jumping¶

Bindings for protocols::jumping namespace

class pyrosetta.rosetta.protocols.jumping.BaseDisulfPairingLibrary¶

Bases: 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_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_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: 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.

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

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.

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

property pos1¶

property pos2¶

property seq_sep¶

property ss_type¶

class pyrosetta.rosetta.protocols.jumping.DisulfPairingLibrary¶

Bases: 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_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_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_object

add_chainbreaks(*args, **kwargs)¶

Overloaded function.

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

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.

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

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.

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

class JumpWeightDef¶

Bases: pybind11_object

property jump_¶

property weight_¶

add_jump(*args, **kwargs)¶

Overloaded function.

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

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

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 &

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

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: BaseJumpSetup

class JumpDef¶

Bases: pybind11_object

property cut_reg_¶

property jump_¶

add_jump(*args, **kwargs)¶

Overloaded function.

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

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

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 &

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

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: 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_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: 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_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: 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_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.

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

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.

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

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.

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

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: BaseJumpSetup

class JumpDef¶

Bases: pybind11_object

property cut_reg_¶

property jump_¶

add_jump(*args, **kwargs)¶

Overloaded function.

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

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

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 &

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

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_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.

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 > > &

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.

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 > > &

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.

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

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.

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

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_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: 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: 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: DisulfPairingLibrary, 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: PairingLibrary, 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.

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
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_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>¶

property value¶

class pyrosetta.rosetta.protocols.jumping.dofType¶

Bases: 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>¶

property value¶

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.

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

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