pregH/molcraft-zoo-data

MolCraftDiffusion Zoo — Data

Corpora and run inputs for MolCraftDiffusion, stored as ASE SQLite databases. Corpora are keyed by corpus and processing, so models that share one share the download.

Assets resolve by name, not by path:

pip install molcraftdiffusion
export HF_TOKEN=hf_xxx                       # these repos are private
MolCraftDiff zoo fetch --model kgdiff
MolCraftDiff generate examples/kgdiff_generate.yaml

Files land in $MOLCRAFT_ASSETS (default ~/.cache/molcraft/zoo), laid out exactly as the paths below.

How things are named

Prefix	Meaning	Example
data/<corpus>/<variant>	a corpus — never named after a model	data/crossdocked/pockets10a
inputs/<name>	a run input — reference structure, single target	inputs/templates
(model name)	weights and their sidecars	kgdiff/pretrained

A corpus belongs to nobody, so CrossDocked pockets are data/crossdocked/pockets10a — read by KGDiff, IPDiff and DiffSBDD alike, and downloaded once.

Code: https://github.com/pregHosh/MolCraftDiffusion

Corpora

asset	size	licence
data/chembl3d/stereo-200	868.0 KB	CC-BY-SA-3.0 (ChEMBL)
data/crossdocked/diffdec	923.2 KB	CC0-1.0
data/crossdocked/diffint	371.4 MB	CC0-1.0
data/crossdocked/diffpharma	4.1 GB	CC0-1.0
data/crossdocked/diffpharma-smoke	4.1 MB	CC0-1.0
data/crossdocked/pmdm	440.0 KB	CC0-1.0
data/crossdocked/pockets10a	1.3 MB	CC0-1.0
data/formed/3k	32.5 MB	MIT
data/formed/full	1.4 GB	MIT
data/geom/ase	618.8 MB	CC0-1.0 (GEOM-Drugs)
data/geom/ase-gcdm	488.0 KB	CC0-1.0
data/geom/graph3d-flowmol3	102.8 MB	CC0-1.0
data/geom/graph3d-val	102.9 MB	CC0-1.0
data/iflp_mof/linkers	33.6 MB	MIT
data/qm9/ase	253.0 MB	CC0-1.0
data/qm9/ase-300	368.0 KB	CC0-1.0
data/qm9/ase-4k	7.4 MB	CC0-1.0 (QM9)
data/qm9/graph3d	191.7 MB	CC0-1.0
data/qm9/graph3d-400-ditmc	552.0 KB	CC0-1.0
data/qm9/graph3d-400-nextmol	552.0 KB	CC0-1.0
data/qm9/graph3d-4k	5.2 MB	CC0-1.0
data/tmc/ligandiff	341.3 MB	CC0-1.0
data/tmc/ligandiff-multi	3.5 GB	CC0-1.0
data/zinc/difflinker	666.1 MB	free-for-academic (ZINC)

Run inputs

asset	size	licence
inputs/apo2mol/8tv6	644.0 KB	MIT
inputs/difflinker/fragments	2.3 KB	free-for-academic (ZINC)
inputs/ligandiff-multi/reference	385.0 B	CC0-1.0
inputs/ligandiff/reference	615.0 B	CC0-1.0
inputs/loqi/stereo-ref	216.4 KB	CC-BY-SA-3.0 (ChEMBL)
inputs/silvr/reference	1.2 KB	CC0-1.0
inputs/templates	4.7 KB	MIT

Provenance

• QM9 — Ramakrishnan et al. 2014 (CC0).
• GEOM-Drugs — Axelrod & Gómez-Bombarelli, Harvard Dataverse.
• CrossDocked2020 — Francoeur et al. 2020; CC0 1.0 per the upstream LICENSE.
• ChEMBL3D — derived from ChEMBL (CC BY-SA 3.0).
• ZINC — via DiffLinker's preprocessed release.
• FORMED, IFLP-MOF — produced for the MolCraftDiffusion manuscript.

The Apo2Mol apo/holo corpus is not here: its upstream dataset is access-gated. MolCraftDiff zoo recipe explains how to obtain it.