fix unit tests for PR #200:

- Ensured that all classes and functions are using instances correctly
- fix all unit and integration test

Author: harryswift01

CodeEntropy/dihedral_tools.py

@@ -10,8 +10,6 @@
     TimeElapsedColumn,
 )
 
-from CodeEntropy.mda_universe_operations import UniverseOperations
-
 logger = logging.getLogger(__name__)
 
 
@@ -21,10 +19,11 @@ class DihedralAnalysis:
     states needed for the conformational entropy functions.
     """
 
-    def __init__(self):
+    def __init__(self, universe_operations=None):
         """
         Initialise with placeholders.
         """
+        self._universe_operations = universe_operations
         self.data_container = None
         self.states_ua = None
         self.states_res = None
@@ -67,7 +66,7 @@ def build_conformational_states(
 
         for group_id in groups.keys():
             molecules = groups[group_id]
-            mol = UniverseOperations.get_molecule_container(data_container, 0)
+            mol = self._universe_operations.get_molecule_container(data_container, 0)
             num_residues = len(mol.residues)
             dihedrals_ua = [[] for _ in range(num_residues)]
             peaks_ua = [{} for _ in range(num_residues)]
@@ -80,11 +79,11 @@ def build_conformational_states(
                     for res_id in range(num_residues):
                         selection1 = mol.residues[res_id].atoms.indices[0]
                         selection2 = mol.residues[res_id].atoms.indices[-1]
-                        res_container = UniverseOperations.new_U_select_atom(
+                        res_container = self._universe_operations.new_U_select_atom(
                             mol,
                             f"index {selection1}:" f"{selection2}",
                         )
-                        heavy_res = UniverseOperations.new_U_select_atom(
+                        heavy_res = self._universe_operations.new_U_select_atom(
                             res_container, "prop mass > 1.1"
                         )
 
@@ -265,7 +264,7 @@ def _identify_peaks(
             # loop over all molecules in the averaging group
             # dihedral angle values have a range from -180 to 180
             for molecule in molecules:
-                mol = UniverseOperations.get_molecule_container(
+                mol = self._universe_operations.get_molecule_container(
                     data_container, molecule
                 )
                 number_frames = len(mol.trajectory)
@@ -342,7 +341,9 @@ def _assign_states(
         # get the values of the angle for the dihedral
         # dihedral angle values have a range from -180 to 180
         for molecule in molecules:
-            mol = UniverseOperations.get_molecule_container(data_container, molecule)
+            mol = self._universe_operations.get_molecule_container(
+                data_container, molecule
+            )
             number_frames = len(mol.trajectory)
             R = Dihedral(dihedrals).run()
             for dihedral_index in range(len(dihedrals)):

CodeEntropy/entropy.py

@@ -15,7 +15,6 @@
 )
 
 from CodeEntropy.config.logging_config import LoggingConfig
-from CodeEntropy.mda_universe_operations import UniverseOperations
 
 logger = logging.getLogger(__name__)
 console = LoggingConfig.get_console()
@@ -36,6 +35,7 @@ def __init__(
         level_manager,
         group_molecules,
         dihedral_analysis,
+        universe_operations,
     ):
         """
         Initializes the EntropyManager with required components.
@@ -56,6 +56,7 @@ def __init__(
         self._level_manager = level_manager
         self._group_molecules = group_molecules
         self._dihedral_analysis = dihedral_analysis
+        self._universe_operations = universe_operations
         self._GAS_CONST = 8.3144598484848
 
     def execute(self):
@@ -85,6 +86,7 @@ def execute(self):
             self._level_manager,
             self._group_molecules,
             self._dihedral_analysis,
+            self._universe_operations,
         )
         ce = ConformationalEntropy(
             self._run_manager,
@@ -94,6 +96,7 @@ def execute(self):
             self._level_manager,
             self._group_molecules,
             self._dihedral_analysis,
+            self._universe_operations,
         )
 
         reduced_atom, number_molecules, levels, groups = self._initialize_molecules()
@@ -274,7 +277,7 @@ def _compute_entropies(
             )
 
             for group_id in groups.keys():
-                mol = UniverseOperations.get_molecule_container(
+                mol = self._universe_operations.get_molecule_container(
                     reduced_atom, groups[group_id][0]
                 )
 
@@ -284,7 +287,7 @@ def _compute_entropies(
                 group_residue_count = len(groups[group_id])
                 group_atom_count = 0
                 for mol_id in groups[group_id]:
-                    each_mol = UniverseOperations.get_molecule_container(
+                    each_mol = self._universe_operations.get_molecule_container(
                         reduced_atom, mol_id
                     )
                     group_atom_count += len(each_mol.atoms)
@@ -398,7 +401,7 @@ def _get_reduced_universe(self):
         # Otherwise create a new (smaller) universe based on the selection
         u = self._universe
         selection_string = self._args.selection_string
-        reduced = UniverseOperations.new_U_select_atom(u, selection_string)
+        reduced = self._universe_operations.new_U_select_atom(u, selection_string)
         name = f"{len(reduced.trajectory)}_frame_dump_atom_selection"
         self._run_manager.write_universe(reduced, name)
 
@@ -810,6 +813,7 @@ def __init__(
         level_manager,
         group_molecules,
         dihedral_analysis,
+        universe_operations,
     ):
         """
         Initializes the VibrationalEntropy manager with all required components and
@@ -823,6 +827,7 @@ def __init__(
             level_manager,
             group_molecules,
             dihedral_analysis,
+            universe_operations,
         )
         self._PLANCK_CONST = 6.62607004081818e-34
 
@@ -958,6 +963,7 @@ def __init__(
         level_manager,
         group_molecules,
         dihedral_analysis,
+        universe_operations,
     ):
         """
         Initializes the ConformationalEntropy manager with all required components and
@@ -971,6 +977,7 @@ def __init__(
             level_manager,
             group_molecules,
             dihedral_analysis,
+            universe_operations,
         )
 
     def conformational_entropy_calculation(self, states):
@@ -1028,6 +1035,7 @@ def __init__(
         level_manager,
         group_molecules,
         dihedral_analysis,
+        universe_operations,
     ):
         """
         Initializes the OrientationalEntropy manager with all required components and
@@ -1041,6 +1049,7 @@ def __init__(
             level_manager,
             group_molecules,
             dihedral_analysis,
+            universe_operations,
         )
 
     def orientational_entropy_calculation(self, neighbours_dict):

CodeEntropy/levels.py

@@ -9,8 +9,6 @@
     TimeElapsedColumn,
 )
 
-from CodeEntropy.mda_universe_operations import UniverseOperations
-
 logger = logging.getLogger(__name__)
 
 
@@ -24,7 +22,7 @@ class LevelManager:
     analysis.
     """
 
-    def __init__(self):
+    def __init__(self, universe_operations):
         """
         Initializes the LevelManager with placeholders for level-related data,
         including translational and rotational axes, number of beads, and a
@@ -35,6 +33,7 @@ def __init__(self):
         self._trans_axes = None
         self._rot_axes = None
         self._number_of_beads = None
+        self._universe_operations = universe_operations
 
     def select_levels(self, data_container):
         """
@@ -699,7 +698,7 @@ def build_covariance_matrices(
             for time_index, _ in zip(indices, reduced_atom.trajectory[start:end:step]):
                 for group_id, molecules in groups.items():
                     for mol_id in molecules:
-                        mol = UniverseOperations.get_molecule_container(
+                        mol = self._universe_operations.get_molecule_container(
                             reduced_atom, mol_id
                         )
                         for level in levels[mol_id]:
@@ -804,7 +803,7 @@ def update_force_torque_matrices(
         if level == "united_atom":
             for res_id, residue in enumerate(mol.residues):
                 key = (group_id, res_id)
-                res = UniverseOperations.new_U_select_atom(
+                res = self._universe_operations.new_U_select_atom(
                     mol, f"index {residue.atoms.indices[0]}:{residue.atoms.indices[-1]}"
                 )
 

CodeEntropy/mda_universe_operations.py

@@ -18,7 +18,7 @@ def __init__(self):
         """
         self._universe = None
 
-    def new_U_select_frame(u, start=None, end=None, step=1):
+    def new_U_select_frame(self, u, start=None, end=None, step=1):
         """Create a reduced universe by dropping frames according to
         user selection.
 
@@ -60,7 +60,7 @@ def new_U_select_frame(u, start=None, end=None, step=1):
 
         return u2
 
-    def new_U_select_atom(u, select_string="all"):
+    def new_U_select_atom(self, u, select_string="all"):
         """Create a reduced universe by dropping atoms according to
         user selection.
 
@@ -95,7 +95,7 @@ def new_U_select_atom(u, select_string="all"):
 
         return u2
 
-    def get_molecule_container(universe, molecule_id):
+    def get_molecule_container(self, universe, molecule_id):
         """
         Extracts the atom group corresponding to a single molecule from the universe.
 
@@ -110,12 +110,9 @@ def get_molecule_container(universe, molecule_id):
         frag = universe.atoms.fragments[molecule_id]
         selection_string = f"index {frag.indices[0]}:{frag.indices[-1]}"
 
-        # Build a new universe with only the one molecule
-        u2 = UniverseOperations.new_U_select_atom(universe, selection_string)
+        return self.new_U_select_atom(universe, selection_string)
 
-        return u2
-
-    def merge_forces(tprfile, trrfile, forcefile, fileformat=None, kcal=False):
+    def merge_forces(self, tprfile, trrfile, forcefile, fileformat=None, kcal=False):
         """
         Creates a universe by merging the coordinates and forces from
         different input files.

CodeEntropy/run.py

@@ -251,24 +251,29 @@ def run_entropy_workflow(self):
                 fileformat = args.file_format
                 kcal_units = args.kcal_force_units
 
+                # Create shared UniverseOperations instance
+                universe_operations = UniverseOperations()
+
                 if forcefile is None:
                     logger.debug(f"Loading Universe with {tprfile} and {trrfile}")
                     u = mda.Universe(tprfile, trrfile, format=fileformat)
                 else:
-                    u = UniverseOperations.merge_forces(
+                    u = universe_operations.merge_forces(
                         tprfile, trrfile, forcefile, fileformat, kcal_units
                     )
 
                 self._config_manager.input_parameters_validation(u, args)
 
                 # Create LevelManager instance
-                level_manager = LevelManager()
+                level_manager = LevelManager(universe_operations)
 
                 # Create GroupMolecules instance
                 group_molecules = GroupMolecules()
 
-                # Create DihedralAnalysis instance
-                dihedral_analysis = DihedralAnalysis()
+                # Create shared DihedralAnalysis with injected universe_operations
+                dihedral_analysis = DihedralAnalysis(
+                    universe_operations=universe_operations
+                )
 
                 # Inject all dependencies into EntropyManager
                 entropy_manager = EntropyManager(
@@ -279,6 +284,7 @@ def run_entropy_workflow(self):
                     level_manager=level_manager,
                     group_molecules=group_molecules,
                     dihedral_analysis=dihedral_analysis,
+                    universe_operations=universe_operations,
                 )
 
                 entropy_manager.execute()