desirebonneau/admet-dataset-cleaner

How desirebonneau/admet-dataset-cleaner works

Dataset Cleaner prepares molecular ADMET CSVs for downstream analysis: users configure batch inputs, then a pipeline validates and standardizes structures, flags duplicates and chemical hazards, assesses structural outliers, predicts pKa, and transfers chirality before producing cleaned data. The multithreaded runner is documented for large datasets; the batch script currently invokes the single-threaded runner. The graph covers the sampled runtime modules and README-described pKa capability; unsampled runner internals are not expanded into unsupported calls.

Main entry points: singlethread_main/main.py Single-thread pipeline · multithread_main/main.py Multithread pipeline · pubchem_utils.py PubChem lookup · outlier_utils.py Outlier detection

Components 15

Entry points

Batch runner batch_cleaning.py
Single-thread pipeline singlethread_main/main.py
Multithread pipeline multithread_main/main.py

Cleaning pipeline

Filter patterns config.py
pKa model pka-model

Chemistry utilities

SMILES handling utils/smiles_utils.py
PubChem lookup utils/pubchem_utils.py
Exact deduplication utils/duplicate_utils.py
Chemical filters utils/chemical_filters.py
Outlier detection utils/outlier_utils.py
Fingerprints utils/tanimoto_utils.py
Chirality transfer utils/chirality_utils.py
File utilities utils/io_utils.py

Other components

Dataset curator
PubChem service

Connections 20

Dataset curator → Batch runner: configures runs README.md
Batch runner → Single-thread pipeline: calls cleaner batch_cleaning.py
Single-thread pipeline → SMILES handling: uses singlethread_main/main.py
Single-thread pipeline → PubChem lookup: uses singlethread_main/main.py
Single-thread pipeline → Exact deduplication: uses singlethread_main/main.py
Single-thread pipeline → Chemical filters: uses singlethread_main/main.py
Single-thread pipeline → Outlier detection: uses singlethread_main/main.py
Single-thread pipeline → Chirality transfer: uses singlethread_main/main.py
Single-thread pipeline → Filter patterns: uses patterns singlethread_main/main.py
Single-thread pipeline → pKa model: predicts with README.md
Multithread pipeline → SMILES handling: uses multithread_main/main.py
Multithread pipeline → PubChem lookup: uses multithread_main/main.py
Multithread pipeline → Exact deduplication: uses multithread_main/main.py
Multithread pipeline → Chemical filters: uses multithread_main/main.py
Multithread pipeline → Outlier detection: uses multithread_main/main.py
Multithread pipeline → Chirality transfer: uses multithread_main/main.py
Multithread pipeline → Filter patterns: uses patterns multithread_main/main.py
Multithread pipeline → pKa model: predicts with README.md
PubChem lookup → PubChem service: requests data utils/pubchem_utils.py
Outlier detection → Fingerprints: generates fingerprints utils/outlier_utils.py

Drawn by GitDiagram on November 12, 2026 from the repository's file tree, README and source files. Read as Markdown ·