KeyError: 'icf'

[QUEST2179]

Tried below script but it gave keyerror, but python projects/tfold_ag/predict.py works though. Could you please help to fix it? Thanks!

import torch
import tfold

Download the pre-trained model of ESM-PPI

ppi_model_path = tfold.model.esm_ppi_650m_ab()

Download the pre-trained model of alphaFold

alphafold_path = tfold.model.alpha_fold_4_ptm()

Download base model for tFold-Ag

tfold_model_path = tfold.model.tfold_ag_base()

Download the ppi model for tFold-Ag

tfold_model_path = tfold.model.tfold_ag_ppi()

Load the model

model = tfold.deploy.AgPredictor(ppi_model_path, alphafold_path, tfold_model_path)

Prepare antibody-antigen sequences

msa_path = 'examples/msa.files/8df5_R.a3m'
with open(msa_path) as f:
msa, deletion_matrix = tfold.protein.parser.parse_a3m(f.read())

data = [
{
"id": "H",
"sequence": "QVQLVQSGAEVKKPGASVKVSCKASGYPFTSYGISWVRQAPGQGLEWMGWISTYNGNTNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCARDYTRGAWFGESLIGGFDNWGQGTLVTVSS"
},
{
"id": "L",
"sequence": "EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVEIK"
},
{
"id": "A",
"sequence": "MGILPSPGMPALLSLVSLLSVLLMGCVAETGTRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGPKKSTHHHHHHHHGGSSGLNDIFEAQKIEWHE",
"msa": msa,
"deletion_matrix": deletion_matrix
}
]

output_path = 'examples/predictions/8df5_A_B_R.pdb'
model.infer_pdb(data, output_path)

Traceback (most recent call last):
File "/mnt/antibody/tfold-master/processTFold.py", line 50, in
model.infer_pdb(data, output_path)
File "/mnt/antibody/tfold-master/tfold/deploy/ag_predictor.py", line 110, in infer_pdb
inputs, outputs = self.infer(chains, icf_path=icf_path, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/miniconda/envs/torch11/lib/python3.11/site-packages/torch/utils/_contextlib.py", line 115, in decorate_context
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/mnt/antibody/tfold-master/tfold/deploy/ag_predictor.py", line 106, in infer
outputs = self.forward(inputs, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/antibody/tfold-master/tfold/deploy/ag_predictor.py", line 97, in forward
outputs = self.model(inputs, chunk_size=chunk_size)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/miniconda/envs/torch11/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1511, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/miniconda/envs/torch11/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1520, in _call_impl
return forward_call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/antibody/tfold-master/tfold/model/arch/ag_model/model.py", line 115, in forward
outputs_cp = self.docking_model(inputs_dock, chunk_size=chunk_size)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/miniconda/envs/torch11/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1511, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/miniconda/envs/torch11/lib/python3.11/site-packages/torch/nn/modules/module.py", line 1520, in _call_impl
return forward_call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/antibody/tfold-master/tfold/model/arch/core/docking_model.py", line 154, in forward
sfea_tns, pfea_tns = self.init_input_feature(inputs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/antibody/tfold-master/tfold/model/arch/core/docking_model.py", line 324, in init_input_feature
if self.use_icf and inputs[complex_id]['feat']['icf'] is not None:
~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^
KeyError: 'icf'