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checkpoints/README.md

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+# 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):
+
+```bash
+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` |

checkpoints/SHA256SUMS

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+ff7b73be01fb57d56087c83a3cea6a36fc9de9179f9eee4642dc78ec4a7648f6  gcpnet_pretrained/model_epoch_115_localpearson_0_616_localspearman_0_532_localkendall_0_385_globalpearson_0_871_globalspearman_0_869_globalkendall_0_676.ckpt
+6dc11e2db6eff3c90f90672af227c647125adb7476de18a2bb860457bdb598ec  gearnet_pretrained/mc_gearnet_edge.pth
+b672ff4ed1492560558dbc666f3df17b57236955dca379008fa2bc60b436c71e  pottsmpnn_ft/potts_ft.pt
+28b1620a71883142eddbc8911136e35324fe5ae025250ad86cef070a1fa1fbcb  pottsmpnn_pretrained/pottsmpnn_20.pt
+f203a69773df41a1b66512dc75a2eec28bfc4f28ec0c549e3f51567747e1607f  pottsmpnn_soluble/sol_pottsmpnn_20.pt
+c9cb4a671d79604111231f8dbfc7c590e06f1197453b7a6854ac6661a642f5bd  proteinmpnn/proteinmpnn_v48_020.pt

checkpoints/gcpnet_pretrained/LICENSE

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+MIT License
+
+Copyright (c) 2023 BioinfoMachineLearning
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

checkpoints/gcpnet_pretrained/model_epoch_115_localpearson_0_616_localspearman_0_532_localkendall_0_385_globalpearson_0_871_globalspearman_0_869_globalkendall_0_676.ckpt

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+version https://git-lfs.github.com/spec/v1
+oid sha256:ff7b73be01fb57d56087c83a3cea6a36fc9de9179f9eee4642dc78ec4a7648f6
+size 14270541

checkpoints/gearnet_pretrained/NOTICE.md

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+# mc_gearnet_edge.pth
+
+Source: Zenodo record "Pre-Trained Models for GearNet", DOI 10.5281/zenodo.7593637
+(<https://zenodo.org/records/7593637>). The file is unmodified; its MD5 (c35402108f14e43f20feb475918f9c26) equals the
+checksum listed in the record.
+
+Licence: Creative Commons Attribution 4.0 International (CC BY 4.0),
+<https://creativecommons.org/licenses/by/4.0/>, as stated in the Zenodo record. When you use this file, credit the
+Zenodo record above and the GearNet paper, "Protein Representation Learning by Geometric Structure Pretraining"
+(ICLR 2023). The GearNet code (github.com/DeepGraphLearning/GearNet) is under the MIT licence.

checkpoints/gearnet_pretrained/mc_gearnet_edge.pth

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+size 80700937

checkpoints/pottsmpnn_ft/LICENSE

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+MIT License
+
+Copyright (c) 2022 Justas Dauparas
+Copyright (c) 2026 Foster Birnbaum, Amy E. Keating.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

checkpoints/pottsmpnn_ft/potts_ft.pt

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+size 20690454

checkpoints/pottsmpnn_pretrained/LICENSE

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+MIT License
+
+Copyright (c) 2022 Justas Dauparas
+Copyright (c) 2026 Foster Birnbaum, Amy E. Keating.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

checkpoints/pottsmpnn_pretrained/pottsmpnn_20.pt

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+version https://git-lfs.github.com/spec/v1
+oid sha256:28b1620a71883142eddbc8911136e35324fe5ae025250ad86cef070a1fa1fbcb
+size 20478391

checkpoints/pottsmpnn_soluble/LICENSE

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+MIT License
+
+Copyright (c) 2022 Justas Dauparas
+Copyright (c) 2026 Foster Birnbaum, Amy E. Keating.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

checkpoints/pottsmpnn_soluble/sol_pottsmpnn_20.pt

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+version https://git-lfs.github.com/spec/v1
+oid sha256:f203a69773df41a1b66512dc75a2eec28bfc4f28ec0c549e3f51567747e1607f
+size 20687317

checkpoints/proteinmpnn/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2022 Justas Dauparas
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

checkpoints/proteinmpnn/proteinmpnn_v48_020.pt

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+version https://git-lfs.github.com/spec/v1
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