data:
  dataset:
    seed: 123
    max_num_res: 128
    cache_num_res: 0
    max_cache_size: 100000
    min_num_res: 0
    subset: null
    samples_per_eval_length: 5
    num_eval_lengths: 8
    min_eval_length: 500
    csv_path: ./preprocessed/metadata.csv
  loader:
    num_workers: 4
    prefetch_factor: 10
  sampler:
    max_batch_size: 100
    max_num_res_squared: 500000
    use_batch_repeats: false
    num_batches: null
interpolant:
  min_t: 0.01
  separate_t: true
  provide_kappa: true
  hierarchical_t: false
  rots:
    train_schedule: linear
    sample_schedule: exp
    exp_rate: 10
  trans:
    batch_ot: true
    train_schedule: linear
    sample_schedule: linear
    sample_temp: 1.0
    vpsde_bmin: 0.1
    vpsde_bmax: 20.0
  sampling:
    num_timesteps: 100
    do_sde: false
  self_condition: ${model.edge_features.self_condition}
model:
  node_embed_size: 256
  edge_embed_size: 128
  symmetric: false
  node_features:
    c_s: ${model.node_embed_size}
    c_pos_emb: 128
    c_timestep_emb: 128
    separate_t: ${interpolant.separate_t}
    embed_diffuse_mask: false
    max_num_res: 2000
    timestep_int: 1000
  edge_features:
    single_bias_transition_n: 2
    c_s: ${model.node_embed_size}
    c_p: ${model.edge_embed_size}
    relpos_k: 64
    use_rbf: true
    num_rbf: 32
    feat_dim: 64
    num_bins: 22
    self_condition: true
  ipa:
    c_s: ${model.node_embed_size}
    c_z: ${model.edge_embed_size}
    c_hidden: 128
    no_heads: 8
    no_qk_points: 8
    no_v_points: 12
    seq_tfmr_num_heads: 4
    seq_tfmr_num_layers: 2
    num_blocks: 6
experiment:
  debug: false
  seed: 123
  num_devices: 2
  warm_start: null
  warm_start_cfg_override: true
  use_swa: false
  batch_ot:
    enabled: true
    cost: kabsch
    noise_per_sample: 1
    permute: false
  training:
    min_plddt_mask: null
    loss: se3_vf_loss
    bb_atom_scale: 0.1
    trans_scale: 0.1
    translation_loss_weight: 2.0
    t_normalize_clip: 0.9
    rotation_loss_weights: 1.0
    aux_loss_weight: 1.0
    aux_loss_t_pass: 0.25
  wandb:
    name: baseline
    project: se3-fm
    save_code: true
    tags: []
  optimizer:
    lr: 0.0001
  trainer:
    overfit_batches: 0
    min_epochs: 1
    max_epochs: 1000
    accelerator: gpu
    log_every_n_steps: 1
    deterministic: false
    strategy: ddp
    check_val_every_n_epoch: 2
    accumulate_grad_batches: 2
  checkpointer:
    dirpath: ckpt/${experiment.wandb.project}/${experiment.wandb.name}/${now:%Y-%m-%d}_${now:%H-%M-%S}
    save_last: true
    save_top_k: 3
    monitor: valid/non_coil_percent
    mode: max