helical_bundle

• parameters

Bindings for protocols::helical_bundle namespace

class pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper

Bases: pybind11_builtins.pybind11_object

BackboneGridSamplerHelper class, which stores options for the PerturbBundle mover.

__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.helical_bundle.BackboneGridSamplerHelper) -> None
2. __init__(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper, arg0: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) -> 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).

assign(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper, : pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) → pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper

C++: protocols::helical_bundle::BackboneGridSamplerHelper::operator=(const class protocols::helical_bundle::BackboneGridSamplerHelper &) –> class protocols::helical_bundle::BackboneGridSamplerHelper &

clone(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) → pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper

Copy this BackboneGridSamplerHelper object( allocate actual memory for it )

C++: protocols::helical_bundle::BackboneGridSamplerHelper::clone() const –> class std::shared_ptr<class protocols::helical_bundle::BackboneGridSamplerHelper>

get_self_ptr(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) → pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper

C++: protocols::helical_bundle::BackboneGridSamplerHelper::get_self_ptr() –> class std::shared_ptr<class protocols::helical_bundle::BackboneGridSamplerHelper>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) → pyrosetta.rosetta.std.weak_ptr_protocols_helical_bundle_BackboneGridSamplerHelper_t

C++: protocols::helical_bundle::BackboneGridSamplerHelper::get_self_weak_ptr() –> class std::weak_ptr<class protocols::helical_bundle::BackboneGridSamplerHelper>

increment_cur_indices(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) → None

RECURSIVE function that increments the current sample index.

This function adds 1 to the last torsion index. If the last torsion index value exceeds the number of samples for that torsion, it resets that torsion index and increments the second-last torsion index by 1 by recursively calling itself. This function is overloaded; the public version by default tries to increment the last index, while the private version can be called recursively.

C++: protocols::helical_bundle::BackboneGridSamplerHelper::increment_cur_indices() –> void

n_torsions(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper, res_index: int) → int

Returns the number of different mainchain torsions that the BackboneGridSampler will sample over.

Returns a value for the residue in the repeating unit with index res_index.

C++: protocols::helical_bundle::BackboneGridSamplerHelper::n_torsions(const unsigned long) const –> unsigned long

n_torsions_total(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) → int

Returns the total number of mainchain torsions over which we will sample.

This is the sum of the n_torsions_ entries for each residue in the repeating

unit, and is initialized by the initialize_samples() function.

C++: protocols::helical_bundle::BackboneGridSamplerHelper::n_torsions_total() const –> unsigned long

reset(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) → None

Reset this BackboneGridSamplerHelper object.

Clears all internal data.

C++: protocols::helical_bundle::BackboneGridSamplerHelper::reset() –> void

residue_index(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper, index: int) → int

Returns the residue index in the repeating unit (1st, 2nd, 3rd etc.) corresponding to a

given torsion index.

C++: protocols::helical_bundle::BackboneGridSamplerHelper::residue_index(const unsigned long) const –> unsigned long

residues_per_repeat(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) → int

Returns the number of residues per repeat, set by the initialize_data() function.

C++: protocols::helical_bundle::BackboneGridSamplerHelper::residues_per_repeat() const –> unsigned long

torsion_id(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper, index: int) → int

Returns the torsion ID for the specified torsion index.

C++: protocols::helical_bundle::BackboneGridSamplerHelper::torsion_id(const unsigned long) const –> unsigned long

torsion_sample_value(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper, index: int) → float

Returns the current sample value for the specified torsion.

C++: protocols::helical_bundle::BackboneGridSamplerHelper::torsion_sample_value(const unsigned long &) const –> double

class pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper

Bases: pybind11_builtins.pybind11_object

BundleGridSamplerHelper class, which stores options for the PerturbBundle mover.

DoF_helix_index(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper, index: int) → int

Returns the helix index of the specified DoF.

C++: protocols::helical_bundle::BundleGridSamplerHelper::DoF_helix_index(const unsigned long &) const –> unsigned long

DoF_name(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper, type: pyrosetta.rosetta.protocols.helical_bundle.DoFType) → str

Return the name of a DoF type given its enum.

C++: protocols::helical_bundle::BundleGridSamplerHelper::DoF_name(const enum protocols::helical_bundle::DoFType &) const –> std::string

DoF_sample_value(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper, index: int) → float

Returns the current sample value for the specified DoF.

C++: protocols::helical_bundle::BundleGridSamplerHelper::DoF_sample_value(const unsigned long &) const –> double

DoF_type(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper, index: int) → pyrosetta.rosetta.protocols.helical_bundle.DoFType

Returns the DoF type of the specified DoF.

C++: protocols::helical_bundle::BundleGridSamplerHelper::DoF_type(const unsigned long &) const –> enum protocols::helical_bundle::DoFType

__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.helical_bundle.BundleGridSamplerHelper) -> None
2. __init__(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper, arg0: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper) -> 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).

add_DoF(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper, doftype: pyrosetta.rosetta.protocols.helical_bundle.DoFType, helix_index: int, n_samples: int, lower_val: float, upper_val: float) → None

Add an allowed DoF that the BundleGridSampler will sample over.

Must specify the DoF type, the helix index, the number of samples, and the lower and upper bounds of the range to be sampled.

C++: protocols::helical_bundle::BundleGridSamplerHelper::add_DoF(const enum protocols::helical_bundle::DoFType, const unsigned long, const unsigned long, const double &, const double &) –> void

assign(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper, : pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper) → pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper

C++: protocols::helical_bundle::BundleGridSamplerHelper::operator=(const class protocols::helical_bundle::BundleGridSamplerHelper &) –> class protocols::helical_bundle::BundleGridSamplerHelper &

clone(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper) → pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper

Copy this BundleGridSamplerHelper object( allocate actual memory for it )

C++: protocols::helical_bundle::BundleGridSamplerHelper::clone() const –> class std::shared_ptr<class protocols::helical_bundle::BundleGridSamplerHelper>

get_self_ptr(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper) → pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper

C++: protocols::helical_bundle::BundleGridSamplerHelper::get_self_ptr() –> class std::shared_ptr<class protocols::helical_bundle::BundleGridSamplerHelper>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper) → pyrosetta.rosetta.std.weak_ptr_protocols_helical_bundle_BundleGridSamplerHelper_t

C++: protocols::helical_bundle::BundleGridSamplerHelper::get_self_weak_ptr() –> class std::weak_ptr<class protocols::helical_bundle::BundleGridSamplerHelper>

increment_cur_indices(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper) → None

RECURSIVE function that increments the current sample index.

This function adds 1 to the last DoF index. If the last DoF index value exceeds the number of samples for that DoF, it resets that DoF index and increments the second-last DoF index by 1 by recursively calling itself. This function is overloaded; the public version by default tries to increment the last index, while the private version can be called recursively.

C++: protocols::helical_bundle::BundleGridSamplerHelper::increment_cur_indices() –> void

initialize_samples(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper) → None

Perform the pre-calculation that sets up the lists of parameter values to be sampled.

C++: protocols::helical_bundle::BundleGridSamplerHelper::initialize_samples() –> void

nDoFs(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper) → int

Returns the number of different DoFs that the BundleGridSampler will sample over.

C++: protocols::helical_bundle::BundleGridSamplerHelper::nDoFs() const –> unsigned long

reset(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper) → None

Reset this BundleGridSamplerHelper object.

Clears all internal data.

C++: protocols::helical_bundle::BundleGridSamplerHelper::reset() –> void

class pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour

Bases: pybind11_builtins.pybind11_object

The behaviour of this filter.

The filter can return true always, false always, or can filter by energy. If you update this enum, add new behaviours to the two set_filter_behaviour() functions (setting by string and by enum).

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(*args, **kwargs)

Overloaded function.

1. __eq__(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour, arg0: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour) -> bool
2. __eq__(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour, arg0: int) -> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour) → tuple

__gt__

Return self>value.

__hash__(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour) → int

__init__(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour, arg0: 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.

__int__(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour) → int

__le__

Return self<=value.

__lt__

Return self<value.

__ne__(*args, **kwargs)

Overloaded function.

1. __ne__(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour, arg0: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour) -> bool
2. __ne__(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour, arg0: int) -> bool

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour) → str

__setattr__

Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour, arg0: tuple) → None

__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).

class pyrosetta.rosetta.protocols.helical_bundle.DoFType

Bases: pybind11_builtins.pybind11_object

The type of bundle parameter that will be sampled by the BundleGridSampler mover.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(*args, **kwargs)

Overloaded function.

1. __eq__(self: pyrosetta.rosetta.protocols.helical_bundle.DoFType, arg0: pyrosetta.rosetta.protocols.helical_bundle.DoFType) -> bool
2. __eq__(self: pyrosetta.rosetta.protocols.helical_bundle.DoFType, arg0: int) -> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.protocols.helical_bundle.DoFType) → tuple

__gt__

Return self>value.

__hash__(self: pyrosetta.rosetta.protocols.helical_bundle.DoFType) → int

__init__(self: pyrosetta.rosetta.protocols.helical_bundle.DoFType, arg0: 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.

__int__(self: pyrosetta.rosetta.protocols.helical_bundle.DoFType) → int

__le__

Return self<=value.

__lt__

Return self<value.

__ne__(*args, **kwargs)

Overloaded function.

1. __ne__(self: pyrosetta.rosetta.protocols.helical_bundle.DoFType, arg0: pyrosetta.rosetta.protocols.helical_bundle.DoFType) -> bool
2. __ne__(self: pyrosetta.rosetta.protocols.helical_bundle.DoFType, arg0: int) -> bool

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__(self: pyrosetta.rosetta.protocols.helical_bundle.DoFType) → str

__setattr__

Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.protocols.helical_bundle.DoFType, arg0: tuple) → None

__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).

class pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc

Bases: pyrosetta.rosetta.core.optimization.Multifunc

Multifunction class for fitting a simple (straight) helix to the Crick parameters.

__call__(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc, vars: pyrosetta.rosetta.utility.vector1_double) → float

Calculate function value (rms squared)

C++: protocols::helical_bundle::FitSimpleHelixMultiFunc::operator()(const class utility::vector1<double, class std::allocator<double> > &) const –> double

__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.helical_bundle.FitSimpleHelixMultiFunc, pose: pyrosetta.rosetta.core.pose.Pose, atom_name: str, first_res_index: int, res_per_repeat: int, start_index: int, end_index: int, minimization_mode: int, rms_offset: float) -> None
2. __init__(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc, arg0: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc) -> 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).

abort_min(self: pyrosetta.rosetta.core.optimization.Multifunc, : pyrosetta.rosetta.utility.vector1_double) → bool

Christophe added the following to allow premature end of minimization

If you want to abort the minimizer under specific circonstances overload this function and return true if you want to stop, false if you want to continue. FOR THE MOMENT, ONLY IN DFPMIN!

C++: core::optimization::Multifunc::abort_min(const class utility::vector1<double, class std::allocator<double> > &) const –> bool

assign(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc, : pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc) → pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc

C++: protocols::helical_bundle::FitSimpleHelixMultiFunc::operator=(const class protocols::helical_bundle::FitSimpleHelixMultiFunc &) –> class protocols::helical_bundle::FitSimpleHelixMultiFunc &

dfunc(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double) → None

Calculate function value derivatives

C++: protocols::helical_bundle::FitSimpleHelixMultiFunc::dfunc(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void

dump(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc, vars: pyrosetta.rosetta.utility.vector1_double, vars2: pyrosetta.rosetta.utility.vector1_double) → None

Error state reached – derivative does not match gradient

C++: protocols::helical_bundle::FitSimpleHelixMultiFunc::dump(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) const –> void

class pyrosetta.rosetta.protocols.helical_bundle.PertType

Bases: pybind11_builtins.pybind11_object

The type of random perturbation that will be used.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(*args, **kwargs)

Overloaded function.

1. __eq__(self: pyrosetta.rosetta.protocols.helical_bundle.PertType, arg0: pyrosetta.rosetta.protocols.helical_bundle.PertType) -> bool
2. __eq__(self: pyrosetta.rosetta.protocols.helical_bundle.PertType, arg0: int) -> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.protocols.helical_bundle.PertType) → tuple

__gt__

Return self>value.

__hash__(self: pyrosetta.rosetta.protocols.helical_bundle.PertType) → int

__init__(self: pyrosetta.rosetta.protocols.helical_bundle.PertType, arg0: 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.

__int__(self: pyrosetta.rosetta.protocols.helical_bundle.PertType) → int

__le__

Return self<=value.

__lt__

Return self<value.

__ne__(*args, **kwargs)

Overloaded function.

1. __ne__(self: pyrosetta.rosetta.protocols.helical_bundle.PertType, arg0: pyrosetta.rosetta.protocols.helical_bundle.PertType) -> bool
2. __ne__(self: pyrosetta.rosetta.protocols.helical_bundle.PertType, arg0: int) -> bool

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__(self: pyrosetta.rosetta.protocols.helical_bundle.PertType) → str

__setattr__

Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.protocols.helical_bundle.PertType, arg0: tuple) → None

__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).

class pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions

Bases: pybind11_builtins.pybind11_object

PerturbBundleOptions class, which stores options for the PerturbBundle mover.

__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.helical_bundle.PerturbBundleOptions) -> None
2. __init__(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, arg0: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) -> 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).

assign(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, : pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions

C++: protocols::helical_bundle::PerturbBundleOptions::operator=(const class protocols::helical_bundle::PerturbBundleOptions &) –> class protocols::helical_bundle::PerturbBundleOptions &

clone(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions

Copy this residue( allocate actual memory for it )

C++: protocols::helical_bundle::PerturbBundleOptions::clone() const –> class std::shared_ptr<class protocols::helical_bundle::PerturbBundleOptions>

default_value(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → float

Returns the default value of this parameter.

This is used by the BundleGridSampler mover, but not the PerturbBundle mover.

C++: protocols::helical_bundle::PerturbBundleOptions::default_value() const –> double

delta(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → float

Function to generate a random value, based on the perturbation type and perturbation magnitude.

Typically, one would then add this value to the current parameter value to perturb it.

C++: protocols::helical_bundle::PerturbBundleOptions::delta() const –> double

get_self_ptr(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions

C++: protocols::helical_bundle::PerturbBundleOptions::get_self_ptr() –> class std::shared_ptr<class protocols::helical_bundle::PerturbBundleOptions>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → pyrosetta.rosetta.std.weak_ptr_protocols_helical_bundle_PerturbBundleOptions_t

C++: protocols::helical_bundle::PerturbBundleOptions::get_self_weak_ptr() –> class std::weak_ptr<class protocols::helical_bundle::PerturbBundleOptions>

helix_index(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → int

Returns the index of the helix that these options refer to.

C++: protocols::helical_bundle::PerturbBundleOptions::helix_index() const –> unsigned long

is_being_set(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → bool

Returns whether this parameter is being set to its default value.

Used by the PerturbBundle mover.

C++: protocols::helical_bundle::PerturbBundleOptions::is_being_set() const –> bool

is_copy(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → bool

Returns whether we’re copying this value from another helix.

C++: protocols::helical_bundle::PerturbBundleOptions::is_copy() const –> bool

is_perturbable(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → bool

Returns whether this option is set to be peturbable.

C++: protocols::helical_bundle::PerturbBundleOptions::is_perturbable() const –> bool

lower_value(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → float

Returns the lower sampled value of this parameter.

This is used by the BundleGridSampler mover, but not the PerturbBundle mover.

C++: protocols::helical_bundle::PerturbBundleOptions::lower_value() const –> double

omega0_copies_pitch_instead(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → bool

Special case: returns whether omega0 copying should use the pitch angle instead of the omega0 value.

Default false.

C++: protocols::helical_bundle::PerturbBundleOptions::omega0_copies_pitch_instead() const –> bool

other_helix(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → int

Returns the other helix index from which we’re copying a value.

C++: protocols::helical_bundle::PerturbBundleOptions::other_helix() const –> unsigned long

perturbation_magnitude(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → float

Returns the perturbation magnitude. Returns 0 if not perturbable.

C++: protocols::helical_bundle::PerturbBundleOptions::perturbation_magnitude() const –> double

perturbation_type(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → pyrosetta.rosetta.protocols.helical_bundle.PertType

Returns the perturbation type.

C++: protocols::helical_bundle::PerturbBundleOptions::perturbation_type() const –> enum protocols::helical_bundle::PertType

samples(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → int

Returns the number of values to sample for this parameter.

This is used by the BundleGridSampler mover, but not the PerturbBundle mover. If the sample value is 0, no sampling occurs.

C++: protocols::helical_bundle::PerturbBundleOptions::samples() const –> unsigned long

set_being_set(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, val: bool) → None

Sets whether this parameter is being set to its default value.

Used by the PerturbBundle mover.

C++: protocols::helical_bundle::PerturbBundleOptions::set_being_set(const bool) –> void

set_default_value(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, val: float) → None

Set the default value of this parameter.

This is used by the BundleGridSampler mover, but not the PerturbBundle mover.

C++: protocols::helical_bundle::PerturbBundleOptions::set_default_value(const double &) –> void

set_helix_index(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, val: int) → None

Sets the index of the helix that these options refer to.

C++: protocols::helical_bundle::PerturbBundleOptions::set_helix_index(const unsigned long) –> void

set_helix_to_copy(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, helix_index: int) → None

Sets the helix from which we should copy a parameter value. If set to zero, no copying occurs.

C++: protocols::helical_bundle::PerturbBundleOptions::set_helix_to_copy(const unsigned long) –> void

set_lower_value(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, val: float) → None

Set the lower sampled value of this parameter.

This is used by the BundleGridSampler mover, but not the PerturbBundle mover.

C++: protocols::helical_bundle::PerturbBundleOptions::set_lower_value(const double &) –> void

set_omega0_copies_pitch_instead(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, copy_pitch: bool) → None

Special case: sets whether omega0 copying should copy the pitch angle instead of the omega0 value.

C++: protocols::helical_bundle::PerturbBundleOptions::set_omega0_copies_pitch_instead(const bool) –> void

set_perturbable(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, val: bool) → None

Sets whether this option is peturbable.

C++: protocols::helical_bundle::PerturbBundleOptions::set_perturbable(const bool) –> void

set_perturbation_magnitude(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, val: float) → None

Sets the perturbation magnitude. Sets perturbable to true in the process.

C++: protocols::helical_bundle::PerturbBundleOptions::set_perturbation_magnitude(const double &) –> void

set_perturbation_type(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, type: pyrosetta.rosetta.protocols.helical_bundle.PertType) → None

Sets the perturbation type.

C++: protocols::helical_bundle::PerturbBundleOptions::set_perturbation_type(const enum protocols::helical_bundle::PertType) –> void

set_samples(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, val: int) → None

Sets the number of values to sample for this parameter.

This is used by the BundleGridSampler mover, but not the PerturbBundle mover. If set to 0, no sampling occurs.

C++: protocols::helical_bundle::PerturbBundleOptions::set_samples(const unsigned long) –> void

set_upper_value(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, val: float) → None

Set the upper sampled value of this parameter.

This is used by the BundleGridSampler mover, but not the PerturbBundle mover.

C++: protocols::helical_bundle::PerturbBundleOptions::set_upper_value(const double &) –> void

set_use_defaults(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, val: bool) → None

Sets whether the default values should be used in lieu of whatever is set here.

C++: protocols::helical_bundle::PerturbBundleOptions::set_use_defaults(const bool) –> void

upper_value(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → float

Returns the upper sampled value of this parameter.

This is used by the BundleGridSampler mover, but not the PerturbBundle mover.

C++: protocols::helical_bundle::PerturbBundleOptions::upper_value() const –> double

use_defaults(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → bool

Returns whether the default values should be used in lieu of whatever is set here.

C++: protocols::helical_bundle::PerturbBundleOptions::use_defaults() const –> bool

pyrosetta.rosetta.protocols.helical_bundle.add_attributes_for_helix_params(subtag_attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None

C++: protocols::helical_bundle::add_attributes_for_helix_params(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.protocols.helical_bundle.add_attributes_for_make_bundle_dofs(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None

C++: protocols::helical_bundle::add_attributes_for_make_bundle_dofs(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.protocols.helical_bundle.add_attributes_for_make_bundle_minorhelix_defaults(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None

C++: protocols::helical_bundle::add_attributes_for_make_bundle_minorhelix_defaults(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.protocols.helical_bundle.add_attributes_for_make_bundle_other_defaults(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None

C++: protocols::helical_bundle::add_attributes_for_make_bundle_other_defaults(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.protocols.helical_bundle.add_attributes_for_make_bundle_symmetry(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None

C++: protocols::helical_bundle::add_attributes_for_make_bundle_symmetry(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.protocols.helical_bundle.add_attributes_for_minor_helix_params(subtag_attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None

C++: protocols::helical_bundle::add_attributes_for_minor_helix_params(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.protocols.helical_bundle.add_attributes_for_other_helix_params(subtag_attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None

C++: protocols::helical_bundle::add_attributes_for_other_helix_params(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.protocols.helical_bundle.align_mainchain_atoms(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, helix_start: int, helix_end: int) → None

Align mainchain atoms of pose to ref_pose mainchain atoms.

C++: protocols::helical_bundle::align_mainchain_atoms(class core::pose::Pose &, const class core::pose::Pose &, const unsigned long, const unsigned long) –> void

pyrosetta.rosetta.protocols.helical_bundle.align_mainchain_atoms_of_residue_range(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, helix_start: int, helix_end: int) → None

Align mainchain atoms of pose to ref_pose mainchain atoms,

moving ONLY the residues involved in the alignment.

C++: protocols::helical_bundle::align_mainchain_atoms_of_residue_range(class core::pose::Pose &, const class core::pose::Pose &, const unsigned long, const unsigned long) –> void

pyrosetta.rosetta.protocols.helical_bundle.copy_helix_bondangles(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, helix_start: int, helix_end: int) → None

Copy backbone bond angle values from one pose, where helix mainchain atom coordinates have been

set with the Crick equations, to another with ideal geometry.

C++: protocols::helical_bundle::copy_helix_bondangles(class core::pose::Pose &, const class core::pose::Pose &, const unsigned long, const unsigned long) –> void

pyrosetta.rosetta.protocols.helical_bundle.copy_helix_bondlengths(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, helix_start: int, helix_end: int) → None

Copy backbone bond length values from one pose, where helix mainchain atom coordinates have been

set with the Crick equations, to another with ideal geometry.

C++: protocols::helical_bundle::copy_helix_bondlengths(class core::pose::Pose &, const class core::pose::Pose &, const unsigned long, const unsigned long) –> void

pyrosetta.rosetta.protocols.helical_bundle.copy_helix_dihedrals(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, helix_start: int, helix_end: int) → None

Copy backbone dihedral values from one pose, where helix mainchain atom coordinates have been

set with the Crick equations, to another with ideal geometry.

C++: protocols::helical_bundle::copy_helix_dihedrals(class core::pose::Pose &, const class core::pose::Pose &, const unsigned long, const unsigned long) –> void

pyrosetta.rosetta.protocols.helical_bundle.generate_atom_positions(outvector: pyrosetta.rosetta.utility.vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t, helixpose: pyrosetta.rosetta.core.pose.Pose, helix_start: int, helix_end: int, r0: float, omega0: float, delta_omega0: float, delta_t: float, z1_offset: float, z0_offset: float, epsilon: float, invert_helix: bool, r1: pyrosetta.rosetta.utility.vector1_double, omega1: float, z1: float, delta_omega1: pyrosetta.rosetta.utility.vector1_double, delta_omega1_all: float, delta_z1: pyrosetta.rosetta.utility.vector1_double, residues_per_repeat: int, atoms_per_residue: pyrosetta.rosetta.utility.vector1_unsigned_long, repeating_unit_offset: int, failed: bool) → None

Generate the x,y,z coordinates of the mainchain atoms using the Crick equations.

Coordinates will be returned as a vector of vectors of xyzVectors. The outer index will refer to residue number, and the inner index will refer to atom number. Returns failed=true if coordinates could not be generated, false otherwise.

C++: protocols::helical_bundle::generate_atom_positions(class utility::vector1<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >, class std::allocator<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > > > &, const class core::pose::Pose &, const unsigned long, const unsigned long, const double &, const double &, const double &, const double &, const double &, const double &, const double &, const bool, const class utility::vector1<double, class std::allocator<double> > &, const double &, const double &, const class utility::vector1<double, class std::allocator<double> > &, const double &, const class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long, bool &) –> void

pyrosetta.rosetta.protocols.helical_bundle.parse_resnames(string_in: str, vect_out: pyrosetta.rosetta.utility.vector1_std_string) → None

Given a comma-separated list of residue names, separate these out into a vector of

residue names.

The string_in string is the input; the vect_out vector is the output (which will be reset by this operation).

C++: protocols::helical_bundle::parse_resnames(const class std::basic_string<char> &, class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> void

pyrosetta.rosetta.protocols.helical_bundle.place_atom_positions(pose: pyrosetta.rosetta.core.pose.Pose, atom_positions: pyrosetta.rosetta.utility.vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t, helix_start: int, helix_end: int) → None

Place the helix mainchain atoms based on the Crick equations.

C++: protocols::helical_bundle::place_atom_positions(class core::pose::Pose &, const class utility::vector1<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >, class std::allocator<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > > > &, const unsigned long, const unsigned long) –> void

pyrosetta.rosetta.protocols.helical_bundle.read_minor_helix_params(filename: str, r1: pyrosetta.rosetta.utility.vector1_double, omega1: float, z1: float, delta_omega1: pyrosetta.rosetta.utility.vector1_double, delta_z1: pyrosetta.rosetta.utility.vector1_double, residues_per_repeat: int, atoms_per_residue: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Read minor helix parameters from a crick_params file.

C++: protocols::helical_bundle::read_minor_helix_params(const class std::basic_string<char> &, class utility::vector1<double, class std::allocator<double> > &, double &, double &, class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, unsigned long &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.protocols.helical_bundle.write_crick_params_file_data(outfile: pyrosetta.rosetta.utility.io.ozstream, r1: pyrosetta.rosetta.utility.vector1_double, omega1: float, z1: float, delta_omega1: pyrosetta.rosetta.utility.vector1_double, delta_z1: pyrosetta.rosetta.utility.vector1_double) → None

Actual write of the crick_params file data.

Called by both write_minor_helix_params variants. The outfile ozstream must already be opened, and will not be closed by this function.

C++: protocols::helical_bundle::write_crick_params_file_data(class utility::io::ozstream &, const class utility::vector1<double, class std::allocator<double> > &, const double &, const double &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) –> void

pyrosetta.rosetta.protocols.helical_bundle.write_minor_helix_params(*args, **kwargs)

Overloaded function.

1. write_minor_helix_params(filename: str, r1: pyrosetta.rosetta.utility.vector1_double, omega1: float, z1: float, delta_omega1: pyrosetta.rosetta.utility.vector1_double, delta_z1: pyrosetta.rosetta.utility.vector1_double) -> None

Write out a crick_params file.

Variant for case of a single-residue repeating unit.

C++: protocols::helical_bundle::write_minor_helix_params(const class std::basic_string<char> &, const class utility::vector1<double, class std::allocator<double> > &, const double &, const double &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) –> void

2. write_minor_helix_params(filename: str, residues_per_repeat: int, atoms_per_residue: pyrosetta.rosetta.utility.vector1_unsigned_long, r1: pyrosetta.rosetta.utility.vector1_double, omega1: float, z1: float, delta_omega1: pyrosetta.rosetta.utility.vector1_double, delta_z1: pyrosetta.rosetta.utility.vector1_double) -> None

Write out a crick_params file.

Variant for case of a multi-residue repeating unit.

C++: protocols::helical_bundle::write_minor_helix_params(const class std::basic_string<char> &, const unsigned long &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<double, class std::allocator<double> > &, const double &, const double &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) –> void