Explicit valence for atom # 219 C, 5, is greater than permitted #8
Description
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