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- builtins.object
-
- Perturber
-
- BondAnglePerturber
- FragmentPerturber
- IdealizeNonPhiPsi
- LogFilePerturber
- OmegaPerturber
- PerturberSet
- Rama2bPerturber
- RamaPerturber
- UniformPerturber
- VicinityPerturber
- WalkingBondAnglePerturber
- WalkingPerturber
class BondAnglePerturber(Perturber) |
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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).
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- Method resolution order:
- BondAnglePerturber
- Perturber
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber) -> str
Perturber::get_name()
- perturb_subset(...) from builtins.PyCapsule
- perturb_subset(self : rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturber::perturb_subset()
Methods inherited from Perturber:
- perturb(...) from builtins.PyCapsule
- perturb(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues.
- perturb_subset_with_balance(...) from builtins.PyCapsule
- perturb_subset_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb the given residues such that detailed balance is obeyed.
- perturb_with_balance(...) from builtins.PyCapsule
- perturb_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues such that detailed balance
is obeyed.
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class FragmentPerturber(Perturber) |
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Pick phi/psi torsions from the given fragment library.
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- Method resolution order:
- FragmentPerturber
- Perturber
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(self : handle, frag_libs : rosetta.utility.vector1_std_shared_ptr_const_core_fragment_FragSet_t) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber) -> str
Perturber::get_name
- perturb_subset(...) from builtins.PyCapsule
- perturb_subset(self : rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturber::get_subset
Methods inherited from Perturber:
- perturb(...) from builtins.PyCapsule
- perturb(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues.
- perturb_subset_with_balance(...) from builtins.PyCapsule
- perturb_subset_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb the given residues such that detailed balance is obeyed.
- perturb_with_balance(...) from builtins.PyCapsule
- perturb_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues such that detailed balance
is obeyed.
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class IdealizeNonPhiPsi(Perturber) |
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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.
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- Method resolution order:
- IdealizeNonPhiPsi
- Perturber
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi) -> str
Perturber::get_name
- perturb_subset(...) from builtins.PyCapsule
- perturb_subset(self : rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturber::get_subset
- perturb_subset_with_balance(...) from builtins.PyCapsule
- perturb_subset_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturber::perturb_subset_with_balance
Methods inherited from Perturber:
- perturb(...) from builtins.PyCapsule
- perturb(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues.
- perturb_with_balance(...) from builtins.PyCapsule
- perturb_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues such that detailed balance
is obeyed.
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class LogFilePerturber(Perturber) |
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Read torsion angles, bond angles, and bond lengths from a log file.
This perturber is meant to be used as a debugging aid.
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- Method resolution order:
- LogFilePerturber
- Perturber
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(self : handle, path : str) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber) -> str
Perturber::get_name
- perturb_subset(...) from builtins.PyCapsule
- perturb_subset(self : rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturber::get_subset
Methods inherited from Perturber:
- perturb(...) from builtins.PyCapsule
- perturb(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues.
- perturb_subset_with_balance(...) from builtins.PyCapsule
- perturb_subset_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb the given residues such that detailed balance is obeyed.
- perturb_with_balance(...) from builtins.PyCapsule
- perturb_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues such that detailed balance
is obeyed.
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class OmegaPerturber(Perturber) |
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- Method resolution order:
- OmegaPerturber
- Perturber
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.kinematic_closure.perturbers.OmegaPerturber) -> str
Perturber::get_name()
- perturb_subset(...) from builtins.PyCapsule
- perturb_subset(self : rosetta.protocols.kinematic_closure.perturbers.OmegaPerturber, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturber::perturb_subset()
Methods inherited from Perturber:
- perturb(...) from builtins.PyCapsule
- perturb(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues.
- perturb_subset_with_balance(...) from builtins.PyCapsule
- perturb_subset_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb the given residues such that detailed balance is obeyed.
- perturb_with_balance(...) from builtins.PyCapsule
- perturb_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues such that detailed balance
is obeyed.
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class Perturber(builtins.object) |
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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.
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.protocols.kinematic_closure.perturbers.Perturber) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.kinematic_closure.perturbers.Perturber) -> str
Return the name of this perturber.
- perturb(...) from builtins.PyCapsule
- perturb(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues.
- perturb_subset(...) from builtins.PyCapsule
- perturb_subset(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb the given residues.
- perturb_subset_with_balance(...) from builtins.PyCapsule
- perturb_subset_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb the given residues such that detailed balance is obeyed.
- perturb_with_balance(...) from builtins.PyCapsule
- perturb_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues such that detailed balance
is obeyed.
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class PerturberSet(Perturber) |
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Maintain a set of perturbers to be executed together.
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- Method resolution order:
- PerturberSet
- Perturber
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add(...) from builtins.PyCapsule
- add(self : rosetta.protocols.kinematic_closure.perturbers.PerturberSet, perturber : rosetta.protocols.kinematic_closure.perturbers.Perturber) -> NoneType
Add a new perturber to the set. Any default perturbers are
removed.
- clear(...) from builtins.PyCapsule
- clear(rosetta.protocols.kinematic_closure.perturbers.PerturberSet) -> NoneType
Remove all perturbers from this set.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.kinematic_closure.perturbers.PerturberSet) -> str
Perturber::get_name
- get_perturber_names(...) from builtins.PyCapsule
- get_perturber_names(*args, **kwargs)
Overloaded function.
1. get_perturber_names(self : rosetta.protocols.kinematic_closure.perturbers.PerturberSet, names : rosetta.utility.vector1_std_string) -> NoneType
Add the names of all the perturbers contained in this set to the
given list. Indentation is used to indicate hierarchy.
2. get_perturber_names(self : rosetta.protocols.kinematic_closure.perturbers.PerturberSet, names : rosetta.utility.vector1_std_string, indent : str) -> NoneType
Add the names of all the perturbers contained in this set to the
given list. Indentation is used to indicate hierarchy.
- mark_as_default(...) from builtins.PyCapsule
- mark_as_default(rosetta.protocols.kinematic_closure.perturbers.PerturberSet) -> NoneType
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.
- perturb_subset(...) from builtins.PyCapsule
- perturb_subset(self : rosetta.protocols.kinematic_closure.perturbers.PerturberSet, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturber::perturb_subset
- perturb_subset_with_balance(...) from builtins.PyCapsule
- perturb_subset_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.PerturberSet, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturber::perturb_subset_with_balance
Methods inherited from Perturber:
- perturb(...) from builtins.PyCapsule
- perturb(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues.
- perturb_with_balance(...) from builtins.PyCapsule
- perturb_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues such that detailed balance
is obeyed.
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class Rama2bPerturber(Perturber) |
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Pick phi/psi pairs from the neighbor-dependent rama distribution.
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| |
- Method resolution order:
- Rama2bPerturber
- Perturber
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber) -> str
Perturber::get_name
- perturb_subset(...) from builtins.PyCapsule
- perturb_subset(self : rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturber::get_subset
Methods inherited from Perturber:
- perturb(...) from builtins.PyCapsule
- perturb(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues.
- perturb_subset_with_balance(...) from builtins.PyCapsule
- perturb_subset_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb the given residues such that detailed balance is obeyed.
- perturb_with_balance(...) from builtins.PyCapsule
- perturb_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues such that detailed balance
is obeyed.
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class RamaPerturber(Perturber) |
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Pick phi/psi pairs from the rama distribution.
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| |
- Method resolution order:
- RamaPerturber
- Perturber
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.kinematic_closure.perturbers.RamaPerturber) -> str
Perturber::get_name
- perturb_subset(...) from builtins.PyCapsule
- perturb_subset(self : rosetta.protocols.kinematic_closure.perturbers.RamaPerturber, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturber::get_subset
- perturb_subset_with_balance(...) from builtins.PyCapsule
- perturb_subset_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.RamaPerturber, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturber::perturb_subset_with_balance
Methods inherited from Perturber:
- perturb(...) from builtins.PyCapsule
- perturb(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues.
- perturb_with_balance(...) from builtins.PyCapsule
- perturb_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues such that detailed balance
is obeyed.
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class UniformPerturber(Perturber) |
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Sample backbone torsions from a uniform distribution.
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| |
- Method resolution order:
- UniformPerturber
- Perturber
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.kinematic_closure.perturbers.UniformPerturber) -> str
Perturber::get_name
- perturb_subset(...) from builtins.PyCapsule
- perturb_subset(self : rosetta.protocols.kinematic_closure.perturbers.UniformPerturber, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturber::perturb_subset()
- perturb_subset_with_balance(...) from builtins.PyCapsule
- perturb_subset_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.UniformPerturber, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturber::perturb_subset_with_balance()
Methods inherited from Perturber:
- perturb(...) from builtins.PyCapsule
- perturb(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues.
- perturb_with_balance(...) from builtins.PyCapsule
- perturb_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues such that detailed balance
is obeyed.
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class VicinityPerturber(Perturber) |
| |
Limit sampling to phi/psi pairs within some distance of a target
loop.
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| |
- Method resolution order:
- VicinityPerturber
- Perturber
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(self : handle, target : rosetta.core.pose.Pose) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber) -> str
Perturber::get_name
- perturb_subset(...) from builtins.PyCapsule
- perturb_subset(self : rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturber::perturb_subset
- perturb_subset_with_balance(...) from builtins.PyCapsule
- perturb_subset_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturber::perturb_subset_with_balance
Methods inherited from Perturber:
- perturb(...) from builtins.PyCapsule
- perturb(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues.
- perturb_with_balance(...) from builtins.PyCapsule
- perturb_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues such that detailed balance
is obeyed.
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class WalkingBondAnglePerturber(Perturber) |
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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).
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- Method resolution order:
- WalkingBondAnglePerturber
- Perturber
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
doc
2. __init__(self : handle, magnitude : float) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber) -> str
Perturber::get_name()
- perturb_subset(...) from builtins.PyCapsule
- perturb_subset(self : rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturber::perturb_subset()
- perturb_subset_with_balance(...) from builtins.PyCapsule
- perturb_subset_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturber::perturb_subset_with_balance
Methods inherited from Perturber:
- perturb(...) from builtins.PyCapsule
- perturb(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues.
- perturb_with_balance(...) from builtins.PyCapsule
- perturb_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues such that detailed balance
is obeyed.
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class WalkingPerturber(Perturber) |
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Make small perturbations to the previous backbone torsions.
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- Method resolution order:
- WalkingPerturber
- Perturber
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
doc
2. __init__(self : handle, magnitude : float) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber) -> str
Perturber::get_name
- perturb_subset(...) from builtins.PyCapsule
- perturb_subset(self : rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturber::perturb_subset
- perturb_subset_with_balance(...) from builtins.PyCapsule
- perturb_subset_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber, pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_unsigned_long, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturber::perturb_subset_with_balance
Methods inherited from Perturber:
- perturb(...) from builtins.PyCapsule
- perturb(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues.
- perturb_with_balance(...) from builtins.PyCapsule
- perturb_with_balance(self : rosetta.protocols.kinematic_closure.perturbers.Perturber, pose : rosetta.core.pose.Pose, problem : rosetta.protocols.kinematic_closure.ClosureProblem) -> NoneType
Perturb all of the non-pivot residues such that detailed balance
is obeyed.
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