| data: | |
| task: hallucination | |
| dataset: pdb | |
| loader: | |
| num_workers: 4 | |
| 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: | |
| debug: false | |
| seed: 123 | |
| num_devices: 4 | |
| warm_start: null | |
| warm_start_cfg_override: true | |
| resume_cfg_path: null | |
| resume_ckpt_path: null | |
| resume: true | |
| 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: 1000 | |
| accelerator: gpu | |
| log_every_n_steps: 1 | |
| deterministic: false | |
| strategy: ddp | |
| check_val_every_n_epoch: 2 | |
| accumulate_grad_batches: 2 | |
| checkpointer: | |
| save_last: false | |
| save_top_k: -1 | |
| dirpath: null | |
| inference_dir: null | |
| shared: | |
| seed: 123 | |
| max_cache_size: 100000 | |
| samples_per_eval_length: 5 | |
| num_eval_lengths: 8 | |
| max_eval_length: 256 | |
| min_motif_percent: 0.05 | |
| max_motif_percent: 0.5 | |
| scope_dataset: | |
| seed: ${shared.seed} | |
| csv_path: ./metadata/scope_metadata.csv | |
| max_cache_size: ${shared.max_cache_size} | |
| cache_num_res: 0 | |
| add_plddt_mask: false | |
| max_eval_length: ${shared.max_eval_length} | |
| inpainting_percent: 1.0 | |
| samples_per_eval_length: ${shared.samples_per_eval_length} | |
| num_eval_lengths: ${shared.num_eval_lengths} | |
| filter: | |
| max_num_res: 128 | |
| min_num_res: 60 | |
| min_motif_percent: ${shared.min_motif_percent} | |
| max_motif_percent: ${shared.max_motif_percent} | |
| pdb_dataset: | |
| seed: ${shared.seed} | |
| 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 | |
| max_eval_length: ${shared.max_eval_length} | |
| samples_per_eval_length: ${shared.samples_per_eval_length} | |
| num_eval_lengths: ${shared.num_eval_lengths} | |
| 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 | |