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