components

Bindings for protocols::denovo_design::components namespace

class pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber

Bases: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

“mutates” a set of mixed architects

__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.

1. __init__(self: pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber) -> None
2. __init__(self: pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber, arg0: pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber) -> 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).

apply(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) → None

C++: protocols::denovo_design::components::StructureDataPerturber::apply(class protocols::denovo_design::components::StructureData &) –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber, : pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber) → pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber

C++: protocols::denovo_design::components::CompoundPerturber::operator=(const class protocols::denovo_design::components::CompoundPerturber &) –> class protocols::denovo_design::components::CompoundPerturber &

class_name() → str

C++: protocols::denovo_design::components::CompoundPerturber::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber) → pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

C++: protocols::denovo_design::components::CompoundPerturber::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::StructureDataPerturber>

create(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

C++: protocols::denovo_design::components::StructureDataPerturber::create(const class utility::tag::Tag &, class basic::datacache::DataMap &) –> class std::shared_ptr<class protocols::denovo_design::components::StructureDataPerturber>

enumerate(self: pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) → pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t

C++: protocols::denovo_design::components::CompoundPerturber::enumerate(const class protocols::denovo_design::components::StructureData &) const –> class utility::vector1<class utility::vector1<class std::shared_ptr<const class protocols::denovo_design::components::Segment>, class std::allocator<class std::shared_ptr<const class protocols::denovo_design::components::Segment> > >, class std::allocator<class utility::vector1<class std::shared_ptr<const class protocols::denovo_design::components::Segment>, class std::allocator<class std::shared_ptr<const class protocols::denovo_design::components::Segment> > > > >

ignored(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, segment_name: str) → bool

C++: protocols::denovo_design::components::StructureDataPerturber::ignored(const class std::basic_string<char> &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::denovo_design::components::CompoundPerturber::parse_my_tag(const class utility::tag::Tag &, class basic::datacache::DataMap &) –> void

set_ignore_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber, ignore_set: pyrosetta.rosetta.std.set_std_string_std_less_std_string_std_allocator_std_string_t) → None

C++: protocols::denovo_design::components::CompoundPerturber::set_ignore_segments(const class std::set<class std::basic_string<char>, struct std::less<class std::basic_string<char> >, class std::allocator<class std::basic_string<char> > > &) –> void

class pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber

Bases: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

“mutates” a connection

__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__(self: pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber) → 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).

apply(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) → None

C++: protocols::denovo_design::components::StructureDataPerturber::apply(class protocols::denovo_design::components::StructureData &) –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber, : pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber) → pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber

C++: protocols::denovo_design::components::ConnectionPerturber::operator=(const class protocols::denovo_design::components::ConnectionPerturber &) –> class protocols::denovo_design::components::ConnectionPerturber &

class_name() → str

C++: protocols::denovo_design::components::ConnectionPerturber::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber) → pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

C++: protocols::denovo_design::components::ConnectionPerturber::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::StructureDataPerturber>

create(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

C++: protocols::denovo_design::components::StructureDataPerturber::create(const class utility::tag::Tag &, class basic::datacache::DataMap &) –> class std::shared_ptr<class protocols::denovo_design::components::StructureDataPerturber>

enumerate(self: pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) → pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t

C++: protocols::denovo_design::components::ConnectionPerturber::enumerate(const class protocols::denovo_design::components::StructureData &) const –> class utility::vector1<class utility::vector1<class std::shared_ptr<const class protocols::denovo_design::components::Segment>, class std::allocator<class std::shared_ptr<const class protocols::denovo_design::components::Segment> > >, class std::allocator<class utility::vector1<class std::shared_ptr<const class protocols::denovo_design::components::Segment>, class std::allocator<class std::shared_ptr<const class protocols::denovo_design::components::Segment> > > > >

ignored(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, segment_name: str) → bool

C++: protocols::denovo_design::components::StructureDataPerturber::ignored(const class std::basic_string<char> &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::denovo_design::components::ConnectionPerturber::parse_my_tag(const class utility::tag::Tag &, class basic::datacache::DataMap &) –> void

set_ignore_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, ignore_set: pyrosetta.rosetta.std.set_std_string_std_less_std_string_std_allocator_std_string_t) → None

C++: protocols::denovo_design::components::StructureDataPerturber::set_ignore_segments(const class std::set<class std::basic_string<char>, struct std::less<class std::basic_string<char> >, class std::allocator<class std::basic_string<char> > > &) –> void

class pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror

Bases: pybind11_builtins.pybind11_object

Splits a denovo structure into pieces, and devises a strategy for folding the structure piece-by-piece

__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__(self: pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror) → 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.denovo_design.components.DivideAndConqueror, : pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror) → pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror

C++: protocols::denovo_design::components::DivideAndConqueror::operator=(const class protocols::denovo_design::components::DivideAndConqueror &) –> class protocols::denovo_design::components::DivideAndConqueror &

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror) → pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror

C++: protocols::denovo_design::components::DivideAndConqueror::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::DivideAndConqueror>

divide_and_conquer(self: pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror, sd: protocols::denovo_design::components::StructureData) → pyrosetta.rosetta.protocols.denovo_design.components.BuildPhases

C++: protocols::denovo_design::components::DivideAndConqueror::divide_and_conquer(const class protocols::denovo_design::components::StructureData &) const –> class protocols::denovo_design::components::BuildPhases

set_start_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror, start_seg_names: pyrosetta.rosetta.std.set_std_string_std_less_std_string_std_allocator_std_string_t) → None

C++: protocols::denovo_design::components::DivideAndConqueror::set_start_segments(const class std::set<class std::basic_string<char>, struct std::less<class std::basic_string<char> >, class std::allocator<class std::basic_string<char> > > &) –> void

set_stop_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror, stop_seg_names: pyrosetta.rosetta.std.set_std_string_std_less_std_string_std_allocator_std_string_t) → None

C++: protocols::denovo_design::components::DivideAndConqueror::set_stop_segments(const class std::set<class std::basic_string<char>, struct std::less<class std::basic_string<char> >, class std::allocator<class std::basic_string<char> > > &) –> void

class pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold

Bases: pyrosetta.rosetta.utility.excn.EXCN_Base

Exception thrown by PoseFolder::apply to indicate folding was not successful

__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.

1. __init__(self: pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold, msg: str) -> None
2. __init__(self: pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold, arg0: pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold) -> 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.utility.excn.EXCN_Base) → 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.denovo_design.components.EXCN_Fold, : pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold) → pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold

C++: protocols::denovo_design::components::EXCN_Fold::operator=(const class protocols::denovo_design::components::EXCN_Fold &) –> class protocols::denovo_design::components::EXCN_Fold &

msg(self: pyrosetta.rosetta.utility.excn.EXCN_Base) → str

C++: utility::excn::EXCN_Base::msg() const –> const std::string

show(self: pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold, os: pyrosetta.rosetta.std.ostream) → None

C++: protocols::denovo_design::components::EXCN_Fold::show(class std::basic_ostream<char> &) const –> void

what(self: pyrosetta.rosetta.utility.excn.EXCN_Base) → str

C++: utility::excn::EXCN_Base::what() const –> const char *

class pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder

Bases: pybind11_builtins.pybind11_object

Builds a pose from StructureData

__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__(self: pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder) → 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).

apply(self: pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder, sd: protocols::denovo_design::components::StructureData) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::denovo_design::components::ExtendedPoseBuilder::apply(const class protocols::denovo_design::components::StructureData &) const –> class std::shared_ptr<class core::pose::Pose>

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder, : pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder) → pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder

C++: protocols::denovo_design::components::ExtendedPoseBuilder::operator=(const class protocols::denovo_design::components::ExtendedPoseBuilder &) –> class protocols::denovo_design::components::ExtendedPoseBuilder &

class pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber

Bases: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

“mutates” a helix

__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__(self: pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber) → 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).

apply(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) → None

C++: protocols::denovo_design::components::StructureDataPerturber::apply(class protocols::denovo_design::components::StructureData &) –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber, : pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber) → pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber

C++: protocols::denovo_design::components::HelixPerturber::operator=(const class protocols::denovo_design::components::HelixPerturber &) –> class protocols::denovo_design::components::HelixPerturber &

class_name() → str

C++: protocols::denovo_design::components::HelixPerturber::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber) → pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

C++: protocols::denovo_design::components::HelixPerturber::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::StructureDataPerturber>

create(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

C++: protocols::denovo_design::components::StructureDataPerturber::create(const class utility::tag::Tag &, class basic::datacache::DataMap &) –> class std::shared_ptr<class protocols::denovo_design::components::StructureDataPerturber>

enumerate(self: pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) → pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t

C++: protocols::denovo_design::components::HelixPerturber::enumerate(const class protocols::denovo_design::components::StructureData &) const –> class utility::vector1<class utility::vector1<class std::shared_ptr<const class protocols::denovo_design::components::Segment>, class std::allocator<class std::shared_ptr<const class protocols::denovo_design::components::Segment> > >, class std::allocator<class utility::vector1<class std::shared_ptr<const class protocols::denovo_design::components::Segment>, class std::allocator<class std::shared_ptr<const class protocols::denovo_design::components::Segment> > > > >

ignored(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, segment_name: str) → bool

C++: protocols::denovo_design::components::StructureDataPerturber::ignored(const class std::basic_string<char> &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::denovo_design::components::HelixPerturber::parse_my_tag(const class utility::tag::Tag &, class basic::datacache::DataMap &) –> void

set_ignore_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, ignore_set: pyrosetta.rosetta.std.set_std_string_std_less_std_string_std_allocator_std_string_t) → None

C++: protocols::denovo_design::components::StructureDataPerturber::set_ignore_segments(const class std::set<class std::basic_string<char>, struct std::less<class std::basic_string<char> >, class std::allocator<class std::basic_string<char> > > &) –> void

class pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator

Bases: pybind11_builtins.pybind11_object

Logic for selection of abego values

__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.

1. __init__(self: pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator, id_val: str) -> None
2. __init__(self: pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator, arg0: pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator) -> 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.denovo_design.components.IdealAbegoGenerator, : pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator) → pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator

C++: protocols::denovo_design::components::IdealAbegoGenerator::operator=(const class protocols::denovo_design::components::IdealAbegoGenerator &) –> class protocols::denovo_design::components::IdealAbegoGenerator &

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator) → pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator

C++: protocols::denovo_design::components::IdealAbegoGenerator::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::IdealAbegoGenerator>

set_extend_ss(self: pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator, extend_ss: bool) → None

if true, secondary structure may be extended to close the loop. Overall size of the insert

will not change. Therefore, a 4 residue loop might extend a helix by 2 residues and have a 2-residue ideal loop if extend_ss is true. If extend_ss is false, a 4 residue loop must have four loop residues.

C++: protocols::denovo_design::components::IdealAbegoGenerator::set_extend_ss(const bool) –> void

class pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber

Bases: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

Perturber that does nothing

__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__(self: pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber) → 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).

apply(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) → None

C++: protocols::denovo_design::components::StructureDataPerturber::apply(class protocols::denovo_design::components::StructureData &) –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber, : pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber) → pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber

C++: protocols::denovo_design::components::NullPerturber::operator=(const class protocols::denovo_design::components::NullPerturber &) –> class protocols::denovo_design::components::NullPerturber &

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber) → pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

C++: protocols::denovo_design::components::NullPerturber::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::StructureDataPerturber>

create(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

C++: protocols::denovo_design::components::StructureDataPerturber::create(const class utility::tag::Tag &, class basic::datacache::DataMap &) –> class std::shared_ptr<class protocols::denovo_design::components::StructureDataPerturber>

enumerate(self: pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) → pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t

C++: protocols::denovo_design::components::NullPerturber::enumerate(const class protocols::denovo_design::components::StructureData &) const –> class utility::vector1<class utility::vector1<class std::shared_ptr<const class protocols::denovo_design::components::Segment>, class std::allocator<class std::shared_ptr<const class protocols::denovo_design::components::Segment> > >, class std::allocator<class utility::vector1<class std::shared_ptr<const class protocols::denovo_design::components::Segment>, class std::allocator<class std::shared_ptr<const class protocols::denovo_design::components::Segment> > > > >

ignored(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, segment_name: str) → bool

C++: protocols::denovo_design::components::StructureDataPerturber::ignored(const class std::basic_string<char> &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::denovo_design::components::NullPerturber::parse_my_tag(const class utility::tag::Tag &, class basic::datacache::DataMap &) –> void

set_ignore_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, ignore_set: pyrosetta.rosetta.std.set_std_string_std_less_std_string_std_allocator_std_string_t) → None

C++: protocols::denovo_design::components::StructureDataPerturber::set_ignore_segments(const class std::set<class std::basic_string<char>, struct std::less<class std::basic_string<char> >, class std::allocator<class std::basic_string<char> > > &) –> void

class pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder

Bases: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder

Folds a pose using random phi/psi torsions

__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.

1. __init__(self: pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder) -> None
2. __init__(self: pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder, arg0: pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder) -> 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).

apply(self: pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder, pose: pyrosetta.rosetta.core.pose.Pose, movable: pyrosetta.rosetta.utility.vector1_bool, loops: pyrosetta.rosetta.protocols.loops.Loops) → None

C++: protocols::denovo_design::components::NullPoseFolder::apply(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const class protocols::loops::Loops &) const –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder, : pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder) → pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder

C++: protocols::denovo_design::components::NullPoseFolder::operator=(const class protocols::denovo_design::components::NullPoseFolder &) –> class protocols::denovo_design::components::NullPoseFolder &

class_name() → str

C++: protocols::denovo_design::components::NullPoseFolder::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder) → pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder

C++: protocols::denovo_design::components::NullPoseFolder::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::PoseFolder>

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::denovo_design::components::PoseFolder::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

type(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder) → str

C++: protocols::denovo_design::components::PoseFolder::type() const –> const std::string &

class pyrosetta.rosetta.protocols.denovo_design.components.Picker

Bases: pyrosetta.rosetta.utility.SingletonBase_protocols_denovo_design_components_Picker_t

class used for picking/caching fragments

__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__(self: pyrosetta.rosetta.protocols.denovo_design.components.Picker) → 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).

fragments_for_permutation(self: pyrosetta.rosetta.protocols.denovo_design.components.Picker, perm: protocols::denovo_design::components::StructureData, comp_ids: pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t, frag_size: int) → pyrosetta.rosetta.core.fragment.ConstantLengthFragSet

picks and caches fragments for the listed components with size frag_size

C++: protocols::denovo_design::components::Picker::fragments_for_permutation(const class protocols::denovo_design::components::StructureData &, const class std::list<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, const unsigned long) –> class std::shared_ptr<class core::fragment::ConstantLengthFragSet>

fragments_for_permutation_take_X_from_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.Picker, perm: protocols::denovo_design::components::StructureData, pose: pyrosetta.rosetta.core.pose.Pose, comp_ids: pyrosetta.rosetta.std.vector_std_string, frag_size: int) → pyrosetta.rosetta.core.fragment.ConstantLengthFragSet

picks and caches fragments for the listed components with size frag_size

C++: protocols::denovo_design::components::Picker::fragments_for_permutation_take_X_from_pose(const class protocols::denovo_design::components::StructureData &, const class core::pose::Pose &, const class std::vector<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, const unsigned long) –> class std::shared_ptr<class core::fragment::ConstantLengthFragSet>

get_instance() → protocols::denovo_design::components::Picker

C++: utility::SingletonBase<protocols::denovo_design::components::Picker>::get_instance() –> class protocols::denovo_design::components::Picker *

pick_and_cache_fragments(*args, **kwargs)

Overloaded function.

1. pick_and_cache_fragments(self: pyrosetta.rosetta.protocols.denovo_design.components.Picker, ss: str, abego: str, loops: pyrosetta.rosetta.protocols.loops.Loops, chain_endings: pyrosetta.rosetta.utility.vector1_unsigned_long, frag_size: int) -> pyrosetta.rosetta.core.fragment.ConstantLengthFragSet

picks and caches fragments for the given segments with size frag_size

C++: protocols::denovo_design::components::Picker::pick_and_cache_fragments(const class std::basic_string<char> &, const class std::basic_string<char> &, const class protocols::loops::Loops &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long) –> class std::shared_ptr<class core::fragment::ConstantLengthFragSet>

2. pick_and_cache_fragments(self: pyrosetta.rosetta.protocols.denovo_design.components.Picker, complete_ss: str, complete_abego: pyrosetta.rosetta.utility.vector1_std_string, chain_endings: pyrosetta.rosetta.utility.vector1_unsigned_long, start_res: int, end_res: int, frag_length: int) -> pyrosetta.rosetta.core.fragment.ConstantLengthFragSet

pick and cache fragments without considering primary sequence

C++: protocols::denovo_design::components::Picker::pick_and_cache_fragments(const class std::basic_string<char> &, const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long, const unsigned long, const unsigned long) –> class std::shared_ptr<class core::fragment::ConstantLengthFragSet>

3. pick_and_cache_fragments(self: pyrosetta.rosetta.protocols.denovo_design.components.Picker, complete_aa: str, complete_ss: str, complete_abego: pyrosetta.rosetta.utility.vector1_std_string, chain_endings: pyrosetta.rosetta.utility.vector1_unsigned_long, start_res: int, end_res: int, frag_length: int) -> pyrosetta.rosetta.core.fragment.ConstantLengthFragSet

pick and cache fragments with a primary sequence in mind

C++: protocols::denovo_design::components::Picker::pick_and_cache_fragments(const class std::basic_string<char> &, const class std::basic_string<char> &, const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long, const unsigned long, const unsigned long) –> class std::shared_ptr<class core::fragment::ConstantLengthFragSet>

set_nfrags(self: pyrosetta.rosetta.protocols.denovo_design.components.Picker, nfrags: int) → None

C++: protocols::denovo_design::components::Picker::set_nfrags(const unsigned long) –> void

class pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder

Bases: pybind11_builtins.pybind11_object

Given a pose with all residues, and a StructureData object, assign a 3D conformation to the pose

__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.

1. __init__(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder, type: str) -> None
2. __init__(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder, arg0: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder) -> 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).

apply(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder, pose: pyrosetta.rosetta.core.pose.Pose, movable: pyrosetta.rosetta.utility.vector1_bool, loops: pyrosetta.rosetta.protocols.loops.Loops) → None

performs folding

• The pose to be folded, with all residues added. The pose should be prepared with

  any necessary cutpoints added before giving to the PoseFolder. Torsions in the pose should be adjusted, and no residues should be added or removed.

• Subset of residues for which new backbone conformations will be sampled. Residues

  specified as ‘True’ in movable must also be present in one or more Loops in order to be folded. Movable’s size must match pose.size()

  • Loops to be folded. Cutpoints specified here must be match the cutpoints found in

    the pose. Residues not within any loop should not be folded. Residues contained in a loop but not in the movable set should not be folded.

EXCN_Fold if anything goes wrong in folding. Derived classes should throw this.

C++: protocols::denovo_design::components::PoseFolder::apply(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const class protocols::loops::Loops &) const –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder, : pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder) → pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder

C++: protocols::denovo_design::components::PoseFolder::operator=(const class protocols::denovo_design::components::PoseFolder &) –> class protocols::denovo_design::components::PoseFolder &

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder) → pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder

C++: protocols::denovo_design::components::PoseFolder::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::PoseFolder>

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::denovo_design::components::PoseFolder::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

type(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder) → str

C++: protocols::denovo_design::components::PoseFolder::type() const –> const std::string &

class pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder

Bases: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder

Folds a pose using random phi/psi torsions

__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.

1. __init__(self: pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder) -> None
2. __init__(self: pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder, arg0: pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder) -> 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).

apply(self: pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder, pose: pyrosetta.rosetta.core.pose.Pose, movable: pyrosetta.rosetta.utility.vector1_bool, loops: pyrosetta.rosetta.protocols.loops.Loops) → None

C++: protocols::denovo_design::components::RandomTorsionPoseFolder::apply(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const class protocols::loops::Loops &) const –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder, : pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder) → pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder

C++: protocols::denovo_design::components::RandomTorsionPoseFolder::operator=(const class protocols::denovo_design::components::RandomTorsionPoseFolder &) –> class protocols::denovo_design::components::RandomTorsionPoseFolder &

class_name() → str

C++: protocols::denovo_design::components::RandomTorsionPoseFolder::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder) → pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder

C++: protocols::denovo_design::components::RandomTorsionPoseFolder::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::PoseFolder>

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::denovo_design::components::PoseFolder::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

type(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder) → str

C++: protocols::denovo_design::components::PoseFolder::type() const –> const std::string &

class pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder

Bases: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder

Folds residues in a pose using RemodelLoopMover

__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.

1. __init__(self: pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder) -> None
2. __init__(self: pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder, arg0: pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder) -> 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).

apply(self: pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder, pose: pyrosetta.rosetta.core.pose.Pose, movable: pyrosetta.rosetta.utility.vector1_bool, loops: pyrosetta.rosetta.protocols.loops.Loops) → None

performs folding

• The pose to be folded, with all residues added. The pose should be prepared with

  any necessary cutpoints added before giving to the PoseFolder. Torsions in the pose should be adjusted, and no residues should be added or removed.

• Subset of residues for which new backbone conformations will be sampled. Residues

  specified as ‘True’ in movable must also be present in one or more Loops in order to be folded. Movable’s size must match pose.size()

  • Loops to be folded. Cutpoints specified here must be match the cutpoints found in

    the pose. Residues not within any loop should not be folded. Residues contained in a loop but not in the movable set should not be folded.

EXCN_Fold if anything goes wrong in folding. Derived classes should throw this.

C++: protocols::denovo_design::components::RemodelLoopMoverPoseFolder::apply(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const class protocols::loops::Loops &) const –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder, : pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder) → pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder

C++: protocols::denovo_design::components::RemodelLoopMoverPoseFolder::operator=(const class protocols::denovo_design::components::RemodelLoopMoverPoseFolder &) –> class protocols::denovo_design::components::RemodelLoopMoverPoseFolder &

class_name() → str

C++: protocols::denovo_design::components::RemodelLoopMoverPoseFolder::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder) → pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder

C++: protocols::denovo_design::components::RemodelLoopMoverPoseFolder::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::PoseFolder>

default_score_function() → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::denovo_design::components::RemodelLoopMoverPoseFolder::default_score_function() –> class std::shared_ptr<class core::scoring::ScoreFunction>

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::denovo_design::components::PoseFolder::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::denovo_design::components::RemodelLoopMoverPoseFolder::set_scorefxn(const class core::scoring::ScoreFunction &) –> void

type(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder) → str

C++: protocols::denovo_design::components::PoseFolder::type() const –> const std::string &

class pyrosetta.rosetta.protocols.denovo_design.components.Segment

Bases: pybind11_builtins.pybind11_object

manages information about segments of residues

__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.

1. __init__(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, id_val: str) -> None
2. __init__(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, id_val: str, ss_val: str, abego_val: str, start_inc: bool, stop_inc: bool) -> None
3. __init__(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, arg0: pyrosetta.rosetta.protocols.denovo_design.components.Segment) -> 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.denovo_design.components.Segment) → 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).

abego(*args, **kwargs)

Overloaded function.

1. abego(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) -> str

C++: protocols::denovo_design::components::Segment::abego() const –> const std::string &

2. abego(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, segment_resid: int) -> str

C++: protocols::denovo_design::components::Segment::abego(const long) const –> char

add_lower_padding(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → None

adds “padding” residue before the fixed portion of this segment

C++: protocols::denovo_design::components::Segment::add_lower_padding() –> void

add_upper_padding(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → None

adds “padding” residue after the fixed portion of this segment

C++: protocols::denovo_design::components::Segment::add_upper_padding() –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, : pyrosetta.rosetta.protocols.denovo_design.components.Segment) → pyrosetta.rosetta.protocols.denovo_design.components.Segment

C++: protocols::denovo_design::components::Segment::operator=(const class protocols::denovo_design::components::Segment &) –> class protocols::denovo_design::components::Segment &

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → pyrosetta.rosetta.protocols.denovo_design.components.Segment

C++: protocols::denovo_design::components::Segment::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::Segment>

contains(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, pose_resid: int) → bool

C++: protocols::denovo_design::components::Segment::contains(const unsigned long) const –> bool

cterm_included(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → bool

C++: protocols::denovo_design::components::Segment::cterm_included() const –> bool

cutpoint(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → int

C++: protocols::denovo_design::components::Segment::cutpoint() const –> unsigned long

cutpoint_segment(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → int

segment residue number for cutpoint

C++: protocols::denovo_design::components::Segment::cutpoint_segment() const –> long

delete_lower_padding(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → None

deletes dummy residues before the fixed portion of this segment

C++: protocols::denovo_design::components::Segment::delete_lower_padding() –> void

delete_residue(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, segment_resid: int) → None

given a segment residue number, delete that residue. Resid for start_local() == 1

C++: protocols::denovo_design::components::Segment::delete_residue(const long) –> void

delete_upper_padding(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → None

deletes dummy residues after the fixed portion of this segment

C++: protocols::denovo_design::components::Segment::delete_upper_padding() –> void

elem_length(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → int

C++: protocols::denovo_design::components::Segment::elem_length() const –> unsigned long

extend(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, secstruct: str, abego: str) → None

appends segment by the given secstruct and abego

C++: protocols::denovo_design::components::Segment::extend(const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

has_free_lower_terminus(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → bool

C++: protocols::denovo_design::components::Segment::has_free_lower_terminus() const –> bool

has_free_upper_terminus(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → bool

C++: protocols::denovo_design::components::Segment::has_free_upper_terminus() const –> bool

has_lower_residue(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → bool

C++: protocols::denovo_design::components::Segment::has_lower_residue() const –> bool

has_template_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → bool

returns whether or not this segment contains a template pose

C++: protocols::denovo_design::components::Segment::has_template_pose() const –> bool

has_upper_residue(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → bool

C++: protocols::denovo_design::components::Segment::has_upper_residue() const –> bool

id(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → str

C++: protocols::denovo_design::components::Segment::id() const –> const std::string &

length(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → int

C++: protocols::denovo_design::components::Segment::length() const –> unsigned long

lower(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → int

C++: protocols::denovo_design::components::Segment::lower() const –> unsigned long

lower_dihedrals(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → pyrosetta.rosetta.protocols.denovo_design.components.ResidueDihedrals

C++: protocols::denovo_design::components::Segment::lower_dihedrals() const –> const class protocols::denovo_design::components::ResidueDihedrals &

lower_local(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → int

on the chopping block

C++: protocols::denovo_design::components::Segment::lower_local() const –> unsigned long

lower_padding(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → int

C++: protocols::denovo_design::components::Segment::lower_padding() const –> unsigned long

lower_residue(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → pyrosetta.rosetta.core.conformation.Residue

C++: protocols::denovo_design::components::Segment::lower_residue() const –> const class core::conformation::Residue &

lower_segment(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → str

C++: protocols::denovo_design::components::Segment::lower_segment() const –> const std::string &

movable_group(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → int

C++: protocols::denovo_design::components::Segment::movable_group() const –> unsigned long

n_residues_after_cutpoint(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → int

number of residues after the cutpoint, length() if cutpoint not set

C++: protocols::denovo_design::components::Segment::n_residues_after_cutpoint() const –> unsigned long

n_residues_before_cutpoint(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → int

number of residues before the cutpoint, 0 if cutpoint not set

C++: protocols::denovo_design::components::Segment::n_residues_before_cutpoint() const –> unsigned long

nterm_included(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → bool

C++: protocols::denovo_design::components::Segment::nterm_included() const –> bool

parse_motif(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, motif_str: str) → None

construct from motif string (i.e. ‘1LX-10HA-1LA-1LB’)

C++: protocols::denovo_design::components::Segment::parse_motif(const class std::basic_string<char> &) –> void

parse_tag(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, tag: pyrosetta.rosetta.utility.tag.Tag) → None

construct from xml tag

C++: protocols::denovo_design::components::Segment::parse_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

pose_to_segment(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, pose_resid: int) → int

converts a internal segment resid to a pose resid

segment_start - 1 + 1 –> 1 segment_start - 1 + 2 –> 2 segment_start - 1 + N –> N

C++: protocols::denovo_design::components::Segment::pose_to_segment(const unsigned long) const –> long

safe(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → int

C++: protocols::denovo_design::components::Segment::safe() const –> unsigned long

safe_segment(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → int

segment residue number for “safe” residue

C++: protocols::denovo_design::components::Segment::safe_segment() const –> long

segment_to_local(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, segment_resid: int) → int

converts a segment resid to a “local” resid

C++: protocols::denovo_design::components::Segment::segment_to_local(const long) const –> unsigned long

segment_to_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, segment_resid: int) → int

converts a internal segment resid to a pose resid

1 –> segment_start - 1 + 1 2 –> segment_start - 1 + 2 N –> segment_start - 1 + N

C++: protocols::denovo_design::components::Segment::segment_to_pose(const long) const –> unsigned long

set_abego(*args, **kwargs)

Overloaded function.

1. set_abego(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, abego_str: str) -> None

C++: protocols::denovo_design::components::Segment::set_abego(const class std::basic_string<char> &) –> void

2. set_abego(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, abego: pyrosetta.rosetta.utility.vector1_std_string) -> None

C++: protocols::denovo_design::components::Segment::set_abego(const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> void

set_cutpoint(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, segment_resid: int) → None

sets cutpoint for this segment to be the ith residue in the segment

cut = segment_start - 1 + cut_res

C++: protocols::denovo_design::components::Segment::set_cutpoint(const long) –> void

set_id(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, id_val: str) → None

C++: protocols::denovo_design::components::Segment::set_id(const class std::basic_string<char> &) –> void

set_lower_segment(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, comp: str) → None

C++: protocols::denovo_design::components::Segment::set_lower_segment(const class std::basic_string<char> &) –> void

set_movable_group(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, mg: int) → None

C++: protocols::denovo_design::components::Segment::set_movable_group(const unsigned long) –> void

set_pose_start(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, pose_resid: int) → None

C++: protocols::denovo_design::components::Segment::set_pose_start(const unsigned long) –> void

set_safe(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, segment_resid: int) → None

sets safe residue for this segment to be the ith residue in the segment

safe = segment_start - 1 + cut_res

C++: protocols::denovo_design::components::Segment::set_safe(const long) –> void

set_ss(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, segment_resid: int, ss_type: str) → None

C++: protocols::denovo_design::components::Segment::set_ss(const long, char) –> void

set_template_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, template_pose: pyrosetta.rosetta.core.pose.Pose, start_resid: int, stop_resid: int) → None

sets template pose to be the given residues from template_pose

C++: protocols::denovo_design::components::Segment::set_template_pose(const class core::pose::Pose &, const unsigned long, const unsigned long) –> void

set_upper_segment(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, comp: str) → None

C++: protocols::denovo_design::components::Segment::set_upper_segment(const class std::basic_string<char> &) –> void

ss(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → str

C++: protocols::denovo_design::components::Segment::ss() const –> const std::string &

start(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → int

C++: protocols::denovo_design::components::Segment::start() const –> unsigned long

start_local(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → int

C++: protocols::denovo_design::components::Segment::start_local() const –> unsigned long

stop(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → int

C++: protocols::denovo_design::components::Segment::stop() const –> unsigned long

stop_local(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → int

C++: protocols::denovo_design::components::Segment::stop_local() const –> unsigned long

template_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → pyrosetta.rosetta.core.pose.Pose

returns template pose

C++: protocols::denovo_design::components::Segment::template_pose() const –> class std::shared_ptr<const class core::pose::Pose>

upper(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → int

C++: protocols::denovo_design::components::Segment::upper() const –> unsigned long

upper_dihedrals(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → pyrosetta.rosetta.protocols.denovo_design.components.ResidueDihedrals

C++: protocols::denovo_design::components::Segment::upper_dihedrals() const –> const class protocols::denovo_design::components::ResidueDihedrals &

upper_local(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → int

C++: protocols::denovo_design::components::Segment::upper_local() const –> unsigned long

upper_padding(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → int

C++: protocols::denovo_design::components::Segment::upper_padding() const –> unsigned long

upper_residue(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → pyrosetta.rosetta.core.conformation.Residue

C++: protocols::denovo_design::components::Segment::upper_residue() const –> const class core::conformation::Residue &

upper_segment(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) → str

C++: protocols::denovo_design::components::Segment::upper_segment() const –> const std::string &

class pyrosetta.rosetta.protocols.denovo_design.components.SheetDB

Bases: pybind11_builtins.pybind11_object

class used to create/manipulate a database of sheets using a list of pdb files

__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.

1. __init__(self: pyrosetta.rosetta.protocols.denovo_design.components.SheetDB) -> None
2. __init__(self: pyrosetta.rosetta.protocols.denovo_design.components.SheetDB, arg0: pyrosetta.rosetta.protocols.denovo_design.components.SheetDB) -> 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_sheet(self: pyrosetta.rosetta.protocols.denovo_design.components.SheetDB, pose: pyrosetta.rosetta.core.pose.Pose, nstrands: int, orientations: str, lengths_shifts: str, check_descriptor_against_pose: bool) → None

add a sheet to the database

C++: protocols::denovo_design::components::SheetDB::add_sheet(class std::shared_ptr<class core::pose::Pose>, const unsigned long, const class std::basic_string<char> &, const class std::basic_string<char> &, const bool) –> void

add_sheets_from_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.SheetDB, pose: pyrosetta.rosetta.core.pose.Pose) → int

adds sheet(s) based on a pose – returns # of sheets added

C++: protocols::denovo_design::components::SheetDB::add_sheets_from_pose(class core::pose::Pose &) –> int

add_sheets_from_spairs(self: pyrosetta.rosetta.protocols.denovo_design.components.SheetDB, pose: pyrosetta.rosetta.core.pose.Pose, spairs: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet, ss_info: protocols::fldsgn::topology::SS_Info2) → int

adds sheet(s) based on a strand pairing set and pose – returns # of sheets added

C++: protocols::denovo_design::components::SheetDB::add_sheets_from_spairs(const class core::pose::Pose &, class protocols::fldsgn::topology::StrandPairingSet &, const class protocols::fldsgn::topology::SS_Info2 &) –> int

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.SheetDB, : pyrosetta.rosetta.protocols.denovo_design.components.SheetDB) → pyrosetta.rosetta.protocols.denovo_design.components.SheetDB

C++: protocols::denovo_design::components::SheetDB::operator=(const class protocols::denovo_design::components::SheetDB &) –> class protocols::denovo_design::components::SheetDB &

lengths_shifts(self: pyrosetta.rosetta.protocols.denovo_design.components.SheetDB, nstrands: int, orientations: str) → pyrosetta.rosetta.utility.vector1_std_string

queries the database for all lengths/shifts with nstrands strands and given orientations

C++: protocols::denovo_design::components::SheetDB::lengths_shifts(const unsigned long, const class std::basic_string<char> &) const –> class utility::vector1<std::string, class std::allocator<std::string > >

nstrand_values(self: pyrosetta.rosetta.protocols.denovo_design.components.SheetDB) → pyrosetta.rosetta.utility.vector1_unsigned_long

queries the database for all strand lengths

C++: protocols::denovo_design::components::SheetDB::nstrand_values() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

orientations(self: pyrosetta.rosetta.protocols.denovo_design.components.SheetDB, nstrands: int) → pyrosetta.rosetta.utility.vector1_std_string

queries the database for all orientations with nstrands strands

C++: protocols::denovo_design::components::SheetDB::orientations(const unsigned long) const –> class utility::vector1<std::string, class std::allocator<std::string > >

set_db_path(self: pyrosetta.rosetta.protocols.denovo_design.components.SheetDB, db_path: str) → None

set location of sheet database files

C++: protocols::denovo_design::components::SheetDB::set_db_path(const class std::basic_string<char> &) –> void

set_idealize(self: pyrosetta.rosetta.protocols.denovo_design.components.SheetDB, idealize_val: bool) → None

C++: protocols::denovo_design::components::SheetDB::set_idealize(const bool) –> void

set_sheetlist(self: pyrosetta.rosetta.protocols.denovo_design.components.SheetDB, list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t, nstrands: int, in_orientations: str, in_lengths: str) → None

add a sheet to the database

C++: protocols::denovo_design::components::SheetDB::set_sheetlist(const class utility::vector1<class std::shared_ptr<const class core::pose::Pose>, class std::allocator<class std::shared_ptr<const class core::pose::Pose> > > &, const unsigned long, const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

set_sheetlist_as_is(self: pyrosetta.rosetta.protocols.denovo_design.components.SheetDB, list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t, nstrands: int, orientations: str, lengths: str) → None

adds a sheet list as it is presented

C++: protocols::denovo_design::components::SheetDB::set_sheetlist_as_is(const class utility::vector1<class std::shared_ptr<const class core::pose::Pose>, class std::allocator<class std::shared_ptr<const class core::pose::Pose> > > &, const unsigned long, const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation

Bases: pybind11_builtins.pybind11_object

Individual strands are oriented pointing either “UP” or “DOWN” If two adjacent strands have the same orientation, they are parallel If two adjacent strands have different orientation, they are antiparallel

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(*args, **kwargs)

Overloaded function.

1. __eq__(self: pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation, arg0: pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation) -> bool
2. __eq__(self: pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation, arg0: int) -> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation) → tuple

__gt__

Return self>value.

__hash__(self: pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation) → int

__init__(self: pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation, arg0: 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.

__int__(self: pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation) → int

__le__

Return self<=value.

__lt__

Return self<value.

__ne__(*args, **kwargs)

Overloaded function.

1. __ne__(self: pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation, arg0: pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation) -> bool
2. __ne__(self: pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation, arg0: int) -> bool

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__(self: pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation) → str

__setattr__

Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation, arg0: tuple) → None

__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).

class pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory

Bases: pyrosetta.rosetta.utility.SingletonBase_protocols_denovo_design_components_StructureDataFactory_t

Singleton for creating StructureData objects

__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).

attach_observer(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, pose: pyrosetta.rosetta.core.pose.Pose) → None

attaches cacheable observer. Sets up cached SD if there isn’t one

C++: protocols::denovo_design::components::StructureDataFactory::attach_observer(class core::pose::Pose &) const –> void

clear_from_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, pose: pyrosetta.rosetta.core.pose.Pose) → None

clears all structuredata information (including cached xml) from

this pose.

C++: protocols::denovo_design::components::StructureDataFactory::clear_from_pose(class core::pose::Pose &) const –> void

create_from_cacheable_data(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, raw_stream: pyrosetta.rosetta.std.istream) → pyrosetta.rosetta.protocols.denovo_design.components.StructureData

creates from CacheableData stream

C++: protocols::denovo_design::components::StructureDataFactory::create_from_cacheable_data(class std::basic_istream<char> &) const –> class protocols::denovo_design::components::StructureData

create_from_motifs(*args, **kwargs)

Overloaded function.

1. create_from_motifs(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, motif_str: str) -> pyrosetta.rosetta.protocols.denovo_design.components.StructureData

creates a StructureData from a motif string

String of secstruct/abego motifs (e.g. “1LX-5EB-2LG-5EB-1LA-1LB-1LG-10HA-1LX” )

StructureData containing one segment per motif with the specified

secondary structure and abego. Each motif is connected to the previous and next motifs. Segments are named by their secondary structure (e.g. L01, E01, L02, E02, L03, H01, L04 )

C++: protocols::denovo_design::components::StructureDataFactory::create_from_motifs(const class std::basic_string<char> &) const –> class protocols::denovo_design::components::StructureData

2. create_from_motifs(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, motif_str: str, prefix: str) -> pyrosetta.rosetta.protocols.denovo_design.components.StructureData

creates a StructureData from a motif string, optionally prefixing a string to the

name of each segment

String of secstruct/abego motifs (e.g. “1LX-5EB-2LG-5EB-1LA-1LB-1LG-10HA-1LX” )

Name to be prepended before the segment names. If empty,

names will be as [ L01, E01, L02, … ]. If set to “myprefix”, names

will be as [ myprefix.L01, myprefix.E01, … ]

StructureData containing one segment per motif with the specified

secondary structure and abego. Each motif is connected to the previous and next motifs. Segments are named by their secondary structure (e.g. L01, E01, L02, E02, L03, H01, L04 )

C++: protocols::denovo_design::components::StructureDataFactory::create_from_motifs(const class std::basic_string<char> &, const class std::basic_string<char> &) const –> class protocols::denovo_design::components::StructureData

create_from_pose(*args, **kwargs)

Overloaded function.

1. create_from_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.protocols.denovo_design.components.StructureData

retrieves a StructureData object from the pose data cache

Creates a StructureData using the pose (but doesn’t store it) if the cached StructureData is not present

The input pose

C++: protocols::denovo_design::components::StructureDataFactory::create_from_pose(const class core::pose::Pose &) const –> class protocols::denovo_design::components::StructureData

2. create_from_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str) -> pyrosetta.rosetta.protocols.denovo_design.components.StructureData

retrieves a StructureData object from the pose data cache

Creates a StructureData using the pose (but doesn’t store it) if the cached StructureData is not present. Adds id_val as a prefix for all new segments

The input pose

A prefix to be added to the segments in the pose. For example, if

prefix is empty, the first helix would be named ‘H01’, but if prefix is set to ‘pose1’, the first helix will be named ‘pose.H01’

C++: protocols::denovo_design::components::StructureDataFactory::create_from_pose(const class core::pose::Pose &, const class std::basic_string<char> &) const –> class protocols::denovo_design::components::StructureData

create_from_remarks(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, rem: pyrosetta.rosetta.core.io.Remarks) → pyrosetta.rosetta.protocols.denovo_design.components.StructureData

creates SD from description stored in PDB remarks

C++: protocols::denovo_design::components::StructureDataFactory::create_from_remarks(const class core::io::Remarks &) const –> class protocols::denovo_design::components::StructureData

create_from_xml(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, xmltag: pyrosetta.rosetta.std.istream) → pyrosetta.rosetta.protocols.denovo_design.components.StructureData

creates a StructureData from an xml stringstream

C++: protocols::denovo_design::components::StructureDataFactory::create_from_xml(class std::basic_istream<char> &) const –> class protocols::denovo_design::components::StructureData

detach_observer(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, pose: pyrosetta.rosetta.core.pose.Pose) → None

detaches cacheable observer and removes from observable cache

C++: protocols::denovo_design::components::StructureDataFactory::detach_observer(class core::pose::Pose &) const –> void

get_from_const_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.denovo_design.components.StructureData

retrieves a StructureData object from the pose observable cache

Creates a StructureData using the pose (but doesn’t attach it) if the cached StructureData could not be retrieved properly

C++: protocols::denovo_design::components::StructureDataFactory::get_from_const_pose(const class core::pose::Pose &) const –> const class protocols::denovo_design::components::StructureData &

get_from_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.denovo_design.components.StructureData

retrieves a StructureData object from the pose observable cache

creates one if necessary

C++: protocols::denovo_design::components::StructureDataFactory::get_from_pose(class core::pose::Pose &) const –> const class protocols::denovo_design::components::StructureData &

get_instance() → protocols::denovo_design::components::StructureDataFactory

C++: utility::SingletonBase<protocols::denovo_design::components::StructureDataFactory>::get_instance() –> class protocols::denovo_design::components::StructureDataFactory *

has_cached_data(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, pose: pyrosetta.rosetta.core.pose.Pose) → bool

checks whether StructureData is stored in the pose’s datacache

C++: protocols::denovo_design::components::StructureDataFactory::has_cached_data(const class core::pose::Pose &) const –> bool

observer_attached(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, pose: pyrosetta.rosetta.core.pose.Pose) → bool

checks for a StructureData in the pose observer cache

Returns true if one is found, false otherwise

C++: protocols::denovo_design::components::StructureDataFactory::observer_attached(const class core::pose::Pose &) const –> bool

retrieve_observer(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, pose: pyrosetta.rosetta.core.pose.Pose) → protocols::denovo_design::components::StructureDataObserver

returns observer pointer if the pose has one cached

pointer returned can be null if no StructureData is present in the cache

C++: protocols::denovo_design::components::StructureDataFactory::retrieve_observer(const class core::pose::Pose &) const –> class std::shared_ptr<const class protocols::denovo_design::components::StructureDataObserver>

save_into_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, pose: pyrosetta.rosetta.core.pose.Pose, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) → None

stores the data of this permutation into a pose for later retrieval

StructureData stored in a pose this way can be retrieved by calling get_from_pose(), or get_from_const_pose()

C++: protocols::denovo_design::components::StructureDataFactory::save_into_pose(class core::pose::Pose &, const class protocols::denovo_design::components::StructureData &) const –> void

class pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver

Bases: pyrosetta.rosetta.core.pose.datacache.CacheableObserver

a cacheable observer that keeps track of what length events occured

__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.

1. __init__(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver) -> None
2. __init__(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) -> 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.denovo_design.components.StructureDataObserver, : pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver) → pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver

C++: protocols::denovo_design::components::StructureDataObserver::operator=(const class protocols::denovo_design::components::StructureDataObserver &) –> class protocols::denovo_design::components::StructureDataObserver &

attach_to(self: pyrosetta.rosetta.core.pose.datacache.CacheableObserver, pose: pyrosetta.rosetta.core.pose.Pose) → None

attach to Pose/Conformation

Derived classes do not overload this method – see attach_impl() instead.

C++: core::pose::datacache::CacheableObserver::attach_to(class core::pose::Pose &) –> void

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver) → pyrosetta.rosetta.core.pose.datacache.CacheableObserver

clone this object

C++: protocols::denovo_design::components::StructureDataObserver::clone() –> class std::shared_ptr<class core::pose::datacache::CacheableObserver>

create(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver) → pyrosetta.rosetta.core.pose.datacache.CacheableObserver

create a new instance of this object

C++: protocols::denovo_design::components::StructureDataObserver::create() –> class std::shared_ptr<class core::pose::datacache::CacheableObserver>

detach_from(self: pyrosetta.rosetta.core.pose.datacache.CacheableObserver) → None

detach from Pose/Conformation

Derived classes do not overload this method – see

detach_impl() instead.

C++: core::pose::datacache::CacheableObserver::detach_from() –> void

is_attached(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver) → bool

is this observer attached to a Pose/Conformation?

C++: protocols::denovo_design::components::StructureDataObserver::is_attached() const –> bool

class pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

Bases: pybind11_builtins.pybind11_object

Classes for altering StructureData objects on the fly

__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__(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber) → 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).

apply(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) → None

C++: protocols::denovo_design::components::StructureDataPerturber::apply(class protocols::denovo_design::components::StructureData &) –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, : pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber) → pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

C++: protocols::denovo_design::components::StructureDataPerturber::operator=(const class protocols::denovo_design::components::StructureDataPerturber &) –> class protocols::denovo_design::components::StructureDataPerturber &

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber) → pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

C++: protocols::denovo_design::components::StructureDataPerturber::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::StructureDataPerturber>

create(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

C++: protocols::denovo_design::components::StructureDataPerturber::create(const class utility::tag::Tag &, class basic::datacache::DataMap &) –> class std::shared_ptr<class protocols::denovo_design::components::StructureDataPerturber>

enumerate(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) → pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t

C++: protocols::denovo_design::components::StructureDataPerturber::enumerate(const class protocols::denovo_design::components::StructureData &) const –> class utility::vector1<class utility::vector1<class std::shared_ptr<const class protocols::denovo_design::components::Segment>, class std::allocator<class std::shared_ptr<const class protocols::denovo_design::components::Segment> > >, class std::allocator<class utility::vector1<class std::shared_ptr<const class protocols::denovo_design::components::Segment>, class std::allocator<class std::shared_ptr<const class protocols::denovo_design::components::Segment> > > > >

ignored(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, segment_name: str) → bool

C++: protocols::denovo_design::components::StructureDataPerturber::ignored(const class std::basic_string<char> &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::denovo_design::components::StructureDataPerturber::parse_my_tag(const class utility::tag::Tag &, class basic::datacache::DataMap &) –> void

set_ignore_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, ignore_set: pyrosetta.rosetta.std.set_std_string_std_less_std_string_std_allocator_std_string_t) → None

C++: protocols::denovo_design::components::StructureDataPerturber::set_ignore_segments(const class std::set<class std::basic_string<char>, struct std::less<class std::basic_string<char> >, class std::allocator<class std::basic_string<char> > > &) –> void

pyrosetta.rosetta.protocols.denovo_design.components.add_segments_for_chain(id_val: str, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, chain_ss: str, chain_abego: str, counts: pyrosetta.rosetta.protocols.denovo_design.components.SegmentCounts) → None

Adds segments to the given SD

Parent ID of the segments. Can be empty

StructureData to be modified

Secondary structure of the full chain

Abego for the full chain

Secondary structure element counters for naming segments

C++: protocols::denovo_design::components::add_segments_for_chain(const class std::basic_string<char> &, class protocols::denovo_design::components::StructureData &, const class std::basic_string<char> &, const class std::basic_string<char> &, class protocols::denovo_design::components::SegmentCounts &) –> void

pyrosetta.rosetta.protocols.denovo_design.components.add_to_pose(newpose: pyrosetta.rosetta.core.pose.Pose, pose: pyrosetta.rosetta.core.pose.Pose, s_start: int, s_stop: int) → int

C++: protocols::denovo_design::components::add_to_pose(class std::shared_ptr<class core::pose::Pose>, const class core::pose::Pose &, unsigned long, unsigned long) –> int

pyrosetta.rosetta.protocols.denovo_design.components.append_new_chain_from_template_segment(pose: pyrosetta.rosetta.core.pose.Pose, segment: protocols::denovo_design::components::Segment) → None

C++: protocols::denovo_design::components::append_new_chain_from_template_segment(class core::pose::Pose &, const class protocols::denovo_design::components::Segment &) –> void

pyrosetta.rosetta.protocols.denovo_design.components.append_new_residues(pose: pyrosetta.rosetta.core.pose.Pose, num_residues: int, insert_pos: int, anchor: int, type: str, upper_dihedrals: protocols::denovo_design::components::ResidueDihedrals) → None

C++: protocols::denovo_design::components::append_new_residues(class core::pose::Pose &, const unsigned long, unsigned long, const unsigned long, const class std::basic_string<char> &, const class protocols::denovo_design::components::ResidueDihedrals &) –> void

pyrosetta.rosetta.protocols.denovo_design.components.append_residues_from_template_segment(pose: pyrosetta.rosetta.core.pose.Pose, prev_segment: protocols::denovo_design::components::Segment, segment: protocols::denovo_design::components::Segment) → None

C++: protocols::denovo_design::components::append_residues_from_template_segment(class core::pose::Pose &, const class protocols::denovo_design::components::Segment &, const class protocols::denovo_design::components::Segment &) –> void

pyrosetta.rosetta.protocols.denovo_design.components.canonicalize(orientations: str, lengths: str) → Tuple[str, str]

C++: protocols::denovo_design::components::canonicalize(const class std::basic_string<char> &, const class std::basic_string<char> &) –> struct std::pair<std::string, std::string >

pyrosetta.rosetta.protocols.denovo_design.components.choose_canonical(l1: str, l2: str) → str

C++: protocols::denovo_design::components::choose_canonical(const class std::basic_string<char> &, const class std::basic_string<char> &) –> const std::string &

pyrosetta.rosetta.protocols.denovo_design.components.clean_for_storage(ss: str) → None

prepare a string to be stored in the string datacache

C++: protocols::denovo_design::components::clean_for_storage(class std::basic_string<char> &) –> void

pyrosetta.rosetta.protocols.denovo_design.components.clean_from_storage(st: str) → None

prepare a string that was stored in string datacache

C++: protocols::denovo_design::components::clean_from_storage(class std::basic_string<char> &) –> void

pyrosetta.rosetta.protocols.denovo_design.components.extract_sheets_from_pose(pose: pyrosetta.rosetta.core.pose.Pose, spairs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_StrandPairing_t, ss_info: protocols::fldsgn::topology::SS_Info2, idealize: bool) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t

C++: protocols::denovo_design::components::extract_sheets_from_pose(const class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::fldsgn::topology::StrandPairing>, class std::allocator<class std::shared_ptr<class protocols::fldsgn::topology::StrandPairing> > > &, const class protocols::fldsgn::topology::SS_Info2 &, const bool) –> class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >

pyrosetta.rosetta.protocols.denovo_design.components.extract_sheets_from_strandlist(strands: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, nstrands: int) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t

C++: protocols::denovo_design::components::extract_sheets_from_strandlist(const class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &, const unsigned long) –> class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >

pyrosetta.rosetta.protocols.denovo_design.components.find_orientations_and_lengths(pose: pyrosetta.rosetta.core.pose.Pose) → Tuple[str, str]

gets a pair of strings, which refer to orientations, and lengths/shifts. Pose secstruct MUST be set

C++: protocols::denovo_design::components::find_orientations_and_lengths(const class core::pose::Pose &) –> struct std::pair<std::string, std::string >

pyrosetta.rosetta.protocols.denovo_design.components.get_closest_chain_ending(chain_endings: pyrosetta.rosetta.utility.vector1_unsigned_long, total_residue: int, end_res: int) → int

C++: protocols::denovo_design::components::get_closest_chain_ending(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, unsigned long, const unsigned long) –> unsigned long

pyrosetta.rosetta.protocols.denovo_design.components.make_strand_info_str(lengths: pyrosetta.rosetta.utility.vector1_unsigned_long, shifts: pyrosetta.rosetta.utility.vector1_long) → str

creates a string key for lengths/shifts based on the given vectors for strand lengths and register shifts

C++: protocols::denovo_design::components::make_strand_info_str(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<long, class std::allocator<long> > &) –> std::string

pyrosetta.rosetta.protocols.denovo_design.components.modify_ft_for_residue_insertion(pose: pyrosetta.rosetta.core.pose.Pose, safe_res: int) → pyrosetta.rosetta.core.kinematics.FoldTree

modifies teh ft in the pose, returns the original

C++: protocols::denovo_design::components::modify_ft_for_residue_insertion(class core::pose::Pose &, const unsigned long) –> class core::kinematics::FoldTree

pyrosetta.rosetta.protocols.denovo_design.components.num_strands(pose: pyrosetta.rosetta.core.pose.Pose) → int

counts number of strands based on number of jumps. Pose must be a disconnected sheet

C++: protocols::denovo_design::components::num_strands(const class core::pose::Pose &) –> unsigned long

pyrosetta.rosetta.protocols.denovo_design.components.parse_lengths(lengths: str) → Tuple[pyrosetta.rosetta.utility.vector1_unsigned_long, pyrosetta.rosetta.utility.vector1_int]

C++: protocols::denovo_design::components::parse_lengths(const class std::basic_string<char> &) –> struct std::pair<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class utility::vector1<int, class std::allocator<int> > >

pyrosetta.rosetta.protocols.denovo_design.components.parse_orientations(orientations: str) → pyrosetta.rosetta.utility.vector1_bool

C++: protocols::denovo_design::components::parse_orientations(const class std::basic_string<char> &) –> class utility::vector1<bool, class std::allocator<bool> >

pyrosetta.rosetta.protocols.denovo_design.components.prepend_new_residues(pose: pyrosetta.rosetta.core.pose.Pose, num_residues: int, insert_pos: int, anchor: int, type: str, lower_dihedrals: protocols::denovo_design::components::ResidueDihedrals) → None

C++: protocols::denovo_design::components::prepend_new_residues(class core::pose::Pose &, const unsigned long, unsigned long, const unsigned long, const class std::basic_string<char> &, const class protocols::denovo_design::components::ResidueDihedrals &) –> void

pyrosetta.rosetta.protocols.denovo_design.components.reverse_chains(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::denovo_design::components::reverse_chains(const class core::pose::Pose &) –> class std::shared_ptr<class core::pose::Pose>

pyrosetta.rosetta.protocols.denovo_design.components.reverse_lengths(orientations: str, lengths: str) → str

C++: protocols::denovo_design::components::reverse_lengths(const class std::basic_string<char> &, const class std::basic_string<char> &) –> std::string

pyrosetta.rosetta.protocols.denovo_design.components.reverse_orientations(orient: str) → str

C++: protocols::denovo_design::components::reverse_orientations(const class std::basic_string<char> &) –> std::string

pyrosetta.rosetta.protocols.denovo_design.components.truncate_abego(complete_abego: pyrosetta.rosetta.utility.vector1_std_string, closest_chain_ending: int) → pyrosetta.rosetta.utility.vector1_std_string

C++: protocols::denovo_design::components::truncate_abego(const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, const unsigned long) –> class utility::vector1<std::string, class std::allocator<std::string > >