Rachel Clune
98b12108c7
Added details and fixed typos in NA binder design examples ( #721 )
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* Fixed spelling and grammar mistakes in the md file for NA binder design examples. Created a .json file containing the code bits for users to easily run the examples.
* NA example clean up
Removed NA examples from foundry docs directory and moved necessary files to the RFD3 docs directory. Added example syntax for how to use `rfd3 design` instead of `python ...`
* Update na_binder_design.md small edits to the hbplus warning sentence
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Co-authored-by: Raktim Mitra <timkartar7879@gmail.com >
2025-12-03 00:34:46 -08:00
Rohith Krishna
faa2935417
remove ipd specific files
2025-12-02 20:56:06 -08:00
Rohith Krishna
db7cbf37d1
fix: fix path in paths for pdb parsing ( #715 )
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* refactor: change modelhub to foundry
* fix: fix path in paths for pdb parsing
* Update run_inf_tutorial.sh
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Co-authored-by: Rohith Krishna <rohith@localhost>
Co-authored-by: Raktim Mitra <timkartar7879@gmail.com >
2025-12-02 17:55:02 -08:00
Jasper Butcher
62cbbe28e5
Finalizing READMEs ( #711 )
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* Draft update to main
* Minor changes
* Add files
* ppi/sm/enzyme.md and input.md/reade.md cleanups
* fix run commands
* fix: typo in ppi md
* fix: Update header dna_binder_design.md
* description of dna_binder_design examples in .md
* fix: Update dna_binder_design.md fix typo
* fix: Update main README.md to add all citations
* fix: filename dna->na
* fix: filename dna->na
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Co-authored-by: Raktim Mitra <raktim@digs.ipd.uw.edu >
Co-authored-by: Raktim Mitra <timkartar7879@gmail.com >
2025-12-02 16:46:33 -08:00
Raktim Mitra
152a0911f1
DRAFT: docs for release, soft code hbplus ( #699 )
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* documentation for release draft start
* trajectory.png
* update readme to rf3-lab paths, annotate TODOs
* add input_pdbs, demo.json
* Update README.md example pngs
* tasks pngs
* Update README.md - restructure pngs and application links
* Update README.md mc
* Update README.md add ipynb kernel export instruction
* mpnn all.ipynb
* open and edit tutorial.zip
* Update run_inf_tutorial.sh
* remove outputs
* cleanup
* rename
* soft code hbplus executable
* rename modelforge to foundry (rfd3) README
* fix: enabled running rfd3, mpnn inline
* cleanup
* remove todos, one remaining
* clear outputs
---------
Co-authored-by: Raktim Mitra <raktim@digs>
Co-authored-by: Raktim Mitra <raktim@localhost>
Co-authored-by: Rohith Krishna <rohith@localhost>
Co-authored-by: Raktim Mitra <raktim@digs.ipd.uw.edu >
2025-12-01 18:23:02 -08:00
Jasper Butcher
7c1a77ff0c
Add enzyme example, refactor io ( #688 )
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* Add enzyme example, refactor io
* udpate
2025-11-25 16:45:25 -08:00
Nathaniel Corley
aa4cb6875f
fix: paths and ipd readme ( #656 )
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fix: update paths; add IPD readme
2025-11-13 17:46:04 -08:00
ncorley
cbbe4c6a6d
wip: save before letting Claude rip
2025-10-01 12:01:05 -07:00
ncorley
2e218aafc2
feat: update ligand templating, bump atomworks version
2025-09-17 21:41:57 -07:00
ncorley
f201cfa1cc
fix: inference for RF3
2025-09-17 04:01:18 -07:00
Nathaniel Corley
05ecfbf046
docs: graphics
2025-08-15 17:27:53 +02:00
