boltzgen / affinity /model.json
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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": {
"max_distance": 22.0,
"normalize_single_input": true,
"num_distogram_bins": 64,
"num_pae_bins": 64,
"num_pair_attention_heads": 16,
"num_pairformer_blocks": 8,
"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": {
"align_reverse_diffusion": true,
"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
}
}