| data: |
| task: hallucination |
| dataset: pdb |
| rectify: true |
| distill: false |
| loader: |
| num_workers: 32 |
| prefetch_factor: 10 |
| sampler: |
| max_batch_size: 128 |
| max_num_res_squared: 1000000 |
| interpolant: |
| min_t: 0.01 |
| twisting: |
| use: false |
| rots: |
| corrupt: true |
| sample_schedule: exp |
| exp_rate: 10 |
| trans: |
| corrupt: true |
| batch_ot: true |
| sample_schedule: linear |
| sample_temp: 1.0 |
| vpsde_bmin: 0.1 |
| vpsde_bmax: 20.0 |
| potential: null |
| potential_t_scaling: false |
| rog: |
| weight: 10.0 |
| cutoff: 5.0 |
| sampling: |
| num_timesteps: 100 |
| do_sde: false |
| self_condition: ${model.edge_features.self_condition} |
| experiment: |
| is_training: true |
| debug: false |
| seed: 123 |
| num_devices: 4 |
| warm_start: null |
| warm_start_cfg_override: true |
| resume_cfg_path: null |
| resume_ckpt_path: null |
| resume: false |
| training: |
| mask_plddt: true |
| bb_atom_scale: 0.1 |
| trans_scale: 0.1 |
| translation_loss_weight: 2.0 |
| t_normalize_clip: 0.9 |
| rotation_loss_weights: 1.0 |
| aux_loss_weight: 1.0 |
| aux_loss_use_bb_loss: true |
| aux_loss_use_pair_loss: true |
| aux_loss_t_pass: 0.5 |
| wandb: |
| name: null |
| project: null |
| optimizer: |
| lr: 0.0001 |
| trainer: |
| overfit_batches: 0 |
| min_epochs: 1 |
| max_epochs: 2000 |
| accelerator: gpu |
| log_every_n_steps: 1 |
| deterministic: false |
| strategy: ddp |
| check_val_every_n_epoch: 1 |
| accumulate_grad_batches: 2 |
| checkpointer: |
| dirpath: null |
| save_last: true |
| save_top_k: -1 |
| inference_dir: null |
| shared: |
| seed: 123 |
| max_cache_size: 100000 |
| min_motif_percent: 0.05 |
| max_motif_percent: 0.5 |
| scope_dataset: |
| seed: ${shared.seed} |
| csv_path: null |
| rectify_csv_path: null |
| max_cache_size: ${shared.max_cache_size} |
| cache_num_res: 0 |
| add_plddt_mask: false |
| min_eval_length: 60 |
| max_eval_length: 128 |
| inpainting_percent: 1.0 |
| samples_per_eval_length: 10 |
| num_eval_lengths: 10 |
| filter: |
| max_num_res: 128 |
| min_num_res: 60 |
| max_coil_percent: 0.5 |
| rog_quantile: 0.96 |
| oligomeric: |
| - monomeric |
| num_chains: |
| - 1 |
| min_motif_percent: ${shared.min_motif_percent} |
| max_motif_percent: ${shared.max_motif_percent} |
| pdb_dataset: |
| seed: ${shared.seed} |
| csv_path: null |
| rectify_csv_path: null |
| cluster_path: ./metadata/pdb.clusters |
| max_cache_size: ${shared.max_cache_size} |
| cache_num_res: 0 |
| inpainting_percent: 1.0 |
| add_plddt_mask: false |
| min_eval_length: 100 |
| max_eval_length: 300 |
| samples_per_eval_length: 10 |
| num_eval_lengths: 10 |
| filter: |
| max_num_res: 512 |
| min_num_res: 60 |
| max_coil_percent: 0.5 |
| rog_quantile: 0.96 |
| oligomeric: |
| - monomeric |
| num_chains: |
| - 1 |
| min_motif_percent: ${shared.min_motif_percent} |
| max_motif_percent: ${shared.max_motif_percent} |
| model: |
| node_embed_size: 256 |
| edge_embed_size: 128 |
| symmetric: false |
| node_features: |
| c_s: ${model.node_embed_size} |
| c_pos_emb: 128 |
| c_timestep_emb: 128 |
| max_num_res: 2000 |
| timestep_int: 1000 |
| embed_chain: false |
| edge_features: |
| single_bias_transition_n: 2 |
| c_s: ${model.node_embed_size} |
| c_p: ${model.edge_embed_size} |
| relpos_k: 64 |
| feat_dim: 64 |
| num_bins: 22 |
| self_condition: true |
| embed_chain: false |
| embed_diffuse_mask: true |
| ipa: |
| c_s: ${model.node_embed_size} |
| c_z: ${model.edge_embed_size} |
| c_hidden: 128 |
| no_heads: 8 |
| no_qk_points: 8 |
| no_v_points: 12 |
| seq_tfmr_num_heads: 4 |
| seq_tfmr_num_layers: 2 |
| num_blocks: 6 |
|
|
