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AIDO.StructureTokenizer

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AIDO.StructureTokenizer
File size: 1,657 Bytes 
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{
  "decoder_config": {
    "folding_trunk": {
      "chunk_size": null,
      "cpu_grad_checkpoint": false,
      "dropout": 0.1,
      "layer_drop": 0,
      "max_recycles": 4,
      "num_blocks": 32,
      "pairwise_head_width": 32,
      "pairwise_state_dim": 128,
      "position_bins": 32,
      "sequence_head_width": 32,
      "sequence_state_dim": 768,
      "structure_module": {
        "c_ipa": 16,
        "c_resnet": 128,
        "c_s": 384,
        "c_z": 128,
        "dropout_rate": 0.1,
        "epsilon": 1e-08,
        "inf": 100000.0,
        "no_angles": 7,
        "no_blocks": 8,
        "no_heads_ipa": 12,
        "no_qk_points": 4,
        "no_resnet_blocks": 2,
        "no_transition_layers": 1,
        "no_v_points": 8,
        "trans_scale_factor": 10
      }
    },
    "lddt_head_hidden_dim": 128,
    "quantize_dim": 384
  },
  "encoder_config": {
    "edge_emb": {
      "bessels": {
        "bessel_const": 40.0,
        "d": 128
      },
      "d": 128,
      "edge_type_emb": {
        "d": 128,
        "dropout": 0.1,
        "max_res_offset": 32,
        "max_sym_offset": 2
      },
      "k_for_knn": 30
    },
    "eqnet": {
      "attn_dropout": 0,
      "d": 128,
      "d_mult": 3,
      "dropout": 0.1,
      "n_head": 4
    },
    "n_eqnet": 12,
    "node_emb": {
      "d": 128,
      "dropout": 0.1,
      "mask_node_type": true,
      "n_chain_type": 100,
      "n_node_type": 200
    },
    "quantize": {
      "decay": 0.99,
      "dim": 384,
      "eps": 1e-05,
      "n_embed": 512,
      "normalize": true,
      "restart": 100,
      "usage_threshold": 1e-09
    }
  },
  "frozen_codebook": false
}