| 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 |
|
|
