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all_atoms: false | |
atom_max_neighbors: 8 | |
atom_radius: 5 | |
batch_size: 16 | |
c_alpha_max_neighbors: 24 | |
cache_path: /data/rsg/nlp/hstark/ligbind/data/cacheNew | |
confidence_dropout: 0.0 | |
confidence_no_batchnorm: false | |
config: null | |
cross_distance_embed_dim: 64 | |
cross_max_distance: 80 | |
cudnn_benchmark: true | |
data_dir: data/PDBBind_processed/ | |
dataset: pdbbind | |
distance_embed_dim: 64 | |
dropout: 0.1 | |
dynamic_max_cross: true | |
ema_rate: 0.999 | |
embedding_scale: 10000 | |
embedding_type: sinusoidal | |
esm_embeddings_path: data/esm2_3billion_embeddings.pt | |
high_confidence_threshold: 5.0 | |
include_confidence_prediction: false | |
inf_pocket_cutoff: 5 | |
inf_pocket_knowledge: false | |
inference_earlystop_goal: max | |
inference_earlystop_metric: valinf_rmsds_lt2 | |
inference_steps: 20 | |
limit_complexes: 0 | |
lm_embeddings_path: null | |
log_dir: workdir | |
lr: 0.001 | |
matching_maxiter: 20 | |
matching_popsize: 20 | |
max_lig_size: null | |
max_radius: 5.0 | |
multiplicity: 1 | |
n_epochs: 850 | |
no_batch_norm: false | |
no_torsion: false | |
norm_by_sigma: false | |
not_full_dataset: false | |
ns: 48 | |
num_conformers: 1 | |
num_conv_layers: 6 | |
num_dataloader_workers: 1 | |
num_gpus: 1 | |
num_inference_complexes: 500 | |
num_workers: 1 | |
nv: 10 | |
odd_parity: false | |
pin_memory: true | |
pretrained_model: null | |
project: diffdock_train | |
receptor_radius: 15.0 | |
remove_hs: true | |
restart_dir: null | |
rot_sigma_max: 1.55 | |
rot_sigma_min: 0.03 | |
rot_weight: 0.33 | |
run_name: big_ema_ESM2emb | |
scale_by_sigma: true | |
scheduler: plateau | |
scheduler_patience: 30 | |
sigma_embed_dim: 64 | |
split_test: data/splits/timesplit_test | |
split_train: data/splits/timesplit_no_lig_overlap_train | |
split_val: data/splits/timesplit_no_lig_overlap_val | |
test_sigma_intervals: true | |
tor_sigma_max: 3.14 | |
tor_sigma_min: 0.0314 | |
tor_weight: 0.33 | |
tr_only_confidence: true | |
tr_sigma_max: 19.0 | |
tr_sigma_min: 0.1 | |
tr_weight: 0.33 | |
train_inference_freq: null | |
train_sampling: linear | |
use_ema: true | |
use_second_order_repr: false | |
val_inference_freq: 5 | |
w_decay: 0.0 | |
wandb: true | |