rc-foundry 0.1.7__tar.gz → 0.1.10__tar.gz

rc_foundry-0.1.10/.git

@@ -0,0 +1 @@
+gitdir: /home/rohith/modelhub/.git/worktrees/release

rc_foundry-0.1.10/.github/workflows/documentation.yml

@@ -0,0 +1,29 @@
+name: documentation
+
+on: [push, pull_request, workflow_dispatch]
+
+permissions:
+  contents: write
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+      - name: Install dependencies
+        run: |
+          pip install sphinx myst_parser furo sphinx-copybutton
+      - name: Sphinx build
+        run: |
+          sphinx-build -M html docs/source/ docs/build/
+      - name: Disable Jekyll
+        run: touch docs/build/html/.nojekyll
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/production' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/build/html
+          force_orphan: true

{rc_foundry-0.1.7 → rc_foundry-0.1.10}/.gitignore

@@ -223,6 +223,9 @@ logs/
 **/distillation/
 **/benchmarks/
 
+# macOS
+.DS_Store
+
 # AI
 **/CLAUDE.md
 **/.claude

{rc_foundry-0.1.7 → rc_foundry-0.1.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rc-foundry
-Version: 0.1.7
+Version: 0.1.10
 Summary: Shared utilities and training infrastructure for biomolecular structure prediction models.
 Author-email: Institute for Protein Design <contact@ipd.uw.edu>
 License: BSD 3-Clause License
@@ -97,12 +97,26 @@ Foundry provides tooling and infrastructure for using and training all classes o
 
 All models within Foundry rely on [AtomWorks](https://github.com/RosettaCommons/atomworks) - a unified framework for manipulating and processing biomolecular structures - for both training and inference. 
 
+
+> [!NOTE]
+> We have a slack now! Join for updates and to get your questions answered [here](https://join.slack.com/t/proteinmodelfoundry/shared_invite/zt-3kpwru8c6-nrmTW6LNHnSE7h16GNnfLA).
+
 ## Getting Started
 ### Quickstart guide
 **Installation**
 ```bash
-pip install rc-foundry[all]
+pip install "rc-foundry[all]"
+```
+
+**Intel XPU Installation**
+
+For Intel XPU devices, install PyTorch with XPU support first, then install Foundry.
+```bash
+pip install torch --index-url https://download.pytorch.org/whl/xpu
+pip install "rc-foundry[all]"
 ```
+> [!NOTE]
+> Use `pip` (not `uv`) for XPU installs since UV re-resolves dependencies and may replace your XPU torch with the standard PyPI version.
 
 **Downloading weights** Models can be downloaded to a target folder with:
 ```

{rc_foundry-0.1.7 → rc_foundry-0.1.10}/README.md

@@ -4,12 +4,26 @@ Foundry provides tooling and infrastructure for using and training all classes o
 
 All models within Foundry rely on [AtomWorks](https://github.com/RosettaCommons/atomworks) - a unified framework for manipulating and processing biomolecular structures - for both training and inference. 
 
+
+> [!NOTE]
+> We have a slack now! Join for updates and to get your questions answered [here](https://join.slack.com/t/proteinmodelfoundry/shared_invite/zt-3kpwru8c6-nrmTW6LNHnSE7h16GNnfLA).
+
 ## Getting Started
 ### Quickstart guide
 **Installation**
 ```bash
-pip install rc-foundry[all]
+pip install "rc-foundry[all]"
+```
+
+**Intel XPU Installation**
+
+For Intel XPU devices, install PyTorch with XPU support first, then install Foundry.
+```bash
+pip install torch --index-url https://download.pytorch.org/whl/xpu
+pip install "rc-foundry[all]"
 ```
+> [!NOTE]
+> Use `pip` (not `uv`) for XPU installs since UV re-resolves dependencies and may replace your XPU torch with the standard PyPI version.
 
 **Downloading weights** Models can be downloaded to a target folder with:
 ```

rc_foundry-0.1.10/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

rc_foundry-0.1.10/docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

rc_foundry-0.1.10/docs/source/conf.py

@@ -0,0 +1,59 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'foundry'
+copyright = '2025, Institute for Protein Design, University of Washington'
+author = 'Institute for Protein Design, University of Washington'
+release = '0.1.7'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ["myst_parser",
+              "sphinx_copybutton"
+              ]
+
+templates_path = ['_templates']
+exclude_patterns = ["readme.md", "readmelink.md", "readme_link.rst"]
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'furo'
+html_static_path = ['_static', '../../models/rfd3/.assets']
+
+html_theme_options = {
+    "sidebar_hide_name":False,
+    #"announcement": "<em>THIS DOCUMENTATION IS CURRENTLY UNDER CONSTRUCTION</em>",
+    "light_css_variables": {
+        "color-brand-primary": "#F68A33", # Rosetta Teal
+        "color-brand-content": "#37939B", # Rosetta Orange
+        #"color-admonition-background": "#CCE8E8", # Rosetta light orange
+        "font-stack": "Open Sans, sans-serif",
+        "font-stack--headings": "Open Sans, sans-serif",
+        "color-background-hover": "#DCE8E8ff",
+        "color-announcement-background" : "#F68A33dd",
+        "color-announcement-text": "#070707",
+        "color-brand-visited": "#37939B",
+        },
+    "dark_css_variables": {
+        "color-brand-primary": "#37939B", # Rosetta teal
+        "color-brand-content": "#F68A33", # Rosetta orange
+        #"color-admonition-background": "#20565B", # Rosetta light orange
+        "font-stack": "Open Sans, sans-serif",
+        "font-stack--headings": "Open Sans, sans-serif",
+        "color-brand-visited": "#37939B",
+        }
+    }
+
+source_suffix = {
+    ".rst": "restructuredtext",
+    ".md": "markdown",
+    }

rc_foundry-0.1.10/docs/source/index.rst

@@ -0,0 +1,25 @@
+.. foundry documentation master file, created by
+   sphinx-quickstart on Wed Dec 17 16:36:38 2025.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to the official documentation for foundry
+=================================================
+
+`foundry <https://github.com/RosettaCommons/foundry/tree/production>`_ is a home for
+many of the machine learning models produced by `Rosetta Commons member labs <https://rosettacommons.org/about/labs/>`_. 
+
+.. toctree::
+   :maxdepth: 1
+   :caption: General
+   
+   license_link.rst
+   installation_faq.md
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Models
+
+   models/rfd3/index
+   models/rf3/index
+   models/mpnn/index

rc_foundry-0.1.10/docs/source/installation_faq.md

@@ -0,0 +1,14 @@
+# Common Installation Issues
+
+<details>
+    <summary><strong>Installation on NVIDIA GeForce RTX 5060 - Blackwell architecture</strong></summary>
+    Taken from [Issue #105](https://github.com/RosettaCommons/foundry/issues/105):
+    If, when installing any of the models included in foundry, you get an error related to CUDA (see linked issue for examples) try installing a version of torch, torchvision and torchaudio that matches your python and CUDA distribution. For CUDA, choose the next lowest available library if there is not a version that matches your exact CUDA build. 
+
+    For example: 
+    ```
+    pip install torch==2.9.1+cu128 torchvision==0.24.1+cu128 torchaudio==2.9.1+cu128 --extra-index-url https://download.pytorch.org/whl/cu128
+    ```
+    This is for Python 2.9.1 and CUDA 12.8.
+
+</details>

rc_foundry-0.1.10/docs/source/license_link.rst

@@ -0,0 +1,5 @@
+LICENSE
+=======
+
+.. include:: ../../LICENSE.md
+   :parser: myst_parser.sphinx_

rc_foundry-0.1.10/docs/source/models/mpnn/index.md

@@ -0,0 +1,22 @@
+# MPNN Documentation
+
+```{warning}
+The documentation for the MPNN model is currently incomplete.
+If you would like to contribute, feel free to open a PR. 
+```
+```{warning}
+The MPNN model is still being benchmarked for comparison to the 
+original ProteinMPNN, LigandMPNN, and SolubleMPNN implementations.
+```
+
+The MPNN model in [foundry](https://github.com/RosettaCommons/foundry)
+has all of the functionality of [ProteinMPNN](https://www.science.org/doi/10.1126/science.add2187), 
+[LigandMPNN](https://www.nature.com/articles/s41592-025-02626-1), 
+and [SolubleMPNN](https://www.nature.com/articles/s41586-024-07601-y), 
+but with the backend support of [atomworks](https://github.com/RosettaCommons/atomworks) and 
+[foundry](https://github.com/RosettaCommons/foundry). More MPNN
+models and weights will be added to foundry in the future. 
+
+Are we missing a model you would like to work with? Create a PR with the 
+necessary files and/or code changes or open an issue requesting it.
+

rc_foundry-0.1.10/docs/source/models/rf3/index.md

@@ -0,0 +1,11 @@
+# RF3 Documentation
+
+```{warning}
+The documentation for RF3 is currently incomplete. If you would like
+to contribute, feel free to open a PR!
+```
+
+RF3 is an all-atom biomolecular structure prediction network 
+competitive with leading open-source models. By including additional features at train-time – implicit chirality representations and atom-level geometric conditioning – we improve performance on tasks such as prediction of chiral ligands and fixed-backbone or fixed-conformer docking.
+
+For more information, please see our preprint, [Accelerating Biomolecular Modeling with AtomWorks and RF3](https://doi.org/10.1101/2025.08.14.670328).

{rc_foundry-0.1.7/models/rfd3/docs → rc_foundry-0.1.10/docs/source/models/rfd3}/demo.json

@@ -29,6 +29,7 @@
         "input": "./input_pdbs/1bna.pdb",
         "contig": "A1-10,/0,B15-24,/0,120-130",
         "length": "140-150",
-        "ori_token": [24,20,10]
+        "ori_token": [24,20,10],
+        "is_non_loopy": true
     }
 }

{rc_foundry-0.1.7/models/rfd3/docs → rc_foundry-0.1.10/docs/source/models/rfd3}/enzyme_design.md

@@ -9,7 +9,7 @@ RFD3 contains several knobs and dials for enzyme design.
 If you would like to run the examples below, `enzyme_design.json`, located in this directory, contains the example code. You can run it via:
 ```
 rfd3 design out_dir=inference_outputs/enzyme/0 \
-ckpt_path=/path/to/rfd3_foundry_2025_12_01.ckpt \
+ckpt_path=/path/to/rfd3_latest.ckpt \
 inputs=./enzyme_design.json
 ```
 
@@ -17,7 +17,7 @@ Or, if you have cloned the repo rather than using `pip install`:
 ```
 python path/to/foundry/models/rfd3/src/rfd3/run_inference.py \
 out_dir=inference_outputs/enzyme/0 \
-ckpt_path=/path/to/rfd3_foundry_2025_12_01.ckpt \
+ckpt_path=/path/to/rfd3_latest.ckpt \
 inputs=./enzyme_design.json 
 ```
 

rc_foundry-0.1.10/docs/source/models/rfd3/index.rst

@@ -0,0 +1,33 @@
+RFdiffusion3 Documentation
+==========================
+
+RFdiffusion3 is a powerful protein design tool that operates on the atomic level to 
+study ligand-protein interactions, create nucleic acid-protein interfaces, and 
+design *de novo* enzymes. It is designed to be highly flexible and 
+user-friendly, making it suitable for a wide range of applications in computational biology and biochemistry.
+
+General
+---------
+.. toctree::
+   :maxdepth: 1
+
+   intro_inference_calculations.md
+   input.md
+
+Tutorials
+---------
+.. toctree::
+   :maxdepth: 1
+
+   ppi_design_tutorial.md
+
+Examples
+--------
+.. toctree::
+   :maxdepth: 1 
+
+   na_binder_design.md
+   sm_binder_design.md
+   protein_binder_design.md
+   symmetry.md
+   enzyme_design.md