--no-atom-ids stored into the Settings class

Author: benoistlaurent

src/grodecoder/main.py

@@ -29,8 +29,9 @@ def main(args: "CliArgs"):
     coordinates_path = args.coordinates_file.path if args.coordinates_file else None
 
     # Storing cli arguments into settings.
-    s = get_settings()
-    s.chain_detection.distance_cutoff = args.bond_threshold
+    settings = get_settings()
+    settings.chain_detection.distance_cutoff = args.bond_threshold
+    settings.output.atom_ids = not args.no_atom_ids
 
     logger.info(f"Processing structure file: {structure_path}")
 
@@ -42,11 +43,12 @@ def main(args: "CliArgs"):
         structure_file_checksum=_get_checksum(structure_path),
         database_version=get_database_version(),
         grodecoder_version=get_version(),
-        input_settings = s,
+        input_settings=settings,
     )
 
     # Serialization.
-    serialization_mode = "compact" if args.no_atom_ids else "full"
+    logger.debug("Creating json output")
+    serialization_mode = "full" if settings.output.atom_ids else "compact"
 
     # Updates run time as late as possible.
     output_json = output.model_dump(context={"serialization_mode": serialization_mode})

src/grodecoder/settings.py

@@ -155,9 +155,15 @@ class ResolutionDetectionSettings(BaseSettings):
     distance_cutoff: float = 1.6
 
 
+class OutputSettings(BaseSettings):
+    # should we output atom ids?
+    atom_ids: bool = True
+
+
 class Settings(BaseSettings):
     resolution_detection: ResolutionDetectionSettings = ResolutionDetectionSettings()
     chain_detection: ChainDetectionSettings = ChainDetectionSettings()
+    output: OutputSettings = OutputSettings()
 
     debug: bool = False