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boltzgen
File size: 2,929 Bytes
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{
  "affinity_heads": [
    {
      "dropout": 0.25,
      "expansion": 2,
      "max_distance": 22.0,
      "num_conditioning_transitions": 2,
      "num_distogram_bins": 64,
      "num_pair_update_blocks": 8,
      "num_triangle_attention_heads": 4,
      "triangle_attention_head_size": 32
    },
    {
      "dropout": 0.25,
      "expansion": 2,
      "max_distance": 22.0,
      "num_conditioning_transitions": 2,
      "num_distogram_bins": 64,
      "num_pair_update_blocks": 4,
      "num_triangle_attention_heads": 4,
      "triangle_attention_head_size": 32
    }
  ],
  "architecture": "boltz2_affinity",
  "atom_feature_size": 388,
  "atom_hidden_size": 128,
  "atom_pair_hidden_size": 16,
  "confidence": {
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    "normalize_single_input": true,
    "num_distogram_bins": 64,
    "num_pae_bins": 64,
    "num_pair_attention_heads": 16,
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    "num_pde_bins": 64,
    "num_plddt_bins": 50,
    "num_triangle_attention_heads": 4,
    "pair_dropout": 0.25,
    "post_layer_norm": false,
    "triangle_attention_head_size": 32
  },
  "denoiser": {
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    "atom_hidden_size": 128,
    "atom_pair_hidden_size": 16,
    "num_atom_attention_heads": 4,
    "num_atom_decoder_blocks": 3,
    "num_atom_encoder_blocks": 3,
    "num_conditioning_transitions": 2,
    "num_key_atoms": 128,
    "num_query_atoms": 32,
    "num_token_encoder_attention_heads": 16,
    "num_token_encoder_blocks": 24,
    "post_layer_norm": false,
    "sigma_data": 16.0
  },
  "fourier_embedding_size": 256,
  "input_embeddings": {
    "add_cyclic_flag": true,
    "add_method_conditioning": true,
    "add_modified_flag": true,
    "add_molecule_type_feature": true,
    "num_atom_encoder_attention_heads": 4,
    "num_atom_encoder_blocks": 3,
    "num_method_types": 12,
    "num_molecule_types": 4,
    "vocab_size": 72
  },
  "max_conditioning_cutoff": 20.0,
  "min_conditioning_cutoff": 4.0,
  "num_bond_types": 7,
  "num_distogram_bins": 64,
  "num_recycles": 6,
  "pair_size": 128,
  "predict_b_factor": false,
  "relative_position_size": 139,
  "sampler": {
    "churn_rate": 0.8,
    "max_noise_level": 160.0,
    "min_noise_level": 0.0001,
    "noise_scale": 1.003,
    "num_sampling_steps": 200,
    "rho": 7.0,
    "step_scale": 1.5
  },
  "single_size": 384,
  "template": null,
  "trunk": {
    "msa_attention_head_size": 32,
    "msa_dropout": 0.15,
    "msa_outer_product_hidden_size": 32,
    "msa_pair_dropout": 0.25,
    "msa_size": 64,
    "msa_triangle_attention_head_size": 32,
    "num_msa_attention_heads": 8,
    "num_msa_blocks": 4,
    "num_msa_triangle_attention_heads": 4,
    "num_pair_attention_heads": 16,
    "num_pairformer_blocks": 64,
    "num_trunk_triangle_attention_heads": 4,
    "post_layer_norm": false,
    "trunk_pair_dropout": 0.25,
    "trunk_triangle_attention_head_size": 32,
    "use_paired_feature": true
  }
}