checkpoints/README.md

Pretrained weights

Local checkpoint files read by the released structure encoders of ProtCompass. Every file here is byte-identical to the upstream release, and loading it with the project's wrapper on CPU reproduces the weight hash (weights_sha256) recorded in the meta.json of the released embeddings. SHA256SUMS lists the full hashes; check them with sha256sum -c SHA256SUMS from this folder.

Folder	File	Size (bytes)	SHA-256 (first 16)	Used by	Source	Licence
proteinmpnn/	proteinmpnn_v48_020.pt	6,681,301	c9cb4a671d796041	ProteinMPNN	github.com/dauparas/ProteinMPNN, vanilla_model_weights/v_48_020.pt (commit 8907e66)	MIT (LICENSE)
gearnet_pretrained/	mc_gearnet_edge.pth	80,700,937	6dc11e2db6eff3c9	GearNet-pre	Zenodo 10.5281/zenodo.7593637	CC BY 4.0 (NOTICE.md)
gcpnet_pretrained/	model_epoch_115_localpearson_0_616_..._globalkendall_0_676.ckpt	14,270,541	ff7b73be01fb57d5	GCPNet-pre; GCPNet (random) reads only its hyper-parameters	github.com/BioinfoMachineLearning/GCPNet, checkpoints/PSR/ (commit 172733b)	MIT (LICENSE)
pottsmpnn_pretrained/	pottsmpnn_20.pt	20,478,391	28b1620a71883142	PottsMPNN-pre	github.com/KeatingLab/PottsMPNN, proteinmpnn_compatible_model_weights/ (commit a6ccac3)	MIT (LICENSE)
pottsmpnn_soluble/	sol_pottsmpnn_20.pt	20,687,317	f203a69773df41a1	PottsMPNN-sol	same repository, soluble_model_weights/	MIT (LICENSE)
pottsmpnn_ft/	potts_ft.pt	20,690,454	b672ff4ed1492560	PottsMPNN-ft	same repository, ft_model_weights/	MIT (LICENSE)

The GCPNet file name is shortened in the table; the full name is in SHA256SUMS. The PottsMPNN repository holds two different files named sol_pottsmpnn_20.pt; the one used is the file in soluble_model_weights/.

Where the code expects each file

The released code reads these files from fixed paths under protcompass/ in the code repository (https://anonymous.4open.science/r/ProEmbedEva-C4F6):

File here	Path the code reads
proteinmpnn/proteinmpnn_v48_020.pt	protcompass/checkpoints/proteinmpnn_v48_020.pt
gearnet_pretrained/mc_gearnet_edge.pth	protcompass/checkpoints/gearnet/mc_gearnet_edge.pth
gcpnet_pretrained/<file>.ckpt	protcompass/external_repos/GCPNet/checkpoints/PSR/<file>.ckpt
pottsmpnn_pretrained/pottsmpnn_20.pt	protcompass/external_repos/PottsMPNN/proteinmpnn_compatible_model_weights/pottsmpnn_20.pt
pottsmpnn_soluble/sol_pottsmpnn_20.pt	protcompass/external_repos/PottsMPNN/soluble_model_weights/sol_pottsmpnn_20.pt
pottsmpnn_ft/potts_ft.pt	protcompass/external_repos/PottsMPNN/ft_model_weights/potts_ft.pt

A clone of the GCPNet and PottsMPNN repositories at the listed commits already contains their files at those paths. Otherwise, link the downloaded files into place from the root of the code repository (HF is the local copy of this Hugging Face repository):

HF=<local copy of this repository>
P=protcompass
mkdir -p $P/checkpoints/gearnet $P/external_repos/GCPNet/checkpoints/PSR \
         $P/external_repos/PottsMPNN/{proteinmpnn_compatible_model_weights,soluble_model_weights,ft_model_weights}
ln -s "$HF/checkpoints/proteinmpnn/proteinmpnn_v48_020.pt" $P/checkpoints/proteinmpnn_v48_020.pt
ln -s "$HF/checkpoints/gearnet_pretrained/mc_gearnet_edge.pth" $P/checkpoints/gearnet/mc_gearnet_edge.pth
ln -s "$HF"/checkpoints/gcpnet_pretrained/*.ckpt $P/external_repos/GCPNet/checkpoints/PSR/
ln -s "$HF/checkpoints/pottsmpnn_pretrained/pottsmpnn_20.pt" $P/external_repos/PottsMPNN/proteinmpnn_compatible_model_weights/
ln -s "$HF/checkpoints/pottsmpnn_soluble/sol_pottsmpnn_20.pt" $P/external_repos/PottsMPNN/soluble_model_weights/
ln -s "$HF/checkpoints/pottsmpnn_ft/potts_ft.pt" $P/external_repos/PottsMPNN/ft_model_weights/

Weights that are not in this folder

Encoder	Where the weights come from
ESM-1b, ESM2 (8M, 35M, 150M, 650M, 3B), ProtBert, ProtT5-XL, Ankh, ProstT5, SaProt	Hugging Face hub, by the id and revision in the checkpoint and checkpoint_revision fields of each meta.json (listed in the main README)
FoldVision	Hugging Face hub, AlexanderKroll/foldvision-encoder, through the model's own from_pretrained
ESM-IF1	downloaded by torch.hub.load("facebookresearch/esm:main", "esm_if1_gvp4_t16_142M_UR50") from the ESM release (MIT)
Foldseek 3Di	computed by the mini3di package, version 0.2.1 (BSD-3-Clause); no separate weights file
ESM3	esm3-sm-open-v1 is distributed by EvolutionaryScale under the Cambrian Non-Commercial License Agreement, which does not allow redistribution. Accept the licence and download it from the gated Hugging Face repository EvolutionaryScale/esm3-sm-open-v1; the code expects it under protcompass/esm3-sm-open-v1/
TFN-pre, IPA-pre	taken from the models' released repositories and not redistributed here; the code expects them at protcompass/checkpoints/tfn_pretrained/best.pt and protcompass/checkpoints/ipa_pretrained/best.pt, and the SHA-256 prefix of each file used is in the checkpoint_sha256 field of its meta.json
randomly initialised encoders (SchNet, TFN, DimeNet, MACE, GearNet, IPA, GVP, GCPNet, CDConv, PottsMPNN)	no weights file; the networks are built with the fixed seed 20260919, and the hash of the resulting weights is in each meta.json