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RepEngineBase Class Documentation

Module: rep_engine_base

Purpose

RepEngineBase is an abstract base class for molecular representation engines. It defines a standard interface and utilities for computing molecular representations from a list of molecules (e.g., SMILES strings), particularly in batched processing. This class is intended to be subclassed, with core functionality like preprocessing and representation computation implemented in derived classes.

Attributes

  • engine (str):
    Name of the representation engine. Typically defined in a subclass or passed during instantiation.

  • rep (str):
    Type of molecular representation (e.g., 'fingerprint', 'embedding').

  • properties (dict):
    A deep copy of the instance's dictionary at initialization. Captures configuration state.

Constructor

def __init__(self, rep: str, **args)

Parameters: - rep (str): Type of molecular representation. - **args (dict): Additional configuration options stored as attributes.

Effect:
Initializes the object, stores rep, and adds all additional keyword arguments to the instance. Also creates a deep copy of all these attributes in self.properties for serialization.

Public Methods

compute_reps

def compute_reps(self, mols: List[str], verbose: Optional[bool] = False, batch_size: Optional[int] = 12) -> Union[np.ndarray, List[np.ndarray]]

Description:
Computes molecular representations in batches using _preprocess_batch and _rep_batch.

Parameters: - mols (List[str]): List of molecular inputs (e.g., SMILES strings). - verbose (bool, optional): If True, shows a progress bar. - batch_size (int, optional): Number of molecules per batch.

Returns:
- np.ndarray if average_pooling is True or unset. - List[np.ndarray] if average_pooling is explicitly set to False.

dim

def dim(self) -> int

Description:
Abstract method. Must return the dimensionality of the computed representation.

Raises:
- NotImplementedError

_rep_batch

def _rep_batch(self, batch: List[str]) -> np.ndarray

Description:
Abstract method. Must compute and return the representation for a batch of molecules.

Raises:
- NotImplementedError

_preprocess_batch

def _preprocess_batch(self, batch: List[str]) -> List[str]

Description:
Abstract method. Must return a preprocessed version of the batch for representation.

Raises:
- NotImplementedError

save

def save(self, filename: str)

Description:
Serializes and saves the engine’s properties to a YAML file.

Parameters: - filename (str): Destination path for the YAML file.

Design Notes

  • This class provides batch processing support and optional average pooling control.
  • The use of batched from itertools supports Python 3.10+ but also includes a fallback implementation for older versions.
  • Intended for extension: Subclasses must implement _rep_batch, _preprocess_batch, and dim.