| data: | |
| name: pl | |
| path: ${ONESCIENCE_DATASETS_DIR}/targetdiff/data/crossdocked_v1.1_rmsd1.0_pocket10 | |
| split: ${ONESCIENCE_DATASETS_DIR}/targetdiff/data/crossdocked_pocket10_pose_split.pt | |
| transform: | |
| ligand_atom_mode: add_aromatic | |
| random_rot: False | |
| model: | |
| model_mean_type: C0 # ['noise', 'C0'] | |
| beta_schedule: sigmoid | |
| beta_start: 1.e-7 | |
| beta_end: 2.e-3 | |
| v_beta_schedule: cosine | |
| v_beta_s: 0.01 | |
| num_diffusion_timesteps: 1000 | |
| loss_v_weight: 100. | |
| sample_time_method: symmetric # ['importance', 'symmetric'] | |
| time_emb_dim: 0 | |
| time_emb_mode: simple | |
| center_pos_mode: protein | |
| node_indicator: True | |
| model_type: uni_o2 | |
| num_blocks: 1 | |
| num_layers: 9 | |
| hidden_dim: 128 | |
| n_heads: 16 | |
| edge_feat_dim: 4 # edge type feat | |
| num_r_gaussian: 20 | |
| knn: 32 # ! | |
| num_node_types: 8 | |
| act_fn: relu | |
| norm: True | |
| cutoff_mode: knn # [radius, none] | |
| ew_net_type: global # [r, m, none] | |
| num_x2h: 1 | |
| num_h2x: 1 | |
| r_max: 10. | |
| x2h_out_fc: False | |
| sync_twoup: False | |
| train: | |
| seed: 2021 | |
| batch_size: 4 | |
| num_workers: 4 | |
| n_acc_batch: 1 | |
| max_iters: 10000000 | |
| val_freq: 100 | |
| pos_noise_std: 0.1 | |
| max_grad_norm: 8.0 | |
| bond_loss_weight: 1.0 | |
| optimizer: | |
| type: adam | |
| lr: 5.e-4 | |
| weight_decay: 0 | |
| beta1: 0.95 | |
| beta2: 0.999 | |
| scheduler: | |
| type: plateau | |
| factor: 0.6 | |
| patience: 10 | |
| min_lr: 1.e-6 | |