| { | |
| "affinity_baseline": false, | |
| "affinity_confidence_different": false, | |
| "affinity_confidence_different_multiple": false, | |
| "affinity_ensemble": false, | |
| "affinity_model_args": { | |
| "affinity_args": { | |
| "groups": { | |
| "0": 1 | |
| }, | |
| "val_groups": [ | |
| 0 | |
| ] | |
| } | |
| }, | |
| "affinity_model_args1": {}, | |
| "affinity_model_args2": {}, | |
| "affinity_mw_correction": true, | |
| "affinity_pair_transformer": false, | |
| "affinity_prediction": false, | |
| "affinity_transformer": false, | |
| "affinity_transformer_atom": false, | |
| "alpha_affinity_absolute": 0.0, | |
| "alpha_affinity_binary": 0.0, | |
| "alpha_affinity_difference": 0.0, | |
| "alpha_affinity_focal": 0.0, | |
| "alpha_affinity_score_binder_binder": 0.0, | |
| "alpha_affinity_score_binder_decoy": 0.0, | |
| "alpha_pae": 1, | |
| "architectures": [ | |
| "BoltzGen" | |
| ], | |
| "atom_feature_dim": 388, | |
| "atom_s": 128, | |
| "atom_z": 16, | |
| "atoms_per_window_keys": 128, | |
| "atoms_per_window_queries": 32, | |
| "bond_type_feature": true, | |
| "chain_sampling_args": null, | |
| "checkpoint_diffusion_conditioning": true, | |
| "compile_confidence": false, | |
| "compile_msa": false, | |
| "compile_pairformer": false, | |
| "compile_structure": false, | |
| "compile_templates": false, | |
| "compute_tistogram": false, | |
| "confidence_imitate_trunk": false, | |
| "confidence_model_args": { | |
| "add_s_input_to_s": true, | |
| "add_s_to_z_prod": true, | |
| "add_z_input_to_z": true, | |
| "confidence_args": { | |
| "num_pae_bins": 64, | |
| "num_pde_bins": 64, | |
| "num_plddt_bins": 50, | |
| "relative_confidence": "none", | |
| "use_separate_heads": true | |
| }, | |
| "max_dist": 22, | |
| "no_trunk_feats": false, | |
| "num_dist_bins": 64, | |
| "pairformer_args": { | |
| "dropout": 0.25, | |
| "num_blocks": 8, | |
| "num_heads": 16 | |
| }, | |
| "use_gaussian": false, | |
| "use_miniformer": false, | |
| "use_s_diffusion": false | |
| }, | |
| "confidence_prediction": true, | |
| "confidence_regression": false, | |
| "cyclic_pos_enc": true, | |
| "diffusion_loss_args": { | |
| "add_bond_loss": false, | |
| "add_smooth_lddt_loss": true, | |
| "filter_by_plddt": 0.0, | |
| "ligand_loss_weight": 10.0, | |
| "nucleotide_loss_weight": 5.0 | |
| }, | |
| "diffusion_process_args": { | |
| "P_mean": -1.2, | |
| "P_std": 1.5, | |
| "alignment_reverse_diff": true, | |
| "coordinate_augmentation": true, | |
| "gamma_0": 0.8, | |
| "gamma_min": 1.0, | |
| "mse_rotational_alignment": true, | |
| "noise_scale": 1.0, | |
| "rho": 7, | |
| "sigma_data": 16.0, | |
| "sigma_max": 160.0, | |
| "sigma_min": 0.0004, | |
| "step_scale": 1.0, | |
| "step_scale_random": [ | |
| 1.0, | |
| 1.1, | |
| 1.2, | |
| 1.3, | |
| 1.4, | |
| 1.5 | |
| ], | |
| "synchronize_sigmas": false | |
| }, | |
| "dtype": "float32", | |
| "dynamic_args": {}, | |
| "ema": true, | |
| "ema_decay": 0.999, | |
| "embedder_args": { | |
| "add_cyclic_flag": true, | |
| "add_method_conditioning": true, | |
| "add_modified_flag": true, | |
| "add_mol_type_feat": true, | |
| "atom_encoder_depth": 3, | |
| "atom_encoder_heads": 4 | |
| }, | |
| "exclude_ions_from_lddt": true, | |
| "fix_sym_check": true, | |
| "freeze_template_weights": false, | |
| "guidance_args": null, | |
| "ignore_ckpt_shape_mismatch": false, | |
| "inference_logging": false, | |
| "inverse_fold": false, | |
| "inverse_fold_args": null, | |
| "masker_args": {}, | |
| "max_dist": 22.0, | |
| "maximum_bond_distance": 0, | |
| "min_dist": 2.0, | |
| "model_type": "boltzgen", | |
| "msa_args": { | |
| "activation_checkpointing": false, | |
| "miniformer_blocks": false, | |
| "msa_blocks": 4, | |
| "msa_dropout": 0.15, | |
| "msa_s": 64, | |
| "pairwise_head_width": 32, | |
| "pairwise_num_heads": 4, | |
| "use_paired_feature": true, | |
| "z_dropout": 0.25 | |
| }, | |
| "num_bins": 64, | |
| "num_distograms": 1, | |
| "num_tistogram_axis": 1, | |
| "num_val_datasets": 4, | |
| "pairformer_args": { | |
| "activation_checkpointing": false, | |
| "dropout": 0.25, | |
| "num_blocks": 64, | |
| "num_heads": 16, | |
| "post_layer_norm": false | |
| }, | |
| "predict_bfactor": true, | |
| "predict_res_type": false, | |
| "recycling_detach": true, | |
| "refolding_validator": null, | |
| "relative_confidence_supervision_weight": 0.0, | |
| "representative_lddt": false, | |
| "score_model_args": { | |
| "activation_checkpointing": false, | |
| "atom_decoder_depth": 3, | |
| "atom_decoder_heads": 4, | |
| "atom_encoder_depth": 3, | |
| "atom_encoder_heads": 4, | |
| "conditioning_transition_layers": 2, | |
| "dim_fourier": 256, | |
| "sigma_data": 16, | |
| "token_transformer_depth": 24, | |
| "token_transformer_heads": 16, | |
| "transformer_post_ln": false | |
| }, | |
| "skip_run_structure": false, | |
| "structure_prediction_training": false, | |
| "symmetry_correction_trunk": false, | |
| "tau_affinity_score": -1.0, | |
| "template_args": { | |
| "activation_checkpointing": false, | |
| "template_blocks": 2, | |
| "template_dim": 64 | |
| }, | |
| "token_distance_args": null, | |
| "token_level_confidence": true, | |
| "token_s": 384, | |
| "token_z": 128, | |
| "training_args": { | |
| "adam_beta_1": 0.9, | |
| "adam_beta_2": 0.95, | |
| "adam_eps": 1e-08, | |
| "affinity_loss_weight": 0.003, | |
| "base_lr": 0.0, | |
| "bfactor_loss_weight": 0.001, | |
| "confidence_loss_weight": 0.3, | |
| "diffusion_loss_weight": 4.0, | |
| "diffusion_multiplicity": 32, | |
| "diffusion_samples": 1, | |
| "distogram_loss_weight": 0.03, | |
| "lr_decay_every_n_steps": 50000, | |
| "lr_decay_factor": 0.95, | |
| "lr_scheduler": "af3", | |
| "lr_start_decay_after_n_steps": 50000, | |
| "lr_warmup_no_steps": 1000, | |
| "max_lr": 0.001, | |
| "recycling_steps": 3, | |
| "sampling_steps": 50, | |
| "sampling_steps_random": [ | |
| 20, | |
| 50, | |
| 200 | |
| ], | |
| "symmetry_correction": true, | |
| "weight_decay": 0.003, | |
| "weight_decay_exclude": true | |
| }, | |
| "transformers_version": "4.57.1", | |
| "trunk_resolved_loss": false, | |
| "use_atom_backbone_feat": false, | |
| "use_kernels": false, | |
| "use_miniformer": false, | |
| "use_miniformer_plus": false, | |
| "use_no_atom_char": false, | |
| "use_residue_feats_atoms": false, | |
| "use_templates": true, | |
| "use_templates_v2": true, | |
| "use_token_distances": false, | |
| "validation_args": { | |
| "diffusion_samples": 5, | |
| "recycling_steps": 3, | |
| "run_confidence_sequentially": true, | |
| "sampling_steps": 200, | |
| "symmetry_correction": true | |
| }, | |
| "validators": "[<__main__.DummyValidator object at 0x00000187A3DBD550>, <__main__.DummyValidator object at 0x00000187A5D718D0>, <__main__.DummyValidator object at 0x00000187A5F44350>, <__main__.DummyValidator object at 0x00000187A415B250>]" | |
| } | |