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# DiffDock CGModel Dataset Evaluation Configuration
#
# IMPORTANT: Update all filesystem paths below to match your environment.
#
# Supported dataset values: pdbbind | moad | generalisation
#
# External dependencies (optional):
# gnina_minimize=true → requires `gnina` executable on PATH
# RMSD computations → requires `spyrmsd` (pip install spyrmsd)
# ============================================================================
runtime:
run_name: diffdock_eval_example
project: diffdock
device: auto
out_dir: examples/biosciences/diffdock/outputs/evaluate
wandb: false
num_cpu: null
restrict_cpu: false
model:
model_dir: /public/home/liuyx19/modelscope/diffdock/outputs/train/diffdock_pdbbind_smoke100_val20_cpu
ckpt: best_model.pt
old_score_model: false # must stay false; old_* score-model paths are intentionally not migrated
no_model: false
force_fixed_center_conv: false
confidence:
confidence_model_dir: null
confidence_ckpt: best_model.pt
old_confidence_model: false # must stay false; old confidence-model paths are intentionally not migrated
data:
dataset: pdbbind # supported: pdbbind | moad | generalisation; unsupported: pdbsidechain | distillation
cache_path: /public/home/liuyx19/modelscope/diffdock/cache
data_dir: /public/share/sugonhpcapp01/onestore/onedatasets/diffdock/datasets/PDBBind_processed
split_path: /public/share/sugonhpcapp01/onestore/onedatasets/diffdock/datasets/splits/timesplit_no_lig_overlap_val
split: val
limit_complexes: 0
num_workers: 1
chain_cutoff: null
protein_file: protein_processed
ligand_file: ligand
esm_embeddings_path: null
moad_esm_embeddings_sequences_path: null
not_knn_only_graph: false
include_miscellaneous_atoms: false
triple_training: false # unsupported in the current migration; will fail fast if set true
unroll_clusters: false
remove_pdbbind: false
min_ligand_size: 0
max_receptor_size: null
remove_promiscuous_targets: null
matching_popsize: 40
matching_maxiter: 40
sampling:
batch_size: 20
inference_steps: 20
actual_steps: null
samples_per_complex: 10
no_random: false
no_final_step_noise: true
ode: false
sigma_schedule: expbeta
inf_sched_alpha: 1.0
inf_sched_beta: 1.0
pocket_knowledge: false
no_random_pocket: false
pocket_tr_max: 3.0
pocket_cutoff: 5.0
different_schedules: false
resample_rdkit: false
skip_matching: false
initial_noise_std_proportion: -1.0
choose_residue: false
limit_failures: 5
tqdm: true
temp_sampling_tr: 1.0
temp_psi_tr: 0.0
temp_sigma_data_tr: 0.5
temp_sampling_rot: 1.0
temp_psi_rot: 0.0
temp_sigma_data_rot: 0.5
temp_sampling_tor: 1.0
temp_psi_tor: 0.0
temp_sigma_data_tor: 0.5
outputs:
save_visualisation: false
save_complexes: false
complexes_save_path: null
gnina:
gnina_minimize: false
gnina_path: gnina
gnina_full_dock: false
save_gnina_metrics: false
gnina_autobox_add: 4.0
gnina_poses_to_optimize: 1
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