moleditpy 5.0.2__tar.gz → 5.0.3__tar.gz

{moleditpy-5.0.2 → moleditpy-5.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 5.0.2
+Version: 5.0.3
 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-Expression: LGPL-3.0-or-later
@@ -28,7 +28,7 @@ Requires-Dist: pyside6-essentials<6.10,>=6.9; python_version < "3.10"
 Requires-Dist: pyside6-essentials<6.12,>=6.10; python_version >= "3.10"
 Requires-Dist: pyvista<0.50
 Requires-Dist: pyvistaqt<0.14
-Requires-Dist: rdkit<2026.4
+Requires-Dist: rdkit<2026.10
 Dynamic: license-file
 
 # MoleditPy — A Python Molecular Editor

{moleditpy-5.0.2 → moleditpy-5.0.3}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "5.0.2"
+version = "5.0.3"
 
 license = "LGPL-3.0-or-later"
 license-files = ["LICENSE", "COPYING", "THIRD_PARTY_NOTICES.md", "DISTRIBUTION.md", "LICENSING.md"]
@@ -39,7 +39,7 @@ dependencies = [
   "pyside6-essentials >= 6.10, < 6.12; python_version >= '3.10'",
   "pyvista < 0.50",
   "pyvistaqt < 0.14",
-  "rdkit < 2026.4"
+  "rdkit < 2026.10"
 ]
 
 [project.urls]

{moleditpy-5.0.2 → moleditpy-5.0.3}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 5.0.2
+Version: 5.0.3
 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-Expression: LGPL-3.0-or-later
@@ -28,7 +28,7 @@ Requires-Dist: pyside6-essentials<6.10,>=6.9; python_version < "3.10"
 Requires-Dist: pyside6-essentials<6.12,>=6.10; python_version >= "3.10"
 Requires-Dist: pyvista<0.50
 Requires-Dist: pyvistaqt<0.14
-Requires-Dist: rdkit<2026.4
+Requires-Dist: rdkit<2026.10
 Dynamic: license-file
 
 # MoleditPy — A Python Molecular Editor

{moleditpy-5.0.2 → moleditpy-5.0.3}/src/MoleditPy.egg-info/SOURCES.txt

@@ -21,6 +21,7 @@ src/moleditpy/assets/icon.png
 src/moleditpy/core/__init__.py
 src/moleditpy/core/mol_geometry.py
 src/moleditpy/core/molecular_data.py
+src/moleditpy/core/project_validation.py
 src/moleditpy/core/stereo_check.py
 src/moleditpy/plugins/__init__.py
 src/moleditpy/plugins/plugin_interface.py

{moleditpy-5.0.2 → moleditpy-5.0.3}/src/MoleditPy.egg-info/requires.txt

@@ -1,7 +1,7 @@
 numpy
 pyvista<0.50
 pyvistaqt<0.14
-rdkit<2026.4
+rdkit<2026.10
 
 [:python_version < "3.10"]
 pyside6-essentials<6.10,>=6.9

{moleditpy-5.0.2 → moleditpy-5.0.3}/src/moleditpy/core/molecular_data.py

@@ -886,6 +886,7 @@ class MolecularData:
                     "y": pos[1],
                     "charge": atom_info.get("charge", 0),
                     "radical": atom_info.get("radical", 0),
+                    **rs_entry(atom_info),
                 }
             )
 

moleditpy-5.0.3/src/moleditpy/core/project_validation.py

@@ -0,0 +1,117 @@
+"""Validate project contents before replacing the live document."""
+
+from __future__ import annotations
+
+import base64
+import math
+from typing import Any
+
+import numpy as np
+from rdkit import Chem
+
+
+def _integer(value: Any, minimum: int = 0) -> int:
+    if not isinstance(value, int) or isinstance(value, bool) or value < minimum:
+        raise ValueError("Project integer field is invalid")
+    return value
+
+
+def _coordinate(value: Any) -> None:
+    try:
+        if isinstance(value, bool) or not math.isfinite(float(value)):
+            raise ValueError("Project coordinates must be finite numbers")
+    except OverflowError as exc:
+        raise ValueError("Project coordinate is out of range") from exc
+
+
+def _validate_2d(structure: Any) -> None:
+    if not isinstance(structure, dict):
+        raise ValueError("2D structure must be an object")
+    atoms, bonds = structure.get("atoms", []), structure.get("bonds", [])
+    if not isinstance(atoms, list) or not isinstance(bonds, list):
+        raise ValueError("Project atoms and bonds must be lists")
+    ids: set[int] = set()
+    for atom in atoms:
+        atom_id = _integer(atom["id"])
+        if atom_id in ids or not isinstance(atom["symbol"], str) or not atom["symbol"]:
+            raise ValueError("Project atoms need unique IDs and element symbols")
+        ids.add(atom_id)
+        _coordinate(atom["x"])
+        _coordinate(atom["y"])
+        _integer(atom.get("charge", 0), -(2**31))
+        if atom.get("charge", 0) >= 2**31:
+            raise ValueError("Project charge is out of range")
+        _integer(atom.get("radical", 0))
+        if atom.get("rs") not in (None, "R", "S"):
+            raise ValueError("Project R/S label must be R or S")
+    seen: set[frozenset[int]] = set()
+    for bond in bonds:
+        first, second = _integer(bond["atom1"]), _integer(bond["atom2"])
+        pair = frozenset((first, second))
+        if first == second or first not in ids or second not in ids or pair in seen:
+            raise ValueError("Project bond has invalid atom references")
+        seen.add(pair)
+        if isinstance(bond["order"], bool) or bond["order"] not in (1, 1.5, 2, 3):
+            raise ValueError("Project bond order is invalid")
+        if _integer(bond.get("stereo", 0)) not in (0, 1, 2, 3, 4):
+            raise ValueError("Project bond stereochemistry is invalid")
+    minimum = max(ids) + 1 if ids else 0
+    _integer(structure.get("next_atom_id", minimum), minimum)
+
+
+def _validate_molecule(binary: Any) -> Chem.Mol:
+    mol = Chem.Mol(binary)
+    for conformer in mol.GetConformers():
+        if not np.isfinite(conformer.GetPositions()).all():
+            raise ValueError("Project 3D coordinates must be finite")
+    return mol
+
+
+def validate_project_data(data: dict[str, Any]) -> None:
+    """Reject corrupt geometry without changing application or plugin state."""
+    if "2d_structure" in data:
+        _validate_2d(data["2d_structure"])
+    structure = data.get("3d_structure")
+    if structure is None:
+        return
+    if not isinstance(structure, dict):
+        raise ValueError("3D structure must be an object")
+    atoms = structure.get("atoms", [])
+    if not isinstance(atoms, list):
+        raise ValueError("3D atoms must be a list")
+    encoded = structure.get("mol_binary_base64")
+    if encoded:
+        binary: Any = base64.b64decode(encoded.encode("ascii"), validate=True)
+        mol = _validate_molecule(binary)
+        if atoms and len(atoms) != mol.GetNumAtoms():
+            raise ValueError("3D atom metadata does not match its molecule")
+    seen: set[int] = set()
+    for atom in atoms:
+        index = _integer(atom["index"])
+        if index >= len(atoms) or index in seen:
+            raise ValueError("3D atom index is invalid")
+        seen.add(index)
+        for axis in ("x", "y", "z"):
+            _coordinate(atom.get(axis, 0.0))
+
+
+def validate_raw_project_data(data: Any) -> None:
+    """Validate legacy pickle geometry before any live state is cleared."""
+    if not isinstance(data, dict):
+        raise ValueError("Raw project must be an object")
+    atoms, bonds = data.get("atoms", {}), data.get("bonds", {})
+    if not isinstance(atoms, dict) or not isinstance(bonds, dict):
+        raise ValueError("Raw project atoms and bonds must be mappings")
+    structure = {
+        "atoms": [
+            dict(atom, id=atom_id, x=atom["pos"][0], y=atom["pos"][1])
+            for atom_id, atom in atoms.items()
+        ],
+        "bonds": [
+            dict(bond, atom1=key[0], atom2=key[1]) for key, bond in bonds.items()
+        ],
+        "next_atom_id": data.get("_next_atom_id", max(atoms) + 1 if atoms else 0),
+    }
+    _validate_2d(structure)
+    if data.get("mol_3d") is not None:
+        _validate_molecule(data["mol_3d"])

{moleditpy-5.0.2 → moleditpy-5.0.3}/src/moleditpy/plugins/plugin_interface.py

@@ -227,7 +227,7 @@ class PluginContext:
         """Set active RDKit molecule and redraw 3D view."""
         mw = self.get_main_window()
         if mw and hasattr(mw, "view_3d_manager"):
-            mw.view_3d_manager.current_mol = mol
+            mw.set_current_molecule(mol)
             mw.view_3d_manager.draw_molecule_3d(mol)
 
     @property
@@ -613,7 +613,10 @@ class PluginContext:
 
             for i in range(num_atoms):
                 pos = conf.GetAtomPosition(i)
-                symbol = mol.GetAtomWithIdx(i).GetSymbol()
+                atom = mol.GetAtomWithIdx(i)
+                symbol = atom.GetSymbol()
+                if atom.GetAtomicNum() == 0 and atom.HasProp("xyz_original_symbol"):
+                    symbol = atom.GetProp("xyz_original_symbol")
                 xyz_lines.append(
                     f"  {symbol:<5}{pos.x:>15.8f}{pos.y:>15.8f}{pos.z:>15.8f}"
                 )

{moleditpy-5.0.2 → moleditpy-5.0.3}/src/moleditpy/plugins/plugin_manager.py

@@ -260,6 +260,19 @@ class PluginManager:
             if os.path.isdir(file_path):
                 # Copy entire directory
                 dest_path = self._safe_install_path(self.plugin_dir, filename)
+                source = os.path.normcase(os.path.realpath(file_path))
+                destination = os.path.normcase(os.path.realpath(dest_path))
+                if source == destination:
+                    raise ValueError(
+                        "Source and installed package are the same directory"
+                    )
+                if (
+                    os.path.splitdrive(source)[0] == os.path.splitdrive(destination)[0]
+                    and os.path.commonpath([source, destination]) == source
+                ):
+                    raise ValueError(
+                        "Cannot install a package inside its source directory"
+                    )
                 if os.path.exists(dest_path):
                     # Option 1: Overwrite (remove then copy) - safer for clean install
                     if os.path.isdir(dest_path):

{moleditpy-5.0.2 → moleditpy-5.0.3}/src/moleditpy/ui/alignment_dialog.py

@@ -55,6 +55,7 @@ class AlignmentDialog(QDialog, Dialog3DPickingMixin):
         Dialog3DPickingMixin.__init__(self)
         self.mol = mol
         self.main_window = main_window
+        self._invalidated = False
         self.axis = axis
         self._selected_atoms = SelectionList()
 
@@ -133,7 +134,7 @@ class AlignmentDialog(QDialog, Dialog3DPickingMixin):
 
     def on_atom_picked(self, atom_idx: int) -> None:
         """Handle atom selection event."""
-        if self.main_window.view_3d_manager.current_mol is None:
+        if self._invalidated or self.main_window.view_3d_manager.current_mol is None:
             return
 
         if atom_idx in self.selected_atoms:
@@ -181,8 +182,16 @@ class AlignmentDialog(QDialog, Dialog3DPickingMixin):
         for i, idx in enumerate(self.selected_atoms, 1):
             self.add_selection_label(idx, f"#{i}")
 
+    def invalidate_molecule(self) -> None:
+        """Close the tool before undo, import or calculation replaces its molecule."""
+        self._invalidated = True
+        self.setEnabled(False)
+        self.reject()
+
     def apply_alignment(self) -> None:
         """Apply the specific axial alignment to the molecule."""
+        if self._invalidated:
+            return
         if len(self.selected_atoms) != 2:
             QMessageBox.warning(
                 self, "Warning", "Please select exactly 2 atoms for alignment."

{moleditpy-5.0.2 → moleditpy-5.0.3}/src/moleditpy/ui/compute_logic.py

@@ -90,6 +90,12 @@ class _CalculationReceiver(QObject):
         # _retain_until_destroyed). Releasing it here would let shiboken
         # delete this receiver inside its own queued slot call.
         self.deleteLater()
+        if (
+            self.manager._close_after_calculation
+            and not self.manager._active_calc_threads
+        ):
+            self.manager._close_after_calculation = False
+            QTimer.singleShot(0, self.manager.host.close)
 
 
 class ComputeManager:
@@ -103,6 +109,7 @@ class ComputeManager:
         self.host = host
         self.last_successful_optimization_method: Optional[str] = None
         self._active_calc_threads: List[QThread] = []
+        self._close_after_calculation = False
         # id(QObject) -> Python objects kept alive until that QObject is destroyed.
         self._calc_objects: Dict[int, Tuple[Any, ...]] = {}
         self.halt_ids: Set[int] = set()
@@ -120,6 +127,18 @@ class ComputeManager:
         """Reset active calculation threads list."""
         self._active_calc_threads = []
 
+    def prepare_calculation_shutdown(self) -> bool:
+        """Cancel calculations and defer window destruction until Qt finishes them."""
+        running = [thread for thread in self._active_calc_threads if thread.isRunning()]
+        if not running:
+            return True
+        self._close_after_calculation = True
+        self.halt_conversion()
+        for thread in running:
+            thread.requestInterruption()
+        self.host.update_status_message("Canceling calculation before closing...")
+        return False
+
     def _safe_disconnect(self, signal: Any) -> None:
         """Disconnect a signal, tolerating one that has nothing connected."""
         try:

{moleditpy-5.0.2 → moleditpy-5.0.3}/src/moleditpy/ui/export_logic.py

@@ -533,6 +533,7 @@ class ExportManager:
                         # This allows glyphs (where all atoms are in one mesh)
                         # to retain individual atom colors when exporting to OBJ/MTL.
                         try:
+                            color_mesh = mesh_copy
                             colors = None
                             pd = mesh_copy.point_data
                             # Use red/green/blue arrays if available
@@ -559,10 +560,10 @@ class ExportManager:
                             if colors is None and "colors" in mesh_copy.cell_data:
                                 try:
                                     # Convert cell_data to point_data
-                                    temp_mesh = mesh_copy.cell_data_to_point_data()
-                                    if "colors" in temp_mesh.point_data:
+                                    color_mesh = mesh_copy.cell_data_to_point_data()
+                                    if "colors" in color_mesh.point_data:
                                         colors = np.asarray(
-                                            temp_mesh.point_data["colors"]
+                                            color_mesh.point_data["colors"]
                                         )
                                 except (
                                     AttributeError,
@@ -616,15 +617,8 @@ class ExportManager:
                                         if point_inds.size == 0:
                                             continue
                                         try:
-                                            # Use temp_mesh if point data available
-                                            target_mesh = (
-                                                temp_mesh
-                                                if "temp_mesh" in locals()
-                                                else mesh_copy
-                                            )
-
                                             # extract_points with adjacent_cells=False to avoid pulling in neighbors
-                                            submesh = target_mesh.extract_points(
+                                            submesh = color_mesh.extract_points(
                                                 point_inds, adjacent_cells=False
                                             )
 

{moleditpy-5.0.2 → moleditpy-5.0.3}/src/moleditpy/ui/geometry_base_dialog.py

@@ -98,9 +98,12 @@ class GeometryBaseDialog(BasePickingDialog):
             if wrap:
                 f_val = (f_val + 180) % 360 - 180
 
-            slider.blockSignals(True)
-            slider.setValue(int(round(f_val * scale)))
-            slider.blockSignals(False)
+            scaled = max(slider.minimum(), min(slider.maximum(), f_val * scale))
+            was_blocked = slider.blockSignals(True)
+            try:
+                slider.setValue(int(round(scaled)))
+            finally:
+                slider.blockSignals(was_blocked)
         except (ValueError, TypeError):
             # Safe defensive fallback catching ValueError, TypeError
             logging.debug("Suppressed non-critical error", exc_info=True)

{moleditpy-5.0.2 → moleditpy-5.0.3}/src/moleditpy/ui/io_logic.py

@@ -13,6 +13,7 @@ DOI: 10.5281/zenodo.17268532
 from __future__ import annotations
 
 import logging
+import math
 import os
 import json
 import pickle
@@ -48,6 +49,8 @@ from rdkit.Chem import (
 )
 
 from ..utils.sdf_records import read_sdf_records
+from ..utils.finite_float import finite_float
+from ..core.project_validation import validate_project_data, validate_raw_project_data
 from .sdf_record_dialog import SdfRecordDialog
 from ..utils.constants import (
     COVALENT_RADII,
@@ -242,11 +245,14 @@ class IOManager:
         nums: list[float] = []
         for tok in tokens:
             try:
-                nums.append(float(tok))
+                value = float(tok)
             except ValueError:
                 if nums:
                     break  # trailing non-numeric column after the coordinates
                 continue  # leading label/separator column before the coordinates
+            if not math.isfinite(value):
+                return None
+            nums.append(value)
             if len(nums) == 3:
                 break
         if len(nums) == 3:
@@ -521,11 +527,17 @@ class IOManager:
         layout.addLayout(hl)
         result = {"accepted": False, "skip": False}
 
+        def _charge_value() -> int:
+            value = finite_float(line_edit.text().strip() or "0")
+            if not value.is_integer() or not -(2**31) <= value < 2**31:
+                raise ValueError("Charge must be a supported integer")
+            return int(value)
+
         def _accept_if_valid() -> None:
             """Validate charge input and accept the dialog if valid."""
             # Invalid input: show inline error and keep the dialog open
             try:
-                int(float(line_edit.text().strip() or "0"))
+                _charge_value()
             except ValueError:
                 error_label.setText("Invalid charge: enter an integer (e.g. 0, -1, 2).")
                 dialog.adjustSize()
@@ -544,7 +556,7 @@ class IOManager:
         if result["skip"]:
             return 0, True, True
         try:
-            val = int(float(line_edit.text().strip() or "0"))
+            val = _charge_value()
             return val, True, False
         except ValueError:
             # Unreachable via OK (validated inline)
@@ -824,6 +836,7 @@ class IOManager:
                 )
                 return
 
+            validate_project_data(json_data)
             if not self.host.edit_actions_manager.clear_all(skip_check=True):
                 return
 
@@ -1251,9 +1264,10 @@ class IOManager:
                 )
                 for i in range(num_atoms):
                     pos = conf.GetAtomPosition(i)
-                    symbol = self.host.view_3d_manager.current_mol.GetAtomWithIdx(
-                        i
-                    ).GetSymbol()
+                    atom = self.host.view_3d_manager.current_mol.GetAtomWithIdx(i)
+                    symbol = atom.GetSymbol()
+                    if atom.GetAtomicNum() == 0 and atom.HasProp("xyz_original_symbol"):
+                        symbol = atom.GetProp("xyz_original_symbol")
                     xyz_lines.append(
                         f"  {symbol:<5}{pos.x:>15.8f}{pos.y:>15.8f}{pos.z:>15.8f}"
                     )
@@ -1311,6 +1325,7 @@ class IOManager:
             # Unpickle before clearing, so an unreadable file keeps the document.
             with open(file_path, "rb") as f:
                 loaded_data = pickle.load(f)
+            validate_raw_project_data(loaded_data)
             if not self.host.edit_actions_manager.clear_all(skip_check=True):
                 return
             self.host.ui_manager.restore_ui_for_editing()

{moleditpy-5.0.2 → moleditpy-5.0.3}/src/moleditpy/ui/main_window_init.py

@@ -51,7 +51,7 @@ from PySide6.QtWidgets import (
     QWidget,
 )
 
-from ..utils.default_settings import DEFAULT_SETTINGS
+from ..utils.default_settings import normalize_settings
 from ..plugins.plugin_manager import PluginManager
 from ..utils.system_utils import detect_system_dark_mode
 
@@ -552,7 +552,7 @@ class MainInitManager:
                     self._migrate_legacy_settings(loaded_settings)
 
                     # 4. Update settings with loaded values
-                    self.settings.update(loaded_settings)
+                    self.settings = normalize_settings(loaded_settings)
         except (AttributeError, RuntimeError, ValueError, TypeError, IOError):
             # Use defaults on any error
             # Safe defensive fallback catching AttributeError, RuntimeError, ValueError, TypeError, IOError
@@ -633,7 +633,7 @@ class MainInitManager:
     # --- Settings and Plugin Helpers ---
     def _get_default_settings(self) -> Dict[str, Any]:
         """Return a dictionary of default application settings."""
-        return DEFAULT_SETTINGS.copy()
+        return normalize_settings({})
 
     def _migrate_legacy_settings(self, loaded_settings: Dict[str, Any]) -> None:
         """Handle migration of legacy settings keys."""

{moleditpy-5.0.2 → moleditpy-5.0.3}/src/moleditpy/ui/molecular_scene_handler.py

@@ -48,6 +48,7 @@ class TemplateMixin:
     mode: Any
     removeItem: Any
     views: Any
+    set_atom_rs_label: Any
 
     def __init__(self, *args: Any, **kwargs: Any) -> None:
         """Initialize template placement mixin."""
@@ -696,6 +697,7 @@ class TemplateMixin:
             atom_item.symbol == symbol
             and atom_item.charge == charge
             and atom_item.radical == radical
+            and atom_item.rs_label == atom_data.get("rs")
         ):
             return
 
@@ -704,6 +706,7 @@ class TemplateMixin:
             atom_item.symbol = symbol
             atom_item.charge = charge
             atom_item.radical = radical
+            self.set_atom_rs_label(atom_item, atom_data.get("rs"))
 
             record = self.data.atoms.get(atom_item.atom_id)
             if record is not None:
@@ -746,6 +749,7 @@ class TemplateMixin:
             radical = atom_data.get("radical", 0)
 
             atom_id = self.create_atom(symbol, pos, charge, radical)
+            self.set_atom_rs_label(self.atom_items[atom_id], atom_data.get("rs"))
             atom_id_map[atom_data["id"]] = atom_id
 
         # Create bonds (bonds_info is always id-based)

{moleditpy-5.0.2 → moleditpy-5.0.3}/src/moleditpy/ui/preview_molecule.py

@@ -20,6 +20,7 @@ from PySide6.QtWidgets import QGraphicsItem, QGraphicsScene
 
 from .atom_item import AtomItem
 from .bond_item import BondItem
+from ..core.molecular_data import rs_entry
 
 
 class PreviewScene(QGraphicsScene):
@@ -96,6 +97,7 @@ def build_preview_items(
             radical=int(atom_data.get("radical", 0) or 0),
         )
         item.setFlag(QGraphicsItem.GraphicsItemFlag.ItemIsMovable, False)
+        item.rs_label = rs_entry(atom_data).get("rs")
         item.setFlag(QGraphicsItem.GraphicsItemFlag.ItemIsSelectable, False)
         item.setAcceptHoverEvents(False)
         atom_items.append(item)

{moleditpy-5.0.2 → moleditpy-5.0.3}/src/moleditpy/ui/template_preview_item.py

@@ -235,6 +235,7 @@ class TemplatePreviewItem(QGraphicsItem):
                     atom.get("symbol", "C"),
                     atom.get("charge", 0),
                     atom.get("radical", 0),
+                    atom.get("rs"),
                 )
                 for atom in preview_atoms
             ),

{moleditpy-5.0.2 → moleditpy-5.0.3}/src/moleditpy/ui/ui_manager.py

@@ -224,7 +224,9 @@ class UIManager(QObject):
         Handle application close logic.
         Returns True if close should proceed, False if it should be cancelled.
         """
-        if not self.host.edit_3d_manager.prepare_optimization_shutdown():
+        calculations_ready = self.host.compute_manager.prepare_calculation_shutdown()
+        optimizations_ready = self.host.edit_3d_manager.prepare_optimization_shutdown()
+        if not calculations_ready or not optimizations_ready:
             return False
         # 1. Persist settings
         try:
@@ -271,17 +273,6 @@ class UIManager(QObject):
                         # Safe defensive fallback catching RuntimeError, TypeError
                         logging.debug("Suppressed non-critical error", exc_info=True)
 
-            # Stop calculation threads
-            active_threads = list(
-                getattr(self.host.compute_manager, "_active_calc_threads", []) or []
-            )
-            for thr in active_threads:
-                try:
-                    thr.quit()
-                    thr.wait(200)
-                except (RuntimeError, TypeError):
-                    # Safe defensive fallback catching RuntimeError, TypeError
-                    logging.debug("Suppressed non-critical error", exc_info=True)
         except (AttributeError, RuntimeError, TypeError, ValueError):
             # Safe defensive fallback catching AttributeError, RuntimeError, TypeError, ValueError
             logging.debug("Suppressed non-critical error", exc_info=True)

{moleditpy-5.0.2 → moleditpy-5.0.3}/src/moleditpy/ui/user_template_dialog.py

@@ -36,6 +36,7 @@ from .preview_molecule import (
 from .template_preview_view import TemplatePreviewView
 
 from ..utils.constants import VERSION
+from ..core.molecular_data import rs_entry
 import json
 import logging
 import os
@@ -402,6 +403,7 @@ class UserTemplateDialog(QDialog):
                 "charge": atom.get("charge", 0),
                 "radical": atom.get("radical", 0),
                 "pos": QPointF(atom["x"], atom["y"]),
+                **rs_entry(atom),
             }
             for atom in atoms
         ]
@@ -545,6 +547,7 @@ class UserTemplateDialog(QDialog):
                     "y": pos[1],
                     "charge": atom_info.get("charge", 0),
                     "radical": atom_info.get("radical", 0),
+                    **rs_entry(atom_info),
                 }
             )
 

{moleditpy-5.0.2 → moleditpy-5.0.3}/src/moleditpy/utils/default_settings.py

@@ -10,6 +10,10 @@ Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """
 
+import copy
+import math
+from typing import Any
+
 from .label_style import DEFAULT_LABEL_SETTINGS
 
 DEFAULT_SETTINGS = {
@@ -96,3 +100,47 @@ DEFAULT_SETTINGS = {
     "cleanup_straighten_bonds_2d": False,
     "cleanup_avoid_clashes_2d": False,
 }
+
+
+def normalize_settings(loaded: dict[str, Any]) -> dict[str, Any]:
+    """Keep plugin settings while replacing unsafe built-in values with defaults."""
+    result = copy.deepcopy(DEFAULT_SETTINGS)
+    result.update(loaded)
+    for key, default in DEFAULT_SETTINGS.items():
+        value = result[key]
+        valid = True
+        if isinstance(default, bool):
+            valid = isinstance(value, bool)
+        elif isinstance(default, (int, float)):
+            try:
+                number = float(value)
+                valid = (
+                    isinstance(value, (int, float))
+                    and not isinstance(value, bool)
+                    and math.isfinite(number)
+                    and 0 <= number <= (2**31 - 1) / 1000
+                )
+                if isinstance(default, int):
+                    valid = valid and number.is_integer()
+                if key.endswith("_resolution") or key in (
+                    "bond_dash_count_2d",
+                    "atom_font_size_2d",
+                ):
+                    valid = valid and number >= 1
+                if valid:
+                    result[key] = int(number) if isinstance(default, int) else number
+            except (ValueError, TypeError, OverflowError):
+                valid = False
+        elif isinstance(default, str):
+            valid = isinstance(value, str) and bool(value.strip())
+        elif isinstance(default, dict):
+            valid = isinstance(value, dict)
+            if valid:
+                result[key] = {
+                    symbol: color
+                    for symbol, color in value.items()
+                    if isinstance(symbol, str) and isinstance(color, str)
+                }
+        if not valid:
+            result[key] = copy.deepcopy(default)
+    return result

{moleditpy-5.0.2 → moleditpy-5.0.3}/src/moleditpy/utils/label_style.py

@@ -13,6 +13,7 @@ DOI: 10.5281/zenodo.17268532
 from __future__ import annotations
 
 import re
+import math
 from collections.abc import Mapping
 from typing import Any, Dict, Tuple
 
@@ -79,7 +80,7 @@ def _get(settings: Any, key: str) -> Any:
 def _color(settings: Any, key: str) -> str:
     """A stored color if it is a valid #RRGGBB, else the default."""
     value = _get(settings, key)
-    if isinstance(value, str) and _HEX_COLOR.match(value):
+    if isinstance(value, str) and _HEX_COLOR.fullmatch(value):
         return value
     return str(DEFAULT_LABEL_SETTINGS[key])
 
@@ -88,7 +89,12 @@ def _number(settings: Any, key: str, low: float, high: float) -> float:
     """A stored number clamped to [low, high], else the default."""
     value = _get(settings, key)
     if isinstance(value, (int, float)) and not isinstance(value, bool):
-        return min(max(float(value), low), high)
+        try:
+            number = float(value)
+        except OverflowError:
+            return float(DEFAULT_LABEL_SETTINGS[key])
+        if math.isfinite(number):
+            return min(max(number, low), high)
     return float(DEFAULT_LABEL_SETTINGS[key])
 
 
@@ -101,7 +107,7 @@ def _flag(settings: Any, key: str) -> bool:
 def _family(settings: Any) -> str:
     """A stored VTK font family, else the default."""
     value = _get(settings, FONT_FAMILY_KEY)
-    if value in {family for family, _ in FONT_FAMILIES}:
+    if isinstance(value, str) and value in {family for family, _ in FONT_FAMILIES}:
         return str(value)
     return str(DEFAULT_LABEL_SETTINGS[FONT_FAMILY_KEY])