MoleditPy-linux 3.0.6__tar.gz → 3.2.0__tar.gz

{moleditpy_linux-3.0.6 → moleditpy_linux-3.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 3.0.6
+Version: 3.2.0
 Summary: A cross-platform, simple, and intuitive molecular structure editor built in Python. It allows 2D molecular drawing and 3D structure visualization. It supports exporting structure files for input to DFT calculation software.
 Author-email: HiroYokoyama <titech.yoko.hiro@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE

{moleditpy_linux-3.0.6 → moleditpy_linux-3.2.0}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy-linux"
 
-version = "3.0.6"
+version = "3.2.0"
 
 license = {file = "LICENSE"}
 

{moleditpy_linux-3.0.6 → moleditpy_linux-3.2.0}/src/MoleditPy_linux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 3.0.6
+Version: 3.2.0
 Summary: A cross-platform, simple, and intuitive molecular structure editor built in Python. It allows 2D molecular drawing and 3D structure visualization. It supports exporting structure files for input to DFT calculation software.
 Author-email: HiroYokoyama <titech.yoko.hiro@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE

{moleditpy_linux-3.0.6 → moleditpy_linux-3.2.0}/src/MoleditPy_linux.egg-info/SOURCES.txt

@@ -55,7 +55,6 @@ src/moleditpy_linux/ui/move_group_dialog.py
 src/moleditpy_linux/ui/periodic_table_dialog.py
 src/moleditpy_linux/ui/planarize_dialog.py
 src/moleditpy_linux/ui/settings_dialog.py
-src/moleditpy_linux/ui/sip_isdeleted_safe.py
 src/moleditpy_linux/ui/string_importers.py
 src/moleditpy_linux/ui/template_preview_item.py
 src/moleditpy_linux/ui/template_preview_view.py

{moleditpy_linux-3.0.6 → moleditpy_linux-3.2.0}/src/moleditpy_linux/__main__.py

@@ -15,9 +15,9 @@ print("MoleditPy - A Python-based molecular editing software")
 print("-----------------------------------------------------\n")
 
 try:
-    from .main import main
+    from .main import main  # type: ignore
 except ImportError:
-    from main import main
+    from main import main  # type: ignore
 
 # --- Application Execution ---
 if __name__ == "__main__":

{moleditpy_linux-3.0.6 → moleditpy_linux-3.2.0}/src/moleditpy_linux/core/mol_geometry.py

@@ -152,7 +152,7 @@ def rodrigues_rotate(v: np.ndarray, axis: np.ndarray, angle: float) -> np.ndarra
     """
     cos_a = np.cos(angle)
     sin_a = np.sin(angle)
-    return v * cos_a + np.cross(axis, v) * sin_a + axis * np.dot(axis, v) * (1 - cos_a)
+    return v * cos_a + np.cross(axis, v) * sin_a + axis * np.dot(axis, v) * (1 - cos_a)  # type: ignore[no-any-return]
 
 
 def adjust_bond_angle(
@@ -421,7 +421,9 @@ def is_problematic_valence(
 # ------------------------------------------------------------------
 
 
-def inject_ez_stereo_to_mol_block(mol_block, rdkit_mol, bonds_data):
+def inject_ez_stereo_to_mol_block(
+    mol_block: str, rdkit_mol: Any, bonds_data: Dict[Tuple[int, int], Any]
+) -> str:
     """Generate a modified MOL block with 'M CFG' lines for E/Z stereochemistry.
 
     Parameters
@@ -502,7 +504,7 @@ def identify_valence_problems(
     problem_atom_ids = []
 
     # Pre-calculate bond orders per atom
-    bond_orders = {}
+    bond_orders: Dict[int, int] = {}
     for (id1, id2), bond in bonds_data.items():
         order = bond.get("order", 1)
         bond_orders[id1] = bond_orders.get(id1, 0) + order
@@ -534,15 +536,22 @@ def optimize_2d_coords(mol: Any) -> Dict[int, Tuple[float, float]]:
     return new_positions
 
 
-def calculate_best_fit_plane_projection(centered_positions, normal, centroid):
+def calculate_best_fit_plane_projection(
+    centered_positions: np.ndarray, normal: np.ndarray, centroid: np.ndarray
+) -> np.ndarray:
     """Project centered points orthogonally onto the plane defined by normal and centroid."""
     projections = centered_positions - np.outer(
         np.dot(centered_positions, normal), normal
     )
-    return projections + centroid
+    return projections + centroid  # type: ignore[no-any-return]
 
 
-def rotate_2d_points(points_map, center_x, center_y, angle_degrees):
+def rotate_2d_points(
+    points_map: Dict[int, Tuple[float, float]],
+    center_x: float,
+    center_y: float,
+    angle_degrees: float,
+) -> Dict[int, Tuple[float, float]]:
     """Rotate 2D points (atom_id -> (x, y)) around a center."""
     rad = math.radians(angle_degrees)
     cos_a = math.cos(rad)
@@ -558,13 +567,13 @@ def rotate_2d_points(points_map, center_x, center_y, angle_degrees):
 
 
 def resolve_2d_overlaps(
-    atom_ids,
-    positions_map,
-    adjacency_list,
-    overlap_threshold=0.5,
-    move_distance=20,
-    has_bond_check_func=None,
-):
+    atom_ids: Iterable[int],
+    positions_map: Dict[int, Tuple[float, float]],
+    adjacency_list: Dict[int, List[int]],
+    overlap_threshold: float = 0.5,
+    move_distance: float = 20,
+    has_bond_check_func: Optional[Any] = None,
+) -> List[Tuple[Set[int], Tuple[float, float]]]:
     """Detect and resolve overlapping atom groups in 2D.
 
     Returns list of (atom_ids_set, translation_vector_tuple).
@@ -592,13 +601,13 @@ def resolve_2d_overlaps(
     # Union-Find for overlap groups
     parent = {aid: aid for aid in atom_ids}
 
-    def find_set(aid):
+    def find_set(aid: Any) -> Any:
         if parent[aid] == aid:
             return aid
         parent[aid] = find_set(parent[aid])
         return parent[aid]
 
-    def unite_sets(aid1, aid2):
+    def unite_sets(aid1: Any, aid2: Any) -> None:
         root1 = find_set(aid1)
         root2 = find_set(aid2)
         if root1 != root2:
@@ -607,7 +616,7 @@ def resolve_2d_overlaps(
     for id1, id2 in overlapping_pairs:
         unite_sets(id1, id2)
 
-    groups_by_root = {}
+    groups_by_root: Dict[int, List[int]] = {}
     for aid in atom_ids:
         root = find_set(aid)
         groups_by_root.setdefault(root, []).append(aid)
@@ -649,7 +658,7 @@ def resolve_2d_overlaps(
                 rep_id1, rep_id2 = i1, i2
                 break
 
-        if rep_id1 is None:
+        if rep_id1 is None or rep_id2 is None:
             continue
 
         frag1 = next((f for f in fragments if rep_id1 in f), None)

{moleditpy_linux-3.0.6 → moleditpy_linux-3.2.0}/src/moleditpy_linux/core/molecular_data.py

@@ -25,10 +25,10 @@ class PointTuple(tuple):
     """Backward-compatible tuple that allows .x() and .y() access like QPointF."""
 
     def x(self) -> float:
-        return self[0]
+        return float(self[0])
 
     def y(self) -> float:
-        return self[1]
+        return float(self[1])
 
 
 class MolecularData:
@@ -248,10 +248,10 @@ class MolecularData:
                 if nbr.GetIdx() == exclude_idx:
                     continue
                 if nbr.GetAtomicNum() > 1:
-                    return nbr.GetIdx()
+                    return int(nbr.GetIdx())
             for nbr in atom.GetNeighbors():
                 if nbr.GetIdx() != exclude_idx:
-                    return nbr.GetIdx()
+                    return int(nbr.GetIdx())
             return None
 
         # Overwrite based on labels (E/Z has highest priority) ---
@@ -275,7 +275,7 @@ class MolecularData:
                 begin_atom_idx = bond.GetBeginAtomIdx()
                 end_atom_idx = bond.GetEndAtomIdx()
 
-                bond_data = info.get("bond_data", {}) or {}
+                bond_data: dict[str, Any] = info.get("bond_data") or {}  # type: ignore[assignment]
                 stereo_atoms_specified = bond_data.get("stereo_atoms")
 
                 if stereo_atoms_specified:
@@ -365,7 +365,10 @@ class MolecularData:
                 if key in self.bonds:
                     rdkit_bond_idx_to_item[bidx] = self.bonds[key].get("item")
 
-        # 5. Initialize/Reset all bond items
+        # 5. Initialize/Reset all bond items and track best ring size
+        bond_to_best_size: Dict[
+            int, int
+        ] = {}  # bond_item_id -> smallest_ring_size_found
         for bond_data in self.bonds.values():
             bond_item = bond_data.get("item")
             if bond_item:
@@ -374,6 +377,7 @@ class MolecularData:
 
         # 6. Apply ring information
         for a_ring, b_ring in zip(atom_rings, bond_rings):
+            ring_size = len(a_ring)
             # Calculate ring center (geometric mean of atom positions)
             positions = []
             for aidx in a_ring:
@@ -395,18 +399,21 @@ class MolecularData:
                 bond_item = rdkit_bond_idx_to_item.get(bidx)
                 if bond_item:
                     bond_item.is_in_ring = True
-                    # Note: Simplified; a bond might be part of multiple rings.
-                    # The inner-bond logic usually picks the smallest ring.
-                    # Since we iterate through all rings, the last one wins.
-                    # RDKit's AtomRings returns SSSR (Smallest Set of Smallest Rings),
-                    # so this is usually correct for 2D drawing.
-                    bond_item.ring_center = ring_center
+                    # Explicitly prioritize smaller rings for double bond shift logic.
+                    # This ensures the double bond is drawn inside the smaller ring in fused systems.
+                    item_id = id(bond_item)
+                    if (
+                        item_id not in bond_to_best_size
+                        or ring_size < bond_to_best_size[item_id]
+                    ):
+                        bond_item.ring_center = ring_center
+                        bond_to_best_size[item_id] = ring_size
 
     def to_mol_block(self) -> Optional[str]:
         mol = self.to_rdkit_mol()
         if mol:
             try:
-                return Chem.MolToMolBlock(mol, includeStereo=True)
+                return Chem.MolToMolBlock(mol, includeStereo=True)  # type: ignore[no-any-return]
             except (RuntimeError, ValueError, TypeError) as e:
                 logging.warning(
                     f"RDKit MolBlock generation failed: {e}"

{moleditpy_linux-3.0.6 → moleditpy_linux-3.2.0}/src/moleditpy_linux/main.py

@@ -15,6 +15,7 @@ import sys
 import argparse
 import logging
 import os
+from typing import Any
 
 try:
     from .utils.constants import VERSION
@@ -35,7 +36,7 @@ except ImportError:
     from moleditpy_linux.ui.main_window import MainWindow
 
 
-def setup_logging():
+def setup_logging() -> None:
     logging.basicConfig(
         level=logging.INFO,
         format="%(asctime)s [%(levelname)s] %(name)s (%(pathname)s:%(lineno)d): %(message)s",
@@ -43,7 +44,7 @@ def setup_logging():
         force=True,
     )
 
-    def handle_exception(exc_type, exc_value, exc_traceback):
+    def handle_exception(exc_type: Any, exc_value: Any, exc_traceback: Any) -> None:
         """Log unhandled exceptions using the configured logging system."""
         if issubclass(exc_type, KeyboardInterrupt):
             # Allow keyboard interrupt to exit normally
@@ -57,7 +58,7 @@ def setup_logging():
     sys.excepthook = handle_exception
 
 
-def main():
+def main() -> None:
     # Setup logging as early as possible
     setup_logging()
 

{moleditpy_linux-3.0.6 → moleditpy_linux-3.2.0}/src/moleditpy_linux/plugins/plugin_interface.py

@@ -19,7 +19,7 @@ class PluginContext:
     It is passed to the `initialize(context)` function of the plugin.
     """
 
-    def __init__(self, manager, plugin_name: str):
+    def __init__(self, manager: Any, plugin_name: str) -> None:
         self._manager = manager
         self._plugin_name = plugin_name
 
@@ -30,7 +30,7 @@ class PluginContext:
         text: Optional[str] = None,
         icon: Optional[str] = None,
         shortcut: Optional[str] = None,
-    ):
+    ) -> None:
         """
         Register a menu action.
 
@@ -52,7 +52,7 @@ class PluginContext:
         callback: Optional[Callable] = None,
         icon: Optional[str] = None,
         shortcut: Optional[str] = None,
-    ):
+    ) -> None:
         """Backward-compatible alias for add_menu_action.
         Supports old 3-arg style: register_menu_action(path, text, callback).
         """
@@ -61,7 +61,8 @@ class PluginContext:
             self.add_menu_action(path, text_or_callback, None, icon, shortcut)
         else:
             # Old style: (path, text, callback)
-            self.add_menu_action(path, callback, text_or_callback, icon, shortcut)
+            if callback is not None:
+                self.add_menu_action(path, callback, text_or_callback, icon, shortcut)
 
     def add_plugin_menu(
         self,
@@ -70,7 +71,7 @@ class PluginContext:
         text: Optional[str] = None,
         icon: Optional[str] = None,
         shortcut: Optional[str] = None,
-    ):
+    ) -> None:
         """
         Register an action nested inside the Plugin menu.
 
@@ -95,7 +96,7 @@ class PluginContext:
         text: str,
         icon: Optional[str] = None,
         tooltip: Optional[str] = None,
-    ):
+    ) -> None:
         """
         Register a toolbar action.
         """
@@ -103,7 +104,9 @@ class PluginContext:
             self._plugin_name, callback, text, icon, tooltip
         )
 
-    def register_drop_handler(self, callback: Callable[[str], bool], priority: int = 0):
+    def register_drop_handler(
+        self, callback: Callable[[str], bool], priority: int = 0
+    ) -> None:
         """
         Register a handler for file drops.
 
@@ -132,7 +135,7 @@ class PluginContext:
         Returns a list of RDKit atom indices currently selected in the 2D or 3D view.
         Note: RDKit indices are returned, which map to the current_mol.
         """
-        return self._manager.get_selected_atom_indices()
+        return self._manager.get_selected_atom_indices()  # type: ignore[no-any-return]
 
     def register_window(self, window_id: str, window: Any) -> None:
         """
@@ -174,7 +177,7 @@ class PluginContext:
         )
 
     @current_mol.setter
-    def current_mol(self, mol: Any):
+    def current_mol(self, mol: Any) -> None:
         mw = self.get_main_window()
         if mw and hasattr(mw, "view_3d_manager"):
             mw.view_3d_manager.current_mol = mol
@@ -186,7 +189,7 @@ class PluginContext:
         return self.current_mol
 
     @current_molecule.setter
-    def current_molecule(self, mol: Any):
+    def current_molecule(self, mol: Any) -> None:
         self.current_mol = mol
 
     @property
@@ -236,7 +239,7 @@ class PluginContext:
         if mw and hasattr(mw, "view_3d_manager") and mw.view_3d_manager.plotter:
             mw.view_3d_manager.plotter.reset_camera()
 
-    def add_export_action(self, label: str, callback: Callable):
+    def add_export_action(self, label: str, callback: Callable) -> None:
         """
         Register a custom export action.
 
@@ -248,7 +251,7 @@ class PluginContext:
 
     def register_optimization_method(
         self, method_name: str, callback: Callable[[Any], bool]
-    ):
+    ) -> None:
         """
         Register a custom 3D optimization method.
 
@@ -263,7 +266,7 @@ class PluginContext:
 
     def register_file_opener(
         self, extension: str, callback: Callable[[str], None], priority: int = 0
-    ):
+    ) -> None:
         """
         Register a handler for opening a specific file extension.
 
@@ -277,7 +280,7 @@ class PluginContext:
             self._plugin_name, extension, callback, priority
         )
 
-    def add_analysis_tool(self, label: str, callback: Callable):
+    def add_analysis_tool(self, label: str, callback: Callable) -> None:
         """
         Register a tool in the Analysis menu.
 
@@ -287,7 +290,7 @@ class PluginContext:
         """
         self._manager.register_analysis_tool(self._plugin_name, label, callback)
 
-    def register_save_handler(self, callback: Callable[[], dict]):
+    def register_save_handler(self, callback: Callable[[], dict]) -> None:
         """
         Register a callback to save state into the project file.
 
@@ -296,7 +299,7 @@ class PluginContext:
         """
         self._manager.register_save_handler(self._plugin_name, callback)
 
-    def register_load_handler(self, callback: Callable[[dict], None]):
+    def register_load_handler(self, callback: Callable[[dict], None]) -> None:
         """
         Register a callback to restore state from the project file.
 
@@ -305,13 +308,15 @@ class PluginContext:
         """
         self._manager.register_load_handler(self._plugin_name, callback)
 
-    def register_3d_context_menu(self, callback: Callable, label: str):
+    def register_3d_context_menu(self, callback: Callable, label: str) -> None:
         """Deprecated: This method does nothing. Kept for backward compatibility."""
         print(
             f"Warning: Plugin '{self._plugin_name}' uses deprecated 'register_3d_context_menu'. This API has been removed."
         )
 
-    def register_3d_style(self, style_name: str, callback: Callable[[Any, Any], None]):
+    def register_3d_style(
+        self, style_name: str, callback: Callable[[Any, Any], None]
+    ) -> None:
         """
         Register a custom 3D rendering style.
 
@@ -322,7 +327,7 @@ class PluginContext:
         """
         self._manager.register_3d_style(self._plugin_name, style_name, callback)
 
-    def register_document_reset_handler(self, callback: Callable[[], None]):
+    def register_document_reset_handler(self, callback: Callable[[], None]) -> None:
         """
         Register a callback to be called when a new document is created (File→New).
 
@@ -370,14 +375,14 @@ class PluginContext:
 class Plugin3DController:
     """Helper to manipulate the 3D scene."""
 
-    def __init__(self, main_window):
+    def __init__(self, main_window: Any) -> None:
         self._mw = main_window
 
-    def _get_v3d(self):
+    def _get_v3d(self) -> Optional[Any]:
         """Helper to get the 3D manager."""
         return getattr(self._mw, "view_3d_manager", None)
 
-    def set_atom_color(self, atom_index: int, color_hex: str):
+    def set_atom_color(self, atom_index: int, color_hex: str) -> None:
         """
         Set the color of a specific atom in the 3D view.
         Args:
@@ -390,7 +395,7 @@ class Plugin3DController:
             if hasattr(self._mw, "plotter") and self._mw.plotter:
                 self._mw.plotter.render()
 
-    def set_bond_color(self, bond_index: int, color_hex: str):
+    def set_bond_color(self, bond_index: int, color_hex: str) -> None:
         """
         Set the color of a specific bond in the 3D view.
 
@@ -404,7 +409,9 @@ class Plugin3DController:
             if hasattr(self._mw, "plotter") and self._mw.plotter:
                 self._mw.plotter.render()
 
-    def set_bond_color_by_atoms(self, atom_idx1: int, atom_idx2: int, color_hex: str):
+    def set_bond_color_by_atoms(
+        self, atom_idx1: int, atom_idx2: int, color_hex: str
+    ) -> None:
         """
         Set the color of the bond between two atoms.
 

{moleditpy_linux-3.0.6 → moleditpy_linux-3.2.0}/src/moleditpy_linux/plugins/plugin_manager.py

@@ -315,7 +315,7 @@ class PluginManager:
             spec = importlib.util.spec_from_file_location(
                 unique_module_name,
                 filepath,
-                submodule_search_locations=([pkg_dir] if is_package else None),
+                submodule_search_locations=([pkg_dir] if is_package else None),  # type: ignore[list-item]
             )
             if spec and spec.loader:
                 module = importlib.util.module_from_spec(spec)
@@ -482,12 +482,16 @@ class PluginManager:
         # Sort by priority desc
         self.drop_handlers.sort(key=lambda x: x["priority"], reverse=True)
 
-    def register_export_action(self, plugin_name, label, callback):
+    def register_export_action(
+        self, plugin_name: str, label: str, callback: Callable
+    ) -> None:
         self.export_actions.append(
             {"plugin": plugin_name, "label": label, "callback": callback}
         )
 
-    def register_optimization_method(self, plugin_name, method_name, callback):
+    def register_optimization_method(
+        self, plugin_name: str, method_name: str, callback: Callable
+    ) -> None:
         # Key by upper-case method name for consistency
         self.optimization_methods[method_name.upper()] = {
             "plugin": plugin_name,
@@ -495,7 +499,9 @@ class PluginManager:
             "label": method_name,
         }
 
-    def register_file_opener(self, plugin_name, extension, callback, priority=0):
+    def register_file_opener(
+        self, plugin_name: str, extension: str, callback: Callable, priority: int = 0
+    ) -> None:
         # Normalize extension to lowercase
         ext = extension.lower()
         if not ext.startswith("."):
@@ -512,25 +518,31 @@ class PluginManager:
         self.file_openers[ext].sort(key=lambda x: x["priority"], reverse=True)
 
     # Analysis Tools registration
-    def register_analysis_tool(self, plugin_name, label, callback):
+    def register_analysis_tool(
+        self, plugin_name: str, label: str, callback: Callable
+    ) -> None:
         self.analysis_tools.append(
             {"plugin": plugin_name, "label": label, "callback": callback}
         )
 
     # State Persistence registration
-    def register_save_handler(self, plugin_name, callback):
+    def register_save_handler(self, plugin_name: str, callback: Callable) -> None:
         self.save_handlers[plugin_name] = callback
 
-    def register_load_handler(self, plugin_name, callback):
+    def register_load_handler(self, plugin_name: str, callback: Callable) -> None:
         self.load_handlers[plugin_name] = callback
 
-    def register_3d_style(self, plugin_name, style_name, callback):
+    def register_3d_style(
+        self, plugin_name: str, style_name: str, callback: Callable
+    ) -> None:
         self.custom_3d_styles[style_name] = {
             "plugin": plugin_name,
             "callback": callback,
         }
 
-    def register_document_reset_handler(self, plugin_name, callback):
+    def register_document_reset_handler(
+        self, plugin_name: str, callback: Callable
+    ) -> None:
         """Register callback to be invoked when a new document is created."""
         self.document_reset_handlers.append(
             {"plugin": plugin_name, "callback": callback}
@@ -637,7 +649,7 @@ class PluginManager:
                     f"Error in document reset handler for {handler['plugin']}: {e}"
                 )
 
-    def get_plugin_info_safe(self, file_path):
+    def get_plugin_info_safe(self, file_path: str) -> Dict[str, str]:
         """Extracts plugin metadata using AST parsing (safe, no execution)."""
         info = {
             "name": os.path.basename(file_path),
@@ -691,25 +703,25 @@ class PluginManager:
 
                         if val is not None:
                             if target.id == "PLUGIN_NAME":
-                                info["name"] = val
+                                info["name"] = str(val)
                             elif target.id == "PLUGIN_VERSION":
-                                info["version"] = val
+                                info["version"] = str(val)
                             elif target.id == "PLUGIN_AUTHOR":
-                                info["author"] = val
+                                info["author"] = str(val)
                             elif target.id == "PLUGIN_DESCRIPTION":
-                                info["description"] = val
+                                info["description"] = str(val)
                             elif target.id == "PLUGIN_CATEGORY":
-                                info["category"] = val
+                                info["category"] = str(val)
                             elif (
                                 target.id == "__version__"
                                 and info["version"] == "Unknown"
                             ):
-                                info["version"] = val
+                                info["version"] = str(val)
                             elif (
                                 target.id == "__author__"
                                 and info["author"] == "Unknown"
                             ):
-                                info["author"] = val
+                                info["author"] = str(val)
 
                 # Docstring extraction
                 if isinstance(node, ast.Expr):