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esmfold2-fast

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esmfold2-fast
File size: 2,818 Bytes
c614031
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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{
  "architecture": "esmfold2",
  "confidence": {
    "folding_stack": {
      "num_blocks": 4
    },
    "max_distance": 50.75,
    "min_distance": 3.25,
    "num_distogram_bins": 39,
    "num_pae_bins": 64,
    "num_pde_bins": 64,
    "num_plddt_bins": 50
  },
  "diffusion_structure_head": {
    "churn_rate": 0.8,
    "denoiser": {
      "atom_hidden_size": 128,
      "expansion": 2,
      "fourier_embedding_size": 256,
      "input_size": 529,
      "num_atom_attention_heads": 4,
      "num_atom_blocks": 3,
      "num_token_encoder_attention_heads": 16,
      "num_token_encoder_blocks": 12,
      "pair_size": 256,
      "sigma_data": 16.0,
      "token_hidden_size": 768
    },
    "max_inference_sigma": 256.0,
    "max_noise_level": 160.0,
    "min_churn_noise_level": 1.0,
    "min_noise_level": 0.0004,
    "noise_scale": 1.003,
    "num_distogram_bins": 64,
    "num_sampling_steps": 14,
    "rho": 7.0,
    "step_scale": 1.5
  },
  "esmc": {
    "attention_bias": false,
    "attention_dropout": 0.0,
    "attention_layer_norm_bias": true,
    "bos_token_id": 1,
    "eos_token_id": 2,
    "feedforward_bias": false,
    "final_layer_norm_bias": false,
    "hidden_act": "swiglu",
    "hidden_dropout": 0.0,
    "hidden_size": 2560,
    "initializer_range": 0.02,
    "intermediate_size": 6912,
    "layer_norm_eps": 1e-05,
    "mask_token_id": 4,
    "max_position_embeddings": 2048,
    "null_token_id": 5,
    "num_attention_heads": 40,
    "num_hidden_layers": 80,
    "pad_token_id": 0,
    "qk_layer_norm": true,
    "qk_layer_norm_bias": false,
    "residue_scaling_factor": 1.4907119849998598,
    "unk_token_id": 3,
    "vocab_size": 37
  },
  "esmc_repository": "multimolecule/esmc-6b",
  "esmc_revision": "62eb94c06f7013fea59a5075955658c8a5a72263",
  "folding_stack": {
    "num_blocks": 24
  },
  "input_embeddings": {
    "atom_encoder": {
      "atom_hidden_size": 128,
      "expansion": 2,
      "num_attention_heads": 4,
      "num_blocks": 3,
      "num_reference_space_rope_pairs": 10,
      "num_spatial_rope_pairs_per_axis": 2,
      "reference_space_rope_base_frequency": 10000.0,
      "sliding_window_size": 128,
      "spatial_rope_base_frequency": 20.0,
      "token_hidden_size": 768
    },
    "input_size": 529
  },
  "language_model_encoder": {
    "dropout": 0.25,
    "enabled": true,
    "num_blocks": 4,
    "per_loop_dropout": true
  },
  "language_model_mask_probability": 0.1,
  "msa_encoder": {
    "enabled": false,
    "hidden_size": 32,
    "msa_attention_head_size": 32,
    "msa_size": 128,
    "num_msa_attention_heads": 8,
    "num_stages": 4
  },
  "msa_encoder_overwrite": true,
  "num_recycles": 4,
  "num_relative_chain_bins": 2,
  "num_relative_residue_bins": 32,
  "pair_size": 256,
  "parcae": {
    "num_coda_blocks": 2
  },
  "single_size": 384
}