refactor: restructure dice environment handling and update Python version requirement

diceplayer/dice/dice_wrapper.py

@@ -1,16 +1,39 @@
-from pydantic import TypeAdapter
-
 import diceplayer.dice.dice_input as dice_input
 from diceplayer.config import DiceConfig
-from diceplayer.environment import System
+
+from pydantic import TypeAdapter
+from pydantic.dataclasses import dataclass
 
 import subprocess
+from itertools import islice
 from pathlib import Path
-from typing import Final
+from typing import Final, List, Self
 
 
-type DiceEnvironment = tuple[str, int, int, int]
-DiceEnvironmentAdapter = TypeAdapter(DiceEnvironment)
+@dataclass(slots=True, frozen=True)
+class DiceEnvironmentItem:
+    atom: str
+    x: float
+    y: float
+    z: float
+
+
+DiceEnvironmentItemAdapter = TypeAdapter(DiceEnvironmentItem)
+
+
+@dataclass(slots=True)
+class DiceEnvironment:
+    number_of_sites: int
+    thickness: List[float]
+    items: List[DiceEnvironmentItem]
+
+    @classmethod
+    def new(cls, thickness: List[float]) -> Self:
+        return cls(number_of_sites=0, thickness=thickness, items=[])
+
+    def add_site(self, site: DiceEnvironmentItem):
+        self.items.append(site)
+        self.number_of_sites += 1
 
 
 DICE_FLAG_LINE: Final[int] = -2
@@ -28,7 +51,10 @@ class DiceWrapper:
 
         with open(output_path, "w") as outfile, open(input_path, "r") as infile:
             exit_status = subprocess.call(
-                self.dice_config.progname, stdin=infile, stdout=outfile, cwd=self.working_directory
+                self.dice_config.progname,
+                stdin=infile,
+                stdout=outfile,
+                cwd=self.working_directory,
             )
 
         if exit_status != 0:
@@ -41,22 +67,37 @@ class DiceWrapper:
 
         raise RuntimeError(f"Dice simulation failed with exit status {exit_status}")
 
-    def parse_results(self, system: System) -> list[DiceEnvironment]:
-        NUMBER_OF_HEADER_LINES = 2
-        NUMBER_OF_PRIMARY_ATOMS = len(system.molecule[0].atom)
-
+    def parse_results(self) -> list[DiceEnvironment]:
         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
+        positions_file = self.working_directory / "phb.xyz"
+        if not positions_file.exists():
+            raise RuntimeError(f"Positions file not found at {self.working_directory}")
 
-                    results.append(
-                        DiceEnvironmentAdapter.validate_python(line.split())
-                    )
+        with open(positions_file, "r") as f:
+            while True:
+                line = f.readline()
+                if not line.startswith("    "):
+                    break
+
+                environment = DiceEnvironment(
+                    number_of_sites=int(line.strip()),
+                    thickness=[float(n) for n in f.readline().split()[-3:]],
+                    items=[],
+                )
+
+                # Skip the comment line
+
+                environment.items.extend(
+                    [
+                        DiceEnvironmentItemAdapter.validate_python(
+                            {"atom": site[0], "x": site[1], "y": site[2], "z": site[3]}
+                        )
+                        for atom in islice(f, environment.number_of_sites)
+                        if (site := atom.strip().split()) and len(site) == 4
+                    ]
+                )
+
+                results.append(environment)
 
         return results