carbohydrates

Bindings for core::scoring::carbohydrates namespace

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

Bases: pybind11_object

Struct for CHI-based dihedral sampling.

Jared Adolf-Bryfogle (jadolfbr.com)

property angles

property linkage_type

property probabilities

property step_size

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

Bases: 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.

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

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

Bases: 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.

Members:

FIRST_LINK_TYPE

ALPHA_LINKS

BETA_LINKS

_2AX_3EQ_4AX_LINKS

_2EQ_3AX_4EQ_LINKS

ALPHA6_LINKS

BETA6_LINKS

N_LINK_TYPES

LINKAGE_NA

ALPHA6_LINKS = <CHIEnergyFunctionLinkageType.ALPHA6_LINKS: 5>

ALPHA_LINKS = <CHIEnergyFunctionLinkageType.FIRST_LINK_TYPE: 1>

BETA6_LINKS = <CHIEnergyFunctionLinkageType.BETA6_LINKS: 6>

BETA_LINKS = <CHIEnergyFunctionLinkageType.BETA_LINKS: 2>

FIRST_LINK_TYPE = <CHIEnergyFunctionLinkageType.FIRST_LINK_TYPE: 1>

LINKAGE_NA = <CHIEnergyFunctionLinkageType.LINKAGE_NA: 7>

N_LINK_TYPES = <CHIEnergyFunctionLinkageType.BETA6_LINKS: 6>

_2AX_3EQ_4AX_LINKS = <CHIEnergyFunctionLinkageType._2AX_3EQ_4AX_LINKS: 3>

_2EQ_3AX_4EQ_LINKS = <CHIEnergyFunctionLinkageType._2EQ_3AX_4EQ_LINKS: 4>

property name

property value

class pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData

Bases: pybind11_object

Struct for Omega-Preference dihedral sampling.

Jared Adolf-Bryfogle (jadolfbr.com)

property angles

property preference_type

property probabilities

property step_size

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

Bases: 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.

Members:

ANTI

GAUCHE_EFFECT

N_OMEGA_PREFERENCE_TYPES

PREFERENCE_NA

ANTI = <OmegaPreferenceType.ANTI: 1>

GAUCHE_EFFECT = <OmegaPreferenceType.GAUCHE_EFFECT: 2>

N_OMEGA_PREFERENCE_TYPES = <OmegaPreferenceType.GAUCHE_EFFECT: 2>

PREFERENCE_NA = <OmegaPreferenceType.PREFERENCE_NA: 3>

property name

property value

class pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction

Bases: pybind11_object

TBD

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

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 psi 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_std_allocator_std_pair_const_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 std::string &) –> 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> > > > >