Source code for baybe.parameters.substance

"""Substance parameters."""

import gc
from functools import cached_property
from typing import Any

import pandas as pd
from attrs import define, field
from attrs.validators import deep_mapping, instance_of, min_len
from typing_extensions import override

from baybe.parameters.base import _DiscreteLabelLikeParameter
from baybe.parameters.enum import SubstanceEncoding
from baybe.parameters.validation import validate_decorrelation
from baybe.utils.basic import group_duplicate_values
from baybe.utils.dataframe import (
    add_noise_to_perturb_degenerate_rows,
    df_drop_single_value_columns,
    df_uncorrelated_features,
)

try:  # For python < 3.11, use the exceptiongroup backport
    ExceptionGroup
except NameError:
    from exceptiongroup import ExceptionGroup

Smiles = str
"""Type alias for SMILES strings."""




@define(frozen=True, slots=False)
class SubstanceParameter(_DiscreteLabelLikeParameter):
    """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.
    """

    # object variables
    data: dict[str, Smiles] = field(
        converter=lambda x: dict(sorted(x.items())),
        validator=deep_mapping(
            mapping_validator=min_len(2),
            key_validator=(instance_of(str), min_len(1)),
        ),
    )
    """A mapping that provides the SMILES strings for all available parameter values."""

    decorrelate: bool | float = field(default=True, validator=validate_decorrelation)
    """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 = field(
        default=SubstanceEncoding.MORDRED, converter=SubstanceEncoding
    )
    # See base class.

    kwargs_fingerprint: dict[str, Any] = field(
        factory=dict, validator=instance_of(dict)
    )
    """Keyword arguments passed to fingerprint generator."""

    kwargs_conformer: dict[str, Any] = field(factory=dict, validator=instance_of(dict))
    """Keyword arguments passed to conformer generator."""

    @data.validator
    def _validate_substance_data(  # noqa: DOC101, DOC103
        self, _: Any, data: dict[str, Smiles]
    ) -> None:
        """Validate that the substance data, provided as SMILES, is valid.

        Raises:
            ValueError: If one or more of the SMILES are invalid.
            ValueError: If the several entries represent the same substance.
        """
        from baybe.utils import chemistry

        # Check for invalid SMILES
        canonical_smiles = {}
        exceptions = []
        for name, smiles in data.items():
            try:
                canonical_smiles[name] = chemistry.get_canonical_smiles(smiles)
            except ValueError:
                exceptions.append(
                    ValueError(
                        f"The SMILES '{smiles}' for molecule '{name}' does "
                        f"not appear to be valid."
                    )
                )
        if exceptions:
            raise ExceptionGroup("invalid SMILES", exceptions)

        # Check for duplicate substances
        if groups := group_duplicate_values(canonical_smiles):
            exceptions = []
            for group, substances in groups.items():
                group_data = {s: data[s] for s in substances}
                exceptions.append(
                    ValueError(
                        f"The following entries all represent the same substance "
                        f"'{group}': {group_data}."
                    )
                )
            raise ExceptionGroup("duplicate substances", exceptions)

    @override
    @property
    def values(self) -> tuple:
        """Returns the labels of the given set of molecules."""
        return tuple(self.data.keys())

    @override
    @cached_property
    def comp_df(self) -> pd.DataFrame:
        from baybe.utils import chemistry

        vals = list(self.data.values())
        pref = self.name

        # Get the raw descriptors
        comp_df = chemistry.smiles_to_fingerprint_features(
            vals,
            encoding=self.encoding,
            prefix=pref,
            kwargs_conformer=self.kwargs_conformer,
            kwargs_fingerprint=self.kwargs_fingerprint,
        )

        # Drop NaN and constant columns
        comp_df = comp_df.loc[:, ~comp_df.isna().any(axis=0)]
        comp_df = df_drop_single_value_columns(comp_df)

        # Label the rows with the molecule names
        comp_df.index = pd.Index(self.values)

        # Get a decorrelated subset of the descriptors
        if self.decorrelate:
            if isinstance(self.decorrelate, bool):
                comp_df = df_uncorrelated_features(comp_df)
            else:
                comp_df = df_uncorrelated_features(comp_df, threshold=self.decorrelate)

        # Add noise to degenerate rows if present
        add_noise_to_perturb_degenerate_rows(comp_df)

        return comp_df



# Collect leftover original slotted classes processed by `attrs.define`
gc.collect()