Fix cube file parsing to follow standard format specification

app.py

@@ -11,41 +11,37 @@ def parse_cube_file(cube_file):
         if len(lines) < 6:
             raise ValueError("Cube file too short")
         
-        # Find the line with natoms (should be the third line or so)
-        for i, line in enumerate(lines):
-            parts = line.split()
-            if len(parts) >= 4:
-                try:
-                    natoms = int(float(parts[0]))  # Try to parse as int, allowing for float strings
-                    if natoms > 0:
-                        break
-                except ValueError:
-                    continue
-        else:
-            raise ValueError("Could not find natoms in cube file")
-        
-        # Now i is the line with natoms
-        origin = np.array([float(x) for x in lines[i].split()[1:4]])
+        # Standard cube format:
+        # Line 0-1: comments
+        # Line 2: natoms, origin_x, origin_y, origin_z
+        # Line 3: nx, voxel_x, 0, 0
+        # Line 4: ny, 0, voxel_y, 0
+        # Line 5: nz, 0, 0, voxel_z
+        # Lines 6 to 6+natoms-1: atom data
+        # Remaining lines: volumetric data
         
-        # Skip atom lines
-        grid_start = i + 1 + natoms
-        if grid_start >= len(lines):
-            raise ValueError("Cube file malformed")
+        # Parse line 2 (natoms and origin)
+        parts = lines[2].split()
+        natoms = abs(int(float(parts[0])))  # abs() handles negative natoms (sometimes used)
+        origin = np.array([float(parts[1]), float(parts[2]), float(parts[3])])
         
-        grid_line = lines[grid_start]
-        nx = int(grid_line.split()[0])
-        dx = float(grid_line.split()[1])
+        # Parse line 3 (nx and voxel spacing)
+        parts = lines[3].split()
+        nx = abs(int(float(parts[0])))
+        dx = float(parts[1])
         
-        grid_line = lines[grid_start + 1]
-        ny = int(grid_line.split()[1])
-        dy = float(grid_line.split()[2])
+        # Parse line 4 (ny and voxel spacing)
+        parts = lines[4].split()
+        ny = abs(int(float(parts[0])))
+        dy = float(parts[2])
         
-        grid_line = lines[grid_start + 2]
-        nz = int(grid_line.split()[2])
-        dz = float(grid_line.split()[3])
+        # Parse line 5 (nz and voxel spacing)
+        parts = lines[5].split()
+        nz = abs(int(float(parts[0])))
+        dz = float(parts[3])
         
-        # Read data
-        data_start = grid_start + 3
+        # Data starts after atom lines
+        data_start = 6 + natoms
         data = []
         for line in lines[data_start:]:
             data.extend([float(x) for x in line.split()])

force_rebuild.txt

@@ -1,2 +1,2 @@
 # Force rebuild
-2025-11-08 v6
+2025-11-08 v7