* Docs: Installation FAQ space and minor RFD3 docs updates
Installation FAQ: created a document to specify any common installation issues and questions. Should be continuously updated based on logged issues and questions. Not specific to any model.
RFD3:
- changed the checkpoint files specified in the examples to rfd3_latest.ckpt
- updated information in input.md to clarify information based on recent issues that had been submitted
* Docs: Symlinks for RF3 and MPNN docs, RFD3 README minor edits
RF3 and MPNN: folders, index files, and symlinks were created in order to provide space for eventual RF3 and MPNN docs.
Several small changes in the RFD3 README to improve readability and add a pointer to the PPI tutorial as a starting point for someone new to RFdiffusion tools.
* First draft of enzyme design tutorial. Minor typo fixes in other documents.
* First draft of nucleic acid binder tutorial, minor edits to the other tutorials
* Completed enzyme design tutorial, removal of NA binder tutorial from index
Made changes based on edits from Saman, added images, and created zip file containing sample outputs for an enzyme design tutorial.
I am waiting on edits for the NA binder design tutorial, so for now I have removed it from the documentation index.
* First drafts of content for NA binder design tutorial
This tutorial is being created in collaboration with Raktim Mitra.
* Adding images to NA binder design tutorial
* Final draft of NA binder tutorial
* Create unfix.zip
* Updated images for na binder tutorial
* fix: restore exact python version constraint (==3.12)
Commit 49187c3 unintentionally reverted requires-python from ==3.12
back to >=3.12 as a side-effect of the inference fix. This restores
the exact version constraint originally introduced in 8aeacba.
* fix: relax python version constraint to allow 3.12.x
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---------
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* RF3 README update and moving RF3 examples
I updated the RF3 README for installation instructions that matched the RFD3 installation instructions. For the first example, I improve the instructions for running and fixed the output file descriptions to match what is now output by running the example. I commented out the 'Templating a Small Molecule' section because many of the files in that section were not present in the repository. The rest of the changes were mostly typo fixes.
I moved the examples from `foundry/docs/releases` to `foundry/models/rf3/docs` to match the organization of RFD3. The changes made to the JSON files just reflect this change of location.
* Changed paths in example JSON files to point to new RF3 examples location
* Updated the landing page for the RF3 documentation so that it links out to the README
* Docs: Installation FAQ space and minor RFD3 docs updates
Installation FAQ: created a document to specify any common installation issues and questions. Should be continuously updated based on logged issues and questions. Not specific to any model.
RFD3:
- changed the checkpoint files specified in the examples to rfd3_latest.ckpt
- updated information in input.md to clarify information based on recent issues that had been submitted
* Docs: Symlinks for RF3 and MPNN docs, RFD3 README minor edits
RF3 and MPNN: folders, index files, and symlinks were created in order to provide space for eventual RF3 and MPNN docs.
Several small changes in the RFD3 README to improve readability and add a pointer to the PPI tutorial as a starting point for someone new to RFdiffusion tools.
* First draft of enzyme design tutorial. Minor typo fixes in other documents.
* First draft of nucleic acid binder tutorial, minor edits to the other tutorials
* Completed enzyme design tutorial, removal of NA binder tutorial from index
Made changes based on edits from Saman, added images, and created zip file containing sample outputs for an enzyme design tutorial.
I am waiting on edits for the NA binder design tutorial, so for now I have removed it from the documentation index.
* Removing file related to in-progress NA binder tutorial
* Removing file related to in-progress NA binder tutorial
* Final version of the enzyme design tutorial
Made small edits, created example files.
* Resolving merge conflicts
* Docs: Installation FAQ space and minor RFD3 docs updates
Installation FAQ: created a document to specify any common installation issues and questions. Should be continuously updated based on logged issues and questions. Not specific to any model.
RFD3:
- changed the checkpoint files specified in the examples to rfd3_latest.ckpt
- updated information in input.md to clarify information based on recent issues that had been submitted
* Docs: Symlinks for RF3 and MPNN docs, RFD3 README minor edits
RF3 and MPNN: folders, index files, and symlinks were created in order to provide space for eventual RF3 and MPNN docs.
Several small changes in the RFD3 README to improve readability and add a pointer to the PPI tutorial as a starting point for someone new to RFdiffusion tools.
* First draft of enzyme design tutorial. Minor typo fixes in other documents.
* First draft of nucleic acid binder tutorial, minor edits to the other tutorials
* Completed enzyme design tutorial, removal of NA binder tutorial from index
Made changes based on edits from Saman, added images, and created zip file containing sample outputs for an enzyme design tutorial.
I am waiting on edits for the NA binder design tutorial, so for now I have removed it from the documentation index.
* Removing file related to in-progress NA binder tutorial
* Removing file related to in-progress NA binder tutorial
* Update ppi_design_tutorial.md
- Added information about useful CLI arguments
- Cleaned up the introduction
- Added section for what one might do with the designs from RFD3
- Added a note about hotspot residues also being in the `contig` (information from Rafi's TTT talk)
- Fixed minor sphinx heading issue
* Reorganizing RFD3 documentation
Reorganized files into an `examples` and a `tutorials` folders to clean up the RFD3 docs folder and align its organization with the RF3 docs folder. Any edits made in the files are related to changing the paths to reflect these changes.
* Docs: Designability vs. Diversity document
Created a document describing the settings that can impact the designability and diversity of structures output by RFdiffusion3, the information is based on the talk Rafi gave at Tech Tea Time in January.
* Minor grammar fixes in designability vs diversity document
* Update models/rfd3/docs/tutorials/ppi_design_tutorial.md
Co-authored-by: Rafael Brent <105883594+RafiBrent@users.noreply.github.com>
* Update models/rfd3/docs/tutorials/enzyme_design_tutorial.md
Co-authored-by: Rafael Brent <105883594+RafiBrent@users.noreply.github.com>
* Update models/rfd3/docs/designability_vs_diversity.md
Co-authored-by: Rafael Brent <105883594+RafiBrent@users.noreply.github.com>
* Update models/rfd3/docs/designability_vs_diversity.md
Co-authored-by: Rafael Brent <105883594+RafiBrent@users.noreply.github.com>
---------
Co-authored-by: Jasper Butcher <66851659+Ubiquinone-dot@users.noreply.github.com>
Co-authored-by: Rafael Brent <105883594+RafiBrent@users.noreply.github.com>
* Create Issue Templates
Created templates for bug reports, feature requests, and usage questions. The main goal is to encourage users to provide files and details required to understand their problem/request/question so that minimal back and forth needs to occur before a solution is reached.
* Revise issue template for clarity and detail
Updated issue template to include a request for images of expected behavior and streamlined the reproduction steps section.
* Upload Dockerfile to examples
* Update Foundry README with Docker information
- There is an image for Foundry on DockerHub
- Example recipe is in `foundry/examples/docker`
---------
Co-authored-by: Rachel Clune <rachel.clune@omsf.io>
* Docs: Installation FAQ space and minor RFD3 docs updates
Installation FAQ: created a document to specify any common installation issues and questions. Should be continuously updated based on logged issues and questions. Not specific to any model.
RFD3:
- changed the checkpoint files specified in the examples to rfd3_latest.ckpt
- updated information in input.md to clarify information based on recent issues that had been submitted
* Docs: Symlinks for RF3 and MPNN docs, RFD3 README minor edits
RF3 and MPNN: folders, index files, and symlinks were created in order to provide space for eventual RF3 and MPNN docs.
Several small changes in the RFD3 README to improve readability and add a pointer to the PPI tutorial as a starting point for someone new to RFdiffusion tools.
feat: Add Intel XPU support for all models
- Add XPU accelerator, precision, and strategy classes
- Update DDP utilities to detect and use Intel XPU
- Add XPU trainer configs for RF3 and RFD3
- Update MPNN inference engine for XPU compatibility
- Update README with XPU documentation
Right now going to the GH pages site just shows the README, this is likely because GH is only building the README with Jekyll even though this workflow should override it without the added lines.
* Starting to put together the foundry and RFD3 external documentation
Set up the foundation for Sphinx to be able to build the external docs, first draft of a ppi_design_tutorial has been completed.
* Add RFdiffusion3 documentation and update toctree
Added initial documentation for RFdiffusion3 under models/rfd3/docs/index.rst and linked it in the main docs toctree. Updated toctree maxdepth for better navigation and added a symlink for the rfd3 model documentation.
* Update and expand RFdiffusion3 documentation
Added introductory and reference documentation files, improved the index structure with general information and examples, and enhanced the PPI design tutorial with additional notes, figures, and clarifications. Also fixed a typo in a PDB filename.
* Update RFD3 documentation and tutorial content
Expanded the Sphinx static path to include RFD3 assets and made minor formatting and clarity improvements in the main and RFD3-specific documentation. The PPI design tutorial was revised for clarity, improved step-by-step instructions, and better separation of setup and execution steps.
* Update RFD3 documentation and tutorials
Added source_suffix to Sphinx conf.py for Markdown support. Updated index.rst to include new documentation sections. Expanded intro_inference_calculations.md with detailed instructions on inference input formats, job configuration, and output files. Improved input.md formatting for appendices and FAQs. Revised ppi_design_tutorial.md for clarity, added details on settings, and expanded explanations for hotspots and batch inference.
* Update RFD3 docs: clarify input specs and file formats
Expanded and clarified the documentation for RFdiffusion3 input specifications, including more detailed explanations of the 'contig' string, input file types, and example YAML/JSON formats. Improved the intro to inference calculations to better explain the structure and usage of settings files, and updated descriptions for job configuration and output files. Added a placeholder for configuration options documentation.
* Update RFdiffusion3 input documentation and examples
Expanded and clarified the documentation for RFdiffusion3 input specification, including detailed explanations of CLI arguments, InputSpecification fields, the InputSelection mini-language, contig string formatting, and advanced options such as partial diffusion and CIF parser arguments. Added more examples, debugging recommendations, and an updated FAQ. Also updated the output file naming explanation for clarity. Removed the obsolete configuration_options.md file.
Note that images are still not being rendered correctly in many of the md files. Fix will be in future commit.
* PPI tutorial and RFD3 docs update
Created output files for PPI tutorial and listed their locations. Made edits to files to add labels to sections to remove sphinx warnings.
* Delete docs/source/conf.py~
This is an auto-save file from emacs - it does not need to be in the repo.
* Delete docs/source/index.rst~
This is an auto-saved copy of index.rst, it does not need to be in the repo
* Adding missing images and fixing docs symlink
* Fix grammatical error in RFdiffusion3 documentation
Fixed typo, clarified enzyme design language.
* Fix typos and enhance clarity in inference docs
Corrected typos and improved clarity in the documentation regarding inference settings and file formats.
* Improve 'unindex' field description in input_parsing.py
Updated the description for the 'unindex' field to clarify its purpose and usage.
* Make format
