bb_sampler

Bindings for protocols::simple_moves::bb_sampler namespace

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

Bases: 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.

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.BBDihedralSampler2D

Bases: BBDihedralSamplerBase

assign(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler2D, : pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler2D) pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler2D

C++: protocols::simple_moves::bb_sampler::BBDihedralSampler2D::operator=(const class protocols::simple_moves::bb_sampler::BBDihedralSampler2D &) –> class protocols::simple_moves::bb_sampler::BBDihedralSampler2D &

clone(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler2D) pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler2D

C++: protocols::simple_moves::bb_sampler::BBDihedralSampler2D::clone() const –> class std::shared_ptr<class protocols::simple_moves::bb_sampler::BBDihedralSampler2D>

get_2d_torsion(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler2D, pose: pyrosetta.rosetta.core.pose.Pose, resnum: int, : Tuple[pyrosetta.rosetta.core.id.MainchainTorsionType, float]) float

Get a torsion angle dependant on another torsion and torsion angle.

C++: protocols::simple_moves::bb_sampler::BBDihedralSampler2D::get_2d_torsion(const class core::pose::Pose &, unsigned long, struct std::pair<enum core::id::MainchainTorsionType, double>) const –> double

get_name(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler2D) str

C++: protocols::simple_moves::bb_sampler::BBDihedralSampler2D::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_2D_torsion_to_pose(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler2D, pose: pyrosetta.rosetta.core.pose.Pose, resnum: int, : Tuple[pyrosetta.rosetta.core.id.MainchainTorsionType, float]) None

C++: protocols::simple_moves::bb_sampler::BBDihedralSampler2D::set_2D_torsion_to_pose(class core::pose::Pose &, unsigned long, struct std::pair<enum core::id::MainchainTorsionType, double>) const –> 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_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.BBDihedralSampler3D

Bases: BBDihedralSamplerBase

assign(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler3D, : pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler3D) pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler3D

C++: protocols::simple_moves::bb_sampler::BBDihedralSampler3D::operator=(const class protocols::simple_moves::bb_sampler::BBDihedralSampler3D &) –> class protocols::simple_moves::bb_sampler::BBDihedralSampler3D &

clone(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler3D) pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler3D

C++: protocols::simple_moves::bb_sampler::BBDihedralSampler3D::clone() const –> class std::shared_ptr<class protocols::simple_moves::bb_sampler::BBDihedralSampler3D>

get_3d_torsion(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler3D, pose: pyrosetta.rosetta.core.pose.Pose, resnum: int, : Tuple[pyrosetta.rosetta.core.id.MainchainTorsionType, float], : Tuple[pyrosetta.rosetta.core.id.MainchainTorsionType, float]) float
Get a torsion angle dependant on two other torsions and torsion angles.

dependendant types and angles are the std::pair.

C++: protocols::simple_moves::bb_sampler::BBDihedralSampler3D::get_3d_torsion(const class core::pose::Pose &, unsigned long, struct std::pair<enum core::id::MainchainTorsionType, double>, struct std::pair<enum core::id::MainchainTorsionType, double>) const –> double

get_name(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler3D) str

C++: protocols::simple_moves::bb_sampler::BBDihedralSampler3D::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_3D_torsion_to_pose(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler3D, pose: pyrosetta.rosetta.core.pose.Pose, resnum: int, : Tuple[pyrosetta.rosetta.core.id.MainchainTorsionType, float], : Tuple[pyrosetta.rosetta.core.id.MainchainTorsionType, float]) None

C++: protocols::simple_moves::bb_sampler::BBDihedralSampler3D::set_3D_torsion_to_pose(class core::pose::Pose &, unsigned long, struct std::pair<enum core::id::MainchainTorsionType, double>, struct std::pair<enum core::id::MainchainTorsionType, double>) const –> 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_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_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 core::Size (due to waay too many in sugars) - we can now remove the ‘BB’ part of this whole thing.

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.BBDihedralSamplerND

Bases: BBDihedralSamplerBase

assign(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerND, : pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerND) pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerND

C++: protocols::simple_moves::bb_sampler::BBDihedralSamplerND::operator=(const class protocols::simple_moves::bb_sampler::BBDihedralSamplerND &) –> class protocols::simple_moves::bb_sampler::BBDihedralSamplerND &

clone(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerND) pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerND

C++: protocols::simple_moves::bb_sampler::BBDihedralSamplerND::clone() const –> class std::shared_ptr<class protocols::simple_moves::bb_sampler::BBDihedralSamplerND>

get_name(self: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSamplerND) str

C++: protocols::simple_moves::bb_sampler::BBDihedralSamplerND::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.BBSampleType

Bases: pybind11_object

Members:

minima

probability

minima = <BBSampleType.minima: 1>
property name
probability = <BBSampleType.probability: 2>
property value
class pyrosetta.rosetta.protocols.simple_moves.bb_sampler.SmallBBSampler

Bases: 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 )

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.

  1. 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

  1. 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

  1. 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: BBDihedralSampler

Sample dihdrals using sugar bb data.

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