refactor(recipe): make BondOperation and Place regular classes instead

of dataclasses

src/kimmdy/analysis.py

@@ -396,9 +396,9 @@ def radical_migration(
         picked_recipes = {}
         for recipes in run_dir.glob("*decide_recipe/recipes.csv"):
             task_nr = int(recipes.parents[0].stem.split(sep="_")[0])
-            rc, picked_recipe = RecipeCollection.from_csv(recipes)
+            _, picked_recipe = RecipeCollection.from_csv(recipes)
             picked_recipes[task_nr] = picked_recipe
-        sorted_recipes = [val for key, val in sorted(picked_recipes.items())]
+        sorted_recipes = [v for _, v in sorted(picked_recipes.items())]
 
         for sorted_recipe in sorted_recipes:
             connectivity_difference = {}
@@ -598,7 +598,7 @@ def reaction_participation(dir: str, open_plot: bool = False):
     reaction_count = {"overall": 0}
     for recipes in run_dir.glob("*decide_recipe/recipes.csv"):
         # get picked recipe
-        rc, picked_rp = RecipeCollection.from_csv(recipes)
+        _, picked_rp = RecipeCollection.from_csv(recipes)
         assert picked_rp, f"No picked recipe found in {recipes}."
         # get involved atoms
         reaction_atom_ids = set()

src/kimmdy/config.py

@@ -328,9 +328,10 @@ def _validate(self, section: str = "config"):
                 )
                 name = self.out.name.split("_")
                 out_end = name[-1]
-                out_start = "_".join(name[:-1])
                 if out_end.isdigit():
-                    self.out = self.out.with_name(f"{out_start}_{int(out_end)+1:03}")
+                    self.out = self.out.with_name(
+                        f"{'_'.join(name[:-1])}_{int(out_end)+1:03}"
+                    )
                 else:
                     self.out = self.out.with_name(self.out.name + "_001")
 

src/kimmdy/coordinates.py

@@ -195,8 +195,12 @@ def merge_dihedrals(
         parameterizedB = None
 
     # construct parameterized Dihedral
-    if parameterizedA and parameterizedB:
+    if parameterizedA is not None and parameterizedB is not None:
         # same
+
+        assert type(parameterizedA) == Dihedral or type(parameterizedA) == DihedralType
+        assert type(parameterizedB) == Dihedral or type(parameterizedB) == DihedralType
+
         dihedralmerge = Dihedral(
             *dihedral_key,
             funct=funct,
@@ -207,8 +211,9 @@ def merge_dihedrals(
             c4=parameterizedB.c1,
             c5=parameterizedB.periodicity,
         )
-    elif parameterizedA:
+    elif parameterizedA is not None:
         # breaking
+        assert type(parameterizedA) == Dihedral or type(parameterizedA) == DihedralType
         dihedralmerge = Dihedral(
             *dihedral_key,
             funct=funct,
@@ -219,8 +224,9 @@ def merge_dihedrals(
             c4="0.00",
             c5=parameterizedA.periodicity,
         )
-    elif parameterizedB:
+    elif parameterizedB is not None:
         # binding
+        assert type(parameterizedB) == Dihedral or type(parameterizedB) == DihedralType
         dihedralmerge = Dihedral(
             *dihedral_key,
             funct="9",
@@ -242,14 +248,10 @@ def merge_top_moleculetypes_slow_growth(
     molA: MoleculeType,
     molB: MoleculeType,
     ff: FF,
-    focus_nr: Optional[list[str]] = None,
 ) -> MoleculeType:
     """Takes two Topologies and joins them for a smooth free-energy like parameter transition simulation"""
     hyperparameters = {"morse_well_depth": 300}  # [kJ mol-1]
 
-    # TODO:
-    # think about how to bring focus_nr into this
-
     # atoms
     for nr in molA.atoms.keys():
         atomA = molA.atoms[nr]
@@ -520,9 +522,7 @@ def merge_top_moleculetypes_slow_growth(
     return molB
 
 
-def merge_top_slow_growth(
-    topA: Topology, topB: Topology, focus_nr: Optional[list[str]] = None
-) -> Topology:
+def merge_top_slow_growth(topA: Topology, topB: Topology) -> Topology:
     """Takes two Topologies and joins them for a smooth free-energy like parameter transition simulation.
 
 
@@ -531,7 +531,7 @@ def merge_top_slow_growth(
 
     molA = topA.moleculetypes[REACTIVE_MOLECULEYPE]
     molB = topB.moleculetypes[REACTIVE_MOLECULEYPE]
-    molB = merge_top_moleculetypes_slow_growth(molA, molB, topB.ff, focus_nr)
+    molB = merge_top_moleculetypes_slow_growth(molA, molB, topB.ff)
 
     return topB
 

src/kimmdy/kmc.py

@@ -235,6 +235,10 @@ def extrande_mod(
         f"\t\texpected tau: {expected_tau}"
     )
 
+    b = None
+    tau = None
+    l = None
+    t_max = None
     for cr_boarders, cr_rates, cr_recipes in zip(
         pairwise(boarders), rate_windows, recipe_windows
     ):
@@ -262,6 +266,9 @@ def extrande_mod(
         if chosen_recipe is not None:
             break
 
+    if None in [b, tau, l, t_max]:
+        logger.error(f"Extrande calculation failed, some variables are None.")
+
     if chosen_recipe is None:
         logger.info(
             f"No reaction was chosen\naccepted: 0, rejected: {rejected}, extra: {n_extra}"
@@ -343,6 +350,8 @@ def extrande(
     )
 
     n_extra = 0
+    tau = None
+    l = None
     while t < t_max:
         crr_window_idx = np.searchsorted(boarders, t, side="right") - 1
         # only 0 rates left -> skip to end
@@ -390,6 +399,9 @@ def extrande(
                 f"{n_extra} extra reactions performed during extrande KMC calculation. Try increasing tau_scale"
             )
 
+    if None in [tau, l]:
+        logger.error(f"Extrande calculation failed, some variables are None.")
+
     if chosen_recipe is None:
         logger.info(
             f"No reaction was chosen\naccepted: 0, rejected: 1, extra: {n_extra}"

src/kimmdy/parsing.py

@@ -524,15 +524,15 @@ def read_distances_dat(distances_dat: Path) -> dict:
 class JSONEncoder(json.JSONEncoder):
     """Encoder that enables writing JSONs with numpy types."""
 
-    def default(self, obj):
-        if isinstance(obj, np.integer):
-            return int(obj)
-        elif isinstance(obj, np.floating):
-            return float(obj)
-        elif isinstance(obj, np.ndarray):
-            return obj.tolist()
+    def default(self, o):
+        if isinstance(o, np.integer):
+            return int(o)
+        elif isinstance(o, np.floating):
+            return float(o)
+        elif isinstance(o, np.ndarray):
+            return o.tolist()
         else:
-            return super(JSONEncoder, self).default(obj)
+            return super(JSONEncoder, self).default(o)
 
 
 def write_json(

src/kimmdy/plugins.py

@@ -106,8 +106,8 @@ def parameterize_topology(self, current_topology: Topology) -> Topology:
 class BasicParameterizer(Parameterizer):
     """reconstruct base force field state"""
 
-    def parameterize_topology(self, current_topology: Topology) -> None:
+    def parameterize_topology(self, current_topology: Topology) -> Topology:
         """Do nothing,
         all necessary actions should already have happened in bind_bond and break_bond of Topology
         """
-        pass
+        return current_topology