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Commits on Sep 30, 2025

• AF2: replace LN with safe LN, add flag for dropout during prediction + loss, simplifying recycling setup. (#34)

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  nboyd

  authored
  79cf981

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Commits on Sep 23, 2025

• Simplifying AF2 interface (#33)

  nboyd

  authored
  1935aea

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Commits on Sep 20, 2025

• Unified interface for structure prediction + loss construction for structure models (#31)

  nboyd

  authored
  a97b575

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Commits on Sep 4, 2025

• add tpu support, fix expanduser bug

  samtomguns

  committed
  4cabf0e

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Commits on Sep 3, 2025

• fix name in README (#30)

  dcroote

  authored
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Commits on Aug 29, 2025

• fix sign error in loss (#29)

  nboyd

  authored
  5399257

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• update optimizers, readme (#28)

  nboyd

  authored
  fc395bb

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• implement ipSAE loss (#27)

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  samtomguns

  authored
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Commits on Aug 25, 2025

• add protenix. add support for stateful loss functions. simplify optimizers.py. rename. (#26)

  nboyd

  authored
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Commits on Jul 19, 2025

• add iptm to boltz1+2 (#25)

  nboyd

  authored
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Commits on Jul 14, 2025

• bump equinox (#24)

  nboyd

  authored
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Commits on Jul 1, 2025

• add boltz iptm. retain sidechain atoms in af2 template.

  nboyd

  committed
  cee8a5a

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Commits on Jun 23, 2025

• add new IF loss. fix bug in AF coords. add templates to boltz2 (#22)

  nboyd

  authored
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Commits on Jun 17, 2025

• fix links

  nboyd

  committed
  c4b0b6c

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• simplify structure prediciton losses. add boltz-2 structure module an… (#21)

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  nboyd

  authored
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Commits on Jun 12, 2025

• download boltz2 cache if missing

  nboyd

  committed
  97c415b

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Commits on Jun 11, 2025

• fix (?) nondeterministic manifest issue

  nboyd

  committed
  5632407

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• add boltz2 (#20)

  nboyd

  authored
  66c093b

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Commits on Jun 6, 2025

• :(

  nboyd

  committed
  85cff46

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• update pyproject, minor QoL improvements

  nboyd

  committed
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Commits on May 31, 2025

• add ptmenergy. remove stop_grad in af2 structure module! (#19)

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  nboyd

  authored
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Commits on May 29, 2025

• fix default kwarg for mpnn encoder (#18)

  nboyd

  authored
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Commits on May 19, 2025

• add ablang pll, gradient clipping and normalization (#17)

  nboyd

  authored
  2a3d937

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Commits on May 15, 2025

• fix esmj source

  nboyd

  committed
  4b78649

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• update README, add ESMC -> stability model. fix a bunch of deps 👎 (#16)

  nboyd

  authored
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Commits on Mar 21, 2025

• upgrade jax to improve TPU performance (#13)

  samtomguns

  authored
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Commits on Feb 20, 2025

• replace internal esm implementation with esm2quinox

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  samtomguns

  authored
  bcb153d

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• move docstring to class

  samtomguns

  committed
  b9d5a20

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• usage docstring

  samtomguns

  committed
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• use esm2eqx alphabet instead of hardcoded tokens

  samtomguns

  committed
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Commits on Feb 19, 2025

• license info

  samtomguns

  committed
  7181071

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• simplify everything

  samtomguns

  committed
  62f274c

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• index before applying head

  samtomguns

  committed
  7f636a9

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• make it an eqx module

  samtomguns

  committed
  deb924b

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• remove unnecessary filter_jit

  samtomguns

  committed
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