| { |
| "affinity_model_args": { |
| "esm_embed_dim": 1280, |
| "pairformer_args": { |
| "activation_checkpointing": true, |
| "dropout": 0.1, |
| "num_blocks": 8, |
| "pairwise_head_width": 32, |
| "pairwise_num_heads": 4, |
| "post_layer_norm": false |
| }, |
| "transformer_args": { |
| "activation_checkpointing": false, |
| "classification_head": true, |
| "num_blocks": 2, |
| "num_heads": 4, |
| "token_s": 384 |
| } |
| }, |
| "affinity_model_args2": { |
| "esm_embed_dim": 1280, |
| "pairformer_args": { |
| "activation_checkpointing": true, |
| "dropout": 0.1, |
| "num_blocks": 8, |
| "pairwise_head_width": 32, |
| "pairwise_num_heads": 4, |
| "post_layer_norm": false |
| }, |
| "transformer_args": { |
| "activation_checkpointing": false, |
| "classification_head": true, |
| "num_blocks": 2, |
| "num_heads": 4, |
| "token_s": 384 |
| } |
| }, |
| "affinity_prediction": true, |
| "atom_feature_dim": 390, |
| "atom_s": 128, |
| "atom_z": 16, |
| "atoms_per_window_keys": 128, |
| "atoms_per_window_queries": 32, |
| "embedder_args": { |
| "add_additional_atom_features": true, |
| "atom_encoder_depth": 3, |
| "atom_encoder_heads": 4, |
| "pocket_conditioning": false |
| }, |
| "esm_module_args": { |
| "dropout": 0.05, |
| "esm_embed_dim": 1280, |
| "esm_num_layers": 34, |
| "use_esm_all_layers": false |
| }, |
| "max_dist": 22.0, |
| "num_dist_bins": 64, |
| "pairformer_model_args": { |
| "activation_checkpointing": true, |
| "dropout": 0.25, |
| "num_blocks": 48, |
| "pairwise_head_width": 32, |
| "pairwise_num_heads": 4, |
| "post_layer_norm": false |
| }, |
| "predict_args": { |
| "pose_protein_cutoff": 15.0, |
| "recycling_steps": 5 |
| }, |
| "token_s": 384, |
| "token_z": 128, |
| "use_kernels": true |
| } |
