Installation

padelpy2 drives the vendored stock PaDEL-Descriptor Java application. You need a system Java runtime in addition to Python dependencies.

Requirements

  • Python 3.9–3.13 (RDKit wheels for oracle-tested versions prefer 3.10+)

  • Java Runtime Environment (JRE) 8 or higher on your PATH (java -version should succeed). CI uses Temurin 17.

Optional extras

  • None (default) — low-level padeldescriptor CLI wrapper (stdlib + Java)

  • [pandas] — DataFrame helpers (qc; used by Calculator)

  • [rdkit] — RDKit molecule I/O for Calculator / compat

  • [calc] — pandas + rdkit (recommended for Calculator)

Install the package

Minimal (padeldescriptor only):

pip install padelpy2

Calculator / DataFrame workflows:

pip install "padelpy2[calc]"

From a source checkout:

pip install -e ".[calc]"

RDKit

Conda (recommended) plus the pandas extra:

conda install -c conda-forge rdkit
pip install "padelpy2[pandas]"

Or the combined PyPI extra (current rdkit wheels; prefer 3.10+):

pip install "padelpy2[calc]"

Stock-JAR oracle fixtures were generated with RDKit 2026.03.x. Prefer conda-forge RDKit when possible.

Java notes

PaDEL-Descriptor will not run without java on PATH. padelpy2 does not bundle or auto-download a JRE; install a system JRE (8+) and ensure java is on PATH. See When to use which package for package choice.

Development extras

pip install -e ".[dev,docs,calc]"

  • [dev] — pytest, coverage, ruff

  • [docs] — Sphinx and the Read the Docs theme

  • [calc] — pandas + RDKit for API autodoc and examples

Build this documentation from a checkout:

cd docs
make html