run_name: 'SE3-inpaint-full'

logdir: '/path/to/logdir'

wandb_params:

  mode: 'online'  # disabled, offline, online

  entity: 'my_username'

dataset: 'crossdock'

datadir: '/path/to/processed_crossdock_noH_full'

enable_progress_bar: True

num_sanity_val_steps: 0

mode: 'joint'  # joint, pocket_conditioning

pocket_representation: 'full-atom'  # CA, full-atom

batch_size: 8

lr: 1.0e-3

noise_factor: 1.0

n_epochs: 1000

num_workers: 0

gpus: 4

clip_grad: True

augment_rotation: False

augment_noise: 0

accumulate_grad_batches: 4

auxiliary_loss: False

loss_params:

  max_weight: 0.001

  schedule: 'linear'

  clamp_lj: 3.0

egnn_params:

  device: 'cuda'

  edge_cutoff_ligand: null

  edge_cutoff_pocket: 5.0

  edge_cutoff_interaction: 5.0

  reflection_equivariant: False

  joint_nf: 32

  hidden_nf: 128

  n_layers: 5

  attention: True

  tanh: True

  norm_constant: 1

  inv_sublayers: 1

  sin_embedding: False

  aggregation_method: 'sum'

  normalization_factor: 100 #1  # used if aggregation_method='sum'

diffusion_params:

  diffusion_steps: 500

  diffusion_noise_schedule: 'polynomial_2'  # learned, cosine

  diffusion_noise_precision: 5.0e-4

  diffusion_loss_type: 'l2'  # vlb, l2

  normalize_factors: [1, 4]  #[10, 4]  # [x, h]

eval_epochs: 50

visualize_sample_epoch: 50

visualize_chain_epoch: 50

eval_params:

  n_eval_samples: 100

  eval_batch_size: 100

  smiles_file: '/path/to/train_smiles.npy'

  n_visualize_samples: 5

  keep_frames: 100