SubstanceParameter

class baybe.parameters.substance.SubstanceParameter[source]

Bases: DiscreteParameter

Generic substances that are treated with cheminformatics descriptors.

Only a decorrelated subset of descriptors should be used as otherwise this can result in a large number of features. For a handful of molecules, keeping only descriptors that have a maximum correlation of 0.7 reduces the number of descriptors to about 5-20. The number might be substantially higher with more labels given.

Public methods

__init__(name, data[, decorrelate, ...])

Method generated by attrs for class SubstanceParameter.

from_dict(dictionary)

Create an object from its dictionary representation.

from_json(string)

Create an object from its JSON representation.

is_in_range(item)

Return whether an item is within the parameter range.

summary()

Return a custom summarization of the parameter.

to_dict()

Create an object's dictionary representation.

to_json()

Create an object's JSON representation.

to_searchspace()

Create a one-dimensional search space from the parameter.

to_subspace()

Create a one-dimensional search space from the parameter.

transform(series, /)

Transform parameter values to computational representation.

Public attributes and properties

comp_df

Return the computational representation of the parameter.

comp_rep_columns

The columns spanning the computational representation.

is_continuous

Boolean indicating if this is a continuous parameter.

is_discrete

Boolean indicating if this is a discrete parameter.

is_numerical

Class variable encoding whether this parameter is numeric.

values

Returns the labels of the given set of molecules.

data

A mapping that provides the SMILES strings for all available parameter values.

decorrelate

Specifies the used decorrelation mode for the parameter encoding.

encoding

An optional encoding for the parameter.

kwargs_fingerprint

Keyword arguments passed to fingerprint generator.

kwargs_conformer

Keyword arguments passed to conformer generator.

name

The name of the parameter

__init__(name: str, data, decorrelate: bool | float = True, encoding=SubstanceEncoding.MORDRED, kwargs_fingerprint: dict[str, Any] = NOTHING, kwargs_conformer: dict[str, Any] = NOTHING)

Method generated by attrs for class SubstanceParameter.

For details on the parameters, see Public attributes and properties.

classmethod from_dict(dictionary: dict)

Create an object from its dictionary representation.

Parameters:

dictionary (dict) – The dictionary representation.

Return type:

TypeVar(_T)

Returns:

The reconstructed object.

classmethod from_json(string: str)

Create an object from its JSON representation.

Parameters:

string (str) – The JSON representation of the object.

Return type:

TypeVar(_T)

Returns:

The reconstructed object.

is_in_range(item: Any)

Return whether an item is within the parameter range.

Parameters:

item (Any) – The item to be checked.

Return type:

bool

Returns:

True if the item is within the parameter range, False otherwise.

summary()

Return a custom summarization of the parameter.

Return type:

dict

to_dict()

Create an object’s dictionary representation.

Return type:

dict

to_json()

Create an object’s JSON representation.

Return type:

str

Returns:

The JSON representation as a string.

to_searchspace()

Create a one-dimensional search space from the parameter.

Return type:

SearchSpace

to_subspace()

Create a one-dimensional search space from the parameter.

Return type:

SubspaceDiscrete

transform(series: Series, /)

Transform parameter values to computational representation.

Parameters:

series (Series) – The parameter values in experimental representation to be transformed.

Return type:

DataFrame

Returns:

A series containing the transformed values. The series name matches that of the input.

property comp_df: DataFrame

Return the computational representation of the parameter.

property comp_rep_columns: tuple[str, ...]

The columns spanning the computational representation.

data: dict[str, str]

A mapping that provides the SMILES strings for all available parameter values.

decorrelate: bool | float

Specifies the used decorrelation mode for the parameter encoding.

  • False: The encoding is used as is.

  • True: The encoding is decorrelated using a default correlation threshold.

  • float in (0, 1): The encoding is decorrelated using the specified threshold.

encoding: SubstanceEncoding

An optional encoding for the parameter.

property is_continuous: bool

Boolean indicating if this is a continuous parameter.

property is_discrete: bool

Boolean indicating if this is a discrete parameter.

is_numerical: ClassVar[bool] = False

Class variable encoding whether this parameter is numeric.

kwargs_conformer: dict[str, Any]

Keyword arguments passed to conformer generator.

kwargs_fingerprint: dict[str, Any]

Keyword arguments passed to fingerprint generator.

name: str

The name of the parameter

property values: tuple

Returns the labels of the given set of molecules.