Pull Request №448 RosettaCommons/RFdiffusion/main ← haoyu-haoyu/RFdiffusion/refactor/extract-magic-numbers
Merge: 9535f1938203a24937d7dadf0cb831d02cb5fc0e←2a7aa2d3a49c4fd3b52bd4cb95e6cc61de90d0d1
refactor: extract magic numbers into named constants module
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Merge commit message:
refactor: extract magic numbers into named constants module
Add rfdiffusion/constants.py centralizing magic numbers used across the
codebase, with documentation of each constant's meaning and provenance.
Replace inline values in 4 files:
- Cbeta reconstruction coefficients (-0.58273431, 0.56802827, -0.54067466)
used in util.py (2x), Embeddings.py, coords6d.py → CBETA_A/B/C
- Amino acid token indices (21=mask, 7=glycine) in run_inference.py
→ AA_MASK_TOKEN, AA_GLYCINE
Also documents additional constants (NO_CONTACT_DIST, CHAIN_BREAK_*,
SE3_*_SCALE, diffusion schedule params) for future refactoring.
Pull Request №445 RosettaCommons/RFdiffusion/main ← haoyu-haoyu/RFdiffusion/fix/replace-deprecated-torch-cuda-amp
Merge: 9535f1938203a24937d7dadf0cb831d02cb5fc0e←a7cc837a05b7944bf06c22795d390adf8821b681
fix: replace deprecated torch.cuda.amp with torch.amp
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Merge commit message:
fix: replace deprecated torch.cuda.amp with torch.amp
`torch.cuda.amp.autocast`, `torch.cuda.amp.GradScaler` were deprecated
in PyTorch 1.13 and will be removed in a future release. Replace with
the device-explicit `torch.amp.autocast('cuda', ...)` and
`torch.amp.GradScaler('cuda', ...)` equivalents.
Files changed:
- rfdiffusion/Track_module.py (decorator on Str2Str.forward)
- env/SE3Transformer/se3_transformer/runtime/inference.py
- env/SE3Transformer/se3_transformer/runtime/training.py (2 instances)
Pull Request №446 RosettaCommons/RFdiffusion/main ← haoyu-haoyu/RFdiffusion/feat/add-input-validation
Merge: 9535f1938203a24937d7dadf0cb831d02cb5fc0e←ac7215240a48d6e41d78dc5ae18204d5a617115b
feat: add input validation for early error detection
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Merge commit message:
feat: add input validation layer for early error detection
Add rfdiffusion/validation.py with validators for:
- PDB file existence and ATOM record format
- Contig string syntax (ranges, chain-residue specs)
- Model checkpoint existence
- Hotspot residue format (chain letter + number)
- Diffuser config parameters (T, partial_T bounds)
Validators are called in Sampler.initialize() and sample_init(), before
GPU allocation and model loading, so users get clear error messages
instead of cryptic tensor shape mismatches.
Pull Request №447 RosettaCommons/RFdiffusion/main ← haoyu-haoyu/RFdiffusion/perf/reduce-gpu-memory-usage
Merge: 9535f1938203a24937d7dadf0cb831d02cb5fc0e←5735aff0e6d512ffa26a4d787613820c2c9bf16f
perf: reduce GPU memory usage during inference
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Merge commit message:
perf: reduce GPU memory usage during inference
- Move trajectory data (px0, x_t, seq, plddt) to CPU immediately after
each denoising step instead of accumulating on GPU. This frees GPU
memory for the next forward pass, reducing peak memory usage
proportional to the number of diffusion steps.
- Remove two unused ComputeAllAtomCoords() instantiations in
get_next_ca() and get_next_pose() that were created every timestep
but never referenced, wasting memory and compute.
Pull Request №426 RosettaCommons/RFdiffusion/main ← RosettaCommons/RFdiffusion/updated_scaffoldguided_fix
Merge: ff20fbafefbdc9b9eb9423754fd418939c32e89e←ecf161b4e2579fdbb9f4a668ac39656bfbc2180a
Updated "Fixed issues with designing in scaffoldguided mode" original PR 386
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Merge commit message:
Move cyclic_reses initialization to a helper function and call it for Sampler and ScaffoldedSampler
Pull Request №426 RosettaCommons/RFdiffusion/main ← RosettaCommons/RFdiffusion/updated_scaffoldguided_fix
Merge: ff20fbafefbdc9b9eb9423754fd418939c32e89e←723a66408c9a5f722812e7bbe13a116fa2fd4f42
Updated "Fixed issues with designing in scaffoldguided mode" original PR 386
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Merge commit message:
Reverting changes to flag name, so you still use scaffoldguided.scaffoldguided=True instead of scaffoldguided_enabled
Pull Request №410 RosettaCommons/RFdiffusion/main ← RosettaCommons/RFdiffusion/fix_test_diffusion
Merge: e22092420281c644b928e64d490044dfca4f9175←dd7643d6406cfbb1332eccaa36e6c0fc786251de
Fix workflow tests that are failing
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Merge commit message:
Revert "Remove try block with except FileExistsError that isn't needed"
After running the test, I found that this was needed
This reverts commit ead721f32670eae379612d9e545690c3f288d251.
Pull Request №410 RosettaCommons/RFdiffusion/main ← RosettaCommons/RFdiffusion/fix_test_diffusion
Merge: e22092420281c644b928e64d490044dfca4f9175←681874e6ea19e763a5ccb35d1a434c9b3f6d8179
Fix workflow tests that are failing
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Merge commit message:
Reduce length for design_tetrahedral_oligos to 600 to reduce run time
Pull Request №410 RosettaCommons/RFdiffusion/main ← RosettaCommons/RFdiffusion/fix_test_diffusion
Merge: e22092420281c644b928e64d490044dfca4f9175←4d870c07da5e645393ee85a557b41e799d8b6371
Fix workflow tests that are failing
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Merge commit message:
In setUpClass check that directory doesn't already exists, so tests do not fail before running examples
Pull Request №410 RosettaCommons/RFdiffusion/main ← RosettaCommons/RFdiffusion/fix_test_diffusion
Merge: e22092420281c644b928e64d490044dfca4f9175←a570b2b8bdce98e979d875cde81d5f9ed0f3d225
Fix workflow tests that are failing
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Merge commit message:
Edit main.yml workflow so if an example fails, the test doesn't pass
Pull Request №410 RosettaCommons/RFdiffusion/main ← RosettaCommons/RFdiffusion/fix_test_diffusion
Merge: e22092420281c644b928e64d490044dfca4f9175←260692d6c2ce4a565fd60cf636c825c3317cc123
Fix workflow tests that are failing
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Merge commit message:
Edits to test_diffusion to make change setUp to setUpClass to make this a class method so examples run only once