chemprop/utils/utils.py

from __future__ import annotations

from enum import StrEnum
from typing import Iterable, Iterator

from rdkit import Chem


class EnumMapping(StrEnum):
    @classmethod
    def get(cls, name: str | EnumMapping) -> EnumMapping:
        if isinstance(name, cls):
            return name

        try:
            return cls[name.upper()]
        except KeyError:
            raise KeyError(
                f"Unsupported {cls.__name__} member! got: '{name}'. expected one of: {cls.keys()}"
            )

    @classmethod
    def keys(cls) -> Iterator[str]:
        return (e.name for e in cls)

    @classmethod
    def values(cls) -> Iterator[str]:
        return (e.value for e in cls)

    @classmethod
    def items(cls) -> Iterator[tuple[str, str]]:
        return zip(cls.keys(), cls.values())


def make_mol(smi: str, keep_h: bool, add_h: bool) -> Chem.Mol:
    """build an RDKit molecule from a SMILES string.

    Parameters
    ----------
    smi : str
        a SMILES string.
    keep_h : bool
        whether to keep hydrogens in the input smiles. This does not add hydrogens, it only keeps them if they are specified
    add_h : bool
        whether to add hydrogens to the molecule

    Returns
    -------
    Chem.Mol
        the RDKit molecule.
    """
    if keep_h:
        mol = Chem.MolFromSmiles(smi, sanitize=False)
        Chem.SanitizeMol(
            mol, sanitizeOps=Chem.SanitizeFlags.SANITIZE_ALL ^ Chem.SanitizeFlags.SANITIZE_ADJUSTHS
        )
    else:
        mol = Chem.MolFromSmiles(smi)

    return Chem.AddHs(mol) if add_h else mol


def pretty_shape(shape: Iterable[int]) -> str:
    """Make a pretty string from an input shape

    Example
    --------
    >>> X = np.random.rand(10, 4)
    >>> X.shape
    (10, 4)
    >>> pretty_shape(X.shape)
    '10 x 4'
    """
    return " x ".join(map(str, shape))