feat: reads potentions from ljc file

diceplayer/utils/potential.py

@@ -0,0 +1,62 @@
+from diceplayer.config import PlayerConfig
+from diceplayer.environment import System, Molecule, Atom
+
+from pathlib import Path
+
+from diceplayer.logger import logger
+from diceplayer.state.state_model import StateModel
+
+
+def read_system_from_phb(config: PlayerConfig) -> System:
+    phb_file = Path(config.dice.ljname)
+    if not phb_file.exists():
+        raise FileNotFoundError
+
+    ljc_data = phb_file.read_text(encoding="utf-8").splitlines()
+
+    combrule = ljc_data.pop(0).strip()
+    if combrule != config.dice.combrule:
+        raise ValueError(
+            f"Invalid combrule defined in {phb_file}. Expected the same value configured in the config file"
+        )
+
+    ntypes = ljc_data.pop(0).strip()
+    if not ntypes.isdigit():
+        raise ValueError(f"Invalid ntypes defined in {phb_file}")
+
+    nmol = int(ntypes)
+    if nmol != len(config.dice.nmol):
+        raise ValueError(f"Invalid nmol defined in {phb_file}")
+
+    sys = System()
+
+    for i in range(nmol):
+        nsites, molname = ljc_data.pop(0).split()
+
+        if not nsites.isdigit():
+            raise ValueError(f"Invalid nsites defined in {phb_file}")
+        nsites = int(nsites)
+
+        mol = Molecule(molname)
+
+        for j in range(nsites):
+            _fields = ljc_data.pop(0).split()
+            mol.add_atom(
+                Atom(*_fields)
+            )
+
+        sys.add_type(mol)
+
+    return sys
+
+
+# def write_phb(phb_file: Path, state: StateModel) -> None:
+#     if phb_file.exists():
+#        raise RuntimeError(f"File {phb_file} already exists")
+#
+#     with open(phb_file, "w") as f:
+#         f.write(f"{state.config.dice.combrule}\n")
+#         f.write(f"{len(state.system.nmols)}\n")
+#         f.write(f"{state.config.dice.nmol}\n")
+
+