abstract structure merge; minor revisions for config

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

src/mindlessgen/Structure_modification/StrucMod.py

@@ -4,6 +4,8 @@
 
 from abc import ABC, abstractmethod
 
+import numpy as np
+
 from mindlessgen.molecules.molecule import Molecule
 from mindlessgen.prog.config import StructureModConfig
 
@@ -52,3 +54,22 @@ def translation(
             xyz[i, 0] += xshift
         mol.xyz = xyz
         return mol
+
+    def combine_structure(
+        self,
+        original_mol: Molecule,
+        new_mol: Molecule,
+        addxyz: np.ndarray,
+    ) -> Molecule:
+        """
+        Combine the original and the modified molecule.
+        """
+        new_mol.xyz = np.vstack((new_mol.xyz, addxyz))
+        # add dimension of addxyz to the number of atoms
+        new_mol.num_atoms += original_mol.num_atoms
+        new_mol.ati = np.hstack((new_mol.ati, original_mol.ati))
+        new_mol.charge += original_mol.charge
+        new_mol.uhf += original_mol.uhf
+        new_mol.atlist += original_mol.atlist
+        new_mol.set_name_from_formula()
+        return new_mol

src/mindlessgen/Structure_modification/inversion.py

@@ -27,12 +27,7 @@ def modify_structure(
         modified_molecule = mol.copy()
         for i in range(mol.num_atoms):
             xyz_inversion[i] = np.dot(inversion_matrix, xyz[i])
-        xyz_combined = np.vstack((xyz, xyz_inversion))
-        modified_molecule.xyz = xyz_combined
-        modified_molecule.num_atoms += mol.num_atoms
-        modified_molecule.ati = np.hstack((modified_molecule.ati, mol.ati))
-        modified_molecule.charge += mol.charge
-        modified_molecule.uhf += mol.uhf
-        modified_molecule.atlist += mol.atlist
-        modified_molecule.set_name_from_formula()
+        modified_molecule = self.combine_structure(
+            mol, modified_molecule, xyz_inversion
+        )
         return modified_molecule

src/mindlessgen/Structure_modification/mirror.py

@@ -28,12 +28,5 @@ def modify_structure(
         for i in range(mol.num_atoms):
             xyz_mirror[i] = np.dot(mirror_matrix, xyz[i])
         # Combine the original and the mirror image
-        xyz_combined = np.vstack((xyz, xyz_mirror))
-        modified_molecule.xyz = xyz_combined
-        modified_molecule.num_atoms += mol.num_atoms
-        modified_molecule.ati = np.hstack((modified_molecule.ati, mol.ati))
-        modified_molecule.charge += mol.charge
-        modified_molecule.uhf += mol.uhf
-        modified_molecule.atlist += mol.atlist
-        modified_molecule.set_name_from_formula()
+        modified_molecule = self.combine_structure(mol, modified_molecule, xyz_mirror)
         return modified_molecule

src/mindlessgen/Structure_modification/rotation.py

@@ -36,12 +36,7 @@ def modify_structure(
         for _ in range(1, n):
             for k in range(mol.num_atoms):
                 xyz_rotation[k] = np.dot(rotation_matrix, xyz_rotation[k])
-            xyz = np.vstack((xyz, xyz_rotation))
-            modified_molecule.num_atoms += mol.num_atoms
-            modified_molecule.ati = np.hstack((modified_molecule.ati, mol.ati))
-            modified_molecule.charge += mol.charge
-            modified_molecule.uhf += mol.uhf
-            modified_molecule.atlist += mol.atlist
-        modified_molecule.xyz = xyz
-        modified_molecule.set_name_from_formula()
+            modified_molecule = self.combine_structure(
+                mol, modified_molecule, xyz_rotation
+            )
         return modified_molecule

src/mindlessgen/prog/config.py

@@ -1171,11 +1171,11 @@ def operation(self, operation: str):
                 raise ValueError(
                     "Rotation operations should be in the format 'c_<n>_rotation' where <n> is an integer."
                 )
-            self._rotation = int(parts[1])
+            self.rotation = int(parts[1])
         else:
-            self._rotation = None
+            self.rotation = None
 
-        if operation.split("_")[0] not in ["translation", "c", "mirror", "inversion"]:
+        if operation.split("_")[0] not in ["c", "mirror", "inversion"]:
             raise ValueError(
                 "Operation can only be translation, c_<n>_rotation, mirror or inversion."
             )