MoleditPy-linux 4.8.2__tar.gz → 4.8.3__tar.gz

{moleditpy_linux-4.8.2 → moleditpy_linux-4.8.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 4.8.2
+Version: 4.8.3
 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:                     GNU GENERAL PUBLIC LICENSE

{moleditpy_linux-4.8.2 → moleditpy_linux-4.8.3}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy-linux"
 
-version = "4.8.2"
+version = "4.8.3"
 
 license = {file = "LICENSE"}
 

{moleditpy_linux-4.8.2 → moleditpy_linux-4.8.3}/src/MoleditPy_linux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 4.8.2
+Version: 4.8.3
 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:                     GNU GENERAL PUBLIC LICENSE

{moleditpy_linux-4.8.2 → moleditpy_linux-4.8.3}/src/moleditpy_linux/core/mol_geometry.py

@@ -593,9 +593,9 @@ def _identify_problems_rdkit(
 
 def optimize_2d_coords(mol: Chem.Mol) -> Dict[int, Tuple[float, float]]:
     """Generate 2D coordinates using RDKit and return a map of (x, y) tuples."""
-    from rdkit.Chem import AllChem
+    from rdkit.Chem import rdDepictor
 
-    AllChem.Compute2DCoords(mol)
+    rdDepictor.Compute2DCoords(mol)
     conf = mol.GetConformer()
     new_positions = {}
     for rdkit_atom in mol.GetAtoms():

{moleditpy_linux-4.8.2 → moleditpy_linux-4.8.3}/src/moleditpy_linux/core/molecular_data.py

@@ -18,7 +18,7 @@ from rdkit import Chem
 from ..utils.constants import ANGSTROM_PER_PIXEL
 
 
-class PointTuple(tuple):
+class PointTuple(Tuple[float, ...]):
     """Backward-compatible tuple that allows .x() and .y() access like QPointF."""
 
     def x(self) -> float:

{moleditpy_linux-4.8.2 → moleditpy_linux-4.8.3}/src/moleditpy_linux/main.py

@@ -20,7 +20,7 @@ import sys
 import argparse
 import time
 import traceback
-from typing import Any, Dict, Optional
+from typing import Any, Dict, Optional, Set
 
 from .utils.constants import VERSION
 
@@ -81,7 +81,7 @@ class _ErrorDialogHandler(logging.Handler):
         # signature -> monotonic timestamp of its last shown dialog.
         self._last_shown: Dict[str, float] = {}
         # Held so a non-blocking box is not garbage-collected before it closes.
-        self._open_boxes: set = set()
+        self._open_boxes: Set[QMessageBox] = set()
         self._log_path = log_path
 
     def emit(self, record: logging.LogRecord) -> None:

{moleditpy_linux-4.8.2 → moleditpy_linux-4.8.3}/src/moleditpy_linux/plugins/plugin_interface.py

@@ -27,7 +27,7 @@ class PluginContext:
     def add_menu_action(
         self,
         path: str,
-        callback: Callable,
+        callback: Callable[..., Any],
         text: Optional[str] = None,
         icon: Optional[str] = None,
         shortcut: Optional[str] = None,
@@ -57,8 +57,8 @@ class PluginContext:
     def register_menu_action(
         self,
         path: str,
-        text_or_callback: Union[str, Callable],
-        callback: Optional[Callable] = None,
+        text_or_callback: Union[str, Callable[..., Any]],
+        callback: Optional[Callable[..., Any]] = None,
         icon: Optional[str] = None,
         shortcut: Optional[str] = None,
     ) -> None:
@@ -76,7 +76,7 @@ class PluginContext:
     def add_plugin_menu(
         self,
         path: str,
-        callback: Callable,
+        callback: Callable[..., Any],
         text: Optional[str] = None,
         icon: Optional[str] = None,
         shortcut: Optional[str] = None,
@@ -103,7 +103,7 @@ class PluginContext:
 
     def add_toolbar_action(
         self,
-        callback: Callable,
+        callback: Callable[..., Any],
         text: str,
         icon: Optional[str] = None,
         tooltip: Optional[str] = None,
@@ -262,7 +262,7 @@ 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) -> None:
+    def add_export_action(self, label: str, callback: Callable[..., Any]) -> None:
         """
         Register a custom export action.
 
@@ -303,7 +303,7 @@ class PluginContext:
             self._plugin_name, extension, callback, priority
         )
 
-    def add_analysis_tool(self, label: str, callback: Callable) -> None:
+    def add_analysis_tool(self, label: str, callback: Callable[..., Any]) -> None:
         """
         Register a tool in the Analysis menu.
 
@@ -313,7 +313,7 @@ class PluginContext:
         """
         self._manager.register_analysis_tool(self._plugin_name, label, callback)
 
-    def register_save_handler(self, callback: Callable[[], dict]) -> None:
+    def register_save_handler(self, callback: Callable[[], Dict[str, Any]]) -> None:
         """
         Register a callback to save state into the project file.
 
@@ -322,7 +322,7 @@ class PluginContext:
         """
         self._manager.register_save_handler(self._plugin_name, callback)
 
-    def register_load_handler(self, callback: Callable[[dict], None]) -> None:
+    def register_load_handler(self, callback: Callable[[Dict[str, Any]], None]) -> None:
         """
         Register a callback to restore state from the project file.
 
@@ -331,7 +331,9 @@ class PluginContext:
         """
         self._manager.register_load_handler(self._plugin_name, callback)
 
-    def register_3d_context_menu(self, callback: Callable, label: str) -> None:
+    def register_3d_context_menu(
+        self, callback: Callable[..., Any], label: str
+    ) -> None:
         """Deprecated: This method does nothing. Kept for backward compatibility."""
         import warnings
 

{moleditpy_linux-4.8.2 → moleditpy_linux-4.8.3}/src/moleditpy_linux/plugins/plugin_manager.py

@@ -92,8 +92,8 @@ class PluginManager:
         self.optimization_methods: Dict[str, Dict[str, Any]] = {}
         self.file_openers: Dict[str, List[Dict[str, Any]]] = {}
         self.analysis_tools: List[Dict[str, Any]] = []
-        self.save_handlers: Dict[str, Callable] = {}
-        self.load_handlers: Dict[str, Callable] = {}
+        self.save_handlers: Dict[str, Callable[..., Any]] = {}
+        self.load_handlers: Dict[str, Callable[..., Any]] = {}
         self.custom_3d_styles: Dict[str, Dict[str, Any]] = {}
         self.document_reset_handlers: List[Dict[str, Any]] = []
         self.atom_drag_handlers: List[Dict[str, Any]] = []
@@ -447,7 +447,7 @@ class PluginManager:
         self,
         plugin_name: str,
         path: str,
-        callback: Callable,
+        callback: Callable[..., Any],
         text: str,
         icon: str,
         shortcut: str,
@@ -471,7 +471,12 @@ class PluginManager:
         )
 
     def register_toolbar_action(
-        self, plugin_name: str, callback: Callable, text: str, icon: str, tooltip: str
+        self,
+        plugin_name: str,
+        callback: Callable[..., Any],
+        text: str,
+        icon: str,
+        tooltip: str,
     ) -> None:
         """Register a plugin toolbar button with its callback and display metadata."""
         self.toolbar_actions.append(
@@ -485,7 +490,7 @@ class PluginManager:
         )
 
     def register_drop_handler(
-        self, plugin_name: str, callback: Callable, priority: int
+        self, plugin_name: str, callback: Callable[..., Any], priority: int
     ) -> None:
         """Register a drag-and-drop handler with a given priority."""
         self.drop_handlers.append(
@@ -495,7 +500,7 @@ class PluginManager:
         self.drop_handlers.sort(key=lambda x: x["priority"], reverse=True)
 
     def register_export_action(
-        self, plugin_name: str, label: str, callback: Callable
+        self, plugin_name: str, label: str, callback: Callable[..., Any]
     ) -> None:
         """Register a plugin export action with its label and callback."""
         self.export_actions.append(
@@ -503,7 +508,7 @@ class PluginManager:
         )
 
     def register_optimization_method(
-        self, plugin_name: str, method_name: str, callback: Callable
+        self, plugin_name: str, method_name: str, callback: Callable[..., Any]
     ) -> None:
         """Register a named 3D optimization method provided by a plugin."""
         method_key = method_name.upper()
@@ -520,7 +525,11 @@ class PluginManager:
             )
 
     def register_file_opener(
-        self, plugin_name: str, extension: str, callback: Callable, priority: int = 0
+        self,
+        plugin_name: str,
+        extension: str,
+        callback: Callable[..., Any],
+        priority: int = 0,
     ) -> None:
         """Register a file-type handler for the given extension."""
         # Normalize extension to lowercase
@@ -540,7 +549,7 @@ class PluginManager:
 
     # Analysis Tools registration
     def register_analysis_tool(
-        self, plugin_name: str, label: str, callback: Callable
+        self, plugin_name: str, label: str, callback: Callable[..., Any]
     ) -> None:
         """Register a plugin analysis tool with its label and callback."""
         self.analysis_tools.append(
@@ -548,16 +557,20 @@ class PluginManager:
         )
 
     # State Persistence registration
-    def register_save_handler(self, plugin_name: str, callback: Callable) -> None:
+    def register_save_handler(
+        self, plugin_name: str, callback: Callable[..., Any]
+    ) -> None:
         """Register a plugin session-save callback."""
         self.save_handlers[plugin_name] = callback
 
-    def register_load_handler(self, plugin_name: str, callback: Callable) -> None:
+    def register_load_handler(
+        self, plugin_name: str, callback: Callable[..., Any]
+    ) -> None:
         """Register a plugin session-load callback."""
         self.load_handlers[plugin_name] = callback
 
     def register_3d_style(
-        self, plugin_name: str, style_name: str, callback: Callable
+        self, plugin_name: str, style_name: str, callback: Callable[..., Any]
     ) -> None:
         """Register a named custom 3D rendering style."""
         self.custom_3d_styles[style_name] = {
@@ -566,14 +579,16 @@ class PluginManager:
         }
 
     def register_document_reset_handler(
-        self, plugin_name: str, callback: Callable
+        self, plugin_name: str, callback: Callable[..., Any]
     ) -> None:
         """Register callback to be invoked when a new document is created."""
         self.document_reset_handlers.append(
             {"plugin": plugin_name, "callback": callback}
         )
 
-    def register_atom_drag_handler(self, plugin_name: str, callback: Callable) -> None:
+    def register_atom_drag_handler(
+        self, plugin_name: str, callback: Callable[..., Any]
+    ) -> None:
         """Register a handler called during 3D atom/group dragging."""
         self.atom_drag_handlers.append({"plugin": plugin_name, "callback": callback})
 
@@ -676,7 +691,7 @@ class PluginManager:
         self,
         event_type: str,
         atom_indices: List[int],
-        positions: Dict[int, tuple],
+        positions: Dict[int, Tuple[float, ...]],
     ) -> None:
         """Call all registered atom drag handlers."""
         for handler in self.atom_drag_handlers:

{moleditpy_linux-4.8.2 → moleditpy_linux-4.8.3}/src/moleditpy_linux/ui/analysis_window.py

@@ -75,7 +75,7 @@ class AnalysisWindow(QDialog):
                 total_atoms = len(xyz_atoms)
                 num_heavy_atoms = 0
 
-                for symbol, x, y, z in xyz_atoms:
+                for symbol, _x, _y, _z in xyz_atoms:
                     atom_counts[symbol] = atom_counts.get(symbol, 0) + 1
                     if symbol != "H":  # Non-hydrogen
                         num_heavy_atoms += 1
@@ -154,12 +154,15 @@ class AnalysisWindow(QDialog):
 
                 # Calculate various properties
                 mol_formula = rdMolDescriptors.CalcMolFormula(self.mol)
-                mol_wt = Descriptors.MolWt(self.mol)
-                exact_mw = Descriptors.ExactMolWt(self.mol)
+                # Descriptors.MolWt is generated at import time from rdkit's
+                # descriptor table, so no stub can declare it; the rest have
+                # direct rdMolDescriptors equivalents used elsewhere here.
+                mol_wt = Descriptors.MolWt(self.mol)  # type: ignore[attr-defined]
+                exact_mw = rdMolDescriptors.CalcExactMolWt(self.mol)
                 num_heavy_atoms = self.mol.GetNumHeavyAtoms()
                 num_rings = rdMolDescriptors.CalcNumRings(self.mol)
-                log_p = Descriptors.MolLogP(self.mol)
-                tpsa = Descriptors.TPSA(self.mol)
+                log_p = rdMolDescriptors.CalcCrippenDescriptors(self.mol)[0]
+                tpsa = rdMolDescriptors.CalcTPSA(self.mol)
                 num_h_donors = rdMolDescriptors.CalcNumHBD(self.mol)
                 num_h_acceptors = rdMolDescriptors.CalcNumHBA(self.mol)
 

{moleditpy_linux-4.8.2 → moleditpy_linux-4.8.3}/src/moleditpy_linux/ui/app_state.py

@@ -19,7 +19,7 @@ import copy
 import logging
 import os
 from ..utils.suppress_log import suppress_log
-from typing import Any, Dict, Optional, Tuple
+from typing import Any, Dict, List, Optional, Tuple
 
 
 import numpy as np
@@ -43,7 +43,7 @@ if TYPE_CHECKING:
 
 
 # --- Class Definition ---
-def _serialize_constraints(constraints: list) -> list:
+def _serialize_constraints(constraints: List[Any]) -> List[List[Any]]:
     """Convert internal constraint tuples to JSON-serializable lists."""
     result = []
     for const in constraints:
@@ -54,7 +54,7 @@ def _serialize_constraints(constraints: list) -> list:
     return result
 
 
-def _deserialize_constraints(raw: list) -> list:
+def _deserialize_constraints(raw: List[Any]) -> List[Tuple[Any, ...]]:
     """Convert JSON-loaded constraint lists back to internal tuples."""
     result = []
     for const in raw:
@@ -228,7 +228,7 @@ class StateManager:
                     if self.host.view_3d_manager.plotter and not getattr(
                         self.host, "is_restoring_state", False
                     ):
-                        self.host.view_3d_manager.plotter.reset_camera()
+                        self.host.view_3d_manager.plotter.reset_camera()  # type: ignore[call-arg]
 
                     self.host.ui_manager.enable_3d_features(True)
                     self.host.view_3d_manager.setup_3d_hover()
@@ -481,7 +481,9 @@ class StateManager:
                     json_data["molecular_info"] = {
                         "num_atoms": self.host.view_3d_manager.current_mol.GetNumAtoms(),
                         "num_bonds": self.host.view_3d_manager.current_mol.GetNumBonds(),
-                        "molecular_weight": Descriptors.MolWt(
+                        # Generated at import time from rdkit's descriptor
+                        # table, so no stub can declare it.
+                        "molecular_weight": Descriptors.MolWt(  # type: ignore[attr-defined]
                             self.host.view_3d_manager.current_mol
                         ),
                         "formula": rdMolDescriptors.CalcMolFormula(
@@ -620,7 +622,11 @@ class StateManager:
                 mol_base64 = structure_3d.get("mol_binary_base64")
                 if mol_base64:
                     mol_binary = base64.b64decode(mol_base64.encode("ascii"))
-                    self.host.set_current_molecule(Chem.Mol(mol_binary))
+                    # Chem.Mol accepts a pickled binary block at runtime;
+                    # the stub only overloads Mol/str.
+                    self.host.set_current_molecule(
+                        Chem.Mol(mol_binary)  # type: ignore[call-overload]
+                    )
                     if self.host.view_3d_manager.current_mol:
                         # Set 3D coordinates
                         if self.host.view_3d_manager.current_mol.GetNumConformers() > 0:
@@ -686,7 +692,7 @@ class StateManager:
                             self.host.set_is_2d_editable(True)
 
                         if self.host.view_3d_manager.plotter:
-                            self.host.view_3d_manager.plotter.reset_camera()
+                            self.host.view_3d_manager.plotter.reset_camera()  # type: ignore[call-arg]
 
                         # Enable 3D-related UI
                         try:

{moleditpy_linux-4.8.2 → moleditpy_linux-4.8.3}/src/moleditpy_linux/ui/base_picking_dialog.py

@@ -11,7 +11,7 @@ DOI: 10.5281/zenodo.17268532
 """
 
 import logging
-from typing import TYPE_CHECKING, Any, Optional, Union
+from typing import Any, List, Optional, Union, TYPE_CHECKING
 
 import numpy as np
 from PyQt6.QtCore import Qt, QTimer
@@ -25,7 +25,7 @@ if TYPE_CHECKING:
     from .main_window import MainWindow
 
 
-class SelectionList(list):
+class SelectionList(List[int]):
     """Order-preserving list that compares equal to sets/lists/tuples of same elements."""
 
     def __eq__(self, other: object) -> bool:

{moleditpy_linux-4.8.2 → moleditpy_linux-4.8.3}/src/moleditpy_linux/ui/calculation_worker.py

@@ -17,13 +17,13 @@ import re
 import numpy as np
 import sys
 import subprocess
-from typing import Any, Callable, Dict, Optional, Set, Tuple
+from typing import Any, Callable, Dict, List, Optional, Set, Tuple
 
 from PyQt6.QtCore import QObject, pyqtSignal, pyqtSlot
 
 # RDKit
 from rdkit import Chem
-from rdkit.Chem import AllChem, rdGeometry
+from rdkit.Chem import rdDistGeom, rdForceFieldHelpers, rdGeometry
 from rdkit.DistanceGeometry import DoTriangleSmoothing
 
 from ..utils.constants import DEFAULT_BOND_LENGTH_ANGSTROM
@@ -235,14 +235,16 @@ def _iterative_optimize(
         )
         ff = None
         if method == "UFF":
-            ff = AllChem.UFFGetMoleculeForceField(
+            ff = rdForceFieldHelpers.UFFGetMoleculeForceField(
                 mol, confId=0, ignoreInterfragInteractions=ignore_interfrag
             )
         elif "MMFF94" in method:
             mmff_variant = "MMFF94" if method == "MMFF94" else "MMFF94s"
-            props = AllChem.MMFFGetMoleculeProperties(mol, mmffVariant=mmff_variant)
+            props = rdForceFieldHelpers.MMFFGetMoleculeProperties(
+                mol, mmffVariant=mmff_variant
+            )
             if props:
-                ff = AllChem.MMFFGetMoleculeForceField(
+                ff = rdForceFieldHelpers.MMFFGetMoleculeForceField(
                     mol, props, confId=0, ignoreInterfragInteractions=ignore_interfrag
                 )
 
@@ -378,8 +380,10 @@ _DIRECT_WEDGE_TILT = math.radians(35.0)
 
 
 def _rescale_2d_layout(
-    coords: list, mol: Chem.Mol, _safe_status: Callable[[str], None]
-) -> list:
+    coords: List[Tuple[float, float, float]],
+    mol: Chem.Mol,
+    _safe_status: Callable[[str], None],
+) -> List[Tuple[float, float, float]]:
     """Scale parsed 2D coordinates so the median bond is a chemically sane length."""
     lengths = []
     for bond in mol.GetBonds():
@@ -419,8 +423,12 @@ def _perform_direct_conversion(
     options: Optional[Dict[str, Any]],
     _check_halted: Callable[[], bool],
     _safe_status: Callable[[str], None],
-) -> Optional[Chem.Mol]:
-    """Direct 3D conversion using 2D coordinates and adding missing H without embedding."""
+) -> Chem.Mol:
+    """Direct 3D conversion using 2D coordinates and adding missing H without embedding.
+
+    Returns the same molecule it was given: the conversion mutates ``mol`` in
+    place and never rebinds it, so the result is never None.
+    """
     parsed_coords, stereo_dirs = [], []
     # Best-effort attempt to parse 2D coordinates from MOL block for direct conversion.
     # We suppress AttributeError/RuntimeError if the block is malformed or RDKit fails internally.
@@ -724,10 +732,10 @@ print(ob_mol.write("mol"))
                     f"Subprocess crashed or failed. Error: {result.stderr.strip()}"
                 )
             out_mol_block = result.stdout
-        except subprocess.TimeoutExpired:
-            raise RuntimeError("Open Babel make3D() timed out.")
+        except subprocess.TimeoutExpired as exc:
+            raise RuntimeError("Open Babel make3D() timed out.") from exc
         except Exception as e:
-            raise RuntimeError(f"Open Babel isolated execution failed: {e}")
+            raise RuntimeError(f"Open Babel isolated execution failed: {e}") from e
 
         rd_mol = Chem.MolFromMolBlock(out_mol_block, removeHs=False)
         if not rd_mol:
@@ -786,7 +794,7 @@ print(ob_mol.write("mol"))
         raise
     except (AttributeError, RuntimeError, ValueError, TypeError) as e:
         if mode == "obabel":
-            raise RuntimeError(f"Open Babel conversion failed: {e}")
+            raise RuntimeError(f"Open Babel conversion failed: {e}") from e
         _safe_status(f"Open Babel failed: {e}. Falling back...")
     return False
 
@@ -953,11 +961,15 @@ class CalculationWorker(QObject):
         _safe_finished = helpers["finished"]
         w_id = options.get("worker_id")
 
-        params = AllChem.ETKDGv2()
-        params.randomSeed = 42
-        params.useExpTorsionAnglePrefs = params.useBasicKnowledge = (
-            params.enforceChirality
-        ) = True
+        # rdkit's stub declares these EmbedParameters properties with bare
+        # `*args, **kwargs` and no annotations, so every assignment through them
+        # is reported as a type error. Unchained here so each one can carry the
+        # narrowest possible ignore.
+        params = rdDistGeom.ETKDGv2()
+        params.randomSeed = 42  # type: ignore[assignment]
+        params.useExpTorsionAnglePrefs = True  # type: ignore[assignment]
+        params.useBasicKnowledge = True  # type: ignore[assignment]
+        params.enforceChirality = True  # type: ignore[assignment]
 
         # Track existing/explicit stereo to restore after embedding
         orig_stereo = []
@@ -980,22 +992,18 @@ class CalculationWorker(QObject):
 
         conf_id = -1
         with suppress_log(RuntimeError, ValueError):
-            conf_id = AllChem.EmbedMolecule(mol, params)
+            conf_id = rdDistGeom.EmbedMolecule(mol, params)
 
         # Fallback embedding strategies
         if conf_id == -1:
             with suppress_log(AttributeError, RuntimeError, ValueError, TypeError):
-                bm = AllChem.GetMoleculeBoundsMatrix(mol)
-                for b_idx, s, satoms in orig_stereo:
+                bm = rdDistGeom.GetMoleculeBoundsMatrix(mol)
+                for _b_idx, s, satoms in orig_stereo:
                     if len(satoms) == 2:
                         t = 3.0 if s == Chem.BondStereo.STEREOZ else 5.0
                         bm[satoms[0]][satoms[1]] = bm[satoms[1]][satoms[0]] = t
                 DoTriangleSmoothing(bm)
-                conf_id = AllChem.EmbedMolecule(mol, bm, params)
-
-        if conf_id == -1:
-            with suppress_log(AttributeError, RuntimeError, ValueError, TypeError):
-                conf_id = AllChem.EmbedMolecule(mol, AllChem.ETKDGv2(randomSeed=42))
+                conf_id = rdDistGeom.EmbedMolecule(mol, bm, params)
 
         if conf_id == -1:
             return False

{moleditpy_linux-4.8.2 → moleditpy_linux-4.8.3}/src/moleditpy_linux/ui/compute_logic.py

@@ -13,13 +13,23 @@ DOI: 10.5281/zenodo.17268532
 from __future__ import annotations
 import logging
 from ..utils.suppress_log import suppress_log
-from typing import Any, Dict, List, Optional, Set, Tuple, Union, TYPE_CHECKING
+from typing import (
+    Any,
+    Dict,
+    List,
+    Optional,
+    Sequence,
+    Set,
+    Tuple,
+    Union,
+    TYPE_CHECKING,
+)
 
 from PyQt6.QtCore import QThread, QTimer, QPoint
 from PyQt6.QtGui import QAction, QColor
 from PyQt6.QtWidgets import QMenu, QMessageBox, QWidget
 from rdkit import Chem
-from rdkit.Chem import AllChem
+from rdkit.Chem import rdDepictor
 
 from . import OBABEL_AVAILABLE
 
@@ -387,6 +397,11 @@ class ComputeManager:
         """
         mol = self.host.view_3d_manager.current_mol
         label = entry.get("label", method)
+        if mol is None:
+            self.host.update_status_message(
+                f"Optimization with {label} needs a 3D structure."
+            )
+            return
         self.host.update_status_message(f"Optimizing 3D structure ({label})...")
         try:
             success = bool(entry["callback"](mol))
@@ -410,7 +425,7 @@ class ComputeManager:
         self._refresh_ui_state()
         self.host.edit_actions_manager.push_undo_state()
         if self.host.view_3d_manager.plotter:
-            self.host.view_3d_manager.plotter.reset_camera()
+            self.host.view_3d_manager.plotter.reset_camera()  # type: ignore[call-arg]
         self.host.update_status_message(f"Process completed ({label}).")
 
     def _prepare_rdkit_mol_for_conversion(self) -> Optional[Chem.Mol]:
@@ -439,7 +454,9 @@ class ComputeManager:
             return None
         return mol
 
-    def _handle_chemistry_problems(self, mol: Chem.Mol, problems: List[Any]) -> None:
+    def _handle_chemistry_problems(
+        self, mol: Chem.Mol, problems: Sequence[Any]
+    ) -> None:
         self.host.init_manager.scene.clear_all_problem_flags()
         msg = f"Error: {len(problems)} chemistry problem(s) found (e.g., hypervalency). Fix the 2D layout before converting."
         self.host.statusBar().showMessage(msg)  # type: ignore[union-attr]
@@ -474,7 +491,7 @@ class ComputeManager:
             # 3D generation; the 2D canvas keeps the user's own layout.
             planar = Chem.Mol(stereo_mol)
             planar.RemoveAllConformers()
-            AllChem.Compute2DCoords(planar)
+            rdDepictor.Compute2DCoords(planar)
             return str(Chem.MolToMolBlock(planar, includeStereo=True))
         except (RuntimeError, ValueError) as e:
             logging.warning("E/Z-consistent 2D layout failed: %s", e)
@@ -556,7 +573,7 @@ class ComputeManager:
         self._refresh_ui_state()
         self.host.edit_actions_manager.push_undo_state()
         if self.host.view_3d_manager.plotter:
-            self.host.view_3d_manager.plotter.reset_camera()
+            self.host.view_3d_manager.plotter.reset_camera()  # type: ignore[call-arg]
 
         # Record the successful optimization method from mol property or current setting
         try:

{moleditpy_linux-4.8.2 → moleditpy_linux-4.8.3}/src/moleditpy_linux/ui/constrained_optimization_dialog.py

@@ -28,7 +28,7 @@ from PyQt6.QtWidgets import (
     QTableWidgetItem,
     QVBoxLayout,
 )
-from rdkit.Chem import AllChem, rdMolTransforms
+from rdkit.Chem import rdForceFieldHelpers, rdMolTransforms
 
 from .dialog_3d_picking_mixin import Dialog3DPickingMixin
 
@@ -378,7 +378,7 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
     def remove_constraint(self) -> None:
         """Delete the selected constraint rows from the table."""
         selected_rows = sorted(
-            list(set(index.row() for index in self.constraint_table.selectedIndexes())),
+            {index.row() for index in self.constraint_table.selectedIndexes()},
             reverse=True,
         )
         if not selected_rows:
@@ -511,8 +511,10 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
                 "optimize_intermolecular_interaction_rdkit", True
             )
             if ff_name.startswith("MMFF"):
-                props = AllChem.MMFFGetMoleculeProperties(self.mol, mmffVariant=ff_name)
-                ff = AllChem.MMFFGetMoleculeForceField(
+                props = rdForceFieldHelpers.MMFFGetMoleculeProperties(
+                    self.mol, mmffVariant=ff_name
+                )
+                ff = rdForceFieldHelpers.MMFFGetMoleculeForceField(
                     self.mol,
                     props,
                     confId=0,
@@ -522,7 +524,7 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
                 add_angle_constraint = ff.MMFFAddAngleConstraint
                 add_torsion_constraint = ff.MMFFAddTorsionConstraint
             else:  # UFF
-                ff = AllChem.UFFGetMoleculeForceField(
+                ff = rdForceFieldHelpers.UFFGetMoleculeForceField(
                     self.mol, confId=0, ignoreInterfragInteractions=ignore_interfrag
                 )
                 add_dist_constraint = ff.UFFAddDistanceConstraint

{moleditpy_linux-4.8.2 → moleditpy_linux-4.8.3}/src/moleditpy_linux/ui/custom_interactor_style.py

@@ -923,7 +923,10 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
             logging.debug("Suppressed non-critical error", exc_info=True)
 
     def _compute_delta_rotation_matrix(
-        self, renderer: Any, start_pos: tuple, current_pos: tuple
+        self,
+        renderer: Any,
+        start_pos: Tuple[float, float],
+        current_pos: Tuple[float, float],
     ) -> Optional[np.ndarray]:
         """Compute 3D rotation matrix from screen mouse displacement (dx, dy)."""
         try: