| run: | |
| name: smoke_test | |
| output_dir: results/smoke_test | |
| max_batches: 2 | |
| random_seed: 7 | |
| data: | |
| target_id: smoke_3ptb | |
| target_path: data/datasets/rdock_3PTB_10k_pubchem/target/rdock_prm/target_raw.pdb | |
| ligand_table: data/ligands/smoke_ligands.csv | |
| benchmark_metadata: data/benchmarks/smoke_metadata.json | |
| backend: | |
| type: rdock | |
| allow_mock_if_missing: false | |
| require_real_backend: true | |
| n_runs: 3 | |
| mapper_radius: 6.0 | |
| pocket_mode: user_fixed_pocket | |
| pocket_center: [-1.7591111111111113, 14.461, 16.915777777777777] | |
| pocket_radius: 6.0 | |
| pocket_relaxation_margin: 0.0 | |
| encoding: | |
| fingerprint_radius: 2 | |
| fingerprint_bits: 512 | |
| generate_3d: false | |
| clustering: | |
| butina_cutoff: 0.4 | |
| n_hyperclusters: 2 | |
| scheduler: | |
| batch_size: 4 | |
| init_coverage_fraction: 0.5 | |
| conservative_deprioritize: false | |
| scoring: | |
| interface_weight: 1.0 | |