

phi(self: pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing) → float¶: C++: protocols::fldsgn::topology::DimerPairing::phi() const –> double

res1(self: pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing) → int¶: C++: protocols::fldsgn::topology::DimerPairing::res1() const –> unsigned long

res2(self: pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing) → int¶: C++: protocols::fldsgn::topology::DimerPairing::res2() const –> unsigned long

score(self: pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing) → float¶: C++: protocols::fldsgn::topology::DimerPairing::score() const –> double

sigma(self: pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing) → float¶: C++: protocols::fldsgn::topology::DimerPairing::sigma() const –> double

sign1(self: pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing) → int¶: C++: protocols::fldsgn::topology::DimerPairing::sign1() const –> unsigned long

sign2(self: pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing) → int¶: C++: protocols::fldsgn::topology::DimerPairing::sign2() const –> unsigned long

theta(self: pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing) → float¶: C++: protocols::fldsgn::topology::DimerPairing::theta() const –> double

valid(*args, **kwargs)¶

Overloaded function.

valid(self: pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing) -> bool

C++: protocols::fldsgn::topology::DimerPairing::valid() const –> bool

valid(self: pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing, v: bool) -> None

C++: protocols::fldsgn::topology::DimerPairing::valid(const bool) –> void

class pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairings¶

Bases: vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t

append(self: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t, arg0: protocols::fldsgn::topology::DimerPairing) → None¶: adds an element to the end

assign(self: pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairings, : pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairings) → pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairings¶: C++: protocols::fldsgn::topology::DimerPairings::operator=(const class protocols::fldsgn::topology::DimerPairings &) –> class protocols::fldsgn::topology::DimerPairings &

back(self: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t) → protocols::fldsgn::topology::DimerPairing¶: access the last element

capacity(self: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t) → int¶: returns the number of elements that can be held in currently allocated storage

clear(self: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t) → None¶: clears the contents

count(self: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t, arg0: protocols::fldsgn::topology::DimerPairing) → int¶: counts the elements that are equal to value

erase(self: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t, arg0: int) → None¶: erases element at index

extend(othervec)¶

finalize(self: pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairings, ss_info: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2) → None¶: C++: protocols::fldsgn::topology::DimerPairings::finalize(const class protocols::fldsgn::topology::SS_Info2 &) –> void

front(self: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t) → protocols::fldsgn::topology::DimerPairing¶: access the first element

l(self: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t) → int¶: lower index

max_size(self: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t) → int¶: returns the maximum possible number of elements

pop(*args, **kwargs)¶

Overloaded function.

pop(self: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t) -> protocols::fldsgn::topology::DimerPairing

remove and return last item

pop(self: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t, arg0: int) -> protocols::fldsgn::topology::DimerPairing

remove and return item at index

remove(self: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t, arg0: protocols::fldsgn::topology::DimerPairing) → None¶: Remove the first item from the list whose value is x. It is an error if there is no such item.

reserve(self: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t, arg0: int) → None¶: reserves storage

resize(self: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t, arg0: int) → None¶: changes the number of elements stored

shrink_to_fit(self: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t) → None¶: reduces memory usage by freeing unused memory

u(self: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_DimerPairing_t) → int¶: upper index

class pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet, : pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet) → pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet¶: C++: protocols::fldsgn::topology::HSSTriplet::operator=(const class protocols::fldsgn::topology::HSSTriplet &) –> class protocols::fldsgn::topology::HSSTriplet &

calc_geometry(self: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet, ssinfo: protocols::fldsgn::topology::SS_Info2) → None¶: C++: protocols::fldsgn::topology::HSSTriplet::calc_geometry(const class std::shared_ptr<const class protocols::fldsgn::topology::SS_Info2>) –> void

geometry_is_initialized(self: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet) → bool¶

geometry is initialized or not

C++: protocols::fldsgn::topology::HSSTriplet::geometry_is_initialized() const –> bool

helix(self: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet) → int¶: C++: protocols::fldsgn::topology::HSSTriplet::helix() const –> unsigned long

hs1_dist(self: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet) → float¶

distance between mid helix and midpoint of 1st strand

C++: protocols::fldsgn::topology::HSSTriplet::hs1_dist() const –> double

hs1_orient(self: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet) → str¶

orientation between helix and 1st strand

C++: protocols::fldsgn::topology::HSSTriplet::hs1_orient() const –> std::string

hs2_dist(self: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet) → float¶

distance between mid helix and midpoint of 2nd strand

C++: protocols::fldsgn::topology::HSSTriplet::hs2_dist() const –> double

hs2_orient(self: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet) → str¶

orientation between helix and 2nd strand

C++: protocols::fldsgn::topology::HSSTriplet::hs2_orient() const –> std::string

hs_angle(self: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet) → float¶

return distance between sheet ( defined by the 2 strands ) and helix

C++: protocols::fldsgn::topology::HSSTriplet::hs_angle() const –> double

hsheet_dist(self: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet) → float¶

reutrn distance between sheet ( defined by the 2 strands ) and helix

C++: protocols::fldsgn::topology::HSSTriplet::hsheet_dist() const –> double

left_handed(self: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet) → bool¶

hsstriplet is left handed or not

C++: protocols::fldsgn::topology::HSSTriplet::left_handed() const –> bool

ss_dist(self: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet) → float¶

distance between midpoints of strands

C++: protocols::fldsgn::topology::HSSTriplet::ss_dist() const –> double

ss_orient(self: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet) → str¶

orientation between strands

C++: protocols::fldsgn::topology::HSSTriplet::ss_orient() const –> std::string

strand1(self: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet) → int¶: C++: protocols::fldsgn::topology::HSSTriplet::strand1() const –> unsigned long

strand2(self: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet) → int¶: C++: protocols::fldsgn::topology::HSSTriplet::strand2() const –> unsigned long

class pyrosetta.rosetta.protocols.fldsgn.topology.HSSTripletSet¶

Bases: pybind11_object

add_hsstriplets(self: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTripletSet, s: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_HSSTriplet_t) → None¶: C++: protocols::fldsgn::topology::HSSTripletSet::add_hsstriplets(const class utility::vector1<class std::shared_ptr<class protocols::fldsgn::topology::HSSTriplet>, class std::allocator<class std::shared_ptr<class protocols::fldsgn::topology::HSSTriplet> > > &) –> void

assign(self: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTripletSet, : pyrosetta.rosetta.protocols.fldsgn.topology.HSSTripletSet) → pyrosetta.rosetta.protocols.fldsgn.topology.HSSTripletSet¶: C++: protocols::fldsgn::topology::HSSTripletSet::operator=(const class protocols::fldsgn::topology::HSSTripletSet &) –> class protocols::fldsgn::topology::HSSTripletSet &

clear(self: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTripletSet) → None¶: C++: protocols::fldsgn::topology::HSSTripletSet::clear() –> void

hss_triplet(self: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTripletSet, helix: int, s1: int, s2: int) → pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet¶

returns the Triplet containing given helix, strand1, and strand2: Exits and throws an error if the triplet isn’t found

C++: protocols::fldsgn::topology::HSSTripletSet::hss_triplet(const unsigned long, const unsigned long, const unsigned long) const –> class std::shared_ptr<class protocols::fldsgn::topology::HSSTriplet>

hss_triplets(*args, **kwargs)¶

Overloaded function.

hss_triplets(self: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTripletSet, helix: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_HSSTriplet_t

returns list of Triplets containing given helix

C++: protocols::fldsgn::topology::HSSTripletSet::hss_triplets(const unsigned long) const –> class utility::vector1<class std::shared_ptr<class protocols::fldsgn::topology::HSSTriplet>, class std::allocator<class std::shared_ptr<class protocols::fldsgn::topology::HSSTriplet> > >

hss_triplets(self: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTripletSet) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_HSSTriplet_t

C++: protocols::fldsgn::topology::HSSTripletSet::hss_triplets() const –> const class utility::vector1<class std::shared_ptr<class protocols::fldsgn::topology::HSSTriplet>, class std::allocator<class std::shared_ptr<class protocols::fldsgn::topology::HSSTriplet> > > &

push_back(self: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTripletSet, hssop: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet) → None¶: C++: protocols::fldsgn::topology::HSSTripletSet::push_back(const class std::shared_ptr<class protocols::fldsgn::topology::HSSTriplet>) –> void

size(self: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTripletSet) → int¶

return the size of vector of hss_triplets_

C++: protocols::fldsgn::topology::HSSTripletSet::size() const –> unsigned long

class pyrosetta.rosetta.protocols.fldsgn.topology.Helix¶

Bases: SS_Base

Cend_orient(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::fldsgn::topology::SS_Base::Cend_orient() const –> class numeric::xyzVector<double>

Cend_pos(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::fldsgn::topology::SS_Base::Cend_pos() const –> class numeric::xyzVector<double>

Nend_orient(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::fldsgn::topology::SS_Base::Nend_orient() const –> class numeric::xyzVector<double>

Nend_pos(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::fldsgn::topology::SS_Base::Nend_pos() const –> class numeric::xyzVector<double>

assign(self: pyrosetta.rosetta.protocols.fldsgn.topology.Helix, : pyrosetta.rosetta.protocols.fldsgn.topology.Helix) → pyrosetta.rosetta.protocols.fldsgn.topology.Helix¶: C++: protocols::fldsgn::topology::Helix::operator=(const class protocols::fldsgn::topology::Helix &) –> class protocols::fldsgn::topology::Helix &

begin(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → int¶: C++: protocols::fldsgn::topology::SS_Base::begin() const –> unsigned long

bend(self: pyrosetta.rosetta.protocols.fldsgn.topology.Helix) → float¶: C++: protocols::fldsgn::topology::Helix::bend() const –> double

calc_geometry(self: pyrosetta.rosetta.protocols.fldsgn.topology.Helix, bbpos: pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos) → None¶

calc geometry of helix

C++: protocols::fldsgn::topology::Helix::calc_geometry(const class protocols::fldsgn::topology::BB_Pos &) –> void

end(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → int¶: C++: protocols::fldsgn::topology::SS_Base::end() const –> unsigned long

is_geometry_initialized(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → bool¶: C++: protocols::fldsgn::topology::SS_Base::is_geometry_initialized() const –> bool

length(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → int¶: C++: protocols::fldsgn::topology::SS_Base::length() const –> unsigned long

mid_pos(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::fldsgn::topology::SS_Base::mid_pos() const –> class numeric::xyzVector<double>

orient(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::fldsgn::topology::SS_Base::orient() const –> class numeric::xyzVector<double>

class pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing¶

Bases: pybind11_object

align_angle(self: pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing) → float¶

helix angle projected on sheet helices belongs to

C++: protocols::fldsgn::topology::HelixPairing::align_angle() const –> double

assign(self: pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing, : pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing) → pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing¶: C++: protocols::fldsgn::topology::HelixPairing::operator=(const class protocols::fldsgn::topology::HelixPairing &) –> class protocols::fldsgn::topology::HelixPairing &

calc_geometry(self: pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing, ss_info: protocols::fldsgn::topology::SS_Info2) → None¶: C++: protocols::fldsgn::topology::HelixPairing::calc_geometry(const class std::shared_ptr<const class protocols::fldsgn::topology::SS_Info2>) –> void

clone(self: pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing) → pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing¶

clone this object

C++: protocols::fldsgn::topology::HelixPairing::clone() –> class std::shared_ptr<class protocols::fldsgn::topology::HelixPairing>

cross_angle(self: pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing) → float¶: C++: protocols::fldsgn::topology::HelixPairing::cross_angle() const –> double

dist(self: pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing) → float¶: C++: protocols::fldsgn::topology::HelixPairing::dist() const –> double

h1(self: pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing) → int¶

the strand number of the 1st strand in strand pairing

C++: protocols::fldsgn::topology::HelixPairing::h1() const –> unsigned long

h2(self: pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing) → int¶

the strand number of the 2nd strand in strand pairing

C++: protocols::fldsgn::topology::HelixPairing::h2() const –> unsigned long

initialize(self: pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing) → None¶: C++: protocols::fldsgn::topology::HelixPairing::initialize() –> void

is_parallel(self: pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing) → bool¶

is parallel

C++: protocols::fldsgn::topology::HelixPairing::is_parallel() const –> bool

name(self: pyrosetta.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

C++: protocols::fldsgn::topology::HelixPairing::name() const –> std::string

orient(self: pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing) → str¶

orientation, parallel or anti-parallel, of helix pairing

C++: protocols::fldsgn::topology::HelixPairing::orient() const –> char

class pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet, : pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet) → pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet¶: C++: protocols::fldsgn::topology::HelixPairingSet::operator=(const class protocols::fldsgn::topology::HelixPairingSet &) –> class protocols::fldsgn::topology::HelixPairingSet &

calc_geometry(self: pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet, ss_info: protocols::fldsgn::topology::SS_Info2) → None¶

calc geomtry of helix pairing

C++: protocols::fldsgn::topology::HelixPairingSet::calc_geometry(class std::shared_ptr<const class protocols::fldsgn::topology::SS_Info2>) –> void

clear(self: pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet) → None¶

clear data of this HelixPairingSet

C++: protocols::fldsgn::topology::HelixPairingSet::clear() –> void

clone(self: pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet) → pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet¶

clone this object

C++: protocols::fldsgn::topology::HelixPairingSet::clone() const –> class std::shared_ptr<class protocols::fldsgn::topology::HelixPairingSet>

helix_pairing(*args, **kwargs)¶

Overloaded function.

helix_pairing(self: pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet, s: int) -> pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing

return one of the strand_pairings given a number

C++: protocols::fldsgn::topology::HelixPairingSet::helix_pairing(const unsigned long) const –> class std::shared_ptr<class protocols::fldsgn::topology::HelixPairing>

helix_pairing(self: pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet, h1: int, h2: int) -> pyrosetta.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

C++: protocols::fldsgn::topology::HelixPairingSet::helix_pairing(const unsigned long, const unsigned long) –> class std::shared_ptr<class protocols::fldsgn::topology::HelixPairing>

helix_pairings(self: pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_HelixPairing_t¶

return all helix pairings

C++: protocols::fldsgn::topology::HelixPairingSet::helix_pairings() const –> const class utility::vector1<class std::shared_ptr<class protocols::fldsgn::topology::HelixPairing>, class std::allocator<class std::shared_ptr<class protocols::fldsgn::topology::HelixPairing> > > &

name(self: pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet) → str¶

the name of HelixPairingSet is expressed by the combination of helix pairings

C++: protocols::fldsgn::topology::HelixPairingSet::name() const –> std::string

push_back(self: pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet, hop: pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing) → None¶

add HelixPairingOP to StrandPairingSet

C++: protocols::fldsgn::topology::HelixPairingSet::push_back(const class std::shared_ptr<class protocols::fldsgn::topology::HelixPairing>) –> void

size(self: pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet) → int¶

return the size of helix_pairings_

C++: protocols::fldsgn::topology::HelixPairingSet::size() const –> unsigned long

class pyrosetta.rosetta.protocols.fldsgn.topology.Loop¶

Bases: SS_Base

Cend_orient(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::fldsgn::topology::SS_Base::Cend_orient() const –> class numeric::xyzVector<double>

Cend_pos(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::fldsgn::topology::SS_Base::Cend_pos() const –> class numeric::xyzVector<double>

Nend_orient(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::fldsgn::topology::SS_Base::Nend_orient() const –> class numeric::xyzVector<double>

Nend_pos(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::fldsgn::topology::SS_Base::Nend_pos() const –> class numeric::xyzVector<double>

assign(self: pyrosetta.rosetta.protocols.fldsgn.topology.Loop, : pyrosetta.rosetta.protocols.fldsgn.topology.Loop) → pyrosetta.rosetta.protocols.fldsgn.topology.Loop¶: C++: protocols::fldsgn::topology::Loop::operator=(const class protocols::fldsgn::topology::Loop &) –> class protocols::fldsgn::topology::Loop &

begin(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → int¶: C++: protocols::fldsgn::topology::SS_Base::begin() const –> unsigned long

end(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → int¶: C++: protocols::fldsgn::topology::SS_Base::end() const –> unsigned long

is_geometry_initialized(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → bool¶: C++: protocols::fldsgn::topology::SS_Base::is_geometry_initialized() const –> bool

length(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → int¶: C++: protocols::fldsgn::topology::SS_Base::length() const –> unsigned long

mid_pos(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::fldsgn::topology::SS_Base::mid_pos() const –> class numeric::xyzVector<double>

orient(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::fldsgn::topology::SS_Base::orient() const –> class numeric::xyzVector<double>

type(self: pyrosetta.rosetta.protocols.fldsgn.topology.Loop) → str¶: C++: protocols::fldsgn::topology::Loop::type() const –> std::string

property type_¶

class pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base¶

Bases: pybind11_object

Cend_orient(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::fldsgn::topology::SS_Base::Cend_orient() const –> class numeric::xyzVector<double>

Cend_pos(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::fldsgn::topology::SS_Base::Cend_pos() const –> class numeric::xyzVector<double>

Nend_orient(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::fldsgn::topology::SS_Base::Nend_orient() const –> class numeric::xyzVector<double>

Nend_pos(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::fldsgn::topology::SS_Base::Nend_pos() const –> class numeric::xyzVector<double>

assign(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base, : pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base¶: C++: protocols::fldsgn::topology::SS_Base::operator=(const class protocols::fldsgn::topology::SS_Base &) –> class protocols::fldsgn::topology::SS_Base &

begin(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → int¶: C++: protocols::fldsgn::topology::SS_Base::begin() const –> unsigned long

end(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → int¶: C++: protocols::fldsgn::topology::SS_Base::end() const –> unsigned long

is_geometry_initialized(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → bool¶: C++: protocols::fldsgn::topology::SS_Base::is_geometry_initialized() const –> bool

length(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → int¶: C++: protocols::fldsgn::topology::SS_Base::length() const –> unsigned long

mid_pos(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::fldsgn::topology::SS_Base::mid_pos() const –> class numeric::xyzVector<double>

orient(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::fldsgn::topology::SS_Base::orient() const –> class numeric::xyzVector<double>

class pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2¶

Bases: CacheableData

assign(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, : pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2) → pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2¶: C++: protocols::fldsgn::topology::SS_Info2::operator=(const class protocols::fldsgn::topology::SS_Info2 &) –> class protocols::fldsgn::topology::SS_Info2 &

bb_pos(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2) → pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos¶

get xyz-coordinates of backbone structure

C++: protocols::fldsgn::topology::SS_Info2::bb_pos() const –> const class protocols::fldsgn::topology::BB_Pos &

bbpos_is_set(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2) → bool¶

get flag for telling whether bb_pos_ was initiliazed by pose or not

C++: protocols::fldsgn::topology::SS_Info2::bbpos_is_set() const –> bool

clear_data(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2) → None¶

clear data

C++: protocols::fldsgn::topology::SS_Info2::clear_data() –> void

clone(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2) → pyrosetta.rosetta.basic.datacache.CacheableData¶

make clone

C++: protocols::fldsgn::topology::SS_Info2::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.basic.datacache.CacheableData¶: C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t¶: C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

helices(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_Helix_t¶

return helices

C++: protocols::fldsgn::topology::SS_Info2::helices() const –> const class utility::vector1<class std::shared_ptr<class protocols::fldsgn::topology::Helix>, class std::allocator<class std::shared_ptr<class protocols::fldsgn::topology::Helix> > > &

helix(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, ih: int) → pyrosetta.rosetta.protocols.fldsgn.topology.Helix¶

return owning pointer of helix given an index of helices

C++: protocols::fldsgn::topology::SS_Info2::helix(unsigned long) const –> const class std::shared_ptr<const class protocols::fldsgn::topology::Helix>

helix_id(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, nres: int) → int¶

return helix index in helices given a residue number

C++: protocols::fldsgn::topology::SS_Info2::helix_id(const unsigned long) const –> unsigned long

initialize(*args, **kwargs)¶

Overloaded function.

initialize(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, secstruct: str) -> None

initialize parameters of this class

C++: protocols::fldsgn::topology::SS_Info2::initialize(const std::string &) –> void

initialize(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, pose: pyrosetta.rosetta.core.pose.Pose) -> None
initialize(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, pose: pyrosetta.rosetta.core.pose.Pose, secstruct: str) -> None

initialize parameters of this class

C++: protocols::fldsgn::topology::SS_Info2::initialize(const class core::pose::Pose &, const std::string &) –> void

loop(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, il: int) → pyrosetta.rosetta.protocols.fldsgn.topology.Loop¶

return owning pointer of loop given an index of loops

C++: protocols::fldsgn::topology::SS_Info2::loop(unsigned long) const –> const class std::shared_ptr<const class protocols::fldsgn::topology::Loop>

loop_id(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, nres: int) → int¶

return loop index in loops given a residue number

C++: protocols::fldsgn::topology::SS_Info2::loop_id(const unsigned long) const –> unsigned long

loops(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_Loop_t¶

return loops

C++: protocols::fldsgn::topology::SS_Info2::loops() const –> const class utility::vector1<class std::shared_ptr<class protocols::fldsgn::topology::Loop>, class std::allocator<class std::shared_ptr<class protocols::fldsgn::topology::Loop> > > &

secstruct(*args, **kwargs)¶

Overloaded function.

secstruct(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2) -> str

string of secondary structure elements

C++: protocols::fldsgn::topology::SS_Info2::secstruct() const –> std::string

secstruct(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, ii: int) -> str

C++: protocols::fldsgn::topology::SS_Info2::secstruct(unsigned long) const –> char

set_SSorient(*args, **kwargs)¶

Overloaded function.

set_SSorient(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, pose: pyrosetta.rosetta.core.pose.Pose) -> None

set orientation vector of secondary structures given a pose

C++: protocols::fldsgn::topology::SS_Info2::set_SSorient(const class core::pose::Pose &) –> void

set_SSorient(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2) -> None

set orientation vector of secondary structures given a pose which is defined in the constructor

C++: protocols::fldsgn::topology::SS_Info2::set_SSorient() –> void

ss_element_id(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, nres: int) → int¶

return the index of secondary structure element given a residue number

C++: protocols::fldsgn::topology::SS_Info2::ss_element_id(const unsigned long) const –> unsigned long

strand(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, is: int) → pyrosetta.rosetta.protocols.fldsgn.topology.Strand¶

return owning pointer of strand given an index of strands

C++: protocols::fldsgn::topology::SS_Info2::strand(unsigned long) const –> const class std::shared_ptr<const class protocols::fldsgn::topology::Strand>

strand_id(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, nres: int) → int¶

return strand index in strands given a residue number

C++: protocols::fldsgn::topology::SS_Info2::strand_id(const unsigned long) const –> unsigned long

strands(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_Strand_t¶

return strands

C++: protocols::fldsgn::topology::SS_Info2::strands() const –> const class utility::vector1<class std::shared_ptr<class protocols::fldsgn::topology::Strand>, class std::allocator<class std::shared_ptr<class protocols::fldsgn::topology::Strand> > > &

class pyrosetta.rosetta.protocols.fldsgn.topology.Sheet¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.fldsgn.topology.Sheet, : pyrosetta.rosetta.protocols.fldsgn.topology.Sheet) → pyrosetta.rosetta.protocols.fldsgn.topology.Sheet¶: C++: protocols::fldsgn::topology::Sheet::operator=(const class protocols::fldsgn::topology::Sheet &) –> class protocols::fldsgn::topology::Sheet &

ca_cb_orient(self: pyrosetta.rosetta.protocols.fldsgn.topology.Sheet, s: int) → int¶: C++: protocols::fldsgn::topology::Sheet::ca_cb_orient(const unsigned long) const –> int

ca_cb_orients(self: pyrosetta.rosetta.protocols.fldsgn.topology.Sheet) → pyrosetta.rosetta.utility.vector1_int¶: C++: protocols::fldsgn::topology::Sheet::ca_cb_orients() const –> class utility::vector1<int, class std::allocator<int> >

calc_geometry(self: pyrosetta.rosetta.protocols.fldsgn.topology.Sheet, ssinfo: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2) → None¶

calc geometry of sheet, sheet_plane_, sheet_center_, ca_cb_orients_

C++: protocols::fldsgn::topology::Sheet::calc_geometry(const class std::shared_ptr<const class protocols::fldsgn::topology::SS_Info2>) –> void

calc_sasa_bothsides(*args, **kwargs)¶

Overloaded function.

calc_sasa_bothsides(self: pyrosetta.rosetta.protocols.fldsgn.topology.Sheet, pose: pyrosetta.rosetta.core.pose.Pose, ssinfo: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2) -> pyrosetta.rosetta.utility.vector1_double
calc_sasa_bothsides(self: pyrosetta.rosetta.protocols.fldsgn.topology.Sheet, pose: pyrosetta.rosetta.core.pose.Pose, ssinfo: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, pore_radius: float) -> pyrosetta.rosetta.utility.vector1_double

calc surface areas only with beta-sheet

C++: protocols::fldsgn::topology::Sheet::calc_sasa_bothsides(const class core::pose::Pose &, const class std::shared_ptr<const class protocols::fldsgn::topology::SS_Info2>, double) –> class utility::vector1<double, class std::allocator<double> >

clone(self: pyrosetta.rosetta.protocols.fldsgn.topology.Sheet) → pyrosetta.rosetta.protocols.fldsgn.topology.Sheet¶

clone this object

C++: protocols::fldsgn::topology::Sheet::clone() –> class std::shared_ptr<class protocols::fldsgn::topology::Sheet>

initialize(self: pyrosetta.rosetta.protocols.fldsgn.topology.Sheet) → None¶

intialize this class

C++: protocols::fldsgn::topology::Sheet::initialize() –> void

is_barrel(self: pyrosetta.rosetta.protocols.fldsgn.topology.Sheet) → bool¶

is this barrel ?

C++: protocols::fldsgn::topology::Sheet::is_barrel() const –> bool

is_member(self: pyrosetta.rosetta.protocols.fldsgn.topology.Sheet, s: int) → bool¶: C++: protocols::fldsgn::topology::Sheet::is_member(const unsigned long) –> bool

num_strands(self: pyrosetta.rosetta.protocols.fldsgn.topology.Sheet) → int¶

the number strands inclued in

C++: protocols::fldsgn::topology::Sheet::num_strands() const –> unsigned long

order_strand(self: pyrosetta.rosetta.protocols.fldsgn.topology.Sheet, s: int) → int¶: C++: protocols::fldsgn::topology::Sheet::order_strand(const unsigned long) const –> unsigned long

order_strands(self: pyrosetta.rosetta.protocols.fldsgn.topology.Sheet) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::fldsgn::topology::Sheet::order_strands() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

orient_strand(self: pyrosetta.rosetta.protocols.fldsgn.topology.Sheet, s: int) → int¶: C++: protocols::fldsgn::topology::Sheet::orient_strand(const unsigned long) const –> int

orient_strands(self: pyrosetta.rosetta.protocols.fldsgn.topology.Sheet) → pyrosetta.rosetta.utility.vector1_int¶: C++: protocols::fldsgn::topology::Sheet::orient_strands() const –> class utility::vector1<int, class std::allocator<int> >

strand_order(self: pyrosetta.rosetta.protocols.fldsgn.topology.Sheet, s: int) → int¶: C++: protocols::fldsgn::topology::Sheet::strand_order(const unsigned long) –> unsigned long

which_side(self: pyrosetta.rosetta.protocols.fldsgn.topology.Sheet, vec: pyrosetta.rosetta.numeric.xyzVector_double_t) → int¶: C++: protocols::fldsgn::topology::Sheet::which_side(const class numeric::xyzVector<double> &) const –> int

class pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType¶

Bases: pybind11_object

List of topologies determined by strand pairings

Members:

BABx1

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

BAB_CFr = <SheetFoldType.BAB_CFr: 15>¶

BABx1 = <SheetFoldType.BABx1: 1>¶

BABx2 = <SheetFoldType.BABx2: 4>¶

BABx3 = <SheetFoldType.BABx3: 12>¶

BEFr = <SheetFoldType.BEFr: 17>¶

BFr = <SheetFoldType.BFr: 6>¶

CDFr = <SheetFoldType.CDFr: 20>¶

CFr = <SheetFoldType.CFr: 8>¶

DFr = <SheetFoldType.DFr: 9>¶

DFr_BAB = <SheetFoldType.DFr_BAB: 16>¶

DFr_HPN = <SheetFoldType.DFr_HPN: 22>¶

EFr = <SheetFoldType.EFr: 7>¶

Fd_like = <SheetFoldType.Fd_like: 18>¶

Flavodoxin = <SheetFoldType.Flavodoxin: 23>¶

HPN_CFr = <SheetFoldType.HPN_CFr: 21>¶

NO_STRANDS = <SheetFoldType.NO_STRANDS: 30>¶

PG_like = <SheetFoldType.PG_like: 13>¶

Ploop2x3 = <SheetFoldType.Ploop2x3: 24>¶

Ploop3x3 = <SheetFoldType.Ploop3x3: 28>¶

RFd_like = <SheetFoldType.RFd_like: 19>¶

RNAseH = <SheetFoldType.RNAseH: 25>¶

RosI = <SheetFoldType.RosI: 2>¶

RosO = <SheetFoldType.RosO: 3>¶

Rsmn2x2 = <SheetFoldType.Rsmn2x2: 10>¶

Rsmn3x3 = <SheetFoldType.Rsmn3x3: 27>¶

Rsmn3x3_Half = <SheetFoldType.Rsmn3x3_Half: 11>¶

Thio = <SheetFoldType.Thio: 5>¶

Thioredoxin = <SheetFoldType.Thioredoxin: 14>¶

Top7 = <SheetFoldType.Top7: 26>¶

UNFOLD = <SheetFoldType.UNFOLD: 29>¶

UNKNOWN = <SheetFoldType.UNKNOWN: 31>¶

n_fold_types = <SheetFoldType.UNKNOWN: 31>¶

property name¶

property value¶

class pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager¶

Bases: pybind11_object

foldtype_from_name(self: pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager, name: str) → pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType¶: C++: protocols::fldsgn::topology::SheetFoldTypeManager::foldtype_from_name(const std::string &) –> enum protocols::fldsgn::topology::SheetFoldType

foldtype_from_spairs(self: pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager, spairs: str) → pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType¶: C++: protocols::fldsgn::topology::SheetFoldTypeManager::foldtype_from_spairs(const std::string &) –> enum protocols::fldsgn::topology::SheetFoldType

is_foldtype(self: pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager, name: str) → bool¶: C++: protocols::fldsgn::topology::SheetFoldTypeManager::is_foldtype(const std::string &) –> bool

is_sparis_foldtype(self: pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager, spairs: str) → bool¶: C++: protocols::fldsgn::topology::SheetFoldTypeManager::is_sparis_foldtype(const std::string &) –> bool

name_from_foldtype(self: pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager, score_type: pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType) → str¶: C++: protocols::fldsgn::topology::SheetFoldTypeManager::name_from_foldtype(enum protocols::fldsgn::topology::SheetFoldType) –> std::string

spairs_from_foldtype(self: pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager, foldtype: pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType) → str¶: C++: protocols::fldsgn::topology::SheetFoldTypeManager::spairs_from_foldtype(enum protocols::fldsgn::topology::SheetFoldType) –> std::string

class pyrosetta.rosetta.protocols.fldsgn.topology.SheetSet¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.fldsgn.topology.SheetSet, : pyrosetta.rosetta.protocols.fldsgn.topology.SheetSet) → pyrosetta.rosetta.protocols.fldsgn.topology.SheetSet¶: C++: protocols::fldsgn::topology::SheetSet::operator=(const class protocols::fldsgn::topology::SheetSet &) –> class protocols::fldsgn::topology::SheetSet &

calc_geometry(self: pyrosetta.rosetta.protocols.fldsgn.topology.SheetSet, ssinfo: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2) → None¶: C++: protocols::fldsgn::topology::SheetSet::calc_geometry(const class std::shared_ptr<const class protocols::fldsgn::topology::SS_Info2>) –> void

clear(self: pyrosetta.rosetta.protocols.fldsgn.topology.SheetSet) → None¶: C++: protocols::fldsgn::topology::SheetSet::clear() –> void

initialize(self: pyrosetta.rosetta.protocols.fldsgn.topology.SheetSet, ssinfo: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, spairset: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet) → None¶: C++: protocols::fldsgn::topology::SheetSet::initialize(const class std::shared_ptr<const class protocols::fldsgn::topology::SS_Info2>, const class std::shared_ptr<const class protocols::fldsgn::topology::StrandPairingSet>) –> void

num_sheets(self: pyrosetta.rosetta.protocols.fldsgn.topology.SheetSet) → int¶

return number of sheets

C++: protocols::fldsgn::topology::SheetSet::num_sheets() const –> unsigned long

push_back(self: pyrosetta.rosetta.protocols.fldsgn.topology.SheetSet, sop: pyrosetta.rosetta.protocols.fldsgn.topology.Sheet) → None¶: C++: protocols::fldsgn::topology::SheetSet::push_back(const class std::shared_ptr<class protocols::fldsgn::topology::Sheet>) –> void

sheet(self: pyrosetta.rosetta.protocols.fldsgn.topology.SheetSet, s: int) → pyrosetta.rosetta.protocols.fldsgn.topology.Sheet¶: C++: protocols::fldsgn::topology::SheetSet::sheet(const unsigned long) const –> class std::shared_ptr<class protocols::fldsgn::topology::Sheet>

sheets(self: pyrosetta.rosetta.protocols.fldsgn.topology.SheetSet) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_Sheet_t¶: C++: protocols::fldsgn::topology::SheetSet::sheets() const –> class utility::vector1<class std::shared_ptr<class protocols::fldsgn::topology::Sheet>, class std::allocator<class std::shared_ptr<class protocols::fldsgn::topology::Sheet> > >

size(self: pyrosetta.rosetta.protocols.fldsgn.topology.SheetSet) → int¶

return number of sheets

C++: protocols::fldsgn::topology::SheetSet::size() const –> unsigned long

spairset(self: pyrosetta.rosetta.protocols.fldsgn.topology.SheetSet) → pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet¶

return strand pairing set

C++: protocols::fldsgn::topology::SheetSet::spairset() const –> class protocols::fldsgn::topology::StrandPairingSet

which_sheet(self: pyrosetta.rosetta.protocols.fldsgn.topology.SheetSet, s: int) → int¶

return the id of sheet that a given strand belongs to.

C++: protocols::fldsgn::topology::SheetSet::which_sheet(const unsigned long) const –> unsigned long

class pyrosetta.rosetta.protocols.fldsgn.topology.Strand¶

Bases: SS_Base

Cend_orient(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::fldsgn::topology::SS_Base::Cend_orient() const –> class numeric::xyzVector<double>

Cend_pos(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::fldsgn::topology::SS_Base::Cend_pos() const –> class numeric::xyzVector<double>

Nend_orient(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::fldsgn::topology::SS_Base::Nend_orient() const –> class numeric::xyzVector<double>

Nend_pos(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::fldsgn::topology::SS_Base::Nend_pos() const –> class numeric::xyzVector<double>

assign(self: pyrosetta.rosetta.protocols.fldsgn.topology.Strand, : pyrosetta.rosetta.protocols.fldsgn.topology.Strand) → pyrosetta.rosetta.protocols.fldsgn.topology.Strand¶: C++: protocols::fldsgn::topology::Strand::operator=(const class protocols::fldsgn::topology::Strand &) –> class protocols::fldsgn::topology::Strand &

begin(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → int¶: C++: protocols::fldsgn::topology::SS_Base::begin() const –> unsigned long

calc_geometry(self: pyrosetta.rosetta.protocols.fldsgn.topology.Strand, bbpos: pyrosetta.rosetta.protocols.fldsgn.topology.BB_Pos) → None¶: C++: protocols::fldsgn::topology::Strand::calc_geometry(const class protocols::fldsgn::topology::BB_Pos &) –> void

end(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → int¶: C++: protocols::fldsgn::topology::SS_Base::end() const –> unsigned long

is_geometry_initialized(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → bool¶: C++: protocols::fldsgn::topology::SS_Base::is_geometry_initialized() const –> bool

length(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → int¶: C++: protocols::fldsgn::topology::SS_Base::length() const –> unsigned long

mid_pos(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::fldsgn::topology::SS_Base::mid_pos() const –> class numeric::xyzVector<double>

orient(self: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: protocols::fldsgn::topology::SS_Base::orient() const –> class numeric::xyzVector<double>

class pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing¶

Bases: pybind11_object

add_pair(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing, r1: int, r2: int, orient: str, rgstr: float) → bool¶: C++: protocols::fldsgn::topology::StrandPairing::add_pair(const unsigned long, const unsigned long, const char, const double) –> bool

assign(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing, : pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing) → pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing¶: C++: protocols::fldsgn::topology::StrandPairing::operator=(const class protocols::fldsgn::topology::StrandPairing &) –> class protocols::fldsgn::topology::StrandPairing &

begin1(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing) → int¶

the residue number of the beginning of 1st strand

C++: protocols::fldsgn::topology::StrandPairing::begin1() const –> unsigned long

begin2(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing) → int¶

the residue number of the beginning of 2nd strand

C++: protocols::fldsgn::topology::StrandPairing::begin2() const –> unsigned long

clone(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing) → pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing¶

clone this object

C++: protocols::fldsgn::topology::StrandPairing::clone() –> class std::shared_ptr<class protocols::fldsgn::topology::StrandPairing>

elongate(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing, r1: int, r2: int, p1: int, p2: int) → bool¶

elongate strand pairings

C++: protocols::fldsgn::topology::StrandPairing::elongate(const unsigned long, const unsigned long, const unsigned long, const unsigned long) –> bool

end1(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing) → int¶

the residue number of the end of 1st strand

C++: protocols::fldsgn::topology::StrandPairing::end1() const –> unsigned long

end2(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing) → int¶

the residue number of the end of 2nd strand

C++: protocols::fldsgn::topology::StrandPairing::end2() const –> unsigned long

has_bulge(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing) → bool¶

whether the strand pairing have bulge or not

C++: protocols::fldsgn::topology::StrandPairing::has_bulge() const –> bool

has_paired_residue(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing, res: int) → bool¶

return residue pairing

C++: protocols::fldsgn::topology::StrandPairing::has_paired_residue(const unsigned long) const –> bool

is_bulge(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing, resid: int) → bool¶

whethe the given residue number is a bulge

C++: protocols::fldsgn::topology::StrandPairing::is_bulge(const unsigned long) const –> bool

is_member(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing, res: int) → bool¶

whether input residue is included in this StrandPairinge or not

C++: protocols::fldsgn::topology::StrandPairing::is_member(const unsigned long) –> bool

is_parallel(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing) → bool¶

is parallel

C++: protocols::fldsgn::topology::StrandPairing::is_parallel() const –> bool

name(self: pyrosetta.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

C++: protocols::fldsgn::topology::StrandPairing::name() const –> std::string

orient(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing) → str¶

orientation, parallel or anti-parallel, of strand pairing

C++: protocols::fldsgn::topology::StrandPairing::orient() const –> char

pleats1(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

the pleating at the begining of strand_pairing

C++: protocols::fldsgn::topology::StrandPairing::pleats1() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pleats2(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

the pleating at the end of strand_pairing

C++: protocols::fldsgn::topology::StrandPairing::pleats2() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

redefine_begin_end(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing, ss_info: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, abego: pyrosetta.rosetta.utility.vector1_std_string) → None¶

reset begin1_, begin2_, and end1_, end2_ based on ssinfo: abego is used for obtaining bulge information if it is non-empty

C++: protocols::fldsgn::topology::StrandPairing::redefine_begin_end(const class std::shared_ptr<const class protocols::fldsgn::topology::SS_Info2>, const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

residue_pair(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing, res: int) → int¶

residue pair

C++: protocols::fldsgn::topology::StrandPairing::residue_pair(const unsigned long) const –> unsigned long

rgstr_shift(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing) → float¶

the number of register shift between the strands

C++: protocols::fldsgn::topology::StrandPairing::rgstr_shift() const –> double

s1(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing) → int¶

the strand number of the 1st strand in strand pairing

C++: protocols::fldsgn::topology::StrandPairing::s1() const –> unsigned long

s2(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing) → int¶

the strand number of the 2nd strand in strand pairing

C++: protocols::fldsgn::topology::StrandPairing::s2() const –> unsigned long

size1(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing) → int¶

the length of 1st strand

C++: protocols::fldsgn::topology::StrandPairing::size1() const –> unsigned long

size2(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing) → int¶

the length of 2nd strand

C++: protocols::fldsgn::topology::StrandPairing::size2() const –> unsigned long

class pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet, : pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet) → pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet¶: C++: protocols::fldsgn::topology::StrandPairingSet::operator=(const class protocols::fldsgn::topology::StrandPairingSet &) –> class protocols::fldsgn::topology::StrandPairingSet &

clear(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet) → None¶

clear data of this StrandPairingSet

C++: protocols::fldsgn::topology::StrandPairingSet::clear() –> void

clone(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet) → pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet¶

clone this object

C++: protocols::fldsgn::topology::StrandPairingSet::clone() const –> class std::shared_ptr<class protocols::fldsgn::topology::StrandPairingSet>

drop_strand_pairs(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet, drop_spairs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_StrandPairing_t) → None¶

remove a set of strand pairings from datay

C++: protocols::fldsgn::topology::StrandPairingSet::drop_strand_pairs(const class utility::vector1<class std::shared_ptr<class protocols::fldsgn::topology::StrandPairing>, class std::allocator<class std::shared_ptr<class protocols::fldsgn::topology::StrandPairing> > > &) –> void

finalize(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet) → None¶

finalize this and create_map_strand_pairings

C++: protocols::fldsgn::topology::StrandPairingSet::finalize() –> void

finalized(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet) → bool¶: C++: protocols::fldsgn::topology::StrandPairingSet::finalized() const –> bool

make_strand_neighbor_two(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet) → None¶

make the number of strand pairing as two

C++: protocols::fldsgn::topology::StrandPairingSet::make_strand_neighbor_two() –> void

name(self: pyrosetta.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

C++: protocols::fldsgn::topology::StrandPairingSet::name() const –> std::string

name_wo_rgstr(self: pyrosetta.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

C++: protocols::fldsgn::topology::StrandPairingSet::name_wo_rgstr() const –> std::string

neighbor_strands(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet, s: int) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

return strand number of neighbor strands of a input strand

C++: protocols::fldsgn::topology::StrandPairingSet::neighbor_strands(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

num_strands(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet) → int¶

return all strand pairings

C++: protocols::fldsgn::topology::StrandPairingSet::num_strands() const –> unsigned long

push_back(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet, sop: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing) → None¶

add StrandPairingOP to StandPairingSet

C++: protocols::fldsgn::topology::StrandPairingSet::push_back(const class std::shared_ptr<class protocols::fldsgn::topology::StrandPairing>) –> void

push_back_and_finalize(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet, sop: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing) → None¶

add StrandPairingOP to StandPairingSet

C++: protocols::fldsgn::topology::StrandPairingSet::push_back_and_finalize(const class std::shared_ptr<class protocols::fldsgn::topology::StrandPairing>) –> void

size(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet) → int¶: C++: protocols::fldsgn::topology::StrandPairingSet::size() const –> unsigned long

strand_pairing(*args, **kwargs)¶

Overloaded function.

strand_pairing(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet, s: int) -> pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing

return one of the strand_pairings given a number

C++: protocols::fldsgn::topology::StrandPairingSet::strand_pairing(const unsigned long) const –> class std::shared_ptr<class protocols::fldsgn::topology::StrandPairing>

strand_pairing(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet, s1: int, s2: int) -> pyrosetta.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

C++: protocols::fldsgn::topology::StrandPairingSet::strand_pairing(const unsigned long, const unsigned long) const –> class std::shared_ptr<class protocols::fldsgn::topology::StrandPairing>

strand_pairings(self: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_StrandPairing_t¶

return all strand pairings

C++: protocols::fldsgn::topology::StrandPairingSet::strand_pairings() const –> const class utility::vector1<class std::shared_ptr<class protocols::fldsgn::topology::StrandPairing>, class std::allocator<class std::shared_ptr<class protocols::fldsgn::topology::StrandPairing> > > &

class pyrosetta.rosetta.protocols.fldsgn.topology.TripletID¶

Bases: pybind11_object

property helix¶

property strand1¶

property strand2¶

pyrosetta.rosetta.protocols.fldsgn.topology.calc_delta_sasa(pose: pyrosetta.rosetta.core.pose.Pose, intervals: pyrosetta.rosetta.utility.vector1_protocols_forge_build_Interval, pore_radius: float) → float¶

calc delta sasa, when a molecule is splited to 2parts.

C++: protocols::fldsgn::topology::calc_delta_sasa(const class core::pose::Pose &, class utility::vector1<struct protocols::forge::build::Interval, class std::allocator<struct protocols::forge::build::Interval> >, const double) –> double

pyrosetta.rosetta.protocols.fldsgn.topology.calc_strand_helix_angle(pose: pyrosetta.rosetta.core.pose.Pose, ssinfo: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, strand_id1: int, strand_id2: int, helix_id: int, geom_type: str) → float¶: C++: protocols::fldsgn::topology::calc_strand_helix_angle(const class core::pose::Pose &, const class std::shared_ptr<const class protocols::fldsgn::topology::SS_Info2>, const unsigned long, const unsigned long, const unsigned long, const std::string &) –> double

pyrosetta.rosetta.protocols.fldsgn.topology.calc_strand_pairing_set(*args, **kwargs)¶

Overloaded function.

calc_strand_pairing_set(pose: pyrosetta.rosetta.core.pose.Pose, ssinfo: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2) -> pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet
calc_strand_pairing_set(pose: pyrosetta.rosetta.core.pose.Pose, ssinfo: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, minimum_pair_length: int) -> pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet

convert StrandParingSet of dssp to fldsgn::topology::StrandPairingSet

C++: protocols::fldsgn::topology::calc_strand_pairing_set(const class core::pose::Pose &, const class std::shared_ptr<const class protocols::fldsgn::topology::SS_Info2>, unsigned long) –> class protocols::fldsgn::topology::StrandPairingSet

pyrosetta.rosetta.protocols.fldsgn.topology.check_kink_helix(pose: pyrosetta.rosetta.core.pose.Pose, begin: int, end: int) → int¶

check kink of helix, return number of loosen hydrogen

C++: protocols::fldsgn::topology::check_kink_helix(const class core::pose::Pose &, const unsigned long, const unsigned long) –> unsigned long