PartiDesign and PartiScore checkpoints

This model repository distributes the original PartiDesign and PartiScore checkpoint files under Apache-2.0. The matching deployment source remains uncommitted for the maintainer's review; weight publication does not imply that the pending source changes are already on the official main branch.

This weight-only package contains the original PartiDesign generation and PartiScore interface-scoring checkpoint binaries. No third-party weights, inference service, model implementation, environment or dataset is included. Use the PartiDesign project to run the checkpoints.

Files and integrity

Path	Use	Bytes	SHA256
ckpts/partidesign.ckpt	Molecular generation	4,909,825,762	ade1da422f89c3817d616195380c68a77ba31a2f71f877803680c6ee09b54944
ckpts/partiscore.ckpt	Molecular-interface scoring	25,350,931	8961ba6612883d0e8a30265cc643ab48ccc97abb24fa25684736327438587506

Both files retain their existing binary format and filename. They were copied and checked byte-for-byte through matching source/copy SHA256 values; no checkpoint conversion, extraction or repackaging was performed.

Compatible source and environments

The tested source package is PartiDesign 0.1.0. Its current deployment candidate is based on source commit d062407fddba918bce4de9c3d7feadd0bb28702d with uncommitted patch SHA256 c77d5655db1e460722c8b6c7ed3d9be8465e64073c4202df099f1581c3bdfe16. That patch fingerprint identifies the reviewed working tree; it is not a new Git commit or a Hugging Face revision. The final source release reference will be recorded when the maintainer accepts and publishes it.

The project links in this card are navigation references: they do not mean that the uncommitted installer changes are already on the official repository's main branch. Use the matching reviewed source and installation guide.

Profile	Python	PyTorch	JAX / GPU plugins	cuEquivariance
CUDA 12	3.12.6	2.9.1+cu128	0.10.2 / CUDA 12	0.10.0
CUDA 13	3.12.6	2.11.0+cu130	0.10.2 / CUDA 13	0.13.0

These are full Linux/NVIDIA environments. The native layer retains OpenMM 8.4.0 and Conda openmmforcefields 0.15.1=pyhcf101f3_1. BioIR is included only with CUDA 13. The private project model implementations remain part of the source/environment; similarly named PyPI projects are not substitutes.

The default installer uses uv/CUDA 12. uv and Conda or Mamba are both prerequisites: uv manages the locked Python/model stack and a paired native Conda prefix provides Python, chemistry libraries and build/search tools.

bash install.sh
source .venv/bin/activate

For CUDA 13, keep a separate virtual environment and native prefix:

bash install.sh --cuda 13 \
  --venv .venv-cu13 --native-prefix .cache/environments/native-cu13
source .venv-cu13/bin/activate

The named Conda route remains available explicitly:

bash install.sh --installer conda --cuda 12
conda activate partidesign

See the matching environment guide for driver requirements, custom paths, updates and recovery. Keep each uv/native pair intact; never combine the two CUDA profiles in one environment.

Downloading and running

Use a full immutable Hugging Face commit hash from this repository's Files and versions history. The matching project download catalog pins its selected release revision. A mutable branch name is not an immutable release identifier; check the matching source documentation for the rollout's current catalog.

Keep the two files under a model root:

/path/to/partidesign-models/
└── ckpts/
    ├── partidesign.ckpt
    └── partiscore.ckpt

Use --model-dir or PARTIDESIGN_MODEL_DIR to select that root. From the matching source checkout, the public command entry points are:

MODEL_DIR=/path/to/partidesign-models

partidesign design configs/examples/protein.yaml \
  --task protein_fixture --batch-size 1 \
  --model-dir "$MODEL_DIR" --ckpt "$MODEL_DIR/ckpts/partidesign.ckpt" \
  --out inference/hf_example

# Score an existing directory of molecular complexes:
partidesign score /path/to/complexes \
  --model-dir "$MODEL_DIR" --ckpt "$MODEL_DIR/ckpts/partiscore.ckpt" \
  --device cpu

The YAML task controls generation inputs, constraints and sampling. PartiScore accepts direct-child PDB/CIF files. It needs eligible contacting partners for an interface score; a monomer can report no eligible interface. See the matching design and scoring guides.

The ordinary shipped pipeline uses ESMFold2-fast for iteration and ESMFold2-standard, with five samples, for final validation. Standard uses MSA for fixed protein context without templates; designed chains and tasks without eligible protein context remain query-only. The explicit PPI preset instead uses AF2-IG models [1,2], one complex/monomer pair each. AF3 and Mol-1 remain optional. Those upstream model weights are excluded from this package and must be prepared separately for the chosen route.

Deployment verification and limits

The deployment candidate was checked on fresh full Conda CUDA12/13 and uv CUDA12/13 environments on an RTX 4080 SUPER host. Installation/native GPU and backend checks completed; 48 real pipeline commands exited successfully. Four ordinary tasks under the original thresholds eliminated normally at round 1; their unexecuted later stages remain pending in those runs. Separate explicitly labeled deployment execution smokes covered the complete three-round and final stages. Fixed-context native MSA use, query-only cases, cache reuse/cache-only, completed resume and explicit search failures were checked independently.

Eight explicit AF3/Mol-1 public validation calls also completed across the four environments, with finite native/public structures and complete input mapping. Those calls used the recorded standalone one-sequence/one-complex budgets and MSA off; they do not establish optional pipeline-final-five or experimental quality. Deployment checks establish software execution, not binding or activity. No additional benchmark accuracy or training-data claims are made by this card.

Transport and source-catalog integration are checked separately from the software deployment results above. Those pre-publication deployment checks do not by themselves establish an anonymous cold download. Use the matching source release's download instructions and acceptance record for that separate gate.

License

The two project-owned checkpoints are prepared for release under Apache-2.0, as specified by the maintainer. The accompanying LICENSE is copied unchanged from the PartiDesign source repository. Third-party model parameters retain their own upstream terms and are not included here.