padelpy

padelpy is a Python wrapper for the PaDEL-Descriptor molecular descriptor and fingerprint engine. It exposes a small public API for SMILES, MDL MolFile, and SDF inputs, and vendors the PaDEL Java bundle so a separate PaDEL install is not required.

A system Java JRE 8+ must be available on PATH. Continuous integration uses Eclipse Temurin 17.

Primary literature for the underlying engine:

• Yap CW. PaDEL-Descriptor: An open source software to calculate molecular descriptors and fingerprints. J Comput Chem. 2011;32(7):1466-1474. DOI: 10.1002/jcc.21707 / PMID: 21425294.

Contents

• Installation
  • Requirements
  • Optional extras
• Quickstart
  • Descriptors from SMILES
  • MDL and SDF files
  • Lower-level CLI wrapper
• API reference
  • from_mdl()
  • from_sdf()
  • from_smiles()
  • padeldescriptor()
• API stability policy
  • Frozen public surface
  • Versioning
  • Oracle parity as a release gate
  • Runtime prerequisite
  • Known limitations
  • Related engine citation