workdir/paper_confidence_model/model_parameters.yml

all_atoms: true
atom_max_neighbors: 8
atom_radius: 5
balance: false
batch_size: 16
best_model_save_frequency: 5
c_alpha_max_neighbors: 24
cache_creation_id: 1
cache_ids_to_combine:
- '1'
- '2'
- '3'
- '4'
cache_path: data/cache
ckpt: best_model.pt
confidence_dropout: 0.0
confidence_loss_weigth: 1
confidence_no_batchnorm: false
confidence_weight: 0.33
config: null
cross_distance_embed_dim: 32
cross_max_distance: 80
data_dir: data/PDBBind_processed/
distance_embed_dim: 32
dropout: 0.1
dynamic_max_cross: true
embedding_scale: 10000
embedding_type: sinusoidal
esm_embeddings_path: data/esm2_3billion_embeddings.pt
high_confidence_threshold: 5.0
include_confidence_prediction: false
inference_steps: 20
limit_complexes: 0
lm_embeddings_path: null
log_dir: workdir
lr: 0.0003
main_metric: loss
main_metric_goal: min
matching_maxiter: 20
matching_popsize: 20
max_lig_size: null
max_radius: 5.0
model_save_frequency: 0
n_epochs: 100
no_batch_norm: false
no_torsion: false
ns: 24
num_conformers: 1
num_conv_layers: 5
num_workers: 1
nv: 6
original_model_dir: workdir/temp_restart_ema_ESM2emb_tr34
project: diffdock_confidence
receptor_radius: 15.0
remove_hs: true
restart_dir: null
rmsd_classification_cutoff:
- 2.0
rmsd_prediction: false
rot_sigma_max: 1.55
rot_sigma_min: 0.03
rot_weight: 0.33
run_name: confidencetrain_samples28_FILTERFROM_ema_ESM2emb_tr34
samples_per_complex: 7
scale_by_sigma: true
scheduler: plateau
scheduler_patience: 50
sigma_embed_dim: 32
split_test: data/splits/timesplit_test
split_train: data/splits/timesplit_no_lig_overlap_train
split_val: data/splits/timesplit_no_lig_overlap_val
tor_sigma_max: 3.14
tor_sigma_min: 0.0314
tor_sigma_schedule: expbeta
tor_weight: 0.33
tr_only_confidence: true
tr_sigma_max: 34.0
tr_sigma_min: 0.1
tr_weight: 0.33
train_sampling: linear
transfer_weights: false
use_original_model_cache: false
use_second_order_repr: false
w_decay: 0.0
wandb: true