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Third-party notices

FastPLMs implements interfaces and checkpoint mappings for independently released protein models. The pinned repositories under vendor/upstream/ are parity oracles. Production code does not import them, and runtime images do not contain them.

This notice is informational and is not legal advice. A checkpoint license can differ from the license covering its source implementation. The typed inventory in src/fastplms/models.toml and the verbatim files under LICENSES/ are the distribution record.

ANKH

The pinned ANKH implementation and the mirrored ANKH checkpoints are identified as CC BY-NC-SA 4.0. FastPLMs displays those terms but does not enforce them in software. Users are responsible for determining whether their use and redistribution comply. The complete text is in LICENSES/ankh/LICENSE.md.

Profluent-E1

Profluent identifies its E1 model code as Apache-2.0. The E1 weights and full release are subject to the Profluent-E1 Clickthrough License Agreement and the incorporated attribution requirements. Any E1 distribution must retain all of the following files:

  • LICENSES/e1/LICENSE, the Profluent-E1 agreement
  • LICENSES/e1/ATTRIBUTION, the attribution guidelines
  • LICENSES/e1/NOTICE, the required notice
  • LICENSES/e1/Apache-2.0.txt, the code license
  • LICENSES/e1/BSD-3-Clause.txt, covering the FlashAttention-derived padding utility identified by the official E1 source
  • LICENSES/e1/MODIFICATIONS.md, the FastPLMs modified-file notice

The exact text Profluent-E1 must remain prominently displayed in E1 documentation and at each launch of an executable E1 workflow, as required by the upstream attribution guidelines. Certain commercial outputs, including specified pharmaceutical and target-related outputs, can require the separate Built with Profluent-E1 statement described in ATTRIBUTION.

DPLM

The pinned ByteDance DPLM repository is Apache-2.0. Its README explicitly defines the repository release as including pretrained DPLM1 and DPLM2 weights, and the same revision carries the complete Apache-2.0 license. FastPLMs records both checkpoint families as Apache-2.0 and distributes the verbatim license plus LICENSES/dplm/PROVENANCE.md. Converted weights retain those terms and remain subject to the ordinary artifact and publication gates.

Biohub

The pinned Biohub ESM implementation is MIT and includes a separate THIRD_PARTY_NOTICE.md; both files are distributed under LICENSES/biohub-esm/. The pinned Biohub Transformers fork is Apache-2.0, with its complete text under LICENSES/biohub-transformers/.

Boltz

The pinned Boltz source is MIT. The verbatim notice is in LICENSES/boltz/LICENSE.

Meta ESM and OpenFold

The pinned Meta ESM source is MIT. The pinned OpenFold source is Apache-2.0. Their verbatim texts and revision-specific provenance notices are under LICENSES/fair-esm/ and LICENSES/openfold/.

The native H100 ESMFold reference image applies the tracked docker/constraints/openfold-sm90.patch to the copied OpenFold setup.py. This build-only change restricts the CUDA extension to sm90 and selects the C++17 standard required by the reference PyTorch version. It leaves the pinned submodule, extension source, model classes, checkpoint data, and public API unchanged. The complete modified-file record is in LICENSES/openfold/MODIFICATIONS.md.

The isolated reference image also includes Apache-2.0 PyTorch Lightning, TorchMetrics, Lightning Utilities, and NVIDIA DLLogger. Their exact versions or revision are pinned in docker/constraints/esmfold.txt; OpenFold imports them eagerly, and FastPLMs production code does not depend on them. DLLogger's exact source identity and installed-license handling are recorded in LICENSES/dllogger/PROVENANCE.md.

ProteinTTT

The optional test-time training workflow is validated against the pinned ProteinTTT repository under its MIT license. Its verbatim license and revision-specific provenance are under LICENSES/protein-ttt/.

Conversion and packaging record

For every supported family, src/fastplms/models.toml records an immutable official checkpoint revision, an immutable FastPLMs checkpoint revision, file digests, a named state transformation, and a mechanism-level conversion record. Generated artifacts reproduce that record in provenance.json. A release or artifact build must fail when a required file identity, legal text, attribution notice, modified-file notice, upstream revision, or conversion record is absent or differs from its manifest digest.