Expand the NPT specification

Author: amorehead

configs/analysis/inference_analysis_casp.yaml

@@ -12,3 +12,4 @@ fault_tolerant: true # whether to continue processing targets if an error occurs
 skip_existing: true # whether to skip processing targets for which output already exists
 score_relaxed_structures: true # whether to score relaxed structures in addition to the original (unrelaxed) structures
 repeat_index: 1 # the run index to use for scoring predictions
+no_pretraining: false # whether to score a model without pretraining

configs/model/ensemble_generation.yaml

@@ -96,6 +96,7 @@ neuralplexer_use_template: true # whether to use the input template protein stru
 neuralplexer_separate_pdb: true # whether to separate the predicted protein structures into dedicated PDB files
 neuralplexer_rank_outputs_by_confidence: true # whether to rank the output conformations, by default, by ligand confidence (if available) and by protein confidence otherwise
 neuralplexer_plddt_ranking_type: ligand # the type of plDDT ranking to apply to generated samples - NOTE: must be one of (`protein`, `ligand`, `protein_ligand`)
+neuralplexer_no_pretraining: false # whether to avoid loading pretrained weights
 # RoseTTAFold-All-Atom inference arguments:
 rfaa_python_exec_path: ${oc.env:PROJECT_ROOT}/forks/RoseTTAFold-All-Atom/RFAA/bin/python3 # the Python executable to use
 rfaa_exec_dir: ${oc.env:PROJECT_ROOT}/forks/RoseTTAFold-All-Atom # the RoseTTAFold-All-Atom directory in which to execute the inference scripts

src/analysis/inference_analysis_casp.py

@@ -183,6 +183,11 @@ def main(cfg: DictConfig):
 
     :param cfg: Configuration dictionary from the hydra YAML file.
     """
+    if cfg.no_pretraining:
+        with open_dict(cfg):
+            cfg.predictions_dir = cfg.predictions_dir.replace(
+                "_ensemble_predictions", "_npt_ensemble_predictions"
+            )
     if cfg.method == "vina":
         with open_dict(cfg):
             cfg.predictions_dir = cfg.predictions_dir.replace(

src/models/ensemble_generation.py

@@ -815,7 +815,7 @@ def get_method_predictions(
     elif method == "neuralplexer":
         ensemble_benchmarking_output_dir = (
             Path(cfg.input_dir if cfg.input_dir else cfg.neuralplexer_out_path).parent
-            / f"neuralplexer_{cfg.ensemble_benchmarking_dataset}_outputs_{cfg.ensemble_benchmarking_repeat_index}"
+            / f"neuralplexer{'_npt' if cfg.neuralplexer_no_pretraining else ''}_{cfg.ensemble_benchmarking_dataset}_outputs_{cfg.ensemble_benchmarking_repeat_index}"
             if cfg.ensemble_benchmarking
             else (cfg.input_dir if cfg.input_dir else cfg.neuralplexer_out_path)
         )