Molecules

This repository stores downloaded 3D molecular datasets collected into one gated Hugging Face dataset repo.

Included datasets

• geom_drugs: GEOM-Drugs (~7GB including QM9, ~304K). Status: uploaded. Uploaded: yes. Cleaned locally: yes, staged size 39.8 GB.
• geom_qm9: GEOM-QM9 (included in GEOM, ~130K). Status: uploaded. Uploaded: yes. Cleaned locally: yes, staged size 148.0 B.
• spice: SPICE v2 (~7GB, ~19K molecules / 1.1M conformers). Status: uploaded. Uploaded: yes. Cleaned locally: yes, staged size 34.9 GB.
• molecule3d: Molecule3D (~15GB, ~3.9M). Status: uploaded. Uploaded: yes. Cleaned locally: yes, staged size 1.9 GB.
• pcqm4mv2: PCQM4Mv2 (~17GB SDF, ~3.8M). Status: uploaded. Uploaded: yes. Cleaned locally: yes, staged size 1.5 GB.
• zinc3d: ZINC20 3D Conformers (SDF) (~50-200GB depending on tranche selection, hundreds of millions). Status: uploaded. Uploaded: yes. Cleaned locally: yes, staged size 463.4 GB.
• pubchem3d: PubChem 3D Conformer (hundreds of GB, ~100M+). Status: uploaded. Uploaded: yes. Cleaned locally: yes, staged size 165.4 GB.

Layout

Each dataset is stored under its own top-level folder in this repo.

Notes

• pubchem3d is very large. The downloader defaults to a limited subset unless --pubchem3d-full is used.
• zinc3d can also become very large depending on tranche selection.
• geom_qm9 reuses the GEOM archive downloaded for geom_drugs.