File size: 1,873 Bytes
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# DiffDock CGModel Sampling Configuration
#
# IMPORTANT: Update all filesystem paths below to match your environment.
# - model_dir: must contain a CGModel checkpoint + model_parameters.yml
# - protein_path: path to receptor PDB
# - ligand_description: SMILES string or path to .sdf/.mol2
#
# CSV batch mode:
# Set protein_ligand_csv instead of the single-complex fields.
# CSV columns: complex_name, protein_path, ligand_description, protein_sequence
#
# Confidence rerank:
# Set confidence_model_dir to a CGModel-based confidence checkpoint dir.
# ============================================================================
runtime:
device: auto
loglevel: INFO
out_dir: examples/biosciences/diffdock/outputs/sample
model:
model_dir: ${ONESCIENCE_DATASETS_DIR}/diffdock/score_model
ckpt: best_ema_inference_epoch_model.pt
old_score_model: false
confidence:
confidence_model_dir: ${ONESCIENCE_DATASETS_DIR}/diffdock/confidence_model
confidence_ckpt: best_model_epoch75.pt
old_confidence_model: false
input:
protein_ligand_csv: null
complex_name: 6o5u_test
protein_path: examples/biosciences/diffdock/data/6o5u_protein_processed.pdb
protein_sequence: null
ligand_description: examples/biosciences/diffdock/data/6o5u_ligand.sdf
lm_embeddings: null
sampling:
samples_per_complex: 10
batch_size: 10
inference_steps: 20
actual_steps: null
sigma_schedule: expbeta
inf_sched_alpha: 1.0
inf_sched_beta: 1.0
no_random: false
no_final_step_noise: true
ode: false
choose_residue: false
initial_noise_std_proportion: 1.0
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
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