pivot_pickers

Bindings for protocols::kinematic_closure::pivot_pickers namespace

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

Bases: PivotPicker

Pick pivots that span the entire loop to sample.

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: PivotPicker

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

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: PivotPicker

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

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: 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.

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: 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.

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_object

Base class for all the pivot picking algorithms.

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: 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.

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