--- a
+++ b/configs/moad_fullatom_joint.yml
@@ -0,0 +1,63 @@
+run_name: 'SE3-joint-fullAtom'
+logdir: '/path/to/logdir'
+wandb_params:
+  mode: 'online'  # disabled, offline, online
+  entity: 'my_username'
+  group: 'bindingmoad'
+dataset: 'bindingmoad'
+datadir: '/path/to//processed_noH_full/'
+enable_progress_bar: False
+num_sanity_val_steps: 0
+
+mode: 'joint'
+pocket_representation: 'full-atom'
+virtual_nodes: False
+batch_size: 16
+lr: 5.0e-4
+n_epochs: 1000
+num_workers: 2
+gpus: 2
+clip_grad: True
+augment_rotation: False
+augment_noise: 0
+
+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: 0.8  # = 4.0 / 5.0
+  edge_cutoff_interaction: 1.4  # = 7.0 / 5.0
+  reflection_equivariant: False
+  edge_embedding_dim: 8
+  joint_nf: 128
+  hidden_nf: 192
+  n_layers: 6
+  attention: True
+  tanh: True
+  norm_constant: 1
+  inv_sublayers: 1
+  sin_embedding: False
+  aggregation_method: 'sum'
+  normalization_factor: 100  # used if aggregation_method='sum'
+
+diffusion_params:
+  diffusion_steps: 500
+  diffusion_noise_schedule: 'polynomial_2'  # learned, cosine
+  diffusion_noise_precision: 1.0e-5
+  diffusion_loss_type: 'l2'  # vlb, l2
+  normalize_factors: [5, 5]  # [x, h]
+
+eval_epochs: 25
+visualize_sample_epoch: 25
+visualize_chain_epoch: 25
+eval_params:
+  n_eval_samples: 100
+  eval_batch_size: 50
+  smiles_file: '/path/to/train_smiles.npy'
+  n_visualize_samples: 5
+  keep_frames: 100
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