Re-introduce HOMO-LUMO gap check

CHANGELOG.md

@@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Return type for `single_molecule_generator`
 - Check for consistency of the `min_num_atoms` and `max_num_atoms` constraint
 - Similar to the `<basename>.CHRG` file, also a `<basename>.UHF` is printed
+- HOMO-LUMO gap check within the refinement step and corresponding Config option called "refine_hlgap"
 
 ## [0.3.0] - 2024-08-20
 ### Breaking Changes

mindlessgen.toml

@@ -42,6 +42,8 @@ forbidden_elements = "57-71"
 max_frag_cycles = 100
 # > Quantum Mechanics (QM) engine to use. Options: 'xtb', 'orca'
 engine = "xtb"
+# > HOMO-LUMO gap threshold applied at the end of the refinement step
+hlgap = 0.5
 # > Debug this step. Leads to more verbose output as soon as the refinement part is reached. Options: <bool>
 # > If `debug` is true, the process is terminated after the first (successful or not) refinement step.
 debug = false

src/mindlessgen/cli/cli_parser.py

@@ -130,6 +130,12 @@ def cli_parser(argv: Sequence[str] | None = None) -> dict:
         required=False,
         help="Maximum number of fragment optimization cycles.",
     )
+    parser.add_argument(
+        "--refine-hlgap",
+        type=float,
+        required=False,
+        help="Minimum HOMO-LUMO gap required in the end of the refinement process",
+    )
     parser.add_argument(
         "--refine-debug",
         action="store_true",
@@ -225,6 +231,7 @@ def cli_parser(argv: Sequence[str] | None = None) -> dict:
     rev_args_dict["refine"] = {
         "engine": args_dict["refine_engine"],
         "max_frag_cycles": args_dict["max_frag_cycles"],
+        "hlgap": args_dict["refine_hlgap"],
         "debug": args_dict["refine_debug"],
     }
     # Molecule generation arguments

src/mindlessgen/molecules/molecule.py

@@ -491,7 +491,7 @@ def write_xyz_to_file(self, filename: str | Path | None = None):
             with open(filename.with_suffix(".UHF"), "w", encoding="utf8") as f:
                 f.write(f"{self.uhf}\n")
 
-    def read_xyz_from_file(self, filename: str | Path):
+    def read_xyz_from_file(self, filename: str | Path) -> None:
         """
         Read the XYZ coordinates of the molecule from a file.
 

src/mindlessgen/molecules/refinement.py

@@ -115,17 +115,14 @@ def iterative_optimization(
             "Final fragment has an invalid number of atoms (less than min or more than max)."
         )
 
-    # IMPORTANT:
-    # TODO: Reintroduce `check_gap` either at this point or in `postprocess.py`
-    # Sample implementation:
-    # try:
-    #     gap_sufficient = engine.check_gap(
-    #         molecule=rev_mol, threshold=0.5, verbosity=verbosity
-    #     )
-    # except RuntimeError as e:
-    #     raise RuntimeError("HOMO-LUMO gap could not be checked.") from e
-    # if not gap_sufficient:
-    #     raise RuntimeError("HOMO-LUMO gap does not meet the lower threshold.")
+    try:
+        gap_sufficient = engine.check_gap(
+            molecule=rev_mol, threshold=config_refine.hlgap, verbosity=verbosity
+        )
+    except RuntimeError as e:
+        raise RuntimeError("HOMO-LUMO gap could not be checked.") from e
+    if not gap_sufficient:
+        raise RuntimeError("HOMO-LUMO gap does not meet the lower threshold.")
 
     return rev_mol
 

src/mindlessgen/prog/config.py

@@ -350,6 +350,7 @@ class RefineConfig(BaseConfig):
     def __init__(self: RefineConfig) -> None:
         self._max_frag_cycles: int = 100
         self._engine: str = "xtb"
+        self._hlgap: float = 0.5
         self._debug: bool = False
 
     def get_identifier(self) -> str:
@@ -391,6 +392,24 @@ def engine(self, engine: str):
             raise ValueError("Refinement engine can only be xtb or orca.")
         self._engine = engine
 
+    @property
+    def hlgap(self):
+        """
+        Get the minimum HOM
+        """
+        return self._hlgap
+
+    @hlgap.setter
+    def hlgap(self, hlgap: float):
+        """
+        Set the minimum HOM
+        """
+        if not isinstance(hlgap, float):
+            raise TypeError("Minimum HL gap should be a float.")
+        if hlgap < 0:
+            raise ValueError("Minimum HL gap should be greater than 0.")
+        self._hlgap = hlgap
+
     @property
     def debug(self):
         """