predictor/config.json

{
  "single_size": 384,
  "pair_size": 128,
  "atom_hidden_size": 128,
  "atom_pair_hidden_size": 16,
  "atom_feature_size": 388,
  "num_bins": 64,
  "num_distograms": 1,
  "fourier_embedding_size": 256,
  "relative_position_size": 139,
  "num_bond_types": 7,
  "initializer_range": 0.02,
  "recycling_steps": 3,
  "recycling_detach": true,
  "fix_sym_check": true,
  "cyclic_pos_enc": true,
  "use_templates": true,
  "use_templates_v2": true,
  "bond_type_feature": true,
  "token_level_confidence": true,
  "predict_bfactor": true,
  "add_s_to_z_prod": true,
  "add_s_input_to_s": true,
  "add_z_input_to_z": true,
  "aggregate_distogram": true,
  "conditioning_cutoff_min": 4.0,
  "conditioning_cutoff_max": 20.0,
  "min_distance": 2.0,
  "max_distance": 22.0,
  "input_embedder": {
    "num_atom_encoder_blocks": 3,
    "num_atom_encoder_attention_heads": 4,
    "vocab_size": 33,
    "msa_profile_size": 34,
    "num_method_types": 12,
    "num_molecule_types": 4,
    "add_method_conditioning": true,
    "add_modified_flag": true,
    "add_cyclic_flag": true,
    "add_mol_type_feat": true
  },
  "trunk": {
    "num_pairformer_blocks": 64,
    "num_pair_attention_heads": 16,
    "num_msa_blocks": 4,
    "msa_size": 64,
    "msa_feature_size": 36,
    "msa_head_dim": 32,
    "num_msa_attention_heads": 8,
    "outer_product_hidden_size": 32,
    "triangle_attention_hidden_size": 32,
    "num_triangle_attention_heads": 4,
    "use_paired_feature": true,
    "operator_backend": "auto",
    "dropout": 0.25,
    "msa_dropout": 0.15
  },
  "template": {
    "hidden_size": 64,
    "num_blocks": 2,
    "num_distogram_bins": 38,
    "vocab_size": 33,
    "expansion": 4,
    "triangle_attention_hidden_size": 32,
    "num_triangle_attention_heads": 4,
    "min_distance": 3.25,
    "max_distance": 50.75
  },
  "diffusion": {
    "num_token_transformer_blocks": 24,
    "num_token_transformer_heads": 16,
    "num_atom_encoder_blocks": 3,
    "num_atom_decoder_blocks": 3,
    "num_atom_attention_heads": 4,
    "atom_hidden_size": 128,
    "atom_pair_hidden_size": 16,
    "num_query_atoms": 32,
    "num_key_atoms": 128,
    "num_conditioning_transitions": 2,
    "sigma_data": 16.0,
    "alignment_reverse_diff": true,
    "operator_backend": "auto"
  },
  "sampler": {
    "solver": "euler",
    "num_sampling_steps": 200,
    "rho": 7.0,
    "max_noise_level": 160.0,
    "min_noise_level": 0.0004,
    "step_scale": 1.5,
    "noise_scale": 1.003,
    "churn_rate": 0.8
  },
  "confidence": {
    "num_pairformer_blocks": 8,
    "num_pair_attention_heads": 16,
    "num_distogram_bins": 64,
    "max_distance": 22.0,
    "num_plddt_bins": 50,
    "num_pae_bins": 64,
    "num_pde_bins": 64,
    "num_bfactor_bins": 64,
    "add_s_to_z_prod": true,
    "add_s_input_to_s": true,
    "add_z_input_to_z": true,
    "use_separate_heads": true,
    "token_level": true
  }
}