bb_sampler¶

Bindings for protocols::simple_moves::bb_sampler namespace

class pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler¶

Bases: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase

This class functions to hold, access, sample on, and set independent and dependent dihedral data. It is an abstract base class for particular types of data. It should eventually be moved out of here.

get_torsion functions should give either the minima on a set of data or sample via the probability.

__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.

__init__(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler) -> None
__init__(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler, arg0: pyrosetta.rosetta.core.id.MainchainTorsionType) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler, torsion_type: pyrosetta.rosetta.core.id.MainchainTorsionType, sampling_type: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBSampleType) -> None
__init__(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler, arg0: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler) -> 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.simple_moves.bb_sampler.BBDihedralSampler, : pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler) → pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler¶: C++: protocols::simple_moves::bb_sampler::BBDihedralSampler::operator=(const class protocols::simple_moves::bb_sampler::BBDihedralSampler &) –> class protocols::simple_moves::bb_sampler::BBDihedralSampler &

clone(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler) → pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler¶: C++: protocols::simple_moves::bb_sampler::BBDihedralSampler::clone() const –> class std::shared_ptr<class protocols::simple_moves::bb_sampler::BBDihedralSampler>

get_name(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler) → str¶: C++: protocols::simple_moves::bb_sampler::BBDihedralSampler::get_name() const –> std::string

get_torsion(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler, pose: pyrosetta.rosetta.core.pose.Pose, resnum: int) → float¶: C++: protocols::simple_moves::bb_sampler::BBDihedralSampler::get_torsion(const class core::pose::Pose &, unsigned long) const –> double

get_torsion_type(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase) → int¶: C++: protocols::simple_moves::bb_sampler::BBDihedralSamplerBase::get_torsion_type() const –> unsigned long

set_sample_type(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase, sampling_type: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBSampleType) → None¶

Set the sampling type. Default is to sample probabilistically on the data.

C++: protocols::simple_moves::bb_sampler::BBDihedralSamplerBase::set_sample_type(enum protocols::simple_moves::bb_sampler::BBSampleType) –> void

set_torsion_to_pose(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler, pose: pyrosetta.rosetta.core.pose.Pose, resnum: int) → None¶

Set torsions to pose

C++: protocols::simple_moves::bb_sampler::BBDihedralSampler::set_torsion_to_pose(class core::pose::Pose &, unsigned long) const –> void

set_torsion_type(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase, torsion_type: pyrosetta.rosetta.core.id.MainchainTorsionType) → None¶

Set the torsion type we will be querying.

C++: protocols::simple_moves::bb_sampler::BBDihedralSamplerBase::set_torsion_type(enum core::id::MainchainTorsionType) –> void

class pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase¶

Bases: pybind11_builtins.pybind11_object

This class functions to hold, access, sample on, and set independent and dependent dihedral data. It is an abstract base class for particular types of data.

get_torsion functions should give either the minima on a set of data or sample via the probability If you are subclassing, you do not necessarily need to use the BBSampleType.

Feel free to implement more types. See the SugarBBSampler and RangedBBSampler as examples.

Technically - with now storing the torsion_types as Size (due to waay too many in sugars) - we can now remove the ‘BB’ part of this whole thing.

__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.

__init__(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase) -> None
__init__(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase, arg0: pyrosetta.rosetta.core.id.MainchainTorsionType) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase, torsion_type: pyrosetta.rosetta.core.id.MainchainTorsionType, sampling_type: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBSampleType) -> None
__init__(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase, arg0: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase) -> 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.simple_moves.bb_sampler.BBDihedralSamplerBase, : pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase) → pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase¶: C++: protocols::simple_moves::bb_sampler::BBDihedralSamplerBase::operator=(const class protocols::simple_moves::bb_sampler::BBDihedralSamplerBase &) –> class protocols::simple_moves::bb_sampler::BBDihedralSamplerBase &

clone(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase) → pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase¶: C++: protocols::simple_moves::bb_sampler::BBDihedralSamplerBase::clone() const –> class std::shared_ptr<class protocols::simple_moves::bb_sampler::BBDihedralSamplerBase>

get_name(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase) → str¶: C++: protocols::simple_moves::bb_sampler::BBDihedralSamplerBase::get_name() const –> std::string

get_torsion_type(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase) → int¶: C++: protocols::simple_moves::bb_sampler::BBDihedralSamplerBase::get_torsion_type() const –> unsigned long

set_sample_type(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase, sampling_type: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBSampleType) → None¶

Set the sampling type. Default is to sample probabilistically on the data.

C++: protocols::simple_moves::bb_sampler::BBDihedralSamplerBase::set_sample_type(enum protocols::simple_moves::bb_sampler::BBSampleType) –> void

set_torsion_type(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase, torsion_type: pyrosetta.rosetta.core.id.MainchainTorsionType) → None¶

Set the torsion type we will be querying.

C++: protocols::simple_moves::bb_sampler::BBDihedralSamplerBase::set_torsion_type(enum core::id::MainchainTorsionType) –> void

class pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler¶

Bases: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler

A bb sampler that samples within a range of a starting angle. Similar to small mover. Samples an angle +/- the current angle. If angle max is not set, will sample any angle.

new_angle = old_angle +/- ( angle_max/2 )

__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.

__init__(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler) -> None
__init__(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler, all_ss_angle_max: float) -> None
__init__(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler, torsion_type: pyrosetta.rosetta.core.id.MainchainTorsionType) -> None
__init__(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler, torsion_type: pyrosetta.rosetta.core.id.MainchainTorsionType, all_ss_angle_max: float) -> None
__init__(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler, arg0: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler) -> 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.simple_moves.bb_sampler.SmallBBSampler, : pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler) → pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler¶: C++: protocols::simple_moves::bb_sampler::SmallBBSampler::operator=(const class protocols::simple_moves::bb_sampler::SmallBBSampler &) –> class protocols::simple_moves::bb_sampler::SmallBBSampler &

clone(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler) → pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler¶: C++: protocols::simple_moves::bb_sampler::SmallBBSampler::clone() const –> class std::shared_ptr<class protocols::simple_moves::bb_sampler::SmallBBSampler>

get_angle_max(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler, type: str) → float¶

Gets the max angle of perturbation for residues with <type>

secondary structure. (<type> must be ‘H’, ‘E’, or ‘L’.)

Example:: bbmover.angle_max(‘H’)
See also:: ShearMover SmallMover

C++: protocols::simple_moves::bb_sampler::SmallBBSampler::get_angle_max(const char) const –> double

get_name(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler) → str¶: C++: protocols::simple_moves::bb_sampler::SmallBBSampler::get_name() const –> std::string

get_torsion(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler, pose: pyrosetta.rosetta.core.pose.Pose, resnum: int) → float¶: C++: protocols::simple_moves::bb_sampler::SmallBBSampler::get_torsion(const class core::pose::Pose &, unsigned long) const –> double

get_torsion_type(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase) → int¶: C++: protocols::simple_moves::bb_sampler::BBDihedralSamplerBase::get_torsion_type() const –> unsigned long

set_angle_max(*args, **kwargs)¶

Overloaded function.

set_angle_max(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler, angle: float) -> None

Sets the maximum angle of perturbation, independent of

secondary structure. new_angle = old_angle +/- ( angle_max/2 )

Example:: bbmover.angle_max(25)
See also:: ShearMover SmallMover

C++: protocols::simple_moves::bb_sampler::SmallBBSampler::set_angle_max(const double) –> void

set_angle_max(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler, type: str, angle: float) -> None

Sets the max angle of perturbation for residues with <type>

secondary structure. (<type> must be ‘H’, ‘E’, or ‘L’.) new_angle = old_angle +/- ( angle_max/2 )

Example:: bbmover.angle_max(‘H’, 25)
See also:: ShearMover SmallMover

C++: protocols::simple_moves::bb_sampler::SmallBBSampler::set_angle_max(const char, const double) –> void

set_angle_max(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler, angle_max_in: pyrosetta.rosetta.std.map_char_double) -> None

Sets the max angle of perturbation, for secondary structures: ‘H’, ‘E’, and ‘L’. new_angle = old_angle +/- ( angle_max/2 )

C++: protocols::simple_moves::bb_sampler::SmallBBSampler::set_angle_max(class std::map<char, double, struct std::less<char>, class std::allocator<struct std::pair<const char, double> > >) –> void

set_sample_type(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase, sampling_type: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBSampleType) → None¶

Set the sampling type. Default is to sample probabilistically on the data.

C++: protocols::simple_moves::bb_sampler::BBDihedralSamplerBase::set_sample_type(enum protocols::simple_moves::bb_sampler::BBSampleType) –> void

set_torsion_to_pose(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler, pose: pyrosetta.rosetta.core.pose.Pose, resnum: int) → None¶: C++: protocols::simple_moves::bb_sampler::SmallBBSampler::set_torsion_to_pose(class core::pose::Pose &, unsigned long) const –> void

set_torsion_type(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase, torsion_type: pyrosetta.rosetta.core.id.MainchainTorsionType) → None¶

Set the torsion type we will be querying.

C++: protocols::simple_moves::bb_sampler::BBDihedralSamplerBase::set_torsion_type(enum core::id::MainchainTorsionType) –> void

class pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler¶

Bases: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler

Sample dihdrals using sugar bb data.

__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.

__init__(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler) -> None
__init__(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler, arg0: pyrosetta.rosetta.core.id.MainchainTorsionType) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler, arg0: pyrosetta.rosetta.core.id.MainchainTorsionType, arg1: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBSampleType) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler, torsion_type: pyrosetta.rosetta.core.id.MainchainTorsionType, sampling_type: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBSampleType, sampling_step_size: float) -> None
__init__(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler, arg0: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler) -> 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.simple_moves.bb_sampler.SugarBBSampler, : pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler) → pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler¶: C++: protocols::simple_moves::bb_sampler::SugarBBSampler::operator=(const class protocols::simple_moves::bb_sampler::SugarBBSampler &) –> class protocols::simple_moves::bb_sampler::SugarBBSampler &

clone(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler) → pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler¶: C++: protocols::simple_moves::bb_sampler::SugarBBSampler::clone() const –> class std::shared_ptr<class protocols::simple_moves::bb_sampler::SugarBBSampler>

get_name(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler) → str¶: C++: protocols::simple_moves::bb_sampler::SugarBBSampler::get_name() const –> std::string

get_torsion(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler, pose: pyrosetta.rosetta.core.pose.Pose, resnum: int) → float¶: C++: protocols::simple_moves::bb_sampler::SugarBBSampler::get_torsion(const class core::pose::Pose &, unsigned long) const –> double

get_torsion_type(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase) → int¶: C++: protocols::simple_moves::bb_sampler::BBDihedralSamplerBase::get_torsion_type() const –> unsigned long

name(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler) → str¶: C++: protocols::simple_moves::bb_sampler::SugarBBSampler::name() const –> std::string

set_sample_type(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase, sampling_type: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBSampleType) → None¶

Set the sampling type. Default is to sample probabilistically on the data.

C++: protocols::simple_moves::bb_sampler::BBDihedralSamplerBase::set_sample_type(enum protocols::simple_moves::bb_sampler::BBSampleType) –> void

set_torsion_to_pose(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SugarBBSampler, pose: pyrosetta.rosetta.core.pose.Pose, resnum: int) → None¶

Set torsions to pose

C++: protocols::simple_moves::bb_sampler::SugarBBSampler::set_torsion_to_pose(class core::pose::Pose &, unsigned long) const –> void

set_torsion_type(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerBase, torsion_type: pyrosetta.rosetta.core.id.MainchainTorsionType) → None¶

Set the torsion type we will be querying.

C++: protocols::simple_moves::bb_sampler::BBDihedralSamplerBase::set_torsion_type(enum core::id::MainchainTorsionType) –> void