| { |
| "architecture": "boltzgen", |
| "atom_feature_size": 388, |
| "atom_hidden_size": 128, |
| "atom_pair_hidden_size": 16, |
| "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_coordinate_gaussians": 0, |
| "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, |
| "token_hidden_size": null, |
| "use_qk_norm": false |
| }, |
| "design": { |
| "num_distance_gaussians": 32, |
| "num_template_blocks": 2, |
| "num_token_distance_blocks": 2, |
| "template_dropout": 0.25, |
| "template_post_layer_norm": false, |
| "template_size": 64, |
| "token_distance_dropout": 0.25, |
| "token_distance_post_layer_norm": false, |
| "token_distance_size": 64, |
| "use_token_distance": true, |
| "use_token_distance_features": true |
| }, |
| "fourier_embedding_size": 256, |
| "input_embeddings": { |
| "add_binding_specification": true, |
| "add_cyclic_flag": true, |
| "add_design_mask": true, |
| "add_method_conditioning": true, |
| "add_modified_flag": true, |
| "add_molecule_type_feature": true, |
| "add_secondary_structure_specification": 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": 4, |
| "pair_size": 128, |
| "relative_position_size": 139, |
| "sampler": { |
| "churn_rate": 0.8, |
| "max_noise_level": 160.0, |
| "max_noise_scale": 1.0, |
| "max_step_scale": 1.0, |
| "min_churn_noise_level": 1.0, |
| "min_noise_level": 0.0004, |
| "min_noise_scale": 1.0, |
| "min_step_scale": 1.0, |
| "noise_scale": 1.0, |
| "noise_scale_alpha": 1.0, |
| "noise_scale_beta": 1.0, |
| "noise_scale_function": "constant", |
| "num_sampling_steps": 200, |
| "rho": 7.0, |
| "sampling_schedule": "dilated", |
| "step_scale": 1.0, |
| "step_scale_alpha": 1.0, |
| "step_scale_beta": 1.0, |
| "step_scale_function": "constant", |
| "step_scale_random": null, |
| "time_dilation": 2.667, |
| "time_dilation_end": 0.8, |
| "time_dilation_start": 0.6 |
| }, |
| "single_size": 384, |
| "template": { |
| "max_distance": 50.75, |
| "min_distance": 3.25, |
| "num_distogram_bins": 38, |
| "num_triangle_attention_heads": 4, |
| "triangle_attention_head_size": 32 |
| }, |
| "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_trunk_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, |
| "use_single_to_pair": false |
| } |
| } |
|
|
