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| train: | |
| home_dir: '' | |
| seed: 0 | |
| checkpoint: ['', 0] | |
| batch_size: 32 | |
| max_epochs: 10000 | |
| eval_freq: 7200 # seconds | |
| checkpoint_freq: 50 | |
| checkpoints: [] | |
| lr: 0.0001 | |
| warmup_steps: 1000 | |
| decay_steps: 2_000_000 | |
| clip_grad_norm: True | |
| grad_clip_val: 1.0 | |
| weight_decay: 0.0 | |
| n_eval_samples: 8 | |
| sample_length_range: [50, 512] | |
| sc_num_seqs: 4 | |
| eval_loss_t: [0.1, 0.3, 0.5, 0.7, 0.9] | |
| self_cond_train_prob: 0.9 | |
| subsample_eval_set: 0.05 | |
| crop_conditional: False | |
| data: | |
| pdb_path: 'datasets/ingraham_cath_dataset' | |
| fixed_size: 384 | |
| n_aatype_tokens: 21 | |
| se3_data_augment: True | |
| sigma_data: 10.0 | |
| diffusion: | |
| training: | |
| function: 'lognormal' | |
| psigma_mean: -1.2 | |
| psigma_std: 1.2 | |
| sampling: | |
| function: 'uniform' | |
| s_min: 0.001 | |
| s_max: 80 | |
| model: | |
| task: 'backbone' # 'backbone', 'allatom', 'seqdes', 'codesign' | |
| pretrained_modules: [] # 'struct_model', 'mpnn_model' | |
| struct_model_checkpoint: '' | |
| mpnn_model_checkpoint: '' | |
| crop_conditional: False | |
| dummy_fill_masked_atoms: False | |
| struct_model: | |
| arch: 'uvit' | |
| n_atoms: 37 # keep same shapes, just zero out sidechains | |
| n_channel: 256 | |
| noise_cond_mult: 4 | |
| uvit: | |
| patch_size: 1 | |
| n_layers: 6 | |
| n_heads: 8 | |
| dim_head: 32 | |
| n_filt_per_layer: [] | |
| n_blocks_per_layer: 2 | |
| cat_pwd_to_conv: False | |
| conv_skip_connection: False | |
| position_embedding_type: 'absolute_residx' | |
| mpnn_model: | |
| use_self_conditioning: True | |
| label_smoothing: 0.1 | |
| n_channel: 128 | |
| n_layers: 3 | |
| n_neighbors: 32 | |
| noise_cond_mult: 4 | |