perturbers

Bindings for protocols::kinematic_closure::perturbers namespace

class pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber

Bases: Perturber

Resample each backbone bond angle from a gaussian distribution.

The parameters for the underlying gaussian distribution were taken from a fit of the bond angle distribution observed in the Top8000 database in 2013. Also note that bond angles (3 atoms) are different than torsion angles (4 atoms).

get_name(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber) → str

Perturber::get_name()

C++: protocols::kinematic_closure::perturbers::BondAnglePerturber::get_name() const –> std::string

perturb(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturber::perturb_subset()

C++: protocols::kinematic_closure::perturbers::BondAnglePerturber::perturb_subset(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb the given residues such that detailed balance is obeyed.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb_subset_with_balance(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues such that detailed balance

is obeyed.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb_with_balance(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

class pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber

Bases: Perturber

Pick phi/psi torsions from the given fragment library.

get_name(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber) → str

Perturber::get_name

C++: protocols::kinematic_closure::perturbers::FragmentPerturber::get_name() const –> std::string

perturb(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturber::get_subset

C++: protocols::kinematic_closure::perturbers::FragmentPerturber::perturb_subset(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb the given residues such that detailed balance is obeyed.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb_subset_with_balance(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues such that detailed balance

is obeyed.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb_with_balance(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

class pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi

Bases: Perturber

Set all the non-phi/psi DOFs to ideal values.

The phi and psi torsion angles don’t really have ideal values; that’s what the Ramachandran distribution is. Use the RamaPerturber to set sample those DOFs and this perturber to idealize all the others. Note that this perturber uses hard-coded ideal values that were inherited from the legacy kinematic closure implementation. I don’t know how they were measured.

get_name(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi) → str

Perturber::get_name

C++: protocols::kinematic_closure::perturbers::IdealizeNonPhiPsi::get_name() const –> std::string

perturb(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturber::get_subset

C++: protocols::kinematic_closure::perturbers::IdealizeNonPhiPsi::perturb_subset(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturber::perturb_subset_with_balance

C++: protocols::kinematic_closure::perturbers::IdealizeNonPhiPsi::perturb_subset_with_balance(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues such that detailed balance

is obeyed.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb_with_balance(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

class pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber

Bases: Perturber

Read torsion angles, bond angles, and bond lengths from a log file.

This perturber is meant to be used as a debugging aid.

get_name(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber) → str

Perturber::get_name

C++: protocols::kinematic_closure::perturbers::LogFilePerturber::get_name() const –> std::string

static log_angles(out: pyrosetta.rosetta.std.ostream, angles: pyrosetta.rosetta.utility.vector1_double) → None

Output the given bond angles in a format that can later be read by

LogFilePerturber.

C++: protocols::kinematic_closure::perturbers::LogFilePerturber::log_angles(std::ostream &, class utility::vector1<double, class std::allocator<double> >) –> void

static log_lengths(out: pyrosetta.rosetta.std.ostream, lengths: pyrosetta.rosetta.utility.vector1_double) → None

Output the given bond lengths in a format that can later be read

by LogFilePerturber.

C++: protocols::kinematic_closure::perturbers::LogFilePerturber::log_lengths(std::ostream &, class utility::vector1<double, class std::allocator<double> >) –> void

static log_torsions(out: pyrosetta.rosetta.std.ostream, torsions: pyrosetta.rosetta.utility.vector1_double) → None

Output the given torsion angles in a format that can later be read

by LogFilePerturber.

C++: protocols::kinematic_closure::perturbers::LogFilePerturber::log_torsions(std::ostream &, class utility::vector1<double, class std::allocator<double> >) –> void

perturb(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturber::get_subset

C++: protocols::kinematic_closure::perturbers::LogFilePerturber::perturb_subset(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb the given residues such that detailed balance is obeyed.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb_subset_with_balance(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues such that detailed balance

is obeyed.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb_with_balance(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

class pyrosetta.rosetta.protocols.kinematic_closure.perturbers.OmegaPerturber

Bases: Perturber

get_name(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.OmegaPerturber) → str

Perturber::get_name()

C++: protocols::kinematic_closure::perturbers::OmegaPerturber::get_name() const –> std::string

perturb(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.OmegaPerturber, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturber::perturb_subset()

C++: protocols::kinematic_closure::perturbers::OmegaPerturber::perturb_subset(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb the given residues such that detailed balance is obeyed.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb_subset_with_balance(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues such that detailed balance

is obeyed.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb_with_balance(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

class pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber

Bases: pybind11_object

Base class for all of the perturber algorithms.

Solving a kinematic closure problem has two steps. The first step is to pick a new torsion angles, bond angles, and/or bond lengths in the region being sampled. The second step is to analytically set six torsions such that the backbone stays closed. Perturber subclasses are responsible for managing the first step.

Every perturber subclass must reimplement perturb_subset(). The arguments to the method are a Pose, a list of residues, and a ClosureProblem. The pose is const and should just be used to look up residue types and other relevant contextual information. The residue list specifies the residues that should be perturbed. In other words, residues not in this list should not be changed. This allows composite perturbers to specify different perturber algorithms for different parts on the loop. For example, for antibody modeling you might use a custom perturber for loop regions with well-known motifs and the standard RamaPerturber everywhere else. Finally, the problem is used to actually set the backbone DOFS via methods like perturb_phi() and perturb_psi().

If your perturber algorithm can be made to obey detailed balance, you should also reimplement perturb_subset_with_balance(). This method is called by BalancedKicMover and it works just like perturb_subset(). If your algorithm doesn’t obey detailed balance, or if you don’t know what detailed balance is, then don’t worry about it.

Currently perturb_phi() and perturb_psi() live in ClosureProblem. This makes sense, because the problem owns the matrices that these methods are perturbing. So you can think of these methods as part of an interface that allows the closure problem to be defined. However, this approach will not work well with non-canonical backbones. An alternative is to expose a much more general interface to the problem (i.e. get_torsion_angles() and set_torsion_angles()). Then subclasses of Perturber that are only meant to work with one sort of backbone can be created, and these subclasses can define methods like perturb_phi() and perturb_psi() which use the more general ClosureProblem interface. In any case, you should be aware that the perturber interface may change in the near future.

It would have been nice if any regular mover could be used to perturb the backbone, instead of being limited to single-purpose Perturber subclasses. I spent a lot of time trying to get this to work, but it was very slow. My belief is that too many AtomTree coordinates were being updated too often.

get_name(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber) → str

Return the name of this perturber.

C++: protocols::kinematic_closure::perturbers::Perturber::get_name() const –> std::string

perturb(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb the given residues.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb_subset(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb the given residues such that detailed balance is obeyed.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb_subset_with_balance(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues such that detailed balance

is obeyed.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb_with_balance(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

class pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet

Bases: Perturber

Maintain a set of perturbers to be executed together.

add(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet, perturber: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber) → None

Add a new perturber to the set. Any default perturbers are

removed.

C++: protocols::kinematic_closure::perturbers::PerturberSet::add(class std::shared_ptr<class protocols::kinematic_closure::perturbers::Perturber>) –> void

clear(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet) → None

Remove all perturbers from this set.

C++: protocols::kinematic_closure::perturbers::PerturberSet::clear() –> void

get_name(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet) → str

Perturber::get_name

C++: protocols::kinematic_closure::perturbers::PerturberSet::get_name() const –> std::string

get_perturber_names(*args, **kwargs)

Overloaded function.

1. get_perturber_names(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet, names: pyrosetta.rosetta.utility.vector1_std_string) -> None

2. get_perturber_names(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet, names: pyrosetta.rosetta.utility.vector1_std_string, indent: str) -> None

Add the names of all the perturbers contained in this set to the

given list. Indentation is used to indicate hierarchy.

C++: protocols::kinematic_closure::perturbers::PerturberSet::get_perturber_names(class utility::vector1<std::string, class std::allocator<std::string > > &, std::string) const –> void

mark_as_default(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet) → None

Indicate that the current set of perturbers is meant as some sort

of default, and should be cleared if a new perturber is manually added.

C++: protocols::kinematic_closure::perturbers::PerturberSet::mark_as_default() –> void

perturb(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturber::perturb_subset

C++: protocols::kinematic_closure::perturbers::PerturberSet::perturb_subset(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturber::perturb_subset_with_balance

C++: protocols::kinematic_closure::perturbers::PerturberSet::perturb_subset_with_balance(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues such that detailed balance

is obeyed.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb_with_balance(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

class pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber

Bases: Perturber

Pick phi/psi pairs from the neighbor-dependent rama distribution.

get_name(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber) → str

Perturber::get_name

C++: protocols::kinematic_closure::perturbers::Rama2bPerturber::get_name() const –> std::string

perturb(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturber::get_subset

C++: protocols::kinematic_closure::perturbers::Rama2bPerturber::perturb_subset(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb the given residues such that detailed balance is obeyed.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb_subset_with_balance(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues such that detailed balance

is obeyed.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb_with_balance(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

class pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber

Bases: Perturber

Pick phi/psi pairs from the rama distribution.

get_name(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber) → str

Perturber::get_name

C++: protocols::kinematic_closure::perturbers::RamaPerturber::get_name() const –> std::string

perturb(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturber::get_subset

C++: protocols::kinematic_closure::perturbers::RamaPerturber::perturb_subset(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturber::perturb_subset_with_balance

C++: protocols::kinematic_closure::perturbers::RamaPerturber::perturb_subset_with_balance(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues such that detailed balance

is obeyed.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb_with_balance(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

class pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber

Bases: Perturber

Sample backbone torsions from a uniform distribution.

get_name(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber) → str

Perturber::get_name

C++: protocols::kinematic_closure::perturbers::UniformPerturber::get_name() const –> std::string

perturb(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturber::perturb_subset()

C++: protocols::kinematic_closure::perturbers::UniformPerturber::perturb_subset(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturber::perturb_subset_with_balance()

C++: protocols::kinematic_closure::perturbers::UniformPerturber::perturb_subset_with_balance(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues such that detailed balance

is obeyed.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb_with_balance(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

class pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber

Bases: Perturber

Limit sampling to phi/psi pairs within some distance of a target loop.

get_name(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber) → str

Perturber::get_name

C++: protocols::kinematic_closure::perturbers::VicinityPerturber::get_name() const –> std::string

perturb(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturber::perturb_subset

C++: protocols::kinematic_closure::perturbers::VicinityPerturber::perturb_subset(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturber::perturb_subset_with_balance

C++: protocols::kinematic_closure::perturbers::VicinityPerturber::perturb_subset_with_balance(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues such that detailed balance

is obeyed.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb_with_balance(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

class pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber

Bases: Perturber

Resample each backbone bond angle from a gaussian distribution.

The parameters for the underlying gaussian distribution were taken from a fit of the bond angle distribution observed in the Top8000 database in 2013. Also note that bond angles (3 atoms) are different than torsion angles (4 atoms).

get_name(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber) → str

Perturber::get_name()

C++: protocols::kinematic_closure::perturbers::WalkingBondAnglePerturber::get_name() const –> std::string

perturb(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturber::perturb_subset()

C++: protocols::kinematic_closure::perturbers::WalkingBondAnglePerturber::perturb_subset(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturber::perturb_subset_with_balance

C++: protocols::kinematic_closure::perturbers::WalkingBondAnglePerturber::perturb_subset_with_balance(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues such that detailed balance

is obeyed.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb_with_balance(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

class pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber

Bases: Perturber

Make small perturbations to the previous backbone torsions.

get_name(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber) → str

Perturber::get_name

C++: protocols::kinematic_closure::perturbers::WalkingPerturber::get_name() const –> std::string

perturb(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturber::perturb_subset

C++: protocols::kinematic_closure::perturbers::WalkingPerturber::perturb_subset(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_subset_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber, pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturber::perturb_subset_with_balance

C++: protocols::kinematic_closure::perturbers::WalkingPerturber::perturb_subset_with_balance(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void

perturb_with_balance(self: pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber, pose: pyrosetta.rosetta.core.pose.Pose, problem: pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem) → None

Perturb all of the non-pivot residues such that detailed balance

is obeyed.

C++: protocols::kinematic_closure::perturbers::Perturber::perturb_with_balance(const class core::pose::Pose &, class std::shared_ptr<class protocols::kinematic_closure::ClosureProblem>) –> void