Publish OFoldX pipeline artifacts

README.md

@@ -6,11 +6,11 @@ tags:
   - "protein"
   - "rna"
   - "dna"
-  - "model"
+  - "pipeline"
   - "alphafold3"
   - "structure-prediction"
   - "protein-structure"
-artifact_kind: "model"
+artifact_kind: "pipeline"
 repo_id: "oteam/protenix-base"
 license: "apache-2.0"
 pipeline_tag: "other"
@@ -34,11 +34,11 @@ widget:
 
 # protenix-base
 
-OFoldX `model` artifact for biomolecular structure prediction, using the `alphafold3` architecture.
+OFoldX `pipeline` artifact for biomolecular structure prediction, using the `alphafold3` architecture.
 
 ## Disclaimer
 
-This model card was generated by the OFoldX team for an OFoldX `model` artifact.
+This model card was generated by the OFoldX team for an OFoldX `pipeline` artifact.
 The upstream model authors did not write this card unless explicitly stated otherwise.
 
 OFoldX is pre-alpha research software. Check the source checkpoint, upstream release, and local validation
@@ -63,12 +63,10 @@ Converted Protenix v0.5.0 structure-prediction weights in an AlphaFold 3-shaped
 | Field | Value |
 | ----- | ----- |
 | Repository | `oteam/protenix-base` |
-| Artifact Kind | `model` |
+| Artifact Kind | `pipeline` |
 | Task | `structure_prediction` |
 | Architecture | `alphafold3` |
-| Entrypoint | `ofoldx.models.alphafold3.model.AlphaFold3Model` |
-| Config | `config.json` |
-| Weights | `model.safetensors` |
+| Entrypoint | `ofoldx.pipelines.structure_prediction.StructurePredictionPipeline` |
 | Source Checkpoint | `protenix_base_default_v0.5.0.pt` |
 
 > [!NOTE]
@@ -80,7 +78,7 @@ Converted Protenix v0.5.0 structure-prediction weights in an AlphaFold 3-shaped
 - **Upstream paper**: [Protenix - Advancing Structure Prediction Through a Comprehensive AlphaFold3 Reproduction](https://doi.org/10.1101/2025.01.08.631967)
 - **Upstream repository**: [Protenix](https://github.com/bytedance/Protenix)
 - **Source checkpoint release**: [https://github.com/bytedance/Protenix/blob/main/docs/supported_models.md](https://github.com/bytedance/Protenix/blob/main/docs/supported_models.md)
-- **Code**: [`ofoldx/models/alphafold3/model.py`](https://github.com/OTeam-AI4S/OFoldX/tree/main/ofoldx/models/alphafold3/model.py)
+- **Code**: [`ofoldx/pipelines/structure_prediction.py`](https://github.com/OTeam-AI4S/OFoldX/tree/main/ofoldx/pipelines/structure_prediction.py)
 - **Project repository**: [https://github.com/OTeam-AI4S/OFoldX](https://github.com/OTeam-AI4S/OFoldX)
 - **Issues**: [https://github.com/OTeam-AI4S/OFoldX/issues](https://github.com/OTeam-AI4S/OFoldX/issues)
 
@@ -92,19 +90,14 @@ The artifact depends on the [`ofoldx`](https://github.com/OTeam-AI4S/OFoldX) lib
 pip install ofoldx
 ```
 
-### Direct Use
+### Pipeline Usage
 
-Load the artifact from `oteam/protenix-base` using the OFoldX `Auto*` interface:
+Load the artifact from `oteam/protenix-base` with the OFoldX task pipeline. Use `AutoModel` or `AutoProcessor` only when you need lower-level control:
 
 ```python
 from ofoldx.pipelines import Pipeline
 
 pipeline = Pipeline.from_pretrained("oteam/protenix-base")
-output = pipeline(...)
-
-from ofoldx import AutoModel
-
-model = AutoModel.from_pretrained("oteam/protenix-base")
 ```
 
 When a matching processor is available, load it with `AutoProcessor.from_pretrained(...)` and pass the
@@ -113,7 +106,7 @@ processed batch to the model.
 ### Interface
 
 - **Task**: `structure_prediction`
-- **Artifact kind**: `model`
+- **Artifact kind**: `pipeline`
 - **Architecture**: `alphafold3`
 - **Runtime files**: `manifest.json`, `config.json`, and `model.safetensors` when present
 
@@ -161,5 +154,5 @@ Please use [OFoldX GitHub issues](https://github.com/OTeam-AI4S/OFoldX/issues) f
 
 ## License
 
-The OFoldX project license is not yet finalized.
+The Hub `license` metadata, when present, reflects the source checkpoint or upstream project license. The OFoldX project license is not yet finalized.
 The source checkpoint is associated with the upstream license noted above: Apache-2.0 for upstream Protenix code and model parameters. Review both OFoldX and upstream terms before redistribution or production use.

manifest.json

@@ -1,18 +1,22 @@
 {
   "format": "biomolecular_pretrained",
   "format_version": 1,
-  "kind": "model",
+  "kind": "pipeline",
   "producer": {
     "package": "ofoldx",
     "version": "0.1.dev1+g9a78c7e44.d20260609"
   },
-  "entrypoint": "ofoldx.models.alphafold3.model.AlphaFold3Model",
+  "entrypoint": "ofoldx.pipelines.structure_prediction.StructurePredictionPipeline",
   "architecture": "alphafold3",
   "task": "structure_prediction",
-  "files": {
-    "config": "config.json"
-  },
-  "weights": {
-    "default": "model.safetensors"
+  "components": {
+    "predictor": {
+      "kind": "component",
+      "path": "predictor"
+    },
+    "processor": {
+      "kind": "component",
+      "path": "processor"
+    }
   }
 }

predictor/README.md

@@ -0,0 +1,165 @@
+---
+library_name: "ofoldx"
+tags:
+  - "biology"
+  - "biomolecular-design"
+  - "protein"
+  - "rna"
+  - "dna"
+  - "model"
+  - "alphafold3"
+  - "structure-prediction"
+  - "protein-structure"
+artifact_kind: "model"
+repo_id: "oteam/protenix-base"
+license: "apache-2.0"
+pipeline_tag: "other"
+task: "structure_prediction"
+model-index:
+  - name: "protenix-base"
+    results:
+      []
+widget:
+  - pipeline_tag: "other"
+    task: "structure_prediction"
+    example_title: "Single-chain protein"
+    text: ">A\nMKTAYIAKQRQISFVKSHFSRQDILD"
+    input_format: "fasta"
+  - pipeline_tag: "other"
+    task: "structure_prediction"
+    example_title: "Protein complex"
+    text: ">A\nMKTAYIAKQRQISFVKSHFSRQDILD\n>B\nGSHMRYFVTAVSRPGRGEPRFI"
+    input_format: "fasta"
+---
+
+# protenix-base
+
+OFoldX `model` artifact for biomolecular structure prediction, using the `alphafold3` architecture.
+
+## Disclaimer
+
+This model card was generated by the OFoldX team for an OFoldX `model` artifact.
+The upstream model authors did not write this card unless explicitly stated otherwise.
+
+OFoldX is pre-alpha research software. Check the source checkpoint, upstream release, and local validation
+before using the artifact for scientific or operational decisions.
+
+## Model Details
+
+AlphaFold 3-shaped structure-prediction model converted for the OFoldX runtime.
+
+Converted Protenix v0.5.0 structure-prediction weights in an AlphaFold 3-shaped OFoldX implementation.
+
+### Model Provenance
+
+- **Upstream Project**: Protenix
+- **Source Checkpoint**: `protenix_base_default_v0.5.0.pt`
+- **Source Release**: [https://github.com/bytedance/Protenix/blob/main/docs/supported_models.md](https://github.com/bytedance/Protenix/blob/main/docs/supported_models.md)
+- **Primary Paper**: [Protenix - Advancing Structure Prediction Through a Comprehensive AlphaFold3 Reproduction](https://doi.org/10.1101/2025.01.08.631967)
+- **Upstream License**: Apache-2.0 for upstream Protenix code and model parameters
+
+### Model Specification
+
+| Field | Value |
+| ----- | ----- |
+| Repository | `oteam/protenix-base` |
+| Artifact Kind | `model` |
+| Task | `structure_prediction` |
+| Architecture | `alphafold3` |
+| Entrypoint | `ofoldx.models.alphafold3.model.AlphaFold3Model` |
+| Config | `config.json` |
+| Weights | `model.safetensors` |
+| Source Checkpoint | `protenix_base_default_v0.5.0.pt` |
+
+> [!NOTE]
+> Source checkpoint: `protenix_base_default_v0.5.0.pt`; `v0.5.0` is the upstream Protenix checkpoint release version, not part of the public repo id.
+
+### Links
+
+- **Hub repository**: [oteam/protenix-base](https://huggingface.co/oteam/protenix-base)
+- **Upstream paper**: [Protenix - Advancing Structure Prediction Through a Comprehensive AlphaFold3 Reproduction](https://doi.org/10.1101/2025.01.08.631967)
+- **Upstream repository**: [Protenix](https://github.com/bytedance/Protenix)
+- **Source checkpoint release**: [https://github.com/bytedance/Protenix/blob/main/docs/supported_models.md](https://github.com/bytedance/Protenix/blob/main/docs/supported_models.md)
+- **Code**: [`ofoldx/models/alphafold3/model.py`](https://github.com/OTeam-AI4S/OFoldX/tree/main/ofoldx/models/alphafold3/model.py)
+- **Project repository**: [https://github.com/OTeam-AI4S/OFoldX](https://github.com/OTeam-AI4S/OFoldX)
+- **Issues**: [https://github.com/OTeam-AI4S/OFoldX/issues](https://github.com/OTeam-AI4S/OFoldX/issues)
+
+## Usage
+
+The artifact depends on the [`ofoldx`](https://github.com/OTeam-AI4S/OFoldX) library. Install it with pip:
+
+```bash
+pip install ofoldx
+```
+
+### Pipeline Usage
+
+Load the artifact from `oteam/protenix-base` with the OFoldX task pipeline. Use `AutoModel` or `AutoProcessor` only when you need lower-level control:
+
+```python
+from ofoldx.pipelines import Pipeline
+
+pipeline = Pipeline.from_pretrained("oteam/protenix-base")
+output = pipeline(...)
+
+from ofoldx import AutoModel
+
+model = AutoModel.from_pretrained("oteam/protenix-base")
+```
+
+When a matching processor is available, load it with `AutoProcessor.from_pretrained(...)` and pass the
+processed batch to the model.
+
+### Interface
+
+- **Task**: `structure_prediction`
+- **Artifact kind**: `model`
+- **Architecture**: `alphafold3`
+- **Runtime files**: `manifest.json`, `config.json`, and `model.safetensors` when present
+
+## Training Details
+
+OFoldX did not train these weights. This repository contains a converted checkpoint and OFoldX runtime
+metadata for loading it.
+
+### Training Data
+
+The upstream Protenix v0.5.0 release reports a 2021-09-30 training-data cutoff. The Protenix training-data pipeline covers released wwPDB/mmCIF bioassemblies, MSAs, CCD cache data, and RCSB sequence clusters. OFoldX does not redistribute the training corpus.
+
+### Training Procedure
+
+The upstream `protenix_base_default_v0.5.0` model is an AF3-shaped all-atom structure-prediction checkpoint. OFoldX converts `protenix_base_default_v0.5.0.pt` to the OFoldX artifact format; it does not retrain the model.
+
+## Evaluation
+
+OFoldX conversion reports and contract tests validate artifact structure and checkpoint loading. Task-level
+scientific evaluation should be checked against the corresponding upstream model release or paper.
+
+## Limitations
+
+- This artifact is distributed for research use.
+- Inputs must match the model-specific processor and expected biomolecular representation.
+- OFoldX is pre-alpha, so APIs and artifact metadata may still change before a stable release.
+
+## Citation
+
+Please cite the upstream Protenix work for the source checkpoint. If OFoldX supports your work, please also cite or link the OFoldX project repository.
+
+```bibtex
+@article{protenix2025advancing,
+  author = {ByteDance AML AI4Science Team and Chen, Xinshi and Zhang, Yuxuan and Lu, Chan and Ma, Wenzhi and Guan, Jiaqi and Gong, Chengyue and Yang, Jincai and Zhang, Hanyu and Zhang, Ke and others},
+  title = {Protenix - Advancing Structure Prediction Through a Comprehensive AlphaFold3 Reproduction},
+  year = {2025},
+  doi = {10.1101/2025.01.08.631967},
+  journal = {bioRxiv}
+}
+```
+
+## Contact
+
+Please use [OFoldX GitHub issues](https://github.com/OTeam-AI4S/OFoldX/issues) for questions or comments about this model card.
+
+## License
+
+The Hub `license` metadata, when present, reflects the source checkpoint or upstream project license. The OFoldX project license is not yet finalized.
+The source checkpoint is associated with the upstream license noted above: Apache-2.0 for upstream Protenix code and model parameters. Review both OFoldX and upstream terms before redistribution or production use.

predictor/manifest.json

@@ -0,0 +1,18 @@
+{
+  "format": "biomolecular_pretrained",
+  "format_version": 1,
+  "kind": "model",
+  "producer": {
+    "package": "ofoldx",
+    "version": "0.1.dev1+g9a78c7e44.d20260609"
+  },
+  "entrypoint": "ofoldx.models.alphafold3.model.AlphaFold3Model",
+  "architecture": "alphafold3",
+  "task": "structure_prediction",
+  "files": {
+    "config": "config.json"
+  },
+  "weights": {
+    "default": "model.safetensors"
+  }
+}

processor/manifest.json

@@ -0,0 +1,13 @@
+{
+  "format": "biomolecular_pretrained",
+  "format_version": 1,
+  "kind": "processor",
+  "producer": {
+    "package": "ofoldx",
+    "version": "0.1.dev1+g9a78c7e44.d20260609"
+  },
+  "entrypoint": "ofoldx.models.alphafold3.processor.AlphaFold3Processor",
+  "files": {
+    "config": "processor_config.json"
+  }
+}

processor/processor_config.json

@@ -0,0 +1,166 @@
+{
+  "single_size": 384,
+  "token_feature_size": 449,
+  "atom_feature_size": 385,
+  "residue_vocabulary": [
+    "ALA",
+    "ARG",
+    "ASN",
+    "ASP",
+    "CYS",
+    "GLN",
+    "GLU",
+    "GLY",
+    "HIS",
+    "ILE",
+    "LEU",
+    "LYS",
+    "MET",
+    "PHE",
+    "PRO",
+    "SER",
+    "THR",
+    "TRP",
+    "TYR",
+    "VAL",
+    "UNK",
+    "A",
+    "G",
+    "C",
+    "U",
+    "N",
+    "DA",
+    "DG",
+    "DC",
+    "DT",
+    "DN",
+    "GAP"
+  ],
+  "element_vocabulary": [
+    "H",
+    "HE",
+    "LI",
+    "BE",
+    "B",
+    "C",
+    "N",
+    "O",
+    "F",
+    "NE",
+    "NA",
+    "MG",
+    "AL",
+    "SI",
+    "P",
+    "S",
+    "CL",
+    "AR",
+    "K",
+    "CA",
+    "SC",
+    "TI",
+    "V",
+    "CR",
+    "MN",
+    "FE",
+    "CO",
+    "NI",
+    "CU",
+    "ZN",
+    "GA",
+    "GE",
+    "AS",
+    "SE",
+    "BR",
+    "KR",
+    "RB",
+    "SR",
+    "Y",
+    "ZR",
+    "NB",
+    "MO",
+    "TC",
+    "RU",
+    "RH",
+    "PD",
+    "AG",
+    "CD",
+    "IN",
+    "SN",
+    "SB",
+    "TE",
+    "I",
+    "XE",
+    "CS",
+    "BA",
+    "LA",
+    "CE",
+    "PR",
+    "ND",
+    "PM",
+    "SM",
+    "EU",
+    "GD",
+    "TB",
+    "DY",
+    "HO",
+    "ER",
+    "TM",
+    "YB",
+    "LU",
+    "HF",
+    "TA",
+    "W",
+    "RE",
+    "OS",
+    "IR",
+    "PT",
+    "AU",
+    "HG",
+    "TL",
+    "PB",
+    "BI",
+    "PO",
+    "AT",
+    "RN",
+    "FR",
+    "RA",
+    "AC",
+    "TH",
+    "PA",
+    "U",
+    "NP",
+    "PU",
+    "AM",
+    "CM",
+    "BK",
+    "CF",
+    "ES",
+    "FM",
+    "MD",
+    "NO",
+    "LR",
+    "RF",
+    "DB",
+    "SG",
+    "BH",
+    "HS",
+    "MT",
+    "DS",
+    "RG",
+    "CN",
+    "NH",
+    "FL",
+    "MC",
+    "LV",
+    "TS",
+    "OG"
+  ],
+  "element_channels": 128,
+  "atom_name_characters_count": 4,
+  "atom_name_character_channels": 64,
+  "reference_conformer_augment": false,
+  "augment_seed": null,
+  "ligand_atom_rename": false,
+  "materialize_missing_atoms": false
+}