KeyError: 'hydropathy' while running design_pdb.py

[Thoudam-A]

Hi, thanks for excellent work! I ran command like this: python design_pdb.py ./data/examples/8X0Y_complex.pdb --config ./configs/test/codesign_single.yml and encountered an error, the result is:

---

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email [email protected] for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta PyRosetta4.Release.python38.ubuntu 2024.19+release.a34b73c40fe9c61558d566d6a63f803cfb15a4fc 2024-05-02T16:22:03] retrieved from: http://www.pyrosetta.org ┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email [email protected] for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta PyRosetta4.Release.python38.ubuntu 2024.19+release.a34b73c40fe9c61558d566d6a63f803cfb15a4fc 2024-05-02T16:22:03] retrieved from: http://www.pyrosetta.org [INFO] Renumbered chain F (K) [INFO] Chain B does not contain valid Fv: Variable chain sequence not recognized: "TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLAPATVCGPK" [INFO] Renumbered chain E (H) [2024-09-16 10:29:59,816::sample::INFO] Data ID: 8X0Y_complex.pdb [2024-09-16 10:29:59,816::sample::INFO] Results will be saved to ./results/codesign_single/8X0Y_complex.pdb_2024_09_16__10_29_59 [2024-09-16 10:29:59,917::sample::INFO] Loading model config and checkpoints: trained_models/ckpt.pt [2024-09-16 10:31:14,701::sample::INFO] <All keys matched successfully> [2024-09-16 10:31:14,858::sample::INFO] Start sampling for: H_CDR3 Sampling: 0%| | 0/500 [00:00<?, ?it/s] 8X0Y_complex.pdb-H_CDR3: 0%| | 0/1 [00:00<?, ?it/s] Traceback (most recent call last): File "design_pdb.py", line 4, in design_for_pdb(args_from_cmdline()) File "/home/disk02/ab_design/zrx/ab_opt-main/AbDesign/diffab/tools/runner/design_for_pdb.py", line 200, in design_for_pdb traj_batch = model.sample(batch, sample_opt={ File "/home/disk02/ab_design/miniconda3/envs/diffab/lib/python3.8/site-packages/torch/autograd/grad_mode.py", line 27, in decorate_context return func(*args, **kwargs) File "/home/disk02/ab_design/zrx/ab_opt-main/AbDesign/diffab/models/diff_gnn.py", line 262, in sample hydropathy = batch['hydropathy'][batch['mask']] KeyError: 'hydropathy'

---

How can I fix it? I tried to set the attribute ‘hydropathy’ false, but it didn't work. I'll be very grateful for your response!