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ckpt
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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