pivot_pickers

Bindings for protocols::kinematic_closure::pivot_pickers namespace

class pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots

Bases: pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker

Pick pivots that span the entire loop to sample.

__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.kinematic_closure.pivot_pickers.EndToEndPivots) → 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).

get_name(self: pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots) → str

PivotPicker::get_name

C++: protocols::kinematic_closure::pivot_pickers::EndToEndPivots::get_name() const –> std::string

pick(self: pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots, pose: pyrosetta.rosetta.core.pose.Pose, loop: pyrosetta.rosetta.protocols.loops.Loop) → pyrosetta.rosetta.protocols.loops.Loop

PivotPicker::pick

C++: protocols::kinematic_closure::pivot_pickers::EndToEndPivots::pick(const class core::pose::Pose &, const class protocols::loops::Loop &) –> class protocols::loops::Loop

class pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots

Bases: pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker

Randomly pick pivots which are always offset by the same amount, but which can appear anywhere in the loop.

__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.kinematic_closure.pivot_pickers.FixedOffsetPivots) -> None

doc

2. __init__(self: pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots, offset: int) -> None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

get_name(self: pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots) → str

PivotPicker::get_name

C++: protocols::kinematic_closure::pivot_pickers::FixedOffsetPivots::get_name() const –> std::string

pick(self: pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots, pose: pyrosetta.rosetta.core.pose.Pose, loop: pyrosetta.rosetta.protocols.loops.Loop) → pyrosetta.rosetta.protocols.loops.Loop

PivotPicker::pick

C++: protocols::kinematic_closure::pivot_pickers::FixedOffsetPivots::pick(const class core::pose::Pose &, const class protocols::loops::Loop &) –> class protocols::loops::Loop

class pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots

Bases: pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker

Randomly pick pivots which are always offsets given in a list but which can appear anywhere in the loop.

__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.kinematic_closure.pivot_pickers.FixedOffsetsPivots, offsets: pyrosetta.rosetta.utility.vector1_unsigned_long) → 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).

get_name(self: pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots) → str

PivotPicker::get_name

C++: protocols::kinematic_closure::pivot_pickers::FixedOffsetsPivots::get_name() const –> std::string

pick(self: pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots, pose: pyrosetta.rosetta.core.pose.Pose, loop: pyrosetta.rosetta.protocols.loops.Loop) → pyrosetta.rosetta.protocols.loops.Loop

PivotPicker::pick

C++: protocols::kinematic_closure::pivot_pickers::FixedOffsetsPivots::pick(const class core::pose::Pose &, const class protocols::loops::Loop &) –> class protocols::loops::Loop

class pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots

Bases: pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker

Use a fixed set of pivots specified in advance.

The pivots are specified in the constructor. Make sure that the pivots will always be contained in the loop being sampled, otherwise strange behavior may occur.

__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.kinematic_closure.pivot_pickers.FixedPivots, start: int, stop: int, cut: int) → None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

get_name(self: pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots) → str

PivotPicker::get_name

C++: protocols::kinematic_closure::pivot_pickers::FixedPivots::get_name() const –> std::string

pick(self: pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots, pose: pyrosetta.rosetta.core.pose.Pose, loop: pyrosetta.rosetta.protocols.loops.Loop) → pyrosetta.rosetta.protocols.loops.Loop

PivotPicker::pick

C++: protocols::kinematic_closure::pivot_pickers::FixedPivots::pick(const class core::pose::Pose &, const class protocols::loops::Loop &) –> class protocols::loops::Loop

class pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots

Bases: pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker

Use the start, stop, and cut points of the given loop as pivots.

This algorithm is meant to be simple and intuitive. The pick() method will be passed a loop, and the pivots will be taken from the parameters of that loop. If the cut point is outside the loop (e.g. if it hasn’t been set), the midpoint of the loop will be used instead.

__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.kinematic_closure.pivot_pickers.LoopPivots) → 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).

get_name(self: pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots) → str

PivotPicker::get_name

C++: protocols::kinematic_closure::pivot_pickers::LoopPivots::get_name() const –> std::string

pick(self: pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots, pose: pyrosetta.rosetta.core.pose.Pose, loop: pyrosetta.rosetta.protocols.loops.Loop) → pyrosetta.rosetta.protocols.loops.Loop

PivotPicker::pick

C++: protocols::kinematic_closure::pivot_pickers::LoopPivots::pick(const class core::pose::Pose &, const class protocols::loops::Loop &) –> class protocols::loops::Loop

class pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker

Bases: pybind11_builtins.pybind11_object

Base class for all the pivot picking algorithms.

__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.kinematic_closure.pivot_pickers.PivotPicker) → 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).

get_name(self: pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker) → str

Return the name of this pivot picker.

C++: protocols::kinematic_closure::pivot_pickers::PivotPicker::get_name() const –> std::string

pick(self: pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker, pose: pyrosetta.rosetta.core.pose.Pose, loop: pyrosetta.rosetta.protocols.loops.Loop) → pyrosetta.rosetta.protocols.loops.Loop

Return a loop object. The pivots will be taken to be the start,

cut and stop residues.

C++: protocols::kinematic_closure::pivot_pickers::PivotPicker::pick(const class core::pose::Pose &, const class protocols::loops::Loop &) –> class protocols::loops::Loop

class pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots

Bases: pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker

Randomly pick pivots in a way that may or may not span the whole loop.

This is the default pivot picking algorithm used by samplers::KicMover. It works well for most applications, and should only really need to be swapped out in in favor of custom pivot pickers that take into account specific knowledge of the loop being sampled. Earlier versions of this algorithm were biased towards the fount half of the loop. This bias has been mitigated, but not completely removed, in the current version.

__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.kinematic_closure.pivot_pickers.StandardPivots) → 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).

get_name(self: pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots) → str

PivotPicker::get_name

C++: protocols::kinematic_closure::pivot_pickers::StandardPivots::get_name() const –> std::string

pick(self: pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots, pose: pyrosetta.rosetta.core.pose.Pose, loop: pyrosetta.rosetta.protocols.loops.Loop) → pyrosetta.rosetta.protocols.loops.Loop

PivotPicker::pick

C++: protocols::kinematic_closure::pivot_pickers::StandardPivots::pick(const class core::pose::Pose &, const class protocols::loops::Loop &) –> class protocols::loops::Loop