Refactor water entropy handling into group-aware pipeline:

- Integrated water entropy into the same group framework as other molecules:
 - Each water group now gets a proper `group_id`, label, residue count, and atom count
 - Entropy components (orientational, vibrational-translational, vibrational-rotational) are logged consistently
- Updated `_handle_water_entropy` to:
 - Compute entropy per water group
 - Exclude water from selection string when `--water-entropy` is enabled
 - Use MDAnalysis residue names to build accurate group labels
- Modified `execute` to:
 - Separate `water_groups` from `nonwater_groups`
 - If `water_entropy=True`: handle waters separately and exclude them from later analysis
 - If `water_entropy=False`: merge water back into non-water groups so they are included in full entropy calculation
- Improved `DataLogger` outputs:
 - Added/cleaned group label mapping table for better tracking
 - Ensured consistent handling of residue names and frame counts

Author: harryswift01

CodeEntropy/config/data_logger.py

@@ -18,6 +18,7 @@ def __init__(self, console=None):
         self.console = console or Console()
         self.molecule_data = []
         self.residue_data = []
+        self.group_labels = {}
 
     def save_dataframes_as_json(self, molecule_df, residue_df, output_file):
         """Save multiple DataFrames into a single JSON file with separate keys"""
@@ -34,20 +35,29 @@ def clean_residue_name(self, resname):
         """Ensures residue names are stripped and cleaned before being stored"""
         return re.sub(r"[-–—]", "", str(resname))
 
-    def add_results_data(self, resname, level, entropy_type, value):
+    def add_results_data(self, group_id, level, entropy_type, value):
         """Add data for molecule-level entries"""
-        resname = self.clean_residue_name(resname)
-        self.molecule_data.append((resname, level, entropy_type, value))
+        self.molecule_data.append((group_id, level, entropy_type, value))
 
-    def add_residue_data(self, resid, resname, level, entropy_type, frame_count, value):
+    def add_residue_data(
+        self, group_id, resname, level, entropy_type, frame_count, value
+    ):
         """Add data for residue-level entries"""
         resname = self.clean_residue_name(resname)
         if isinstance(frame_count, np.ndarray):
             frame_count = frame_count.tolist()
         self.residue_data.append(
-            [resid, resname, level, entropy_type, frame_count, value]
+            [group_id, resname, level, entropy_type, frame_count, value]
         )
 
+    def add_group_label(self, group_id, label, residue_count=None, atom_count=None):
+        """Store a mapping from group ID to a descriptive label and metadata"""
+        self.group_labels[group_id] = {
+            "label": label,
+            "residue_count": residue_count,
+            "atom_count": atom_count,
+        }
+
     def log_tables(self):
         """Display rich tables in terminal"""
 
@@ -67,7 +77,7 @@ def log_tables(self):
 
         if self.residue_data:
             table = Table(title="Residue Entropy Results", show_lines=True, expand=True)
-            table.add_column("Residue ID", justify="center", style="bold cyan")
+            table.add_column("Group ID", justify="center", style="bold cyan")
             table.add_column("Residue Name", justify="center", style="cyan")
             table.add_column("Level", justify="center", style="magenta")
             table.add_column("Type", justify="center", style="green")
@@ -78,3 +88,22 @@ def log_tables(self):
                 table.add_row(*[str(cell) for cell in row])
 
             console.print(table)
+
+        if self.group_labels:
+            label_table = Table(
+                title="Group ID to Residue Label Mapping", show_lines=True, expand=True
+            )
+            label_table.add_column("Group ID", justify="center", style="bold cyan")
+            label_table.add_column("Residue Label", justify="center", style="green")
+            label_table.add_column("Residue Count", justify="center", style="magenta")
+            label_table.add_column("Atom Count", justify="center", style="yellow")
+
+            for group_id, info in self.group_labels.items():
+                label_table.add_row(
+                    str(group_id),
+                    info["label"],
+                    str(info.get("residue_count", "")),
+                    str(info.get("atom_count", "")),
+                )
+
+            console.print(label_table)