Document webLigandMPNN browser model assets

README.md

@@ -8,6 +8,7 @@ tags:
   - webgpu
   - protein-design
   - proteinmpnn
+  - ligandmpnn
 ---
 
 # MurrellLab webports
@@ -32,7 +33,7 @@ each `manifest.json`. A collection-wide index is available at
 Code, usage documentation, and validation details are maintained at
 https://github.com/MurrellGroup/webProteinMPNN.
 
-## License and attribution
+### License and attribution
 
 The upstream ProteinMPNN code and checkpoints are MIT licensed. The upstream
 notice is preserved in `webProteinMPNN/LICENSE.ProteinMPNN`, with additional
@@ -42,7 +43,7 @@ provenance in `webProteinMPNN/THIRD_PARTY_NOTICES.md`. Please cite:
 > protein sequence design using ProteinMPNN. Science. 2022;378(6615):49-56.
 > https://doi.org/10.1126/science.add2187
 
-## Intended use and limitations
+### Intended use and limitations
 
 The bundles are intended for research use in protein sequence design from
 protein backbone or CA-only coordinates. They preserve the behavior and
@@ -51,3 +52,37 @@ constitute new training or biological validation. Generated sequences require
 independent computational and experimental evaluation. These files are not a
 hosted inference API and are not suitable for clinical decision-making.
 
+## webLigandMPNN
+
+`webLigandMPNN/` contains four LigandMPNN sequence-design bundles and one
+learned side-chain packing bundle converted to ONNX for browser and Node.js
+inference through ONNX Runtime Web. It contains converted web assets only; the
+original PyTorch `.pt` checkpoints are not stored in this repository.
+
+The models were trained and released by the original LigandMPNN authors.
+MurrellLab converted the checkpoints into browser-oriented graphs; it did not
+train the underlying models. Each bundle records the original checkpoint hash,
+locked upstream revision, converted-file hashes, dimensions, validation status,
+and applicable notices. A collection-wide index is available at
+`webLigandMPNN/catalog.json`.
+
+Code, usage documentation, and validation details are maintained at
+https://github.com/MurrellGroup/webLigandMPNN.
+
+### License and attribution
+
+The upstream LigandMPNN code and model parameters are MIT licensed. The locked
+upstream license and additional attribution are preserved under
+`webLigandMPNN/`. Packing geometry derived from OpenFold constants retains the
+applicable Apache-2.0 license and source notice in the packing bundle. Please
+cite the original LigandMPNN publication and repository as described by the
+upstream project.
+
+### Intended use and limitations
+
+These bundles are intended for research use in ligand-conditioned protein
+sequence design and side-chain packing. Conversion does not constitute new
+training or independent biological validation. Generated structures and
+sequences require independent computational and experimental evaluation. These
+files are static model assets, not a hosted inference API, and are not suitable
+for clinical decision-making.

webLigandMPNN/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 webLigandMPNN contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

webLigandMPNN/README.md

@@ -0,0 +1,35 @@
+# webLigandMPNN model assets
+
+Browser-ready ONNX bundles for the unofficial
+[`webLigandMPNN`](https://github.com/MurrellGroup/webLigandMPNN) port. These
+files were converted from checkpoints trained and released by the original
+[`dauparas/LigandMPNN`](https://github.com/dauparas/LigandMPNN) authors.
+MurrellLab performed the web conversion and did not train the models.
+
+## Layout
+
+`models/` contains four LigandMPNN sequence models and the learned side-chain
+packer:
+
+- `ligandmpnn_v_32_005_25`
+- `ligandmpnn_v_32_010_25` (default sequence model)
+- `ligandmpnn_v_32_020_25`
+- `ligandmpnn_v_32_030_25`
+- `ligandmpnn_sc_v_32_002_16` (side-chain packer)
+
+Each directory is a self-contained web bundle. `manifest.json` lists the files
+needed at runtime and records their sizes and SHA-256 hashes. Additional parity
+and validation JSON files document the conversion checks. `catalog.json`
+indexes every hosted file and its digest. No original PyTorch `.pt` checkpoint
+is included.
+
+## Provenance and licenses
+
+`upstream.lock.json` pins upstream LigandMPNN revision
+`26ec57ac976ade5379920dbd43c7f97a91cf82de` and records the original checkpoint
+hashes and source URLs without redistributing those checkpoint files. The
+LigandMPNN license is included in every bundle. The packing bundle also retains
+the Apache-2.0 license and notice for geometry derived from OpenFold constants.
+
+See `THIRD_PARTY_NOTICES.md` and the source repository documentation for full
+attribution, validation scope, API usage, and scientific limitations.

webLigandMPNN/THIRD_PARTY_NOTICES.md

@@ -0,0 +1,31 @@
+# Third-party notices
+
+The neural feature equations, decoding procedure, and packing algorithm follow
+[dauparas/LigandMPNN](https://github.com/dauparas/LigandMPNN), copyright 2024 Justas
+Dauparas, MIT. The upstream project states that its code and model parameters
+are MIT-licensed. Its license is preserved in `vendor/LigandMPNN-LICENSE.txt`.
+The exporter also copies the actual license from the locked upstream revision
+into every generated bundle. New library and tooling code is MIT-licensed.
+
+Packing geometry is derived, at conversion time, from the OpenFold residue
+constants distributed inside LigandMPNN. This code descends from OpenFold and
+AlphaFold and carries Apache-2.0 notices. The exporter retains the exact source
+header and supplies `vendor/Apache-2.0.txt` with the derived geometry asset.
+No OpenFold neural network is required, and no AlphaFold model weights are used.
+The complete release archive includes the locked upstream sources and original
+checkpoints, along with their license. Exported bundles include the derived
+geometry constants and their license/notice files.
+
+[webProteinMPNN](https://github.com/MurrellGroup/webProteinMPNN) is the architectural
+reference for a library-only TypeScript/ONNX Runtime Web port. Its source code and
+model artifacts are not redistributed in this repository.
+
+[ONNX Runtime](https://github.com/microsoft/onnxruntime) is MIT-licensed. Installing
+`onnxruntime-web` brings its own licenses and third-party notices; retain them
+when redistributing its WASM/JavaScript binaries. The asset-copying tool copies
+available license/notice files as well as runtime assets. Python export/test
+packages retain their respective licenses and are not browser dependencies.
+
+Because the ORT 1.22.0 npm archive omits the root license files, this release also
+vendors `LICENSE` and `ThirdPartyNotices.txt` from Microsoft's exact `v1.22.0`
+tag and copies them to `public/ort/`. Updating ORT requires matching notices.

webLigandMPNN/catalog.json

@@ -0,0 +1,251 @@
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+}

webLigandMPNN/upstream.lock.json

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+}