refactor: update dice handling and optimization flow to return structured results

diceplayer/dice/dice_wrapper.py

@@ -1,3 +1,5 @@
+from pydantic import TypeAdapter
+
 import diceplayer.dice.dice_input as dice_input
 from diceplayer.config import DiceConfig
 from diceplayer.environment import System
@@ -7,6 +9,10 @@ from pathlib import Path
 from typing import Final
 
 
+type DiceEnvironment = tuple[str, int, int, int]
+DiceEnvironmentAdapter = TypeAdapter(DiceEnvironment)
+
+
 DICE_FLAG_LINE: Final[int] = -2
 DICE_END_FLAG: Final[str] = "End of simulation"
 
@@ -35,9 +41,22 @@ class DiceWrapper:
 
         raise RuntimeError(f"Dice simulation failed with exit status {exit_status}")
 
-    def parse_results(self, system: System) -> dict:
-        results = {}
+    def parse_results(self, system: System) -> list[DiceEnvironment]:
+        NUMBER_OF_HEADER_LINES = 2
+        NUMBER_OF_PRIMARY_ATOMS = len(system.molecule[0].atom)
+
+        results = []
         for output_file in sorted(self.working_directory.glob("phb*.xyz")):
-            ...
+            with open(output_file, "r") as f:
+                for _ in range(NUMBER_OF_HEADER_LINES + NUMBER_OF_PRIMARY_ATOMS):
+                    next(f, None)
+
+                for line in f:
+                    if line.strip() == "":
+                        break
+
+                    results.append(
+                        DiceEnvironmentAdapter.validate_python(line.split())
+                    )
 
         return results