pyCSRML documentation

pyCSRML is an attempt to provide a pure-Python implementation of the Chemical Subgraph Representation Markup Language (CSRML). It parses CSRML XML files, converts subgraph patterns to SMARTS, and computes binary chemotype fingerprints for molecules using RDKit.

Two fingerprint sets are bundled and accessible via path constants:

• ToxPrint v2.0 — 729 general toxicologically-relevant chemotypes (TOXPRINT_PATH)

• TxP_PFAS v1.0 — 129 per- and polyfluoroalkyl substance (PFAS) chemotypes (TXPPFAS_PATH)

Concordance with the reference ChemoTyper tool:

• 99.99 % overall accuracy across 14 710 PFAS compounds from Richard et al. (2023), using the TxP_PFAS v1.0 fingerprint.

• 98.17 % overall accuracy on the full ToxCast library (9 014 compounds, 711 / 729 bits ≥ 90 %) for ToxPrint v2.0.

• 99.98 % overall accuracy on the ToxCast CF-containing subset (808 compounds, all 129 bits ≥ 90 %) for TxP_PFAS v1.0.

• CLinventory (pharmaceutical/industrial chemical set) — ToxPrint v2.0 and TxP_PFAS v1.0 results are generated automatically when running the test suite; see tests/concordance_report.md for the latest figures.

Run pytest tests/test_chemotyper_concordance.py -v -s to reproduce; results (including per-bit MCC, balanced accuracy, and ROC-AUC) are written to tests/concordance_report.md. Known residual discrepancies (G/Q pseudo-element approximations, RDKit vs ChemoTyper aromaticity for fluorinated heterocycles) are documented in README.md under the Known discrepancies heading.

User guide

• Installation
  • Requirements
  • Optional dependencies
  • From PyPI (pip)
  • Conda users
  • Development install
• Quick start
  • Computing fingerprints for a single molecule
  • Using the bundled TxP_PFAS definition
  • Batch processing
  • Using a custom CSRML XML file
• Timing Benchmarks
  • Benchmark sets
  • pyCSRML timing results
  • Reproducing the benchmarks
  • System information
• CSRML format
  • File structure
  • Atom features (matchIf)
  • Pseudo-elements
  • combineAtomFeatures (QRY atoms)
  • Exception handling
  • Low-level API
  • Known limitations
• Custom fingerprints: JSON and YAML format
  • File format
  • Field reference
  • Loading a custom file
  • Exporting the bundled specs to JSON
  • YAML installation

API reference

• Fingerprinter API
  • Pattern matching strategy
  • TOXPRINT_PATH
  • TXPPFAS_PATH
  • Fingerprinter
• CSRML parser API
  • parse_csrml_xml()
  • ordered_bit_list()

About

• Changelog

Indices and tables

• Index

• Module Index

• Search Page