kathyli2023
commented
1 month ago I tried to increase the "num_samples" or decrease the "num_atom", but still got the above error "File "/disk1/liyan/PMDM-main/models/encoders/egnn.py", line 215, in forward hidden_out, coors_out = self.propagate(edge_index, x=feats, edge_attr=edge_attr_feats, ValueError: too many values to unpack (expected 2)"
There is something wrong with the returned values in the function "self.propagate" of the script "egnn.py"?
Layne-Huang
Dear Dr. Huang, I have encountered following errors when applying the sample_for_pdb.py . Would you please help me with it? Many thanks.
python -u sample_for_pdb.py --ckpt pretrained/500.pt --pdb_path 5fc4_md.pdb --num_atom 32 --num_samples 20 --sampling_type generalized sh: module: command not found /home/public/.conda/envs/mol/lib/python3.9/site-packages/torchvision/io/image.py:13: UserWarning: Failed to load image Python extension: '/home/public/.conda/envs/mol/lib/python3.9/site-packages/torchvision/image.so: undefined symbol: _ZN5torch3jit17parseSchemaOrNameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE'If you don't plan on using image functionality from
pos_gen, pos_gen_traj, atom_type, atom_traj = model.langevin_dynamics_sample(
File "/disk1/liyan/PMDM-main/models/epsnet/MDM_pocket_coor_shared.py", line 790, in langevin_dynamics_sample
net_out = self.net(
File "/disk1/liyan/PMDM-main/models/epsnet/MDM_pocket_coor_shared.py", line 478, in net
node_attr_global, pos_attr_global = self.encoder_global(
File "/home/public/.conda/envs/mol/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1518, in _wrapped_call_impl
return self._call_impl( args, kwargs)
File "/home/public/.conda/envs/mol/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1527, in _call_impl
return forward_call(*args, *kwargs)
File "/disk1/liyan/PMDM-main/models/encoders/egnn.py", line 476, in forward
x = layer(x, edge_index, edge_attr, batch=batch, ligand_batch=ligand_batch, size=bsize, linker_mask=linker_mask)
File "/home/public/.conda/envs/mol/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1518, in _wrapped_call_impl
return self._call_impl(args, kwargs)
File "/home/public/.conda/envs/mol/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1527, in _call_impl
return forward_call(*args, **kwargs)
File "/disk1/liyan/PMDM-main/models/encoders/egnn.py", line 215, in forward
hidden_out, coors_out = self.propagate(edge_index, x=feats, edge_attr=edge_attr_feats,
ValueError: too many values to unpack (expected 2)
torchvision.io, you can ignore this warning. Otherwise, there might be something wrong with your environment. Did you havelibjpegorlibpnginstalled before buildingtorchvisionfrom source? warn( Entropy of n_nodes: H[N] -1.3862943649291992 [2024-05-12 13:49:16,210::test::INFO] Namespace(pdb_path='5fc4_md.pdb', sdf_path=None, num_atom=32, build_method='reconstruct', config=None, cuda=True, ckpt='pretrained/500.pt', save_traj=False, num_samples=20, batch_size=10, resume=None, tag='', clip=1000.0, n_steps=1000, global_start_sigma=inf, w_global_pos=1.0, w_local_pos=1.0, w_global_node=1.0, w_local_node=1.0, sampling_type='generalized', eta=1.0) [2024-05-12 13:49:16,210::test::INFO] {'model': {'type': 'diffusion', 'network': 'MDM_full_pocket_coor_shared', 'hidden_dim': 128, 'protein_hidden_dim': 128, 'num_convs': 3, 'num_convs_local': 3, 'protein_num_convs': 2, 'cutoff': 3.0, 'g_cutoff': 6.0, 'encoder_cutoff': 6.0, 'time_emb': True, 'atom_num_emb': False, 'mlp_act': 'relu', 'beta_schedule': 'sigmoid', 'beta_start': 1e-07, 'beta_end': 0.002, 'num_diffusion_timesteps': 1000, 'edge_order': 3, 'edge_encoder': 'mlp', 'smooth_conv': False, 'num_layer': 9, 'feats_dim': 5, 'soft_edge': True, 'norm_coors': True, 'm_dim': 128, 'context': 'None', 'vae_context': False, 'num_atom': 10, 'protein_feature_dim': 31}, 'train': {'seed': 2021, 'batch_size': 16, 'val_freq': 250, 'max_iters': 500, 'max_grad_norm': 10.0, 'num_workers': 4, 'anneal_power': 2.0, 'optimizer': {'type': 'adam', 'lr': 0.001, 'weight_decay': 0.0, 'beta1': 0.95, 'beta2': 0.999}, 'scheduler': {'type': 'plateau', 'factor': 0.6, 'patience': 10, 'min_lr': 1e-06}, 'transform': {'mask': {'type': 'mixed', 'min_ratio': 0.0, 'max_ratio': 1.2, 'min_num_masked': 1, 'min_num_unmasked': 0, 'p_random': 0.5, 'p_bfs': 0.25, 'p_invbfs': 0.25}, 'contrastive': {'num_real': 50, 'num_fake': 50, 'pos_real_std': 0.05, 'pos_fake_std': 2.0}}}, 'dataset': {'name': 'crossdock', 'type': 'pl', 'path': './data/crossdocked_pocket10', 'split': './data/split_by_name.pt'}} [2024-05-12 13:49:16,211::test::INFO] Loading crossdock data... Entropy of n_nodes: H[N] -3.543935775756836 [2024-05-12 13:49:16,212::test::INFO] Loading data... [2024-05-12 13:49:16,257::test::INFO] Building model... [2024-05-12 13:49:16,257::test::INFO] MDM_full_pocket_coor_shared {'type': 'diffusion', 'network': 'MDM_full_pocket_coor_shared', 'hidden_dim': 128, 'protein_hidden_dim': 128, 'num_convs': 3, 'num_convs_local': 3, 'protein_num_convs': 2, 'cutoff': 3.0, 'g_cutoff': 6.0, 'encoder_cutoff': 6.0, 'time_emb': True, 'atom_num_emb': False, 'mlp_act': 'relu', 'beta_schedule': 'sigmoid', 'beta_start': 1e-07, 'beta_end': 0.002, 'num_diffusion_timesteps': 1000, 'edge_order': 3, 'edge_encoder': 'mlp', 'smooth_conv': False, 'num_layer': 9, 'feats_dim': 5, 'soft_edge': True, 'norm_coors': True, 'm_dim': 128, 'context': 'None', 'vae_context': False, 'num_atom': 10, 'protein_feature_dim': 31} sdf idr: generate_ref Entropy of n_nodes: H[N] -3.543935775756836 100%|████████████████████████████████████████████████████████████████████████████████████| 4/4 [00:00<00:00, 147.77it/s] 0%| | 0/4 [00:00<?, ?it/s]1 /disk1/liyan/PMDM-main/models/common.py:485: UserWarning: torch.sparse.SparseTensor(indices, values, shape, , device=) is deprecated. Please use torch.sparse_coo_tensor(indices, values, shape, dtype=, device=). (Triggered internally at ../torch/csrc/utils/tensor_new.cpp:605.) bgraph_adj = torch.sparse.LongTensor( sample: 0it [00:00, ?it/s] 0%| | 0/4 [00:00<?, ?it/s] Traceback (most recent call last): File "/disk1/liyan/PMDM-main/sample_for_pdb.py", line 350, in