Quickstart

padelpy wraps the PaDEL-Descriptor Java engine (Yap, 2011; DOI 10.1002/jcc.21707). Ensure Java 8+ is on PATH before calling the API (see Installation).

Descriptors from SMILES

from padelpy import from_smiles

descriptors = from_smiles("CCC")
print(descriptors["MW"], descriptors["nC"])

# list input → list of mappings
rows = from_smiles(["CCC", "CCCC"])

# PubChem fingerprints only
fps = from_smiles("CCC", fingerprints=True, descriptors=False)

MDL and SDF files

from padelpy import from_mdl, from_sdf

mdl_rows = from_mdl("mols.mdl")
sdf_rows = from_sdf("mols.sdf")

Lower-level CLI wrapper

from padelpy import padeldescriptor

padeldescriptor(
    mol_dir="molecules.smi",
    d_file="descriptors.csv",
    d_2d=True,
    d_3d=True,
    retainorder=True,
    headless=True,
)

Full signatures appear in API reference. Compatibility expectations are described in API stability policy.