Enable generic DynamicBind ensemble inference

configs/model/ensemble_generation.yaml

@@ -1,11 +1,4 @@
-ensemble_methods: [
-    diffdock,
-    dynamicbind,
-    neuralplexer,
-    rfaa,
-    vina,
-    tulip,
-  ] # the methods from which to gather predictions for ensembling - NOTE: must be one of (`diffdock`, `dynamicbind`, `neuralplexer`, `rfaa`, `vina`, `tulip`)
+ensemble_methods: [diffdock, dynamicbind, neuralplexer, rfaa, vina, tulip] # the methods from which to gather predictions for ensembling - NOTE: must be one of (`diffdock`, `dynamicbind`, `neuralplexer`, `rfaa`, `vina`, `tulip`)
 generate_vina_scripts: false # whether to generate Vina scripts using other methods' binding site predictions - NOTE: `resume` must also be `true` when this is `true`, meaning other methods' predictions must have already been generated locally
 rank_single_method_intrinsically: true # whether to rank single-method predictions using either `consensus` or `vina` ranking (false) or instead using their intrinsic (explicit) rank assignment (true)
 output_bash_file_dir: ensemble_generation_scripts # the directory in which to save the generated Bash scripts
@@ -66,6 +59,7 @@ diffdock_skip_existing: true # whether to skip existing predictions
 # DynamicBind inference arguments:
 dynamicbind_python_exec_path: ${oc.env:PROJECT_ROOT}/forks/DynamicBind/DynamicBind/bin/python3 # the Python executable to use
 dynamicbind_exec_dir: ${oc.env:PROJECT_ROOT}/forks/DynamicBind # the DynamicBind directory in which to execute the inference scripts
+dynamicbind_dataset: ensemble # the dataset to use for inference - NOTE: must be one of (`ensemble`)
 dynamicbind_input_protein_data_dir: ${oc.env:PROJECT_ROOT}/forks/DynamicBind/inference/ensemble_esmfold_structures # the input protein-ligand complex directory to recursively parse for protein inputs
 dynamicbind_input_ligand_csv_dir: ${oc.env:PROJECT_ROOT}/forks/DynamicBind/inference/dynamicbind_ensemble_inputs # the input CSV directory with which to run inference
 dynamicbind_samples_per_complex: 40 # the number of samples to generate per complex

src/models/ensemble_generation.py

@@ -246,6 +246,7 @@ def create_dynamicbind_bash_script(
     cuda_device_index={cfg.cuda_device_index} \\
     python_exec_path={cfg.dynamicbind_python_exec_path} \\
     dynamicbind_exec_dir={cfg.dynamicbind_exec_dir} \\
+    dataset={cfg.dynamicbind_dataset} \\
     input_data_dir={cfg.dynamicbind_input_protein_data_dir} \\
     input_ligand_csv_dir={cfg.dynamicbind_input_ligand_csv_dir} \\
     samples_per_complex={min(cfg.dynamicbind_samples_per_complex, cfg.max_method_predictions)} \\