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RepEngineFP — Fingerprint Representation Engine

Module: autopeptideml.reps.fps
Inherits from: RepEngineBase

Overview

RepEngineFP computes fixed-length molecular fingerprint bit vectors using RDKit. It supports Extended-Connectivity Fingerprints (ECFP / Morgan), Feature-class Fingerprints (FCFP), and peptide-specific fingerprints via PepFuNN.

Requires: pip install rdkit
PepFuNN fingerprints additionally require: pip install git+https://github.com/novonordisk-research/pepfunn

Attributes

Attribute Type Description
engine str Fixed to 'fp'.
nbits int Fingerprint bit-vector length.
radius int Neighbourhood radius for the Morgan algorithm.
name str Auto-generated identifier in the form fp-<rep>-<nbits>-<radius>.
generator object RDKit fingerprint generator instance (or PepFunn_Generator for PepFuNN).
count bool If True, uses count-simulation fingerprints instead of binary.

Constructor

RepEngineFP(rep: str, nbits: int, radius: int)
Parameter Type Description
rep str Fingerprint type. Accepted values: 'ecfp', 'ecfp-count', 'morgan', 'fcfp', 'fcfp-count', 'pepfunn'.
nbits int Number of bits in the fingerprint vector (e.g. 1024, 2048).
radius int Morgan radius (e.g. 2 for ECFP4, 4 for ECFP8).

Methods

compute_reps (inherited)

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

Compute fingerprints for a list of SMILES strings. Returns an array of shape (n_mols, nbits).

dim

dim() -> int

Returns self.nbits.

_preprocess_batch

_preprocess_batch(batch: List[str]) -> List[str]

For standard fingerprints, returns the batch unchanged. For PepFuNN fingerprints, converts SMILES to BILN notation using the SmilesToBiln transformer.

_rep_batch

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

Converts each SMILES to an RDKit Mol object and computes the fingerprint. Invalid molecules (where MolFromSmiles returns None) produce zero vectors of length nbits.

_load_generator

_load_generator(rep: str) -> object

Instantiates the appropriate RDKit generator based on rep:

rep value Generator
'ecfp' / 'morgan' rdFingerprintGenerator.GetMorganGenerator
'ecfp-count' GetMorganGenerator with countSimulation=True
'fcfp' GetMorganGenerator with GetMorganFeatureAtomInvGen()
'pepfunn' PepFunn_Generator

Representation Shortcuts in build_models

When passing reps to AutoPeptideML.build_models, fingerprints can be specified as:

Format Example Meaning
<name> 'ecfp' Uses default radius 8, 1024 bits
<name>-<radius> 'ecfp-4' Uses 1024 bits, radius 4
<name>-<radius>-<nbits> 'ecfp-4-2048' Explicit radius and bit size

Example

from autopeptideml.reps.fps import RepEngineFP

engine = RepEngineFP(rep='ecfp', nbits=1024, radius=4)

smiles = [
    'CC(=O)NC(CCC(N)=O)C(=O)NC(CCC(N)=O)C(=O)O',
    'CC(N)C(=O)O',
]

fps = engine.compute_reps(smiles, verbose=False)
print(fps.shape)  # (2, 1024)
print(engine.dim())  # 1024