Foundry atom23#245

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timkartar wants to merge 49 commits intoproductionfrom

Commits on Mar 20, 2026

Install bug

Ubiquinone-dot
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Raktim Mitra
committed
Bugfixes for confidence training

fdimaio
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Raktim Mitra
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feat: atom23 porting

Raktim Mitra
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Raktim Mitra
committed
feat: atom23 inference changes and training fixes

Raktim Mitra
authored and
Raktim Mitra
committed
feat: atom23 porting

Raktim Mitra
authored and
Raktim Mitra
committed
feat: atom23 inference changes and training fixes

Raktim Mitra
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Raktim Mitra
committed
add .env, can remove paths later

Raktim Mitra
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Raktim Mitra
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Add nucleic SS metrics + conditioning + pseudoknot dataset config

andrewfavor95
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Raktim Mitra
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train and inference atom23 with custom datasets and na ss transform

Raktim Mitra
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Raktim Mitra
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inference fixes for legacy_input_parsing
Raktim Mitra
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feat: atom23 porting

Raktim Mitra
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Raktim Mitra
committed
fix: atom23 constants import error
Raktim Mitra
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mor einference fixes
Raktim Mitra
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fix: tiny legacy parsing bug
Raktim Mitra
committed
inference fixes
Raktim Mitra
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ligand chain fix; add ori_jitter option in new dialect

Raktim Mitra
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Raktim Mitra
committed
make 2oken_2d_features/embedder optional
Raktim Mitra
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dll bug fix
Raktim Mitra
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cleaned up NA-SS conditioning code before rebase

andrewfavor95
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Raktim Mitra
committed
fixed behavior for conditional sampling of NA SS condition

andrewfavor95
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Raktim Mitra
committed
val metric logging fix

Raktim Mitra
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Raktim Mitra
committed
prevalidate on

Raktim Mitra
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Raktim Mitra
committed
skip ss computation when not ss example
Raktim Mitra
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cleanup; aptamer metric; monomer dist on; send trainininggit status

Raktim Mitra
authored and
Raktim Mitra
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run time fixes; inference fix for readout seq from struct
Raktim Mitra
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time to fix ss metric line 242
Raktim Mitra
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fixed na ss metric calculation

andrewfavor95
authored and
Raktim Mitra
committed
fix atom14 scheme cases

Raktim Mitra
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Raktim Mitra
committed
fix: permute U in association_schemes_stripped

Raktim Mitra
authored and
Raktim Mitra
committed
time to fix ss metric line 242
Raktim Mitra
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add failsafe for nucleic ss metric

Raktim Mitra
authored and
Raktim Mitra
committed
extra filter for huge base pair centroid distances, and also cleaned inference specification code

andrewfavor95
authored and
Raktim Mitra
committed
mc: yaml changes
Raktim Mitra
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refactor ss metric computatino section to be called during inference to write in the json
Raktim Mitra
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cfg for bp_partners feature

Raktim Mitra
authored and
Raktim Mitra
committed
unindex fix final for real

Raktim Mitra
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Raktim Mitra
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unindex train fix

Raktim Mitra
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Raktim Mitra
committed
remove rf3 config which tagegd along
Raktim Mitra
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remove extra rfd3na configs
Raktim Mitra
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debug cleanup
Raktim Mitra
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leftover rebase bugs cleanup, atom14 inference demo working
Raktim Mitra
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Commits on Mar 23, 2026

cleanup configs
Raktim Mitra
committed

Commits on Mar 27, 2026

ruff format
Raktim Mitra
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ruff_format_2
Raktim Mitra
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cleanup debug comment
Raktim Mitra
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docs and json progress
Raktim Mitra
committed

Commits on Mar 28, 2026

more extensive documentation
Raktim Mitra
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cleanup
Raktim Mitra
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main readme updates
Raktim Mitra
committed