rename some file and Class names to typical conventions

Signed-off-by: Marcel Müller <[email protected]>

src/mindlessgen/generator/main.py

@@ -39,8 +39,8 @@
     ResourceMonitor,
     setup_blocks,
 )
-from ..Structure_modification import (
-    StrucMod,
+from ..symmetrization import (
+    Symmetrizer,
     CnRotation,
     Mirror,
     Inversion,
@@ -84,7 +84,7 @@ def generator(config: ConfigManager) -> tuple[list[Molecule], int]:
     )
 
     if config.general.structure_mod:
-        structure_mod_model: StrucMod | None = setup_structure_modification_model(
+        structure_mod_model: Symmetrizer | None = setup_structure_modification_model(
             config.modification.operation, config.modification
         )
     else:
@@ -201,7 +201,7 @@ def single_molecule_generator(
     resources: ResourceMonitor,
     refine_engine: QMMethod,
     postprocess_engine: QMMethod | None,
-    structure_mod_model: StrucMod,
+    structure_mod_model: Symmetrizer,
     ncores: int,
 ) -> Molecule | None:
     """
@@ -272,7 +272,7 @@ def single_molecule_step(
     resources_local: ResourceMonitor,
     refine_engine: QMMethod,
     postprocess_engine: QMMethod | None,
-    structure_mod_model: StrucMod,
+    structure_mod_model: Symmetrizer,
     cycle: int,
     stop_event: Event,
 ) -> Molecule | None:
@@ -461,7 +461,7 @@ def setup_engines(
 
 def setup_structure_modification_model(
     structure_mod_type: str, config: StructureModConfig
-) -> StrucMod:
+) -> Symmetrizer:
     """
     Set up the structure modification model.
     """

src/mindlessgen/Structure_modification/__init__.py → src/mindlessgen/symmetrization/__init__.py

@@ -2,14 +2,14 @@
 This module contains all structure modification classes.
 """
 
-from .StrucMod import StrucMod
+from .base import Symmetrizer
 from .mirror import Mirror
 from .inversion import Inversion
 from .rotation import CnRotation
 
 
 __all__ = [
-    "StrucMod",
+    "Symmetrizer",
     "Mirror",
     "Inversion",
     "CnRotation",

src/mindlessgen/Structure_modification/StrucMod.py → src/mindlessgen/symmetrization/base.py

@@ -10,7 +10,7 @@
 from ..molecules import check_distances, Molecule
 
 
-class StrucMod(ABC):
+class Symmetrizer(ABC):
     """
     This abstract base class defines the interface for all structure modification methods.
     """

src/mindlessgen/Structure_modification/inversion.py → src/mindlessgen/symmetrization/inversion.py

@@ -4,11 +4,11 @@
 
 import numpy as np
 
-from .StrucMod import StrucMod
+from .base import Symmetrizer
 from ..molecules.molecule import Molecule
 
 
-class Inversion(StrucMod):
+class Inversion(Symmetrizer):
     """
     This class handles the Inversion structure modification.
     """

src/mindlessgen/Structure_modification/mirror.py → src/mindlessgen/symmetrization/mirror.py

@@ -4,11 +4,11 @@
 
 import numpy as np
 
-from .StrucMod import StrucMod
+from .base import Symmetrizer
 from ..molecules.molecule import Molecule
 
 
-class Mirror(StrucMod):
+class Mirror(Symmetrizer):
     """
     This class handles the translation structure modification.
     """

src/mindlessgen/Structure_modification/rotation.py → src/mindlessgen/symmetrization/rotation.py

@@ -4,11 +4,11 @@
 
 import numpy as np
 
-from .StrucMod import StrucMod
+from .base import Symmetrizer
 from ..molecules.molecule import Molecule
 
 
-class CnRotation(StrucMod):
+class CnRotation(Symmetrizer):
     """
     This class handles the rotation structure modification.
     """

test/test_Structure_modification/test_inversion.py

@@ -1,5 +1,5 @@
 import numpy as np
-from mindlessgen.Structure_modification.inversion import Inversion  # type: ignore
+from mindlessgen.symmetrization.inversion import Inversion  # type: ignore
 from mindlessgen.molecules.molecule import Molecule, ati_to_atlist  # type: ignore
 from mindlessgen.prog.config import StructureModConfig  # type: ignore
 

test/test_Structure_modification/test_mirror.py

@@ -1,6 +1,6 @@
 import pytest
 import numpy as np
-from mindlessgen.Structure_modification.mirror import Mirror  # type: ignore
+from mindlessgen.symmetrization.mirror import Mirror  # type: ignore
 from mindlessgen.molecules.molecule import Molecule, ati_to_atlist  # type: ignore
 from mindlessgen.prog.config import StructureModConfig  # type: ignore
 

test/test_Structure_modification/test_rotation.py

@@ -1,5 +1,5 @@
 import numpy as np
-from mindlessgen.Structure_modification.rotation import CnRotation  # type: ignore
+from mindlessgen.symmetrization.rotation import CnRotation  # type: ignore
 from mindlessgen.molecules.molecule import Molecule, ati_to_atlist  # type: ignore
 from mindlessgen.prog.config import StructureModConfig  # type: ignore