| adam: | |
| beta1: 0.9 | |
| beta2: 0.95 | |
| lr: 0.0018 | |
| use_adamw: false | |
| weight_decay: 1.0e-08 | |
| af3_lr_scheduler: | |
| decay_every_n_steps: 50000 | |
| decay_factor: 0.95 | |
| lr: 0.0018 | |
| warmup_steps: 10 | |
| atom_permutation: | |
| global_align_wo_symmetric_atom: false | |
| permute_by_pocket: true | |
| test: | |
| diffusion_sample: true | |
| train: | |
| diffusion_sample: false | |
| mini_rollout: true | |
| base_dir: /home/toolkit/ewpo/outputs/sampling | |
| blocks_per_ckpt: 1 | |
| c_atom: 128 | |
| c_atompair: 16 | |
| c_s: 384 | |
| c_s_inputs: 449 | |
| c_token: 384 | |
| c_z: 128 | |
| chain_permutation: | |
| configs: | |
| accept_it_as_it_is: false | |
| enumerate_all_anchor_pairs: false | |
| find_gt_anchor_first: false | |
| selection_metric: aligned_rmsd | |
| use_center_rmsd: false | |
| permute_by_pocket: true | |
| test: | |
| diffusion_sample: true | |
| train: | |
| diffusion_sample: false | |
| mini_rollout: true | |
| checkpoint_interval: -1 | |
| data: | |
| atlas: | |
| base_info: | |
| bioassembly_dict_dir: /home/toolkit/ewpo/data_atlas/mmcif_bioassembly | |
| indices_fpath: /home/toolkit/ewpo/data_atlas/indices.csv | |
| max_n_token: -1 | |
| mmcif_dir: /home/toolkit/ewpo/data_atlas/mmcif | |
| pdb_list: '' | |
| random_sample_if_failed: true | |
| use_reference_chains_only: true | |
| cropping_configs: | |
| crop_size: 256 | |
| method_weights: | |
| - 0.5 | |
| - 0.5 | |
| - 0.0 | |
| lig_atom_rename: false | |
| limits: -1 | |
| precomputed_emb_dir: /home/toolkit/ewpo/dumps | |
| sample_weight: 0.5 | |
| sampler_configs: | |
| sampler_type: uniform | |
| shuffle_mols: false | |
| shuffle_sym_ids: false | |
| atlas_repr: | |
| base_info: | |
| bioassembly_dict_dir: /home/toolkit/ewpo/data_atlas/mmcif_bioassembly | |
| indices_fpath: /home/toolkit/ewpo/data_atlas/indices_repr.csv | |
| max_n_token: -1 | |
| mmcif_dir: /home/toolkit/ewpo/data_atlas/mmcif | |
| pdb_list: '' | |
| random_sample_if_failed: true | |
| use_reference_chains_only: true | |
| cropping_configs: | |
| crop_size: -1 | |
| method_weights: | |
| - 0.0 | |
| - 0.0 | |
| - 1.0 | |
| lig_atom_rename: false | |
| limits: -1 | |
| precomputed_emb_dir: /home/toolkit/ewpo/dumps | |
| sample_weight: 0.5 | |
| sampler_configs: | |
| sampler_type: uniform | |
| shuffle_mols: false | |
| shuffle_sym_ids: false | |
| atlas_test: | |
| base_info: | |
| bioassembly_dict_dir: /home/toolkit/ewpo/data_atlas/mmcif_bioassembly | |
| indices_fpath: /home/toolkit/ewpo/data_atlas/indices_test.csv | |
| max_n_token: -1 | |
| mmcif_dir: /home/toolkit/ewpo/data_atlas/mmcif | |
| pdb_list: '' | |
| random_sample_if_failed: true | |
| use_reference_chains_only: true | |
| cropping_configs: | |
| crop_size: -1 | |
| method_weights: | |
| - 0.0 | |
| - 0.0 | |
| - 1.0 | |
| lig_atom_rename: false | |
| limits: -1 | |
| precomputed_emb_dir: /home/toolkit/ewpo/dumps | |
| sample_weight: 0.5 | |
| sampler_configs: | |
| sampler_type: uniform | |
| shuffle_mols: false | |
| shuffle_sym_ids: false | |
| atlas_test_repr: | |
| base_info: | |
| bioassembly_dict_dir: /home/toolkit/ewpo/data_atlas/mmcif_bioassembly | |
| indices_fpath: /home/toolkit/ewpo/data_atlas/indices_test_repr.csv | |
| max_n_token: -1 | |
| mmcif_dir: /home/toolkit/ewpo/data_atlas/mmcif | |
| pdb_list: '' | |
| random_sample_if_failed: true | |
| use_reference_chains_only: true | |
| cropping_configs: | |
| crop_size: -1 | |
| method_weights: | |
| - 0.0 | |
| - 0.0 | |
| - 1.0 | |
| lig_atom_rename: false | |
| limits: -1 | |
| precomputed_emb_dir: /home/toolkit/ewpo/dumps | |
| sample_weight: 0.5 | |
| sampler_configs: | |
| sampler_type: uniform | |
| shuffle_mols: false | |
| shuffle_sym_ids: false | |
| atlas_train: | |
| base_info: | |
| bioassembly_dict_dir: /home/toolkit/ewpo/data_atlas/mmcif_bioassembly | |
| indices_fpath: /home/toolkit/ewpo/data_atlas/indices_train.csv | |
| max_n_token: -1 | |
| mmcif_dir: /home/toolkit/ewpo/data_atlas/mmcif | |
| pdb_list: '' | |
| random_sample_if_failed: true | |
| use_reference_chains_only: true | |
| cropping_configs: | |
| crop_size: 256 | |
| method_weights: | |
| - 0.5 | |
| - 0.5 | |
| - 0.0 | |
| lig_atom_rename: false | |
| limits: -1 | |
| precomputed_emb_dir: /home/toolkit/ewpo/dumps | |
| sample_weight: 0.5 | |
| sampler_configs: | |
| sampler_type: uniform | |
| shuffle_mols: false | |
| shuffle_sym_ids: false | |
| atlas_train_dpo: | |
| base_info: | |
| annotation_csv: /home/toolkit/ewpo/data_atlas/minimization_results_all.csv | |
| bioassembly_dict_dir: /home/toolkit/ewpo/data_atlas/mmcif_bioassembly | |
| indices_fpath: /home/toolkit/ewpo/data_atlas/indices_train.csv | |
| max_n_token: 384 | |
| mmcif_dir: /home/toolkit/ewpo/data_atlas/mmcif | |
| pdb_list: '' | |
| preference_mode: true | |
| random_sample_if_failed: true | |
| retrieval_k: 2 | |
| use_reference_chains_only: true | |
| cropping_configs: | |
| crop_size: -1 | |
| method_weights: | |
| - 0.5 | |
| - 0.5 | |
| - 0.0 | |
| lig_atom_rename: false | |
| limits: -1 | |
| precomputed_emb_dir: /home/toolkit/ewpo/dumps | |
| sample_weight: 0.5 | |
| sampler_configs: | |
| sampler_type: uniform | |
| shuffle_mols: false | |
| shuffle_sym_ids: false | |
| atlas_val: | |
| base_info: | |
| bioassembly_dict_dir: /home/toolkit/ewpo/data_atlas/mmcif_bioassembly | |
| indices_fpath: /home/toolkit/ewpo/data_atlas/indices_val.csv | |
| max_n_token: -1 | |
| mmcif_dir: /home/toolkit/ewpo/data_atlas/mmcif | |
| pdb_list: '' | |
| random_sample_if_failed: true | |
| use_reference_chains_only: true | |
| cropping_configs: | |
| crop_size: -1 | |
| method_weights: | |
| - 0.0 | |
| - 0.0 | |
| - 1.0 | |
| lig_atom_rename: false | |
| limits: -1 | |
| precomputed_emb_dir: /home/toolkit/ewpo/dumps | |
| sample_weight: 0.5 | |
| sampler_configs: | |
| sampler_type: uniform | |
| shuffle_mols: false | |
| shuffle_sym_ids: false | |
| ccd_components_file: /home/toolkit/ewpo/ewpo/release_data/ccd_cache/components.v20240608.cif | |
| ccd_components_rdkit_mol_file: /home/toolkit/ewpo/ewpo/release_data/ccd_cache/components.v20240608.cif.rdkit_mol.pkl | |
| epoch_size: 10000 | |
| msa: | |
| enable: true | |
| enable_rna_msa: false | |
| max_size: | |
| test: 16384 | |
| train: 16384 | |
| merge_method: dense_max | |
| min_size: | |
| test: 2048 | |
| train: 1 | |
| prot: | |
| indexing_method: sequence | |
| non_pairing_db: mmseqs_other | |
| pairing_db: uniref100 | |
| pdb_mmseqs_dir: /home/toolkit/ewpo/release_data/mmcif_msa | |
| seq_to_pdb_idx_path: /home/toolkit/ewpo/release_data/seq_to_pdb_index.json | |
| rna: | |
| indexing_method: sequence | |
| rna_msa_dir: '' | |
| seq_to_pdb_idx_path: '' | |
| sample_cutoff: | |
| test: 2048 | |
| train: 2048 | |
| strategy: random | |
| num_dl_workers: 16 | |
| posebusters_0925: | |
| base_info: | |
| bioassembly_dict_dir: /home/toolkit/ewpo/release_data/posebusters_bioassembly | |
| find_all_pockets: false | |
| find_pocket: true | |
| indices_fpath: /home/toolkit/ewpo/release_data/indices/posebusters_indices_mainchain_interface.csv | |
| max_n_token: -1 | |
| mmcif_dir: /home/toolkit/ewpo/release_data/posebusters_mmcif | |
| pdb_list: '' | |
| cropping_configs: | |
| crop_size: -1 | |
| method_weights: | |
| - 0.0 | |
| - 0.0 | |
| - 1.0 | |
| lig_atom_rename: false | |
| sampler_configs: | |
| sampler_type: uniform | |
| shuffle_mols: false | |
| shuffle_sym_ids: false | |
| recentPDB_1536_sample384_0925: | |
| base_info: | |
| bioassembly_dict_dir: /home/toolkit/ewpo/release_data/recentPDB_bioassembly | |
| find_eval_chain_interface: true | |
| group_by_pdb_id: true | |
| indices_fpath: /home/toolkit/ewpo/release_data/indices/recentPDB_low_homology_maxtoken1536.csv | |
| max_n_token: -1 | |
| mmcif_dir: /home/toolkit/ewpo/release_data/mmcif | |
| pdb_list: /home/toolkit/ewpo/release_data/indices/recentPDB_low_homology_maxtoken1024_sample384_pdb_id.txt | |
| sort_by_n_token: false | |
| cropping_configs: | |
| crop_size: -1 | |
| method_weights: | |
| - 0.0 | |
| - 0.0 | |
| - 1.0 | |
| lig_atom_rename: false | |
| sampler_configs: | |
| sampler_type: uniform | |
| shuffle_mols: false | |
| shuffle_sym_ids: false | |
| template: | |
| enable: false | |
| test_ref_pos_augment: true | |
| test_sets: | |
| - atlas_test_repr | |
| train_ref_pos_augment: true | |
| train_sampler: | |
| sampler_type: weighted | |
| train_sample_weights: | |
| - 1.0 | |
| train_sets: | |
| - atlas_train | |
| weightedPDB_before2109_wopb_nometalc_0925: | |
| base_info: | |
| bioassembly_dict_dir: /home/toolkit/ewpo/release_data/mmcif_bioassembly | |
| exclusion: | |
| mol_1_type: | |
| - ions | |
| mol_2_type: | |
| - ions | |
| indices_fpath: /home/toolkit/ewpo/release_data/indices/weightedPDB_indices_before_2021-09-30_wo_posebusters_resolution_below_9.csv.gz | |
| max_n_token: -1 | |
| mmcif_dir: /home/toolkit/ewpo/release_data/mmcif | |
| pdb_list: '' | |
| random_sample_if_failed: true | |
| use_reference_chains_only: false | |
| cropping_configs: | |
| crop_size: 256 | |
| method_weights: | |
| - 0.2 | |
| - 0.4 | |
| - 0.4 | |
| lig_atom_rename: false | |
| limits: -1 | |
| sample_weight: 0.5 | |
| sampler_configs: | |
| alpha_dict: | |
| ligand: 1 | |
| nuc: 3 | |
| prot: 3 | |
| beta_dict: | |
| chain: 0.5 | |
| interface: 1 | |
| force_recompute_weight: true | |
| sampler_type: weighted | |
| shuffle_mols: false | |
| shuffle_sym_ids: false | |
| decay_every_n_steps: 50000 | |
| deterministic: false | |
| diffusion_batch_size: 48 | |
| diffusion_chunk_size: 4 | |
| dpo_training: false | |
| dtype: bf16 | |
| dump_embeddings: false | |
| ema_decay: 0.999 | |
| ema_mutable_param_keywords: | |
| - '' | |
| eval_ema_only: false | |
| eval_first: false | |
| eval_interval: 400 | |
| eval_only: false | |
| find_unused_parameters: false | |
| grad_clip_norm: 10 | |
| infer_setting: | |
| chunk_size: 64 | |
| lddt_metrics_chunk_size: 1 | |
| lddt_metrics_sparse_enable: true | |
| sample_diffusion_chunk_size: 4 | |
| inference_noise_scheduler: | |
| rho: 7 | |
| s_max: 160.0 | |
| s_min: 0.0004 | |
| sigma_data: 16.0 | |
| iters_to_accumulate: 1 | |
| load_checkpoint_path: /home/toolkit/ewpo/outputs/dpo/dpo_train_12999_ewpo_20250128_013045/checkpoints/999.pt | |
| load_ema_checkpoint_path: /home/toolkit/ewpo/outputs/dpo/dpo_train_12999_ewpo_20250128_013045/checkpoints/999.pt | |
| load_params_only: true | |
| load_strict: true | |
| log_interval: 50 | |
| loss: | |
| diffusion: | |
| beta_dpo: 1 | |
| beta_ewpo: 0.4 | |
| bond: | |
| eps: 1.0e-06 | |
| dpo_enabled: false | |
| ewpo_enabled: false | |
| ewpo_with_ref: false | |
| linear_ew: false | |
| mse: | |
| eps: 1.0e-06 | |
| weight_dna: 5.0 | |
| weight_ligand: 10.0 | |
| weight_mse: 0.3333333333333333 | |
| weight_rna: 5.0 | |
| norm_by_len: false | |
| smooth_lddt: | |
| eps: 1.0e-06 | |
| diffusion_bond_chunk_size: 1 | |
| diffusion_chunk_size_outer: -1 | |
| diffusion_lddt_chunk_size: 1 | |
| diffusion_lddt_loss_dense: true | |
| diffusion_sparse_loss_enable: true | |
| distogram: | |
| eps: 1.0e-06 | |
| max_bin: 21.6875 | |
| min_bin: 2.3125 | |
| no_bins: 64 | |
| pae: | |
| eps: 1.0e-06 | |
| max_bin: 32 | |
| min_bin: 0 | |
| no_bins: 64 | |
| pde: | |
| eps: 1.0e-06 | |
| max_bin: 32 | |
| min_bin: 0 | |
| no_bins: 64 | |
| plddt: | |
| eps: 1.0e-06 | |
| max_bin: 1.0 | |
| min_bin: 0 | |
| no_bins: 50 | |
| normalize: true | |
| resolution: | |
| max: 4.0 | |
| min: 0.1 | |
| resolved: | |
| eps: 1.0e-06 | |
| weight: | |
| alpha_bond: 0.0 | |
| alpha_confidence: 0.0001 | |
| alpha_diffusion: 4.0 | |
| alpha_distogram: 0.03 | |
| alpha_except_pae: 1.0 | |
| alpha_pae: 0.0 | |
| smooth_lddt: 1.0 | |
| loss_metrics_sparse_enable: true | |
| lr: 0.0018 | |
| lr_scheduler: af3 | |
| max_atoms_per_token: 24 | |
| max_steps: 100000 | |
| metrics: | |
| chain_ranker_keys: | |
| - chain_ptm | |
| - chain_plddt | |
| clash: | |
| af3_clash_threshold: 1.1 | |
| vdw_clash_threshold: 0.75 | |
| complex_ranker_keys: | |
| - plddt | |
| - gpde | |
| - ranking_score | |
| interface_ranker_keys: | |
| - chain_pair_iptm | |
| - chain_pair_iptm_global | |
| - chain_pair_plddt | |
| lddt: | |
| eps: 1.0e-06 | |
| min_lr_ratio: 0.1 | |
| model: | |
| N_cycle: 4 | |
| N_model_seed: 1 | |
| confidence_head: | |
| blocks_per_ckpt: 1 | |
| c_s: 384 | |
| c_s_inputs: 449 | |
| c_z: 128 | |
| distance_bin_end: 52.0 | |
| distance_bin_start: 3.25 | |
| distance_bin_step: 1.25 | |
| max_atoms_per_token: 24 | |
| n_blocks: 4 | |
| pairformer_dropout: 0.0 | |
| stop_gradient: true | |
| diffusion_module: | |
| atom_decoder: | |
| n_blocks: 3 | |
| n_heads: 4 | |
| atom_encoder: | |
| n_blocks: 3 | |
| n_heads: 4 | |
| blocks_per_ckpt: 1 | |
| c_atom: 128 | |
| c_atompair: 16 | |
| c_s: 384 | |
| c_s_inputs: 449 | |
| c_token: 768 | |
| c_z: 128 | |
| initialization: | |
| glorot_init_self_attention: false | |
| he_normal_init_atom_encoder_output: false | |
| he_normal_init_atom_encoder_small_mlp: false | |
| zero_init_adaln: true | |
| zero_init_atom_decoder_linear: false | |
| zero_init_atom_encoder_residual_linear: false | |
| zero_init_condition_transition: false | |
| zero_init_dit_output: true | |
| zero_init_residual_condition_transition: false | |
| sigma_data: 16.0 | |
| transformer: | |
| n_blocks: 24 | |
| n_heads: 16 | |
| use_fine_grained_checkpoint: true | |
| distogram_head: | |
| c_z: 128 | |
| no_bins: 64 | |
| input_embedder: | |
| c_atom: 128 | |
| c_atompair: 16 | |
| c_token: 384 | |
| msa_module: | |
| blocks_per_ckpt: 1 | |
| c_m: 64 | |
| c_s_inputs: 449 | |
| c_z: 128 | |
| msa_dropout: 0.15 | |
| n_blocks: 4 | |
| pair_dropout: 0.25 | |
| pairformer: | |
| blocks_per_ckpt: 1 | |
| c_s: 384 | |
| c_z: 128 | |
| dropout: 0.25 | |
| n_blocks: 48 | |
| n_heads: 16 | |
| relative_position_encoding: | |
| c_z: 128 | |
| r_max: 32 | |
| s_max: 2 | |
| template_embedder: | |
| blocks_per_ckpt: 1 | |
| c: 64 | |
| c_z: 128 | |
| dropout: 0.25 | |
| n_blocks: 0 | |
| n_blocks: 48 | |
| need_atom_confidence: false | |
| no_bins: 64 | |
| predict_only: true | |
| project: protenix | |
| run_name: '13045_250' | |
| sample_diffusion: | |
| N_sample: 250 | |
| N_sample_mini_rollout: 1 | |
| N_step: 20 | |
| N_step_mini_rollout: 20 | |
| gamma0: 0.8 | |
| gamma_min: 1.0 | |
| noise_scale_lambda: 1.75 | |
| step_scale_eta: 1.25 | |
| seed: 42 | |
| sigma_data: 16.0 | |
| skip_amp: | |
| confidence_head: true | |
| loss: true | |
| sample_diffusion: true | |
| sample_diffusion_training: true | |
| skip_confidence_and_permutation: false | |
| skip_load_optimizer: false | |
| skip_load_scheduler: false | |
| skip_load_step: false | |
| sorted_by_ranking_score: false | |
| test_lig_atom_rename: false | |
| test_max_n_token: -1 | |
| test_shuffle_mols: false | |
| test_shuffle_sym_ids: false | |
| train_confidence_only: false | |
| train_crop_size: 256 | |
| train_lig_atom_rename: false | |
| train_noise_sampler: | |
| p_mean: -1.2 | |
| p_std: 1.5 | |
| sigma_data: 16.0 | |
| train_shuffle_mols: false | |
| train_shuffle_sym_ids: false | |
| use_deepspeed_evo_attention: false | |
| use_flash: false | |
| use_lma: false | |
| use_memory_efficient_kernel: false | |
| use_wandb: false | |
| use_xformer: false | |
| wandb_id: '' | |
| warmup_steps: 10 | |