carbohydrates

Bindings for core::scoring::carbohydrates namespace

class pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData

Bases: pybind11_builtins.pybind11_object

Struct for CHI-based dihedral sampling.

Jared Adolf-Bryfogle (jadolfbr.com)

__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__(self: pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData) → 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).

class pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction

Bases: pybind11_builtins.pybind11_object

This is an implementation of the “CarboHydrate Intrinsic” (CHI) energy function developed by Woods Lab. The Gaussian parameters for the function depend on whether the glycosidic bond in question is a phi or psi angle. The parameters further depend on if the phi angles are at alpha or beta linkages and on if the psi angles are at ->2-axial, ->3-equatorial, or ->4-axial OR ->2-equatorial, ->3-axial, or ->4-equatorial linkages. If at exocyclic linkages, psi instead depends on whether the linkage is alpha or beta. Functions for omega angles and (2->3) and (2->6) linkages (found in ketoses) could not be developed with QM, so knowledge-based functions were created instead.

__call__(self: pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction, type: pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType, x: float) → float

C++: core::scoring::carbohydrates::CHIEnergyFunction::operator()(enum core::scoring::carbohydrates::CHIEnergyFunctionLinkageType, 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__(self: pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction) → 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.core.scoring.carbohydrates.CHIEnergyFunction, : pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction) → pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction

C++: core::scoring::carbohydrates::CHIEnergyFunction::operator=(const class core::scoring::carbohydrates::CHIEnergyFunction &) –> class core::scoring::carbohydrates::CHIEnergyFunction &

evaluate_derivative(self: pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction, type: pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType, x: float) → float

C++: core::scoring::carbohydrates::CHIEnergyFunction::evaluate_derivative(enum core::scoring::carbohydrates::CHIEnergyFunctionLinkageType, double) const –> double

get_sampling_data(self: pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction, type: pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType) → pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData

C++: core::scoring::carbohydrates::CHIEnergyFunction::get_sampling_data(enum core::scoring::carbohydrates::CHIEnergyFunctionLinkageType) const –> const struct core::scoring::carbohydrates::CHIDihedralSamplingData &

sampling_data_setup(*args, **kwargs)

Overloaded function.

1. sampling_data_setup(self: pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction) -> bool

C++: core::scoring::carbohydrates::CHIEnergyFunction::sampling_data_setup() const –> bool

2. sampling_data_setup(self: pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction, linkage_type: pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType) -> bool

C++: core::scoring::carbohydrates::CHIEnergyFunction::sampling_data_setup(enum core::scoring::carbohydrates::CHIEnergyFunctionLinkageType) const –> bool

setup_for_sampling(*args, **kwargs)

Overloaded function.

1. setup_for_sampling(self: pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction) -> None
2. setup_for_sampling(self: pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction, step_size: float) -> None

Set up CHI sampling data.

C++: core::scoring::carbohydrates::CHIEnergyFunction::setup_for_sampling(double) –> void

class pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType

Bases: pybind11_builtins.pybind11_object

Labels for the CHI Energy Function linkage type of the carbohydrate phi or psi angle.

The CHI energy functions depend on the type of linkage.

Parameters for the Gaussian functions that compose the CHI Energy Functions are stored in a vector indexed by these labels.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(*args, **kwargs)

Overloaded function.

1. __eq__(self: pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType, arg0: pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType) -> bool
2. __eq__(self: pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType, arg0: int) -> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType) → tuple

__gt__

Return self>value.

__hash__(self: pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType) → int

__init__(self: pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType, 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.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType) → int

__le__

Return self<=value.

__lt__

Return self<value.

__ne__(*args, **kwargs)

Overloaded function.

1. __ne__(self: pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType, arg0: pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType) -> bool
2. __ne__(self: pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType, 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.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType) → str

__setattr__

Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType, 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.core.scoring.carbohydrates.OmegaPreferenceSamplingData

Bases: pybind11_builtins.pybind11_object

Struct for Omega-Preference dihedral sampling.

Jared Adolf-Bryfogle (jadolfbr.com)

__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__(self: pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData) → 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).

class pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType

Bases: pybind11_builtins.pybind11_object

Labels for the omega torsion preference type used to select the proper OmegaPreferencesFunction form.

In saccharide residues where the hydroxyl group of the carbon atom two carbons previous to the exocyclic

carbon is equatorial, the “gauche effect” occurs, in which the exocyclic torsion angle prefers one of the two gauche orientations instead of the expected anti configuration.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(*args, **kwargs)

Overloaded function.

1. __eq__(self: pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType, arg0: pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType) -> bool
2. __eq__(self: pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType, arg0: int) -> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType) → tuple

__gt__

Return self>value.

__hash__(self: pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType) → int

__init__(self: pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType, 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.core.scoring.carbohydrates.OmegaPreferenceType) → int

__le__

Return self<=value.

__lt__

Return self<value.

__ne__(*args, **kwargs)

Overloaded function.

1. __ne__(self: pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType, arg0: pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType) -> bool
2. __ne__(self: pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType, 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.core.scoring.carbohydrates.OmegaPreferenceType) → str

__setattr__

Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType, 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.core.scoring.carbohydrates.OmegaPreferencesFunction

Bases: pybind11_builtins.pybind11_object

TBD

__call__(self: pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction, preference: pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType, x: float) → float

C++: core::scoring::carbohydrates::OmegaPreferencesFunction::operator()(enum core::scoring::carbohydrates::OmegaPreferenceType, 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.core.scoring.carbohydrates.OmegaPreferencesFunction) -> None
2. __init__(self: pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction, arg0: pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction) -> 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).

evaluate_derivative(self: pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction, preference: pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType, x: float) → float

C++: core::scoring::carbohydrates::OmegaPreferencesFunction::evaluate_derivative(enum core::scoring::carbohydrates::OmegaPreferenceType, double) const –> double

get_sampling_data(self: pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction, type: pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType) → pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData

C++: core::scoring::carbohydrates::OmegaPreferencesFunction::get_sampling_data(const enum core::scoring::carbohydrates::OmegaPreferenceType) const –> const struct core::scoring::carbohydrates::OmegaPreferenceSamplingData &

sampling_data_setup(*args, **kwargs)

Overloaded function.

1. sampling_data_setup(self: pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction) -> bool

C++: core::scoring::carbohydrates::OmegaPreferencesFunction::sampling_data_setup() const –> bool

2. sampling_data_setup(self: pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction, linkage_type: pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType) -> bool

C++: core::scoring::carbohydrates::OmegaPreferencesFunction::sampling_data_setup(const enum core::scoring::carbohydrates::OmegaPreferenceType) const –> bool

setup_for_sampling(*args, **kwargs)

Overloaded function.

1. setup_for_sampling(self: pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction) -> None
2. setup_for_sampling(self: pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction, step_size: float) -> None

Set up CHI sampling data.

C++: core::scoring::carbohydrates::OmegaPreferencesFunction::setup_for_sampling(double) –> void

pyrosetta.rosetta.core.scoring.carbohydrates.get_CHI_energy_function_linkage_type_for_phi_for_residue_in_pose(pose: pyrosetta.rosetta.core.pose.Pose, rsd_num: int) → pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType

Get the CHI Energy Function linkage type for phi for a particular residue.

C++: core::scoring::carbohydrates::get_CHI_energy_function_linkage_type_for_phi_for_residue_in_pose(const class core::pose::Pose &, unsigned long) –> enum core::scoring::carbohydrates::CHIEnergyFunctionLinkageType

pyrosetta.rosetta.core.scoring.carbohydrates.get_CHI_energy_function_linkage_type_for_psi_for_residue_in_pose(pose: pyrosetta.rosetta.core.pose.Pose, rsd_num: int) → pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType

Get the CHI Energy Function linkage type for phi for a particular residue.

C++: core::scoring::carbohydrates::get_CHI_energy_function_linkage_type_for_psi_for_residue_in_pose(const class core::pose::Pose &, unsigned long) –> enum core::scoring::carbohydrates::CHIEnergyFunctionLinkageType

pyrosetta.rosetta.core.scoring.carbohydrates.get_CHI_energy_function_linkage_type_for_residue_in_pose(torsion: pyrosetta.rosetta.core.id.MainchainTorsionType, pose: pyrosetta.rosetta.core.pose.Pose, rsd_num: int) → pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType

Get the CHI Energy Function linkage type for the given torsion angle of a particular residue.

C++: core::scoring::carbohydrates::get_CHI_energy_function_linkage_type_for_residue_in_pose(enum core::id::MainchainTorsionType, const class core::pose::Pose &, unsigned long) –> enum core::scoring::carbohydrates::CHIEnergyFunctionLinkageType

pyrosetta.rosetta.core.scoring.carbohydrates.get_omega_preference_for_residue_in_pose(pose: pyrosetta.rosetta.core.pose.Pose, rsd_num: int) → pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType

Get the omega preference for a particular residue.

C++: core::scoring::carbohydrates::get_omega_preference_for_residue_in_pose(const class core::pose::Pose &, unsigned long) –> enum core::scoring::carbohydrates::OmegaPreferenceType

pyrosetta.rosetta.core.scoring.carbohydrates.read_Gaussian_parameters_from_database_file(filename: str) → pyrosetta.rosetta.std.map_char_utility_vector1_double_std_allocator_double_t

Return a table of Gaussian parameters read from a database file.

C++: core::scoring::carbohydrates::read_Gaussian_parameters_from_database_file(const class std::basic_string<char> &) –> class std::map<char, class utility::vector1<double, class std::allocator<double> >, struct std::less<char>, class std::allocator<struct std::pair<const char, class utility::vector1<double, class std::allocator<double> > > > >