solution_pickers

Bindings for protocols::kinematic_closure::solution_pickers namespace

class pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions

Bases: pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker

Apply rama and bump checks to quickly filter out bad solutions.

The rama check only considers the pivot torsions, since it is assumed that the non-pivot torsions were set as desired. This check employs a Monte Carlo acceptance step, which means that the pivot torsions will really be sampled from a rama distribution (ignoring the inherent geometric biases in the closure algorithm) when this check is enabled. However, note that the rama distribution will be double-counted if the score function also contains a rama term, which it usually does.

The bump check checks for clashes between the N, CA, C, O, and CB atoms of every residue in the loop versus every other residue in the protein. This filter is O(n^2) and is much slower than the constant time rama check. The rama check is also very selective; it usually filters out more than 90% of proposed solutions. For these reasons, it is important that the rama check be run before the bump check. You can disable the rama check, but this would probably lead to a noticeable drop in performance.

__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.solution_pickers.FilteredSolutions) -> None

doc

2. __init__(self: pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions, arg0: bool) -> None

doc

3. __init__(self: pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions, arg0: bool, arg1: bool) -> None

doc

4. __init__(self: pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions, check_rama: bool, check_overlap: bool, be_lenient: bool) -> 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).

be_lenient(self: pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions) → None

Make the bump check more lenient.

C++: protocols::kinematic_closure::solution_pickers::FilteredSolutions::be_lenient() –> void

check_overlap(self: pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions) → None

Enable the bump check.

C++: protocols::kinematic_closure::solution_pickers::FilteredSolutions::check_overlap() –> void

check_rama(self: pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions) → None

Enable the rama check.

C++: protocols::kinematic_closure::solution_pickers::FilteredSolutions::check_rama() –> void

dont_be_lenient(self: pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions) → None

Make the bump check more lenient.

C++: protocols::kinematic_closure::solution_pickers::FilteredSolutions::dont_be_lenient() –> void

dont_check_overlap(self: pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions) → None

Disable the bump check.

C++: protocols::kinematic_closure::solution_pickers::FilteredSolutions::dont_check_overlap() –> void

dont_check_rama(self: pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions) → None

Disable the rama check.

C++: protocols::kinematic_closure::solution_pickers::FilteredSolutions::dont_check_rama() –> void

pick_and_apply(self: pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions, pose: pyrosetta.rosetta.core.pose.Pose, solutions: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_kinematic_closure_ClosureSolution_t) → bool

SolutionPicker::pick_and_apply

C++: protocols::kinematic_closure::solution_pickers::FilteredSolutions::pick_and_apply(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<const class protocols::kinematic_closure::ClosureSolution>, class std::allocator<class std::shared_ptr<const class protocols::kinematic_closure::ClosureSolution> > > &) –> bool

class pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions

Bases: pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker

Pick a completely random solution to return.

__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.solution_pickers.RandomSolutions) → 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).

pick_and_apply(self: pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions, pose: pyrosetta.rosetta.core.pose.Pose, solutions: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_kinematic_closure_ClosureSolution_t) → bool

SolutionPicker::pick_and_apply

C++: protocols::kinematic_closure::solution_pickers::RandomSolutions::pick_and_apply(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<const class protocols::kinematic_closure::ClosureSolution>, class std::allocator<class std::shared_ptr<const class protocols::kinematic_closure::ClosureSolution> > > &) –> bool

class pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker

Bases: pybind11_builtins.pybind11_object

Base class for all the solution 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.solution_pickers.SolutionPicker) → 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).

pick_and_apply(self: pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker, pose: pyrosetta.rosetta.core.pose.Pose, solutions: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_kinematic_closure_ClosureSolution_t) → bool

Pick a solution from the given list, and if apply it to the given

pose. If no solution is satisfactory, don’t do anything.

C++: protocols::kinematic_closure::solution_pickers::SolutionPicker::pick_and_apply(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<const class protocols::kinematic_closure::ClosureSolution>, class std::allocator<class std::shared_ptr<const class protocols::kinematic_closure::ClosureSolution> > > &) –> bool