| { |
| "architecture": "alphafold2", |
| "evoformer": { |
| "block": { |
| "msa_row_attention_with_pair_bias": { |
| "dropout": 0.15, |
| "num_attention_heads": 8 |
| }, |
| "msa_transition": { |
| "expansion": 4 |
| }, |
| "outer_product_mean": { |
| "first": false, |
| "hidden_size": 32 |
| }, |
| "pair_transition": { |
| "expansion": 4 |
| }, |
| "triangle_attention_starting_node": { |
| "dropout": 0.25, |
| "head_size": 32, |
| "num_attention_heads": 4 |
| }, |
| "triangle_multiplication_outgoing": { |
| "hidden_size": 128 |
| } |
| }, |
| "extra_msa_size": 64, |
| "msa_size": 256, |
| "num_blocks": 48, |
| "num_extra_msa_blocks": 4, |
| "pair_size": 128, |
| "single_size": 384 |
| }, |
| "heads": { |
| "distogram": { |
| "num_distogram_bins": 64 |
| }, |
| "experimentally_resolved": { |
| "num_atom_types": 37 |
| }, |
| "predicted_aligned_error": { |
| "enabled": true, |
| "max_error_bin": 31.0, |
| "num_pae_bins": 64 |
| }, |
| "predicted_lddt": { |
| "hidden_size": 128, |
| "num_plddt_bins": 50 |
| } |
| }, |
| "input_embeddings": { |
| "max_relative_feature": 32, |
| "token_feature_size": 73 |
| }, |
| "msa": { |
| "gap_agreement_weight": 0.0, |
| "masked_msa_enabled": true, |
| "masked_msa_profile_prob": 0.1, |
| "masked_msa_replace_fraction": 0.15, |
| "masked_msa_same_prob": 0.1, |
| "masked_msa_uniform_prob": 0.1, |
| "max_extra_msa": 5120, |
| "max_msa_clusters": 512, |
| "msa_cluster_features": true, |
| "resample_msa_in_recycling": true |
| }, |
| "num_ensembles": 1, |
| "num_recycles": 4, |
| "recycling": { |
| "previous_positions": { |
| "max_distance": 20.75, |
| "min_distance": 3.25, |
| "num_distogram_bins": 15 |
| }, |
| "recycle_features": true, |
| "recycle_positions": true |
| }, |
| "structure_module": { |
| "dropout": 0.1, |
| "hidden_size": 384, |
| "num_attention_heads": 12, |
| "num_blocks": 8, |
| "num_point_qk": 4, |
| "num_point_v": 8, |
| "num_transition_projections": 3, |
| "position_scale": 10.0, |
| "scalar_query_key_size": 16, |
| "scalar_value_size": 16, |
| "sidechain": { |
| "hidden_size": 128, |
| "num_blocks": 2 |
| } |
| }, |
| "template": { |
| "attention": { |
| "num_attention_heads": 4 |
| }, |
| "embed_torsion_angles": true, |
| "enabled": false, |
| "max_distance": 50.75, |
| "min_distance": 3.25, |
| "num_distogram_bins": 39, |
| "template_pair_stack": { |
| "num_blocks": 2, |
| "pair_size": 64, |
| "transition": { |
| "expansion": 2 |
| }, |
| "triangle_attention_starting_node": { |
| "dropout": 0.25, |
| "head_size": 16, |
| "num_attention_heads": 4 |
| }, |
| "triangle_multiplication_outgoing": { |
| "hidden_size": 64 |
| } |
| }, |
| "use_template_unit_vector": false, |
| "vocab_size": 22 |
| } |
| } |
|
|
