jumping

Bindings for protocols::jumping namespace

class pyrosetta.rosetta.protocols.jumping.BaseDisulfPairingLibrary

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.jumping.BaseDisulfPairingLibrary, : pyrosetta.rosetta.protocols.jumping.BaseDisulfPairingLibrary) pyrosetta.rosetta.protocols.jumping.BaseDisulfPairingLibrary

C++: protocols::jumping::BaseDisulfPairingLibrary::operator=(const class protocols::jumping::BaseDisulfPairingLibrary &) –> class protocols::jumping::BaseDisulfPairingLibrary &

class pyrosetta.rosetta.protocols.jumping.BaseJumpSetup

Bases: pybind11_builtins.pybind11_object

virtual base class: can create a set of jumps and cuts

assign(self: pyrosetta.rosetta.protocols.jumping.BaseJumpSetup, : pyrosetta.rosetta.protocols.jumping.BaseJumpSetup) pyrosetta.rosetta.protocols.jumping.BaseJumpSetup

C++: protocols::jumping::BaseJumpSetup::operator=(const class protocols::jumping::BaseJumpSetup &) –> class protocols::jumping::BaseJumpSetup &

clean_jumps(self: pyrosetta.rosetta.protocols.jumping.BaseJumpSetup, : pyrosetta.rosetta.protocols.jumping.JumpSample) pyrosetta.rosetta.protocols.jumping.JumpSample

take from a given JumpSample only those Jumps, which could also have been created by create_jump_sample()

C++: protocols::jumping::BaseJumpSetup::clean_jumps(const class protocols::jumping::JumpSample &) const –> class protocols::jumping::JumpSample

create_jump_sample(self: pyrosetta.rosetta.protocols.jumping.BaseJumpSetup) pyrosetta.rosetta.protocols.jumping.JumpSample

C++: protocols::jumping::BaseJumpSetup::create_jump_sample() const –> class protocols::jumping::JumpSample

generate_jump_frags(self: pyrosetta.rosetta.protocols.jumping.BaseJumpSetup, : pyrosetta.rosetta.protocols.jumping.JumpSample, mm: pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet
returns an ordered FragSet that is compatible with the JumpSample

default: generate jumps from ss-library according to JumpSample

C++: protocols::jumping::BaseJumpSetup::generate_jump_frags(const class protocols::jumping::JumpSample &, const class core::kinematics::MoveMap &) const –> class std::shared_ptr<class core::fragment::FragSet>

type_name(self: pyrosetta.rosetta.protocols.jumping.BaseJumpSetup) str

C++: protocols::jumping::BaseJumpSetup::type_name() const –> std::string

class pyrosetta.rosetta.protocols.jumping.BasePairingLibrary

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.jumping.BasePairingLibrary, : pyrosetta.rosetta.protocols.jumping.BasePairingLibrary) pyrosetta.rosetta.protocols.jumping.BasePairingLibrary

C++: protocols::jumping::BasePairingLibrary::operator=(const class protocols::jumping::BasePairingLibrary &) –> class protocols::jumping::BasePairingLibrary &

create_jump_fragments(self: pyrosetta.rosetta.protocols.jumping.BasePairingLibrary, orientation: int, pleating: int, bWithTorsion: bool, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragData_t) None

C++: protocols::jumping::BasePairingLibrary::create_jump_fragments(const int, const int, bool, class utility::vector1<class std::shared_ptr<class core::fragment::FragData>, class std::allocator<class std::shared_ptr<class core::fragment::FragData> > > &) const –> void

generate_jump_frags(self: pyrosetta.rosetta.protocols.jumping.BasePairingLibrary, pairings: pyrosetta.rosetta.utility.vector1_core_scoring_dssp_Pairing, mm: pyrosetta.rosetta.core.kinematics.MoveMap, bWithTorsion: bool, frags_accumulator: pyrosetta.rosetta.core.fragment.FragSet) None

C++: protocols::jumping::BasePairingLibrary::generate_jump_frags(const class utility::vector1<class core::scoring::dssp::Pairing, class std::allocator<class core::scoring::dssp::Pairing> > &, const class core::kinematics::MoveMap &, bool, class core::fragment::FragSet &) –> void

class pyrosetta.rosetta.protocols.jumping.ChainbreakDistFunc

Bases: pyrosetta.rosetta.core.scoring.func.Func

assign(self: pyrosetta.rosetta.protocols.jumping.ChainbreakDistFunc, : pyrosetta.rosetta.protocols.jumping.ChainbreakDistFunc) pyrosetta.rosetta.protocols.jumping.ChainbreakDistFunc

C++: protocols::jumping::ChainbreakDistFunc::operator=(const class protocols::jumping::ChainbreakDistFunc &) –> class protocols::jumping::ChainbreakDistFunc &

clone(self: pyrosetta.rosetta.protocols.jumping.ChainbreakDistFunc) pyrosetta.rosetta.core.scoring.func.Func

C++: protocols::jumping::ChainbreakDistFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.protocols.jumping.ChainbreakDistFunc, x: float) float

C++: protocols::jumping::ChainbreakDistFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)

Overloaded function.

  1. estimate_dfunc(self: pyrosetta.rosetta.core.scoring.func.Func, r: float) -> float

Estimates the derivative of this function at a given radius by

calculating the slope of the secant line from func(r) and func(r+1e-05).

C++: core::scoring::func::Func::estimate_dfunc(const double) const –> double

  1. estimate_dfunc(self: pyrosetta.rosetta.core.scoring.func.Func, r: float, h: float) -> float

Estimates the derivative of this function at a given radius by

calculating the slope of the secant line from func(r) and func(r+h).

C++: core::scoring::func::Func::estimate_dfunc(const double, const double) const –> double

func(self: pyrosetta.rosetta.protocols.jumping.ChainbreakDistFunc, x: float) float

C++: protocols::jumping::ChainbreakDistFunc::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.Func, : pyrosetta.rosetta.std.istream) None

initialize this Func from the given std::istream.

C++: core::scoring::func::Func::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.protocols.jumping.ChainbreakDistFunc, other: pyrosetta.rosetta.core.scoring.func.Func) bool

C++: protocols::jumping::ChainbreakDistFunc::same_type_as_me(const class core::scoring::func::Func &) const –> bool

show(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream) None
Prints out space-delimited columns for r, func, dfunc and

dfunc_est. The values for func, dfunc and dfunc_est are plotted as a function of r, which is varied from 2-20 in steps of 0.5. The value for dfunc_est is the estimated by the method estimate_dfunc( r ).

C++: core::scoring::func::Func::show(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream) None
shows the definition of this function, usually the string type of

function and the parameters passed in to the constructor.

C++: core::scoring::func::Func::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

  1. show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int

  2. show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int, threshold: float) -> int

show some sort of stringified representation of the violations for

this constraint.

C++: core::scoring::func::Func::show_violations(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.protocols.jumping.DisulfPairing

Bases: pybind11_builtins.pybind11_object

property pos1
property pos2
property seq_sep
property ss_type
class pyrosetta.rosetta.protocols.jumping.DisulfPairingLibrary

Bases: pyrosetta.rosetta.protocols.jumping.BaseDisulfPairingLibrary

assign(self: pyrosetta.rosetta.protocols.jumping.DisulfPairingLibrary, : pyrosetta.rosetta.protocols.jumping.DisulfPairingLibrary) pyrosetta.rosetta.protocols.jumping.DisulfPairingLibrary

C++: protocols::jumping::DisulfPairingLibrary::operator=(const class protocols::jumping::DisulfPairingLibrary &) –> class protocols::jumping::DisulfPairingLibrary &

create_jump_fragments(self: pyrosetta.rosetta.protocols.jumping.DisulfPairingLibrary, bWithTorsion: bool, frags: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragData_t) None

C++: protocols::jumping::DisulfPairingLibrary::create_jump_fragments(bool, class utility::vector1<class std::shared_ptr<class core::fragment::FragData>, class std::allocator<class std::shared_ptr<class core::fragment::FragData> > > &) const –> void

generate_jump_frags(self: pyrosetta.rosetta.protocols.jumping.DisulfPairingLibrary, pairings: pyrosetta.rosetta.utility.vector1_protocols_jumping_DisulfPairing, mm: pyrosetta.rosetta.core.kinematics.MoveMap, bWithTorsion: bool, frags_accumulator: pyrosetta.rosetta.core.fragment.FragSet) None

C++: protocols::jumping::DisulfPairingLibrary::generate_jump_frags(const class utility::vector1<class protocols::jumping::DisulfPairing, class std::allocator<class protocols::jumping::DisulfPairing> > &, const class core::kinematics::MoveMap &, bool, class core::fragment::FragSet &) const –> void

read_from_file(self: pyrosetta.rosetta.protocols.jumping.DisulfPairingLibrary, fn: str) None

C++: protocols::jumping::DisulfPairingLibrary::read_from_file(const std::string &) –> void

size(self: pyrosetta.rosetta.protocols.jumping.DisulfPairingLibrary) int

C++: protocols::jumping::DisulfPairingLibrary::size() const –> unsigned long

class pyrosetta.rosetta.protocols.jumping.DisulfTemplate

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.jumping.DisulfTemplate, : pyrosetta.rosetta.protocols.jumping.DisulfTemplate) pyrosetta.rosetta.protocols.jumping.DisulfTemplate

C++: protocols::jumping::DisulfTemplate::operator=(const class protocols::jumping::DisulfTemplate &) –> class protocols::jumping::DisulfTemplate &

property atoms_downstream_
property atoms_upstream_
property omega
property phi
property psi
property rt_
property secstruct
class pyrosetta.rosetta.protocols.jumping.Interval

Bases: pybind11_builtins.pybind11_object

two numbers, i.e., jump start end residue, or cut-regions…

end(self: pyrosetta.rosetta.protocols.jumping.Interval) int

C++: protocols::jumping::Interval::end() –> unsigned long

property end_
start(self: pyrosetta.rosetta.protocols.jumping.Interval) int

C++: protocols::jumping::Interval::start() –> unsigned long

property start_
stop(self: pyrosetta.rosetta.protocols.jumping.Interval) int

C++: protocols::jumping::Interval::stop() –> unsigned long

class pyrosetta.rosetta.protocols.jumping.JumpSample

Bases: pybind11_builtins.pybind11_object

add_chainbreaks(*args, **kwargs)

Overloaded function.

  1. add_chainbreaks(self: pyrosetta.rosetta.protocols.jumping.JumpSample, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::jumping::JumpSample::add_chainbreaks(class core::pose::Pose &) const –> void

  1. add_chainbreaks(self: pyrosetta.rosetta.protocols.jumping.JumpSample, pose: pyrosetta.rosetta.core.pose.Pose, max_dist: int, : pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree) -> None

C++: protocols::jumping::JumpSample::add_chainbreaks(class core::pose::Pose &, unsigned long, const class core::kinematics::ShortestPathInFoldTree &) const –> void

add_chainbreaks_as_distance_constraint(*args, **kwargs)

Overloaded function.

  1. add_chainbreaks_as_distance_constraint(self: pyrosetta.rosetta.protocols.jumping.JumpSample, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::jumping::JumpSample::add_chainbreaks_as_distance_constraint(class core::pose::Pose &) const –> void

  1. add_chainbreaks_as_distance_constraint(self: pyrosetta.rosetta.protocols.jumping.JumpSample, pose: pyrosetta.rosetta.core.pose.Pose, max_dist: int, sp: pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree) -> None

C++: protocols::jumping::JumpSample::add_chainbreaks_as_distance_constraint(class core::pose::Pose &, unsigned long, const class core::kinematics::ShortestPathInFoldTree &) const –> void

assign(self: pyrosetta.rosetta.protocols.jumping.JumpSample, : pyrosetta.rosetta.protocols.jumping.JumpSample) pyrosetta.rosetta.protocols.jumping.JumpSample

C++: protocols::jumping::JumpSample::operator=(const class protocols::jumping::JumpSample &) –> class protocols::jumping::JumpSample &

cuts(self: pyrosetta.rosetta.protocols.jumping.JumpSample) pyrosetta.rosetta.ObjexxFCL.FArray1D_unsigned_long_t

C++: protocols::jumping::JumpSample::cuts() const –> const class ObjexxFCL::FArray1D<unsigned long> &

downstream_res_nr(self: pyrosetta.rosetta.protocols.jumping.JumpSample, jump_nr: int) int

C++: protocols::jumping::JumpSample::downstream_res_nr(unsigned long) const –> unsigned long

dump_pymol(self: pyrosetta.rosetta.protocols.jumping.JumpSample, fn: str) None

dump file with little pymol script that shows jumps and cuts

C++: protocols::jumping::JumpSample::dump_pymol(std::string) const –> void

fold_tree(self: pyrosetta.rosetta.protocols.jumping.JumpSample) pyrosetta.rosetta.core.kinematics.FoldTree

C++: protocols::jumping::JumpSample::fold_tree() const –> const class core::kinematics::FoldTree &

generate_jump_frags(self: pyrosetta.rosetta.protocols.jumping.JumpSample, pairings: protocols::jumping::PairingLibrary, : pyrosetta.rosetta.core.kinematics.MoveMap, bWithTorsion: bool, : pyrosetta.rosetta.core.fragment.FrameList) None

C++: protocols::jumping::JumpSample::generate_jump_frags(const class protocols::jumping::PairingLibrary &, const class core::kinematics::MoveMap &, bool, class core::fragment::FrameList &) const –> void

generate_jump_frames(*args, **kwargs)

Overloaded function.

  1. generate_jump_frames(self: pyrosetta.rosetta.protocols.jumping.JumpSample, : pyrosetta.rosetta.core.fragment.FrameList, : pyrosetta.rosetta.core.kinematics.MoveMap) -> None

  2. generate_jump_frames(self: pyrosetta.rosetta.protocols.jumping.JumpSample, : pyrosetta.rosetta.core.fragment.FrameList, : pyrosetta.rosetta.core.kinematics.MoveMap, bWithTorsion: bool) -> None

C++: protocols::jumping::JumpSample::generate_jump_frames(class core::fragment::FrameList &, const class core::kinematics::MoveMap &, bool) const –> void

get_pairing(self: pyrosetta.rosetta.protocols.jumping.JumpSample, res1: int, res2: int) pyrosetta.rosetta.core.scoring.dssp.Pairing

C++: protocols::jumping::JumpSample::get_pairing(unsigned long, unsigned long) const –> class core::scoring::dssp::Pairing

has_orientation_and_pleating(self: pyrosetta.rosetta.protocols.jumping.JumpSample) bool

C++: protocols::jumping::JumpSample::has_orientation_and_pleating() const –> bool

is_valid(self: pyrosetta.rosetta.protocols.jumping.JumpSample) bool

C++: protocols::jumping::JumpSample::is_valid() const –> bool

jump_atoms(self: pyrosetta.rosetta.protocols.jumping.JumpSample) pyrosetta.rosetta.ObjexxFCL.FArray2D_std_string_t

C++: protocols::jumping::JumpSample::jump_atoms() const –> const class ObjexxFCL::FArray2D<std::string > &

jumps(self: pyrosetta.rosetta.protocols.jumping.JumpSample) pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_long_t

C++: protocols::jumping::JumpSample::jumps() const –> const class ObjexxFCL::FArray2D<unsigned long> &

remove_chainbreaks(self: pyrosetta.rosetta.protocols.jumping.JumpSample, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::jumping::JumpSample::remove_chainbreaks(class core::pose::Pose &) const –> void

resize(self: pyrosetta.rosetta.protocols.jumping.JumpSample, njump: int) None

C++: protocols::jumping::JumpSample::resize(unsigned long) –> void

safe_secstruct(self: pyrosetta.rosetta.protocols.jumping.JumpSample, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::jumping::JumpSample::safe_secstruct(class core::pose::Pose &) const –> void

set_fold_tree_and_chainbreaks(self: pyrosetta.rosetta.protocols.jumping.JumpSample, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::jumping::JumpSample::set_fold_tree_and_chainbreaks(class core::pose::Pose &) const –> void

set_fold_tree_in_pose(self: pyrosetta.rosetta.protocols.jumping.JumpSample, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::jumping::JumpSample::set_fold_tree_in_pose(class core::pose::Pose &) const –> void

size(self: pyrosetta.rosetta.protocols.jumping.JumpSample) int

C++: protocols::jumping::JumpSample::size() const –> unsigned long

steal_jumps(self: pyrosetta.rosetta.protocols.jumping.JumpSample, native_pose: pyrosetta.rosetta.core.pose.Pose, begin: pyrosetta.rosetta.core.fragment.FrameIterator, end: pyrosetta.rosetta.core.fragment.FrameIterator) None

C++: protocols::jumping::JumpSample::steal_jumps(class core::pose::Pose &, const class core::fragment::FrameIterator &, const class core::fragment::FrameIterator &) const –> void

steal_orientation_and_pleating(self: pyrosetta.rosetta.protocols.jumping.JumpSample, native_pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::jumping::JumpSample::steal_orientation_and_pleating(class core::pose::Pose &) –> void

total_residue(self: pyrosetta.rosetta.protocols.jumping.JumpSample) int

C++: protocols::jumping::JumpSample::total_residue() const –> unsigned long

transfer_jumps(self: pyrosetta.rosetta.protocols.jumping.JumpSample, pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::jumping::JumpSample::transfer_jumps(class core::pose::Pose &, class core::pose::Pose &) const –> void

class pyrosetta.rosetta.protocols.jumping.JumpSelector

Bases: pyrosetta.rosetta.protocols.jumping.BaseJumpSetup

class JumpWeightDef

Bases: pybind11_builtins.pybind11_object

property jump_
property weight_
add_jump(*args, **kwargs)

Overloaded function.

  1. add_jump(self: pyrosetta.rosetta.protocols.jumping.JumpSelector, jd: protocols::jumping::JumpSelector::JumpWeightDef) -> None

C++: protocols::jumping::JumpSelector::add_jump(const class protocols::jumping::JumpSelector::JumpWeightDef &) –> void

  1. add_jump(self: pyrosetta.rosetta.protocols.jumping.JumpSelector, jump: pyrosetta.rosetta.protocols.jumping.Interval, weight: float) -> None

C++: protocols::jumping::JumpSelector::add_jump(const class protocols::jumping::Interval &, double) –> void

  1. add_jump(self: pyrosetta.rosetta.protocols.jumping.JumpSelector, js: int, je: int, weight: float) -> None

C++: protocols::jumping::JumpSelector::add_jump(unsigned long, unsigned long, double) –> void

assign(self: pyrosetta.rosetta.protocols.jumping.JumpSelector, : pyrosetta.rosetta.protocols.jumping.JumpSelector) pyrosetta.rosetta.protocols.jumping.JumpSelector

C++: protocols::jumping::JumpSelector::operator=(const class protocols::jumping::JumpSelector &) –> class protocols::jumping::JumpSelector &

begin(self: pyrosetta.rosetta.protocols.jumping.JumpSelector) __gnu_cxx::__normal_iterator<protocols::jumping::JumpSelector::JumpWeightDef const*, std::vector<protocols::jumping::JumpSelector::JumpWeightDef, std::allocator<protocols::jumping::JumpSelector::JumpWeightDef> > >

C++: protocols::jumping::JumpSelector::begin() const –> class __gnu_cxx::__normal_iterator<const class protocols::jumping::JumpSelector::JumpWeightDef *, class std::vector<class protocols::jumping::JumpSelector::JumpWeightDef, class std::allocator<class protocols::jumping::JumpSelector::JumpWeightDef> > >

clean_jumps(self: pyrosetta.rosetta.protocols.jumping.JumpSelector, js: pyrosetta.rosetta.protocols.jumping.JumpSample) pyrosetta.rosetta.protocols.jumping.JumpSample

C++: protocols::jumping::JumpSelector::clean_jumps(const class protocols::jumping::JumpSample &) const –> class protocols::jumping::JumpSample

create_jump_sample(self: pyrosetta.rosetta.protocols.jumping.JumpSelector) pyrosetta.rosetta.protocols.jumping.JumpSample

C++: protocols::jumping::JumpSelector::create_jump_sample() const –> class protocols::jumping::JumpSample

end(self: pyrosetta.rosetta.protocols.jumping.JumpSelector) __gnu_cxx::__normal_iterator<protocols::jumping::JumpSelector::JumpWeightDef const*, std::vector<protocols::jumping::JumpSelector::JumpWeightDef, std::allocator<protocols::jumping::JumpSelector::JumpWeightDef> > >

C++: protocols::jumping::JumpSelector::end() const –> class __gnu_cxx::__normal_iterator<const class protocols::jumping::JumpSelector::JumpWeightDef *, class std::vector<class protocols::jumping::JumpSelector::JumpWeightDef, class std::allocator<class protocols::jumping::JumpSelector::JumpWeightDef> > >

generate_jump_frags(self: pyrosetta.rosetta.protocols.jumping.BaseJumpSetup, : pyrosetta.rosetta.protocols.jumping.JumpSample, mm: pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet
returns an ordered FragSet that is compatible with the JumpSample

default: generate jumps from ss-library according to JumpSample

C++: protocols::jumping::BaseJumpSetup::generate_jump_frags(const class protocols::jumping::JumpSample &, const class core::kinematics::MoveMap &) const –> class std::shared_ptr<class core::fragment::FragSet>

read_file(self: pyrosetta.rosetta.protocols.jumping.JumpSelector, file: str) None

C++: protocols::jumping::JumpSelector::read_file(std::string) –> void

select_random(self: pyrosetta.rosetta.protocols.jumping.JumpSelector) pyrosetta.rosetta.protocols.jumping.Interval

C++: protocols::jumping::JumpSelector::select_random() const –> class protocols::jumping::Interval

set_secstruct(self: pyrosetta.rosetta.protocols.jumping.JumpSelector, ss: str) None

C++: protocols::jumping::JumpSelector::set_secstruct(std::string) –> void

size(self: pyrosetta.rosetta.protocols.jumping.JumpSelector) int

C++: protocols::jumping::JumpSelector::size() const –> unsigned long

type_name(self: pyrosetta.rosetta.protocols.jumping.JumpSelector) str

C++: protocols::jumping::JumpSelector::type_name() const –> std::string

class pyrosetta.rosetta.protocols.jumping.JumpSetup

Bases: pyrosetta.rosetta.protocols.jumping.BaseJumpSetup

class JumpDef

Bases: pybind11_builtins.pybind11_object

property cut_reg_
property jump_
add_jump(*args, **kwargs)

Overloaded function.

  1. add_jump(self: pyrosetta.rosetta.protocols.jumping.JumpSetup, jd: protocols::jumping::JumpSetup::JumpDef) -> None

C++: protocols::jumping::JumpSetup::add_jump(const class protocols::jumping::JumpSetup::JumpDef &) –> void

  1. add_jump(self: pyrosetta.rosetta.protocols.jumping.JumpSetup, jump: pyrosetta.rosetta.protocols.jumping.Interval, cut_reg: pyrosetta.rosetta.protocols.jumping.Interval) -> None

C++: protocols::jumping::JumpSetup::add_jump(const class protocols::jumping::Interval &, const class protocols::jumping::Interval &) –> void

  1. add_jump(self: pyrosetta.rosetta.protocols.jumping.JumpSetup, js: int, je: int, crs: int, cre: int) -> None

C++: protocols::jumping::JumpSetup::add_jump(unsigned long, unsigned long, unsigned long, unsigned long) –> void

assign(self: pyrosetta.rosetta.protocols.jumping.JumpSetup, : pyrosetta.rosetta.protocols.jumping.JumpSetup) pyrosetta.rosetta.protocols.jumping.JumpSetup

C++: protocols::jumping::JumpSetup::operator=(const class protocols::jumping::JumpSetup &) –> class protocols::jumping::JumpSetup &

begin(self: pyrosetta.rosetta.protocols.jumping.JumpSetup) __gnu_cxx::__normal_iterator<protocols::jumping::JumpSetup::JumpDef const*, std::vector<protocols::jumping::JumpSetup::JumpDef, std::allocator<protocols::jumping::JumpSetup::JumpDef> > >

C++: protocols::jumping::JumpSetup::begin() const –> class __gnu_cxx::__normal_iterator<const class protocols::jumping::JumpSetup::JumpDef *, class std::vector<class protocols::jumping::JumpSetup::JumpDef, class std::allocator<class protocols::jumping::JumpSetup::JumpDef> > >

clean_jumps(self: pyrosetta.rosetta.protocols.jumping.JumpSetup, js: pyrosetta.rosetta.protocols.jumping.JumpSample) pyrosetta.rosetta.protocols.jumping.JumpSample

C++: protocols::jumping::JumpSetup::clean_jumps(const class protocols::jumping::JumpSample &) const –> class protocols::jumping::JumpSample

clear(self: pyrosetta.rosetta.protocols.jumping.JumpSetup) None

C++: protocols::jumping::JumpSetup::clear() –> void

create_jump_sample(self: pyrosetta.rosetta.protocols.jumping.JumpSetup) pyrosetta.rosetta.protocols.jumping.JumpSample

C++: protocols::jumping::JumpSetup::create_jump_sample() const –> class protocols::jumping::JumpSample

end(self: pyrosetta.rosetta.protocols.jumping.JumpSetup) __gnu_cxx::__normal_iterator<protocols::jumping::JumpSetup::JumpDef const*, std::vector<protocols::jumping::JumpSetup::JumpDef, std::allocator<protocols::jumping::JumpSetup::JumpDef> > >

C++: protocols::jumping::JumpSetup::end() const –> class __gnu_cxx::__normal_iterator<const class protocols::jumping::JumpSetup::JumpDef *, class std::vector<class protocols::jumping::JumpSetup::JumpDef, class std::allocator<class protocols::jumping::JumpSetup::JumpDef> > >

generate_jump_frags(self: pyrosetta.rosetta.protocols.jumping.BaseJumpSetup, : pyrosetta.rosetta.protocols.jumping.JumpSample, mm: pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet
returns an ordered FragSet that is compatible with the JumpSample

default: generate jumps from ss-library according to JumpSample

C++: protocols::jumping::BaseJumpSetup::generate_jump_frags(const class protocols::jumping::JumpSample &, const class core::kinematics::MoveMap &) const –> class std::shared_ptr<class core::fragment::FragSet>

read_file(self: pyrosetta.rosetta.protocols.jumping.JumpSetup, file: str) None

C++: protocols::jumping::JumpSetup::read_file(std::string) –> void

set_jump_sample(self: pyrosetta.rosetta.protocols.jumping.JumpSetup, jump_sample: pyrosetta.rosetta.protocols.jumping.JumpSample) None

C++: protocols::jumping::JumpSetup::set_jump_sample(const class protocols::jumping::JumpSample &) –> void

size(self: pyrosetta.rosetta.protocols.jumping.JumpSetup) int

C++: protocols::jumping::JumpSetup::size() const –> unsigned long

total_residue(self: pyrosetta.rosetta.protocols.jumping.JumpSetup) int

C++: protocols::jumping::JumpSetup::total_residue() const –> unsigned long

type_name(self: pyrosetta.rosetta.protocols.jumping.JumpSetup) str

C++: protocols::jumping::JumpSetup::type_name() const –> std::string

class pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings

Bases: pyrosetta.rosetta.protocols.jumping.BaseJumpSetup

assign(self: pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings, : pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings) pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings

C++: protocols::jumping::JumpsFromAllPairings::operator=(const class protocols::jumping::JumpsFromAllPairings &) –> class protocols::jumping::JumpsFromAllPairings &

clean_jumps(self: pyrosetta.rosetta.protocols.jumping.BaseJumpSetup, : pyrosetta.rosetta.protocols.jumping.JumpSample) pyrosetta.rosetta.protocols.jumping.JumpSample

take from a given JumpSample only those Jumps, which could also have been created by create_jump_sample()

C++: protocols::jumping::BaseJumpSetup::clean_jumps(const class protocols::jumping::JumpSample &) const –> class protocols::jumping::JumpSample

create_jump_sample(self: pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings) pyrosetta.rosetta.protocols.jumping.JumpSample

C++: protocols::jumping::JumpsFromAllPairings::create_jump_sample() const –> class protocols::jumping::JumpSample

generate_jump_frags(self: pyrosetta.rosetta.protocols.jumping.BaseJumpSetup, : pyrosetta.rosetta.protocols.jumping.JumpSample, mm: pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet
returns an ordered FragSet that is compatible with the JumpSample

default: generate jumps from ss-library according to JumpSample

C++: protocols::jumping::BaseJumpSetup::generate_jump_frags(const class protocols::jumping::JumpSample &, const class core::kinematics::MoveMap &) const –> class std::shared_ptr<class core::fragment::FragSet>

type_name(self: pyrosetta.rosetta.protocols.jumping.BaseJumpSetup) str

C++: protocols::jumping::BaseJumpSetup::type_name() const –> std::string

class pyrosetta.rosetta.protocols.jumping.MembraneJump

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.jumping.MembraneJump, : pyrosetta.rosetta.protocols.jumping.MembraneJump) pyrosetta.rosetta.protocols.jumping.MembraneJump

C++: protocols::jumping::MembraneJump::operator=(const class protocols::jumping::MembraneJump &) –> class protocols::jumping::MembraneJump &

defined(self: pyrosetta.rosetta.protocols.jumping.MembraneJump) bool

C++: protocols::jumping::MembraneJump::defined() const –> bool

init(self: pyrosetta.rosetta.protocols.jumping.MembraneJump, template_file: str, pairings_file: str) None

C++: protocols::jumping::MembraneJump::init(const std::string &, const std::string &) –> void

pairings_size(self: pyrosetta.rosetta.protocols.jumping.MembraneJump) int

C++: protocols::jumping::MembraneJump::pairings_size() const –> unsigned long

rt_templates(self: pyrosetta.rosetta.protocols.jumping.MembraneJump, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::jumping::MembraneJump::rt_templates(class core::pose::Pose &) –> void

setup_fold_tree(self: pyrosetta.rosetta.protocols.jumping.MembraneJump, pose: pyrosetta.rosetta.core.pose.Pose, njumps: int) None

C++: protocols::jumping::MembraneJump::setup_fold_tree(class core::pose::Pose &, unsigned long) –> void

template_size(self: pyrosetta.rosetta.protocols.jumping.MembraneJump) int

C++: protocols::jumping::MembraneJump::template_size() const –> unsigned long

class pyrosetta.rosetta.protocols.jumping.PairingLibrary

Bases: pyrosetta.rosetta.protocols.jumping.BasePairingLibrary

assign(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary, : pyrosetta.rosetta.protocols.jumping.PairingLibrary) pyrosetta.rosetta.protocols.jumping.PairingLibrary

C++: protocols::jumping::PairingLibrary::operator=(const class protocols::jumping::PairingLibrary &) –> class protocols::jumping::PairingLibrary &

create_jump_fragments(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary, orientation: int, pleating: int, bWithTorsion: bool, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragData_t) None
puts all jump-geometries that fit the orientation and pleating into

list of FragData’s. Try to reuse these FragData for different Frames that have same orientation and pleating This creates Fragments with single JumpSRFD — PairingLibrary also stores phi/psi/omega of start and end residue use bWithTorsion = true to get FragData with BBTorsionSRFD and JumpSRFD length of single FragData is

noTorsion 1 withTorsion 3

bWithTorsion = true length of single FragData is 3 start jump end

C++: protocols::jumping::PairingLibrary::create_jump_fragments(const int, const int, bool, class utility::vector1<class std::shared_ptr<class core::fragment::FragData>, class std::allocator<class std::shared_ptr<class core::fragment::FragData> > > &) const –> void

generate_jump_frags(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary, pairings: pyrosetta.rosetta.utility.vector1_core_scoring_dssp_Pairing, mm: pyrosetta.rosetta.core.kinematics.MoveMap, bWithTorsion: bool, frags_accumulator: pyrosetta.rosetta.core.fragment.FragSet) None

C++: protocols::jumping::PairingLibrary::generate_jump_frags(const class utility::vector1<class core::scoring::dssp::Pairing, class std::allocator<class core::scoring::dssp::Pairing> > &, const class core::kinematics::MoveMap &, bool, class core::fragment::FragSet &) –> void

get_random_beta_sheet_jump(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary, orientation: int, pleating: int) pyrosetta.rosetta.core.kinematics.RT

classic rosetta++ accessor

C++: protocols::jumping::PairingLibrary::get_random_beta_sheet_jump(const int, const int) const –> class core::kinematics::RT

get_random_tmh_jump(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary, orientation: int, pos1: int, pos2: int) pyrosetta.rosetta.core.kinematics.RT

classic rosetta++ accessor

C++: protocols::jumping::PairingLibrary::get_random_tmh_jump(const int, const int, const int) const –> class core::kinematics::RT

read_from_file(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary, fn: str) None

C++: protocols::jumping::PairingLibrary::read_from_file(const std::string &) –> void

read_from_file_no_filters(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary, fn: str) None

C++: protocols::jumping::PairingLibrary::read_from_file_no_filters(const std::string &) –> void

set_tmh_jump(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary, pose: pyrosetta.rosetta.core.pose.Pose, jump_number: int, orientation: int, pos1: int, pos2: int) None

C++: protocols::jumping::PairingLibrary::set_tmh_jump(class core::pose::Pose, const int, const int, const int, const int) const –> void

size(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary) int

C++: protocols::jumping::PairingLibrary::size() const –> unsigned long

class pyrosetta.rosetta.protocols.jumping.PairingTemplate

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.jumping.PairingTemplate, : pyrosetta.rosetta.protocols.jumping.PairingTemplate) pyrosetta.rosetta.protocols.jumping.PairingTemplate

C++: protocols::jumping::PairingTemplate::operator=(const class protocols::jumping::PairingTemplate &) –> class protocols::jumping::PairingTemplate &

property atoms_downstream_
property atoms_upstream_
property omega
property phi
property psi
property rt_
property secstruct
class pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder

Bases: pyrosetta.rosetta.protocols.jumping.SheetBuilder

select jumps to build a given topology

this class encapsulates the functionality of choose_random_pairings in jumping_pairings.cc of Rosetta++

assign(self: pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder, : pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder) pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder

C++: protocols::jumping::RandomSheetBuilder::operator=(const class protocols::jumping::RandomSheetBuilder &) –> class protocols::jumping::RandomSheetBuilder &

clean_jumps(self: pyrosetta.rosetta.protocols.jumping.SheetBuilder, js: pyrosetta.rosetta.protocols.jumping.JumpSample) pyrosetta.rosetta.protocols.jumping.JumpSample

C++: protocols::jumping::SheetBuilder::clean_jumps(const class protocols::jumping::JumpSample &) const –> class protocols::jumping::JumpSample

create_jump_sample(self: pyrosetta.rosetta.protocols.jumping.SheetBuilder) pyrosetta.rosetta.protocols.jumping.JumpSample

C++: protocols::jumping::SheetBuilder::create_jump_sample() const –> class protocols::jumping::JumpSample

generate_jump_frags(self: pyrosetta.rosetta.protocols.jumping.BaseJumpSetup, : pyrosetta.rosetta.protocols.jumping.JumpSample, mm: pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet
returns an ordered FragSet that is compatible with the JumpSample

default: generate jumps from ss-library according to JumpSample

C++: protocols::jumping::BaseJumpSetup::generate_jump_frags(const class protocols::jumping::JumpSample &, const class core::kinematics::MoveMap &) const –> class std::shared_ptr<class core::fragment::FragSet>

total_residue(self: pyrosetta.rosetta.protocols.jumping.SheetBuilder) int

C++: protocols::jumping::SheetBuilder::total_residue() const –> unsigned long

type_name(self: pyrosetta.rosetta.protocols.jumping.SheetBuilder) str

C++: protocols::jumping::SheetBuilder::type_name() const –> std::string

class pyrosetta.rosetta.protocols.jumping.ResiduePairJump

Bases: pybind11_builtins.pybind11_object

add_residue_pair(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJump, residue1: pyrosetta.rosetta.core.chemical.ResidueType, residue2: pyrosetta.rosetta.core.chemical.ResidueType) None

C++: protocols::jumping::ResiduePairJump::add_residue_pair(const class core::chemical::ResidueType &, const class core::chemical::ResidueType &) –> void

add_residue_single(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJump, residue: pyrosetta.rosetta.core.chemical.ResidueType) None

C++: protocols::jumping::ResiduePairJump::add_residue_single(const class core::chemical::ResidueType &) –> void

assign(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJump, : pyrosetta.rosetta.protocols.jumping.ResiduePairJump) pyrosetta.rosetta.protocols.jumping.ResiduePairJump

C++: protocols::jumping::ResiduePairJump::operator=(const class protocols::jumping::ResiduePairJump &) –> class protocols::jumping::ResiduePairJump &

build_cst_conformer_jumps(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJump) None

C++: protocols::jumping::ResiduePairJump::build_cst_conformer_jumps() –> void

build_sidechain_rotamers(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJump) None

C++: protocols::jumping::ResiduePairJump::build_sidechain_rotamers() –> void

cstAtoms(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJump, i: int) pyrosetta.rosetta.utility.vector1_std_string

C++: protocols::jumping::ResiduePairJump::cstAtoms(unsigned long) const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

cstAtoms_defined(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJump) bool

C++: protocols::jumping::ResiduePairJump::cstAtoms_defined() const –> bool

cstInfoMap_defined(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJump) bool

C++: protocols::jumping::ResiduePairJump::cstInfoMap_defined() const –> bool

diversify_cst_conformers(*args, **kwargs)

Overloaded function.

  1. diversify_cst_conformers(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJump, type: pyrosetta.rosetta.protocols.jumping.cstType, max_index: int) -> None

C++: protocols::jumping::ResiduePairJump::diversify_cst_conformers(enum protocols::jumping::cstType, unsigned long) –> void

  1. diversify_cst_conformers(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJump) -> None

C++: protocols::jumping::ResiduePairJump::diversify_cst_conformers() –> void

diversify_dof_conformers(*args, **kwargs)

Overloaded function.

  1. diversify_dof_conformers(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJump, type: pyrosetta.rosetta.protocols.jumping.dofType, max_index: int) -> None

C++: protocols::jumping::ResiduePairJump::diversify_dof_conformers(enum protocols::jumping::dofType, unsigned long) –> void

  1. diversify_dof_conformers(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJump) -> None

C++: protocols::jumping::ResiduePairJump::diversify_dof_conformers() –> void

generate_frame(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJump) pyrosetta.rosetta.core.fragment.Frame

C++: protocols::jumping::ResiduePairJump::generate_frame() –> class std::shared_ptr<class core::fragment::Frame>

init_mini_pose(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJump) None

C++: protocols::jumping::ResiduePairJump::init_mini_pose() –> void

jumpAtoms(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJump, i: int) pyrosetta.rosetta.utility.vector1_std_string

C++: protocols::jumping::ResiduePairJump::jumpAtoms(unsigned long) const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

jumpAtoms_defined(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJump) bool

C++: protocols::jumping::ResiduePairJump::jumpAtoms_defined() const –> bool

set_cstAtoms(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJump, rsd: int, atom: int, name: str) None

C++: protocols::jumping::ResiduePairJump::set_cstAtoms(unsigned long, unsigned long, std::string) –> void

set_cstInfo(*args, **kwargs)

Overloaded function.

  1. set_cstInfo(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJump, type: pyrosetta.rosetta.protocols.jumping.cstType, value: float) -> None

C++: protocols::jumping::ResiduePairJump::set_cstInfo(enum protocols::jumping::cstType, double) –> void

  1. set_cstInfo(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJump, type: pyrosetta.rosetta.protocols.jumping.cstType, values: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::jumping::ResiduePairJump::set_cstInfo(enum protocols::jumping::cstType, const class utility::vector1<double, class std::allocator<double> > &) –> void

set_jumpAtoms(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJump, rsd: int, atom: int, name: str) None

C++: protocols::jumping::ResiduePairJump::set_jumpAtoms(unsigned long, unsigned long, std::string) –> void

class pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup

Bases: pyrosetta.rosetta.protocols.jumping.BaseJumpSetup

class JumpDef

Bases: pybind11_builtins.pybind11_object

property cut_reg_
property jump_
add_jump(*args, **kwargs)

Overloaded function.

  1. add_jump(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup, jd: protocols::jumping::ResiduePairJumpSetup::JumpDef) -> None

C++: protocols::jumping::ResiduePairJumpSetup::add_jump(const class protocols::jumping::ResiduePairJumpSetup::JumpDef &) –> void

  1. add_jump(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup, jump: pyrosetta.rosetta.protocols.jumping.Interval, cut_reg: pyrosetta.rosetta.protocols.jumping.Interval) -> None

C++: protocols::jumping::ResiduePairJumpSetup::add_jump(const class protocols::jumping::Interval &, const class protocols::jumping::Interval &) –> void

  1. add_jump(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup, js: int, je: int, crs: int, cre: int) -> None

C++: protocols::jumping::ResiduePairJumpSetup::add_jump(unsigned long, unsigned long, unsigned long, unsigned long) –> void

add_residue_pair_jump(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup, ptr: pyrosetta.rosetta.protocols.jumping.ResiduePairJump) None

C++: protocols::jumping::ResiduePairJumpSetup::add_residue_pair_jump(class std::shared_ptr<class protocols::jumping::ResiduePairJump>) –> void

assign(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup, : pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup) pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup

C++: protocols::jumping::ResiduePairJumpSetup::operator=(const class protocols::jumping::ResiduePairJumpSetup &) –> class protocols::jumping::ResiduePairJumpSetup &

begin(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup) __gnu_cxx::__normal_iterator<protocols::jumping::ResiduePairJumpSetup::JumpDef const*, std::vector<protocols::jumping::ResiduePairJumpSetup::JumpDef, std::allocator<protocols::jumping::ResiduePairJumpSetup::JumpDef> > >

C++: protocols::jumping::ResiduePairJumpSetup::begin() const –> class __gnu_cxx::__normal_iterator<const class protocols::jumping::ResiduePairJumpSetup::JumpDef *, class std::vector<class protocols::jumping::ResiduePairJumpSetup::JumpDef, class std::allocator<class protocols::jumping::ResiduePairJumpSetup::JumpDef> > >

clean_jumps(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup, js: pyrosetta.rosetta.protocols.jumping.JumpSample) pyrosetta.rosetta.protocols.jumping.JumpSample

C++: protocols::jumping::ResiduePairJumpSetup::clean_jumps(const class protocols::jumping::JumpSample &) const –> class protocols::jumping::JumpSample

clear(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup) None

C++: protocols::jumping::ResiduePairJumpSetup::clear() –> void

create_jump_sample(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup) pyrosetta.rosetta.protocols.jumping.JumpSample

C++: protocols::jumping::ResiduePairJumpSetup::create_jump_sample() const –> class protocols::jumping::JumpSample

end(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup) __gnu_cxx::__normal_iterator<protocols::jumping::ResiduePairJumpSetup::JumpDef const*, std::vector<protocols::jumping::ResiduePairJumpSetup::JumpDef, std::allocator<protocols::jumping::ResiduePairJumpSetup::JumpDef> > >

C++: protocols::jumping::ResiduePairJumpSetup::end() const –> class __gnu_cxx::__normal_iterator<const class protocols::jumping::ResiduePairJumpSetup::JumpDef *, class std::vector<class protocols::jumping::ResiduePairJumpSetup::JumpDef, class std::allocator<class protocols::jumping::ResiduePairJumpSetup::JumpDef> > >

generate_jump_frags(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup, : pyrosetta.rosetta.protocols.jumping.JumpSample, mm: pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet

C++: protocols::jumping::ResiduePairJumpSetup::generate_jump_frags(const class protocols::jumping::JumpSample &, const class core::kinematics::MoveMap &) const –> class std::shared_ptr<class core::fragment::FragSet>

read_file(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup, file: str) None

C++: protocols::jumping::ResiduePairJumpSetup::read_file(std::string) –> void

root(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup) int

C++: protocols::jumping::ResiduePairJumpSetup::root() const –> unsigned long

set_root(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup, root: int) None

C++: protocols::jumping::ResiduePairJumpSetup::set_root(unsigned long) –> void

size(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup) int

C++: protocols::jumping::ResiduePairJumpSetup::size() const –> unsigned long

total_residue(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup) int

C++: protocols::jumping::ResiduePairJumpSetup::total_residue() const –> unsigned long

type_name(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup) str

C++: protocols::jumping::ResiduePairJumpSetup::type_name() const –> std::string

class pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle

Bases: pybind11_builtins.pybind11_object

a single residue component of a ResiduePairJump class

a residue type with information which atoms to be used to define a jump

and cst.

assign(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle, : pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle) pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle

C++: protocols::jumping::ResiduePairJumpSingle::operator=(const class protocols::jumping::ResiduePairJumpSingle &) –> class protocols::jumping::ResiduePairJumpSingle &

cstAtoms(*args, **kwargs)

Overloaded function.

  1. cstAtoms(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle) -> pyrosetta.rosetta.utility.vector1_std_string

access all three cstAtoms at once

C++: protocols::jumping::ResiduePairJumpSingle::cstAtoms() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

  1. cstAtoms(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle, i: int) -> str

access single cstAtom one at a time

C++: protocols::jumping::ResiduePairJumpSingle::cstAtoms(unsigned long) const –> const std::string

cstAtoms_defined(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle) bool

have cstAtoms been defined?

C++: protocols::jumping::ResiduePairJumpSingle::cstAtoms_defined() const –> bool

fixResidue(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle) bool

whether this residue has internal flexibility

C++: protocols::jumping::ResiduePairJumpSingle::fixResidue() const –> bool

jumpAtoms(*args, **kwargs)

Overloaded function.

  1. jumpAtoms(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle) -> pyrosetta.rosetta.utility.vector1_std_string

access all three jumpAtoms at once

C++: protocols::jumping::ResiduePairJumpSingle::jumpAtoms() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

  1. jumpAtoms(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle, i: int) -> str

access single jumpAtom one at a time

C++: protocols::jumping::ResiduePairJumpSingle::jumpAtoms(unsigned long) const –> const std::string

jumpAtoms_defined(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle) bool

have jumpAtoms been defined?

C++: protocols::jumping::ResiduePairJumpSingle::jumpAtoms_defined() const –> bool

residueType(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle) pyrosetta.rosetta.core.chemical.ResidueType

access residue type

C++: protocols::jumping::ResiduePairJumpSingle::residueType() const –> class std::shared_ptr<const class core::chemical::ResidueType>

set_cstAtoms(*args, **kwargs)

Overloaded function.

  1. set_cstAtoms(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle, cst_atoms: pyrosetta.rosetta.utility.vector1_std_string) -> None

set all three cstAtoms at once

C++: protocols::jumping::ResiduePairJumpSingle::set_cstAtoms(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

  1. set_cstAtoms(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle, i: int, atom_name: str) -> None

set all single cstAtom one at a time

C++: protocols::jumping::ResiduePairJumpSingle::set_cstAtoms(unsigned long, const std::string &) –> void

set_jumpAtoms(*args, **kwargs)

Overloaded function.

  1. set_jumpAtoms(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle, jump_atoms: pyrosetta.rosetta.utility.vector1_std_string) -> None

set all three jumpAtoms at once

C++: protocols::jumping::ResiduePairJumpSingle::set_jumpAtoms(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

  1. set_jumpAtoms(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle, i: int, atom_name: str) -> None

set single jumpAtom one at a time

C++: protocols::jumping::ResiduePairJumpSingle::set_jumpAtoms(unsigned long, const std::string &) –> void

class pyrosetta.rosetta.protocols.jumping.SameStrand

Bases: pybind11_builtins.pybind11_object

tiny helper class that knows the relative fractions of secondary structure L,H,E

so far these fractions can be computed from a FragSet other input strategies are conceivable but not implemented, yet: eg. psipred files, a bunch of poses,

assign(self: pyrosetta.rosetta.protocols.jumping.SameStrand, : pyrosetta.rosetta.protocols.jumping.SameStrand) pyrosetta.rosetta.protocols.jumping.SameStrand

C++: protocols::jumping::SameStrand::operator=(const class protocols::jumping::SameStrand &) –> class protocols::jumping::SameStrand &

eval(self: pyrosetta.rosetta.protocols.jumping.SameStrand, i: int, j: int) bool

return whether residue i and j are on the same strand

C++: protocols::jumping::SameStrand::eval(unsigned long, unsigned long) const –> bool

redo(self: pyrosetta.rosetta.protocols.jumping.SameStrand) None

new stochastic choices for strand boundaries

C++: protocols::jumping::SameStrand::redo() const –> void

show(self: pyrosetta.rosetta.protocols.jumping.SameStrand, os: pyrosetta.rosetta.std.ostream) None

print current choice to stream

C++: protocols::jumping::SameStrand::show(std::ostream &) const –> void

total_residue(self: pyrosetta.rosetta.protocols.jumping.SameStrand) int

C++: protocols::jumping::SameStrand::total_residue() const –> unsigned long

class pyrosetta.rosetta.protocols.jumping.SheetBuilder

Bases: pyrosetta.rosetta.protocols.jumping.BaseJumpSetup

select jumps to build a given topology

this class encapsulates the functionality of choose_random_pairings in jumping_pairings.cc of Rosetta++

assign(self: pyrosetta.rosetta.protocols.jumping.SheetBuilder, : pyrosetta.rosetta.protocols.jumping.SheetBuilder) pyrosetta.rosetta.protocols.jumping.SheetBuilder

C++: protocols::jumping::SheetBuilder::operator=(const class protocols::jumping::SheetBuilder &) –> class protocols::jumping::SheetBuilder &

clean_jumps(self: pyrosetta.rosetta.protocols.jumping.SheetBuilder, js: pyrosetta.rosetta.protocols.jumping.JumpSample) pyrosetta.rosetta.protocols.jumping.JumpSample

C++: protocols::jumping::SheetBuilder::clean_jumps(const class protocols::jumping::JumpSample &) const –> class protocols::jumping::JumpSample

create_jump_sample(self: pyrosetta.rosetta.protocols.jumping.SheetBuilder) pyrosetta.rosetta.protocols.jumping.JumpSample

C++: protocols::jumping::SheetBuilder::create_jump_sample() const –> class protocols::jumping::JumpSample

generate_jump_frags(self: pyrosetta.rosetta.protocols.jumping.BaseJumpSetup, : pyrosetta.rosetta.protocols.jumping.JumpSample, mm: pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet
returns an ordered FragSet that is compatible with the JumpSample

default: generate jumps from ss-library according to JumpSample

C++: protocols::jumping::BaseJumpSetup::generate_jump_frags(const class protocols::jumping::JumpSample &, const class core::kinematics::MoveMap &) const –> class std::shared_ptr<class core::fragment::FragSet>

total_residue(self: pyrosetta.rosetta.protocols.jumping.SheetBuilder) int

C++: protocols::jumping::SheetBuilder::total_residue() const –> unsigned long

type_name(self: pyrosetta.rosetta.protocols.jumping.SheetBuilder) str

C++: protocols::jumping::SheetBuilder::type_name() const –> std::string

class pyrosetta.rosetta.protocols.jumping.SpecificGeometryLibrary

Bases: pyrosetta.rosetta.protocols.jumping.PairingLibrary

assign(self: pyrosetta.rosetta.protocols.jumping.SpecificGeometryLibrary, : pyrosetta.rosetta.protocols.jumping.SpecificGeometryLibrary) pyrosetta.rosetta.protocols.jumping.SpecificGeometryLibrary

C++: protocols::jumping::SpecificGeometryLibrary::operator=(const class protocols::jumping::SpecificGeometryLibrary &) –> class protocols::jumping::SpecificGeometryLibrary &

create_jump_fragments(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary, orientation: int, pleating: int, bWithTorsion: bool, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragData_t) None
puts all jump-geometries that fit the orientation and pleating into

list of FragData’s. Try to reuse these FragData for different Frames that have same orientation and pleating This creates Fragments with single JumpSRFD — PairingLibrary also stores phi/psi/omega of start and end residue use bWithTorsion = true to get FragData with BBTorsionSRFD and JumpSRFD length of single FragData is

noTorsion 1 withTorsion 3

bWithTorsion = true length of single FragData is 3 start jump end

C++: protocols::jumping::PairingLibrary::create_jump_fragments(const int, const int, bool, class utility::vector1<class std::shared_ptr<class core::fragment::FragData>, class std::allocator<class std::shared_ptr<class core::fragment::FragData> > > &) const –> void

generate_jump_frags(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary, pairings: pyrosetta.rosetta.utility.vector1_core_scoring_dssp_Pairing, mm: pyrosetta.rosetta.core.kinematics.MoveMap, bWithTorsion: bool, frags_accumulator: pyrosetta.rosetta.core.fragment.FragSet) None

C++: protocols::jumping::PairingLibrary::generate_jump_frags(const class utility::vector1<class core::scoring::dssp::Pairing, class std::allocator<class core::scoring::dssp::Pairing> > &, const class core::kinematics::MoveMap &, bool, class core::fragment::FragSet &) –> void

get_random_beta_sheet_jump(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary, orientation: int, pleating: int) pyrosetta.rosetta.core.kinematics.RT

classic rosetta++ accessor

C++: protocols::jumping::PairingLibrary::get_random_beta_sheet_jump(const int, const int) const –> class core::kinematics::RT

get_random_tmh_jump(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary, orientation: int, pos1: int, pos2: int) pyrosetta.rosetta.core.kinematics.RT

classic rosetta++ accessor

C++: protocols::jumping::PairingLibrary::get_random_tmh_jump(const int, const int, const int) const –> class core::kinematics::RT

read_from_file(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary, fn: str) None

C++: protocols::jumping::PairingLibrary::read_from_file(const std::string &) –> void

read_from_file_no_filters(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary, fn: str) None

C++: protocols::jumping::PairingLibrary::read_from_file_no_filters(const std::string &) –> void

set_tmh_jump(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary, pose: pyrosetta.rosetta.core.pose.Pose, jump_number: int, orientation: int, pos1: int, pos2: int) None

C++: protocols::jumping::PairingLibrary::set_tmh_jump(class core::pose::Pose, const int, const int, const int, const int) const –> void

size(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary) int

C++: protocols::jumping::PairingLibrary::size() const –> unsigned long

class pyrosetta.rosetta.protocols.jumping.StandardDisulfPairingLibrary

Bases: pyrosetta.rosetta.protocols.jumping.DisulfPairingLibrary, pyrosetta.rosetta.utility.SingletonBase_protocols_jumping_StandardDisulfPairingLibrary_t

The %StandardDisulfPairingsLibrary initializes itself in its constructor from the sampling/disulfide_jump_database_wip.dat file in the database. Users should not in any circumstance invoke any of its non-const methods that are defined in the subclass. This class ought to be reworked to ensure that it is threadsafe.

assign(self: pyrosetta.rosetta.protocols.jumping.DisulfPairingLibrary, : pyrosetta.rosetta.protocols.jumping.DisulfPairingLibrary) pyrosetta.rosetta.protocols.jumping.DisulfPairingLibrary

C++: protocols::jumping::DisulfPairingLibrary::operator=(const class protocols::jumping::DisulfPairingLibrary &) –> class protocols::jumping::DisulfPairingLibrary &

create_jump_fragments(self: pyrosetta.rosetta.protocols.jumping.DisulfPairingLibrary, bWithTorsion: bool, frags: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragData_t) None

C++: protocols::jumping::DisulfPairingLibrary::create_jump_fragments(bool, class utility::vector1<class std::shared_ptr<class core::fragment::FragData>, class std::allocator<class std::shared_ptr<class core::fragment::FragData> > > &) const –> void

generate_jump_frags(self: pyrosetta.rosetta.protocols.jumping.DisulfPairingLibrary, pairings: pyrosetta.rosetta.utility.vector1_protocols_jumping_DisulfPairing, mm: pyrosetta.rosetta.core.kinematics.MoveMap, bWithTorsion: bool, frags_accumulator: pyrosetta.rosetta.core.fragment.FragSet) None

C++: protocols::jumping::DisulfPairingLibrary::generate_jump_frags(const class utility::vector1<class protocols::jumping::DisulfPairing, class std::allocator<class protocols::jumping::DisulfPairing> > &, const class core::kinematics::MoveMap &, bool, class core::fragment::FragSet &) const –> void

static get_instance() protocols::jumping::StandardDisulfPairingLibrary

C++: utility::SingletonBase<protocols::jumping::StandardDisulfPairingLibrary>::get_instance() –> class protocols::jumping::StandardDisulfPairingLibrary *

read_from_file(self: pyrosetta.rosetta.protocols.jumping.DisulfPairingLibrary, fn: str) None

C++: protocols::jumping::DisulfPairingLibrary::read_from_file(const std::string &) –> void

size(self: pyrosetta.rosetta.protocols.jumping.DisulfPairingLibrary) int

C++: protocols::jumping::DisulfPairingLibrary::size() const –> unsigned long

class pyrosetta.rosetta.protocols.jumping.StandardPairingLibrary

Bases: pyrosetta.rosetta.protocols.jumping.PairingLibrary, pyrosetta.rosetta.utility.SingletonBase_protocols_jumping_StandardPairingLibrary_t

This class is thread-unsafe, though, if perhaps none of its non-const functions were accessible, then it wouldn’t be.

assign(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary, : pyrosetta.rosetta.protocols.jumping.PairingLibrary) pyrosetta.rosetta.protocols.jumping.PairingLibrary

C++: protocols::jumping::PairingLibrary::operator=(const class protocols::jumping::PairingLibrary &) –> class protocols::jumping::PairingLibrary &

create_jump_fragments(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary, orientation: int, pleating: int, bWithTorsion: bool, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragData_t) None
puts all jump-geometries that fit the orientation and pleating into

list of FragData’s. Try to reuse these FragData for different Frames that have same orientation and pleating This creates Fragments with single JumpSRFD — PairingLibrary also stores phi/psi/omega of start and end residue use bWithTorsion = true to get FragData with BBTorsionSRFD and JumpSRFD length of single FragData is

noTorsion 1 withTorsion 3

bWithTorsion = true length of single FragData is 3 start jump end

C++: protocols::jumping::PairingLibrary::create_jump_fragments(const int, const int, bool, class utility::vector1<class std::shared_ptr<class core::fragment::FragData>, class std::allocator<class std::shared_ptr<class core::fragment::FragData> > > &) const –> void

generate_jump_frags(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary, pairings: pyrosetta.rosetta.utility.vector1_core_scoring_dssp_Pairing, mm: pyrosetta.rosetta.core.kinematics.MoveMap, bWithTorsion: bool, frags_accumulator: pyrosetta.rosetta.core.fragment.FragSet) None

C++: protocols::jumping::PairingLibrary::generate_jump_frags(const class utility::vector1<class core::scoring::dssp::Pairing, class std::allocator<class core::scoring::dssp::Pairing> > &, const class core::kinematics::MoveMap &, bool, class core::fragment::FragSet &) –> void

static get_instance() protocols::jumping::StandardPairingLibrary

C++: utility::SingletonBase<protocols::jumping::StandardPairingLibrary>::get_instance() –> class protocols::jumping::StandardPairingLibrary *

get_random_beta_sheet_jump(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary, orientation: int, pleating: int) pyrosetta.rosetta.core.kinematics.RT

classic rosetta++ accessor

C++: protocols::jumping::PairingLibrary::get_random_beta_sheet_jump(const int, const int) const –> class core::kinematics::RT

get_random_tmh_jump(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary, orientation: int, pos1: int, pos2: int) pyrosetta.rosetta.core.kinematics.RT

classic rosetta++ accessor

C++: protocols::jumping::PairingLibrary::get_random_tmh_jump(const int, const int, const int) const –> class core::kinematics::RT

read_from_file(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary, fn: str) None

C++: protocols::jumping::PairingLibrary::read_from_file(const std::string &) –> void

read_from_file_no_filters(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary, fn: str) None

C++: protocols::jumping::PairingLibrary::read_from_file_no_filters(const std::string &) –> void

set_tmh_jump(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary, pose: pyrosetta.rosetta.core.pose.Pose, jump_number: int, orientation: int, pos1: int, pos2: int) None

C++: protocols::jumping::PairingLibrary::set_tmh_jump(class core::pose::Pose, const int, const int, const int, const int) const –> void

size(self: pyrosetta.rosetta.protocols.jumping.PairingLibrary) int

C++: protocols::jumping::PairingLibrary::size() const –> unsigned long

pyrosetta.rosetta.protocols.jumping.assign_ss_dssp(pose: pyrosetta.rosetta.core.pose.Pose) None

Assign secondary structure using DSSP.

C++: protocols::jumping::assign_ss_dssp(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.jumping.close_chainbreaks(*args, **kwargs)

Overloaded function.

  1. close_chainbreaks(closure_protocol: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure, pose: pyrosetta.rosetta.core.pose.Pose, checkpoint: pyrosetta.rosetta.protocols.checkpoint.CheckPointer, decoy_tag: str) -> None

  2. close_chainbreaks(closure_protocol: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure, pose: pyrosetta.rosetta.core.pose.Pose, checkpoint: pyrosetta.rosetta.protocols.checkpoint.CheckPointer, decoy_tag: str, final_fold_tree: pyrosetta.rosetta.core.kinematics.FoldTree) -> None

C++: protocols::jumping::close_chainbreaks(class std::shared_ptr<class protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure>, class core::pose::Pose &, class protocols::checkpoint::CheckPointer &, const std::string &, const class core::kinematics::FoldTree &) –> void

class pyrosetta.rosetta.protocols.jumping.cstType

Bases: pybind11_builtins.pybind11_object

Members:

disAB

angleA

angleB

dihedralA

dihedralAB

dihedralB

num_cstType

angleA = <cstType.angleA: 2>
angleB = <cstType.angleB: 3>
dihedralA = <cstType.dihedralA: 4>
dihedralAB = <cstType.dihedralAB: 5>
dihedralB = <cstType.dihedralB: 6>
disAB = <cstType.disAB: 1>
property name
num_cstType = <cstType.dihedralB: 6>
class pyrosetta.rosetta.protocols.jumping.dofType

Bases: pybind11_builtins.pybind11_object

Members:

rot1

rot2

cstJump

num_dofType

cstJump = <dofType.cstJump: 3>
property name
num_dofType = <dofType.cstJump: 3>
rot1 = <dofType.rot1: 1>
rot2 = <dofType.rot2: 2>
pyrosetta.rosetta.protocols.jumping.generate_empty_jump_frame(startpos: int, endpos: int, length: int) pyrosetta.rosetta.core.fragment.JumpingFrame

C++: protocols::jumping::generate_empty_jump_frame(unsigned long, unsigned long, unsigned long) –> class std::shared_ptr<class core::fragment::JumpingFrame>

pyrosetta.rosetta.protocols.jumping.generate_jump_frame(startpos: int, endpos: int, bWithTorsion: bool) pyrosetta.rosetta.core.fragment.JumpingFrame

C++: protocols::jumping::generate_jump_frame(unsigned long, unsigned long, bool) –> class std::shared_ptr<class core::fragment::JumpingFrame>

pyrosetta.rosetta.protocols.jumping.get_pairing_geometry(pose: pyrosetta.rosetta.core.pose.Pose, res1: int, res2: int, orientation: float, pleating1: float, pleating2: float) None

C++: protocols::jumping::get_pairing_geometry(const class core::pose::Pose &, const unsigned long, const unsigned long, double &, double &, double &) –> void

pyrosetta.rosetta.protocols.jumping.get_pleating(pose: pyrosetta.rosetta.core.pose.Pose, pos1: int, pos2: int, orientation: int, pleating: int) None

C++: protocols::jumping::get_pleating(const class core::pose::Pose &, const unsigned long, const unsigned long, unsigned long &, unsigned long &) –> void

pyrosetta.rosetta.protocols.jumping.read_disulf_pairing_list(is: pyrosetta.rosetta.std.istream, disulf_pairings: pyrosetta.rosetta.utility.vector1_protocols_jumping_DisulfPairing) None

C++: protocols::jumping::read_disulf_pairing_list(std::istream &, class utility::vector1<class protocols::jumping::DisulfPairing, class std::allocator<class protocols::jumping::DisulfPairing> > &) –> void

pyrosetta.rosetta.protocols.jumping.remove_cut(*args, **kwargs)

Overloaded function.

  1. remove_cut(cutpoint: int, pose: pyrosetta.rosetta.core.pose.Pose) -> bool

  2. remove_cut(cutpoint: int, pose: pyrosetta.rosetta.core.pose.Pose, final_fold_tree: pyrosetta.rosetta.core.kinematics.FoldTree) -> bool

C++: protocols::jumping::remove_cut(unsigned long, class core::pose::Pose &, const class core::kinematics::FoldTree &) –> bool

  1. remove_cut(cutpoint: int, fold_tree: pyrosetta.rosetta.core.kinematics.FoldTree) -> bool

  2. remove_cut(cutpoint: int, fold_tree: pyrosetta.rosetta.core.kinematics.FoldTree, final_fold_tree: pyrosetta.rosetta.core.kinematics.FoldTree) -> bool

C++: protocols::jumping::remove_cut(unsigned long, class core::kinematics::FoldTree &, const class core::kinematics::FoldTree &) –> bool

pyrosetta.rosetta.protocols.jumping.safe_secstruct(pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::jumping::safe_secstruct(class core::pose::Pose &) –> void