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boltzgen

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PyTorch
BoltzGen
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boltzgen
File size: 6,445 Bytes 
628366e
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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{
  "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>]"
}