some renamings, better docstrings, remove useless variable copies

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

src/mindlessgen/generator/main.py

@@ -346,8 +346,8 @@ def single_molecule_step(
         except RuntimeError as e:
             if config.general.verbosity > 0:
                 print(f"Structure modification failed for cycle {cycle + 1}.")
-            if config.general.verbosity > 1:
-                print(e)
+                if config.general.verbosity > 1:
+                    print(e)
             return None
 
     if config.general.postprocess:

src/mindlessgen/prog/config.py

@@ -173,14 +173,14 @@ def write_xyz(self, write_xyz: bool):
     @property
     def symmetrization(self):
         """
-        Get the structure_mod flag.
+        Get the symmetrization flag.
         """
         return self._symmetrization
 
     @symmetrization.setter
     def symmetrization(self, symmetrization: bool):
         """
-        Set the structure_mod flag.
+        Set the symmetrization flag.
         """
         if not isinstance(symmetrization, bool):
             raise TypeError("Symmetrization should be a boolean.")

src/mindlessgen/symmetrization/base.py

@@ -1,5 +1,5 @@
 """
-This module defines the abstract base class for all structure modification methods.
+This module defines the abstract base class for all symmetrization methods.
 """
 
 from abc import ABC, abstractmethod
@@ -12,12 +12,12 @@
 
 class Symmetrizer(ABC):
     """
-    This abstract base class defines the interface for all structure modification methods.
+    This abstract base class defines the interface for all symmetrization methods.
     """
 
     def __init__(self, config: SymmetrizationConfig):
         """
-        Initialize the structure modification class.
+        Initialize the symmetrization class.
         """
         self.cfg = config
 
@@ -28,11 +28,11 @@ def _modify_structure(
         translation_distance: float,
     ) -> Molecule:
         """
-        Define the structure modification process.
+        Define the symmetrization process.
 
         Arguments:
         molecule (Molecule): Molecule to modify
-        config (StructureModConfig): Configuration for the structure modification
+        translation_distance (float): Distance to translate the molecule
 
         Returns:
         Molecule: Modified molecule
@@ -46,6 +46,13 @@ def translation(
     ) -> Molecule:
         """
         Translate the molecule and add a little extra distance to the x axis.
+
+        Arguments:
+        mol (Molecule): Molecule to translate
+        x_vec_translation (float): Translation distance in x direction
+
+        Returns:
+        Molecule: Translated molecule
         """
         xyz = mol.xyz
         # Find the translation vector in x direction
@@ -67,6 +74,14 @@ def combine_structure(
     ) -> Molecule:
         """
         Combine the original and the modified molecule.
+
+        Arguments:
+        original_mol (Molecule): Original molecule
+        new_mol (Molecule): Modified molecule
+        addxyz (np.ndarray): Coordinates to add to the molecule
+
+        Returns:
+        Molecule: Combined molecule
         """
         new_mol.xyz = np.vstack((new_mol.xyz, addxyz))
         # add dimension of addxyz to the number of atoms
@@ -84,6 +99,12 @@ def get_symmetric_structure(
     ) -> Molecule:
         """
         Get the symmetric structure of the molecule.
+
+        Arguments:
+        mol (Molecule): Molecule to symmetrize
+
+        Returns:
+        Molecule: Symmetric molecule
         """
         orig_mol = mol.copy()
         if not check_distances(mol.xyz, mol.ati, 0.6):

src/mindlessgen/symmetrization/inversion.py

@@ -22,12 +22,11 @@ def _modify_structure(
         Invert the molecule.
         """
         mol = self.translation(mol, translation_distance)
-        xyz = mol.xyz
         inversion_matrix = np.array([[-1, 0, 0], [0, -1, 0], [0, 0, -1]])
-        xyz_inversion = xyz.copy()
+        xyz_inversion = mol.xyz.copy()
         modified_molecule = mol.copy()
         for i in range(mol.num_atoms):
-            xyz_inversion[i] = np.dot(inversion_matrix, xyz[i])
+            xyz_inversion[i] = np.dot(inversion_matrix, mol.xyz[i])
         modified_molecule = self.combine_structure(
             mol, modified_molecule, xyz_inversion
         )

src/mindlessgen/symmetrization/mirror.py

@@ -22,12 +22,11 @@ def _modify_structure(
         Mirror the molecule.
         """
         mol = self.translation(mol, translation_distance)
-        xyz = mol.xyz
         mirror_matrix = np.array([[-1, 0, 0], [0, 1, 0], [0, 0, 1]])
-        xyz_mirror = xyz.copy()
+        xyz_mirror = mol.xyz.copy()
         modified_molecule = mol.copy()
         for i in range(mol.num_atoms):
-            xyz_mirror[i] = np.dot(mirror_matrix, xyz[i])
+            xyz_mirror[i] = np.dot(mirror_matrix, mol.xyz[i])
         # Combine the original and the mirror image
         modified_molecule = self.combine_structure(mol, modified_molecule, xyz_mirror)
         return modified_molecule

src/mindlessgen/symmetrization/rotation.py

@@ -22,7 +22,6 @@ def _modify_structure(
         Rotate the molecule around the z-axis.
         """
         mol = self.translation(mol, translation_distance)
-        xyz = mol.xyz
         n = self.cfg.rotation
         rotation_matrix = np.array(
             [
@@ -31,7 +30,7 @@ def _modify_structure(
                 [0, 0, 1],
             ]
         )
-        xyz_rotation = xyz.copy()
+        xyz_rotation = mol.xyz.copy()
         modified_molecule = mol.copy()
         # For loop to get n times the molecule
         for _ in range(1, n):