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When I run diffpack on an antibody design I generated from diffab, I get the above error and it writes nothing to disk and just exits.
This is the pdb file (just change the extension to .pdb) output.txt
#!/usr/bin/env bash # # exec python script/inference.py -c config/inference_confidence.yaml \ --seed 2023 \ --output_dir path/to/output \ --pdb_files $@
| ./run_example.sh output.pdb 16:45:24 Config file: /home/ws/projects/diffpack/DiffPack/config/inference_confidence.yaml 16:45:24 {'engine': {'batch_size': 32, 'gpus': [0], 'log_interval': 1000}, 'model_checkpoint': '~/scratch/trained_model/diffpack/gearnet_edge_confidence_converted.pth', 'optimizer': {'class': 'Adam', 'lr': 0.0001}, 'task': {'class': 'ConfidencePrediction', 'confidence_model': {'batch_norm': True, 'class': 'GearNet', 'concat_hidden': True, 'edge_input_dim': 58, 'hidden_dims': [128, 128, 128, 128, 128, 128], 'input_dim': 39, 'num_angle_bin': 8, 'num_relation': 6, 'readout': 'sum', 'short_cut': True}, 'graph_construction_model': {'class': 'GraphConstruction', 'edge_feature': 'gearnet', 'edge_layers': [{'class': 'BondEdge'}, {'class': 'SpatialEdge', 'min_distance': 2, 'radius': 4.5}, {'class': 'KNNEdge', 'k': 10, 'min_distance': 0}]}, 'model': {'batch_norm': True, 'class': 'GearNet', 'concat_hidden': True, 'edge_input_dim': 58, 'hidden_dims': [128, 128, 128, 128, 128, 128], 'input_dim': 128, 'num_angle_bin': 8, 'num_relation': 6, 'readout': 'sum', 'short_cut': True}, 'num_mlp_layer': 3, 'num_sample': 4, 'schedule_1pi_periodic': {'annealed_temp': 3, 'cache_folder': '~/scratch/output/diffpack', 'class': 'SO2VESchedule', 'mode': 'ode', 'pi_periodic': True}, 'schedule_2pi_periodic': {'annealed_temp': 3, 'cache_folder': '~/scratch/output/diffpack', 'class': 'SO2VESchedule', 'mode': 'ode', 'pi_periodic': False}, 'sigma_embedding': {'class': 'SigmaEmbeddingLayer', 'hidden_dims': [64, 128], 'input_dim': 39, 'sigma_dim': 64}, 'torsion_mlp_hidden_dims': [64, 128], 'train_chi_id': None}, 'test_set': {'atom_feature': 'residue_symbol', 'bond_feature': None, 'class': 'SideChainDataset', 'mol_feature': None, 'path': None, 'pdb_files': ['output_test.pdb'], 'removeHs': True, 'residue_feature': None, 'sanitize': True, 'transform': {'class': 'Compose', 'transforms': []}}, 'train': {'num_epoch': 0}} 16:45:24 Output dir: /home/ws/projects/diffpack/DiffPack/path/to/output 16:45:34 Preprocess training set 16:45:37 {'batch_size': 32, 'class': 'core.Engine', 'gpus': [0], 'gradient_interval': 1, 'log_interval': 1000, 'logger': 'logging', 'num_worker': 0, 'optimizer': None, 'scheduler': None, 'task': {'class': 'tasks.ConfidencePrediction', 'graph_construction_model': {'class': 'layers.GraphConstruction', 'edge_feature': 'gearnet', 'edge_layers': [{'class': 'layers.geometry.BondEdge'}, {'class': 'layers.geometry.SpatialEdge', 'max_distance': None, 'max_num_neighbors': 32, 'min_distance': 2, 'radius': 4.5}, {'class': 'layers.geometry.KNNEdge', 'k': 10, 'max_distance': None, 'min_distance': 0}], 'node_layers': None}, 'model': {'activation': 'relu', 'batch_norm': True, 'class': 'models.GearNet', 'concat_hidden': True, 'edge_input_dim': 58, 'hidden_dims': [128, 128, 128, 128, 128, 128], 'input_dim': 128, 'num_angle_bin': 8, 'num_relation': 6, 'readout': 'sum', 'short_cut': True}, 'schedule_1pi_periodic': {'PI': 1.5707963267948966, 'cache_folder': '~/scratch/output/diffpack', 'class': 'SO2VESchedule'}, 'schedule_2pi_periodic': {'PI': 3.141592653589793, 'cache_folder': '~/scratch/output/diffpack', 'class': 'SO2VESchedule'}, 'sigma_embedding': {'class': 'layers.SigmaEmbeddingLayer', 'embed_type': 'sinusoidal', 'hidden_dims': [64, 128], 'input_dim': 39, 'operation': 'post_add', 'sigma_dim': 64}, 'torsion_mlp_hidden_dims': [64, 128], 'train_chi_id': None, 'verbose': 0}, 'test_set': None, 'train_set': None, 'valid_set': None} 16:45:37 #parameter: 9351987 16:45:37 Loading dataset from pdb files Constructing proteins from pdbs: 0%| | 0/1 [00:00<?, ?it/s][16:45:37] Explicit valence for atom # 219 C, 5, is greater than permitted Constructing proteins from pdbs: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 9.68it/s] 16:45:37 Test on SideChainDataset( #sample: 0) 16:45:37 /home/ws/projects/diffpack/DiffPack/path/to/output
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When I run diffpack on an antibody design I generated from diffab, I get the above error and it writes nothing to disk and just exits.
This is the pdb file (just change the extension to .pdb)
output.txt
The text was updated successfully, but these errors were encountered: