jumping¶

Bindings for protocols::jumping namespace

class pyrosetta.rosetta.protocols.jumping.BaseJumpSetup¶

Bases: pybind11_builtins.pybind11_object

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

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.jumping.BaseJumpSetup, arg0: pyrosetta.rosetta.protocols.jumping.BaseJumpSetup) -> None
__init__(self: pyrosetta.rosetta.protocols.jumping.BaseJumpSetup) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.Interval¶

Bases: pybind11_builtins.pybind11_object

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

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.jumping.Interval) -> None
__init__(self: pyrosetta.rosetta.protocols.jumping.Interval, start: int, end: int) -> None
__init__(self: pyrosetta.rosetta.protocols.jumping.Interval, arg0: pyrosetta.rosetta.protocols.jumping.Interval) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

end(self: pyrosetta.rosetta.protocols.jumping.Interval) → int¶: C++: protocols::jumping::Interval::end() –> unsigned long

start(self: pyrosetta.rosetta.protocols.jumping.Interval) → int¶: C++: protocols::jumping::Interval::start() –> unsigned long

stop(self: pyrosetta.rosetta.protocols.jumping.Interval) → int¶: C++: protocols::jumping::Interval::stop() –> unsigned long

class pyrosetta.rosetta.protocols.jumping.JumpSelector¶

Bases: pyrosetta.rosetta.protocols.jumping.BaseJumpSetup

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.jumping.JumpSelector) -> None
__init__(self: pyrosetta.rosetta.protocols.jumping.JumpSelector, ss: str) -> None
__init__(self: pyrosetta.rosetta.protocols.jumping.JumpSelector, arg0: pyrosetta.rosetta.protocols.jumping.JumpSelector) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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 &

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(class std::basic_string<char>) –> 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(class std::basic_string<char>) –> 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

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.jumping.JumpSetup, total_residue: int) -> None
__init__(self: pyrosetta.rosetta.protocols.jumping.JumpSetup, arg0: pyrosetta.rosetta.protocols.jumping.JumpSetup) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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 &

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(class std::basic_string<char>) –> 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

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings, total_residue: int, jumps: pyrosetta.rosetta.utility.vector1_core_scoring_dssp_Pairing, cut_probability: ObjexxFCL::FArray1D<float>) -> None
__init__(self: pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings, arg0: pyrosetta.rosetta.protocols.jumping.JumpsFromAllPairings) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.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++

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder, : pyrosetta.rosetta.core.fragment.SecondaryStructure, : pyrosetta.rosetta.utility.vector1_core_scoring_dssp_Pairing, : pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
__init__(self: pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder, arg0: pyrosetta.rosetta.protocols.jumping.RandomSheetBuilder) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.ResiduePairJumpSetup¶

Bases: pyrosetta.rosetta.protocols.jumping.BaseJumpSetup

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup) -> None
__init__(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup, total_residue: int) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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 &

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(class std::basic_string<char>) –> 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.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle) -> None
__init__(self: pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle, residue_type: pyrosetta.rosetta.core.chemical.ResidueType) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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<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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> 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 class std::basic_string<char> &) –> 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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> 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 class std::basic_string<char> &) –> 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,

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.jumping.SameStrand, : pyrosetta.rosetta.core.fragment.SecondaryStructure) -> None
__init__(self: pyrosetta.rosetta.protocols.jumping.SameStrand, arg0: pyrosetta.rosetta.protocols.jumping.SameStrand) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.protocols.jumping.SameStrand) → str¶

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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(class std::basic_ostream<char> &) 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++

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.jumping.SheetBuilder, : pyrosetta.rosetta.core.fragment.SecondaryStructure, : pyrosetta.rosetta.utility.vector1_core_scoring_dssp_Pairing, : pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
__init__(self: pyrosetta.rosetta.protocols.jumping.SheetBuilder, arg0: pyrosetta.rosetta.protocols.jumping.SheetBuilder) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.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.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__¶: Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

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 class std::basic_string<char> &) –> 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.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__¶: Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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_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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &) –> 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: pyrosetta.rosetta.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: pyrosetta.rosetta.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 class std::basic_string<char> &, const class core::kinematics::FoldTree &) –> void

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(class std::basic_istream<char> &, 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