MoleditPy-linux 4.1.4__py3-none-any.whl → 4.2.1__py3-none-any.whl

moleditpy_linux/core/mol_geometry.py

@@ -517,6 +517,14 @@ def identify_valence_problems(
     list
         IDs of atoms with problematic valence.
     """
+    # Preferred: RDKit's own detection on an unsanitized mol. Unlike the
+    # heuristic table below, it knows every element and accounts for formal
+    # charges and radical electrons (e.g. hypervalent N+, S, B, radicals).
+    rdkit_ids = _identify_problems_rdkit(atoms_data, bonds_data)
+    if rdkit_ids is not None:
+        return rdkit_ids
+
+    # Fallback heuristic when RDKit cannot even construct the atoms
     problem_atom_ids = []
 
     # Pre-calculate bond orders per atom
@@ -537,6 +545,52 @@ def identify_valence_problems(
     return problem_atom_ids
 
 
+def _identify_problems_rdkit(
+    atoms_data: Dict[int, Any], bonds_data: Dict[Tuple[int, int], Any]
+) -> Optional[List[int]]:
+    """Find problem atoms via Chem.DetectChemistryProblems (no sanitization).
+
+    Returns None when the molecule cannot be constructed at all (unknown
+    symbols etc.), signalling the caller to use the heuristic fallback.
+    """
+    try:
+        from rdkit import Chem as _Chem
+
+        mol = _Chem.RWMol()
+        id_to_idx = {}
+        for atom_id, data in atoms_data.items():
+            atom = _Chem.Atom(data["symbol"])
+            atom.SetFormalCharge(data.get("charge", 0))
+            atom.SetNumRadicalElectrons(data.get("radical", 0))
+            atom.SetNoImplicit(False)
+            id_to_idx[atom_id] = mol.AddAtom(atom)
+
+        bond_type_map = {
+            1.0: _Chem.BondType.SINGLE,
+            1.5: _Chem.BondType.AROMATIC,
+            2.0: _Chem.BondType.DOUBLE,
+            3.0: _Chem.BondType.TRIPLE,
+        }
+        for (id1, id2), bond in bonds_data.items():
+            if id1 not in id_to_idx or id2 not in id_to_idx:
+                continue
+            order = bond_type_map.get(
+                float(bond.get("order", 1)), _Chem.BondType.SINGLE
+            )
+            mol.AddBond(id_to_idx[id1], id_to_idx[id2], order)
+
+        idx_to_id = {v: k for k, v in id_to_idx.items()}
+        problem_ids = set()
+        for prob in _Chem.DetectChemistryProblems(mol.GetMol()):
+            if hasattr(prob, "GetAtomIdx"):
+                problem_ids.add(idx_to_id[prob.GetAtomIdx()])
+            elif hasattr(prob, "GetAtomIndices"):
+                problem_ids.update(idx_to_id[i] for i in prob.GetAtomIndices())
+        return sorted(problem_ids)
+    except (RuntimeError, ValueError, TypeError, KeyError):
+        return None
+
+
 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
@@ -618,10 +672,13 @@ def resolve_2d_overlaps(
     parent = {aid: aid for aid in atom_ids}
 
     def find_set(aid: int) -> int:
-        if parent[aid] == aid:
-            return aid
-        parent[aid] = find_set(parent[aid])
-        return parent[aid]
+        # Iterative path compression avoids recursion limits
+        root = aid
+        while parent[root] != root:
+            root = parent[root]
+        while parent[aid] != root:
+            parent[aid], aid = root, parent[aid]
+        return root
 
     def unite_sets(aid1: int, aid2: int) -> None:
         root1 = find_set(aid1)

moleditpy_linux/core/molecular_data.py

@@ -101,9 +101,14 @@ class MolecularData:
         if (id1, id2) in self.bonds:
             self.bonds[(id1, id2)].update(bond_data)
             return (id1, id2), "updated"
-        else:
-            self.bonds[(id1, id2)] = bond_data
-            return (id1, id2), "created"
+        if (id2, id1) in self.bonds:
+            # Re-key reversed entry (stereo direction changed) to avoid duplicates
+            existing = self.bonds.pop((id2, id1))
+            existing.update(bond_data)
+            self.bonds[(id1, id2)] = existing
+            return (id1, id2), "updated"
+        self.bonds[(id1, id2)] = bond_data
+        return (id1, id2), "created"
 
     def remove_atom(self, atom_id: int) -> None:
         """Remove an atom and all bonds involving it from the data model."""
@@ -171,7 +176,9 @@ class MolecularData:
             atom_id_to_idx_map[atom_id] = idx
 
         # save bonds & stereo info (label info is kept here)
-        bond_stereo_info = {}  # bond_idx -> {'type': int, 'atom_ids': (id1,id2), 'bond_data': bond_data}
+        bond_stereo_info: Dict[
+            int, Dict[str, Any]
+        ] = {}  # bond_idx -> {'type', 'atom_ids', 'bond_data'}
         for (id1, id2), bond_data in self.bonds.items():
             if id1 not in atom_id_to_idx_map or id2 not in atom_id_to_idx_map:
                 continue
@@ -279,8 +286,8 @@ class MolecularData:
                 begin_atom_idx = bond.GetBeginAtomIdx()
                 end_atom_idx = bond.GetEndAtomIdx()
 
-                bond_data: dict[str, Any] = info.get("bond_data") or {}  # type: ignore[assignment]
-                stereo_atoms_specified = bond_data.get("stereo_atoms")
+                label_bond_data = info.get("bond_data") or {}
+                stereo_atoms_specified = label_bond_data.get("stereo_atoms")
 
                 if stereo_atoms_specified:
                     try:
@@ -338,10 +345,10 @@ class MolecularData:
 
         if not self.atoms:
             return None
-        atom_map = {old_id: new_id for new_id, old_id in enumerate(self.atoms.keys())}
-        num_atoms, num_bonds = len(self.atoms), len(self.bonds)
-        mol_block = "\n  MoleditPy\n\n"
-        mol_block += f"{num_atoms:3d}{num_bonds:3d}  0  0  0  0  0  0  0  0999 V2000\n"
+
+        # Counts line and bond indices must only reflect atoms actually written
+        atom_map: Dict[int, int] = {}
+        atom_lines: List[str] = []
         for old_id, atom in self.atoms.items():
             # Convert scene pixel coordinates to angstroms when emitting MOL block
             pos = atom.get("pos")
@@ -373,10 +380,19 @@ class MolecularData:
             elif charge == -3:
                 chg_code = 7
 
-            mol_block += f"{x:10.4f}{y:10.4f}{z:10.4f} {symbol:<3} 0  0  0{chg_code:3d}  0  0  0  0  0  0  0\n"
+            atom_map[old_id] = len(atom_lines)
+            atom_lines.append(
+                f"{x:10.4f}{y:10.4f}{z:10.4f} {symbol:<3} 0  0  0{chg_code:3d}  0  0  0  0  0  0  0\n"
+            )
 
+        bond_lines = []
         for (id1, id2), bond in self.bonds.items():
-            idx1, idx2, order = atom_map[id1] + 1, atom_map[id2] + 1, bond["order"]
+            if id1 not in atom_map or id2 not in atom_map:
+                continue
+            idx1, idx2 = atom_map[id1] + 1, atom_map[id2] + 1
+            # Bond order may be a float (1.5 = aromatic); V2000 uses code 4.
+            order_val = float(bond["order"])
+            order = 4 if order_val == 1.5 else int(order_val)
             stereo_code = 0
             bond_stereo = bond.get("stereo", 0)
             if bond_stereo == 1:
@@ -384,8 +400,14 @@ class MolecularData:
             elif bond_stereo == 2:
                 stereo_code = 6
 
-            mol_block += f"{idx1:3d}{idx2:3d}{order:3d}{stereo_code:3d}  0  0  0\n"
+            bond_lines.append(
+                f"{idx1:3d}{idx2:3d}{order:3d}{stereo_code:3d}  0  0  0\n"
+            )
 
+        mol_block = "\n  MoleditPy\n\n"
+        mol_block += f"{len(atom_lines):3d}{len(bond_lines):3d}  0  0  0  0  0  0  0  0999 V2000\n"
+        mol_block += "".join(atom_lines)
+        mol_block += "".join(bond_lines)
         mol_block += "M  END\n"
         return mol_block
 

moleditpy_linux/main.py

@@ -17,7 +17,7 @@ import logging.handlers
 import os
 import sys
 import argparse
-from typing import Any
+from typing import Any, Optional
 
 from .utils.constants import VERSION
 
@@ -39,8 +39,9 @@ _QT_LOG_LEVEL = {
 _DOWNGRADED_QT_PATTERNS = ("Retrying to obtain clipboard",)
 
 
-def _qt_message_handler(mode: QtMsgType, _context: Any, message: str) -> None:
+def _qt_message_handler(mode: QtMsgType, _context: Any, message: Optional[str]) -> None:
     """Route Qt log messages to Python logging, downgrading known noisy warnings."""
+    message = message or ""
     for pattern in _DOWNGRADED_QT_PATTERNS:
         if pattern in message:
             logging.debug("Qt: %s", message)
@@ -109,7 +110,9 @@ def main() -> None:
     setup_logging()
 
     if sys.platform == "win32":
-        myappid = "hyoko.moleditpy_linux.1.0"
+        # Taskbar grouping ID follows the major version
+        major = VERSION.split(".")[0] if VERSION and VERSION != "Unknown" else "0"
+        myappid = f"hyoko.moleditpy_linux.{major}"
         ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID(myappid)
 
     parser = argparse.ArgumentParser(
@@ -201,6 +204,6 @@ def main() -> None:
         except (
             Exception
         ):  # [COSMETIC] Icon refresh is best-effort; Qt timing errors are non-fatal.
-            pass
+            logging.debug("Suppressed non-critical error", exc_info=True)
 
     sys.exit(app.exec())

moleditpy_linux/plugins/plugin_interface.py

@@ -133,7 +133,7 @@ class PluginContext:
 
     def get_selected_atom_indices(self) -> List[int]:
         """
-        Returns a list of RDKit atom indices currently selected in the 2D or 3D view.
+        Returns a list of RDKit atom indices currently selected in the 2D view.
         Note: RDKit indices are returned, which map to the current_mol.
         """
         return self._manager.get_selected_atom_indices()  # type: ignore[no-any-return]
@@ -397,7 +397,7 @@ class PluginContext:
                 if fn:
                     fn()
             except Exception:
-                pass
+                logging.debug("mark_project_modified failed", exc_info=True)
 
     def refresh_ui(self) -> None:
         """Refresh all UI state after modifying the molecule.

moleditpy_linux/plugins/plugin_manager.py

@@ -151,21 +151,24 @@ class PluginManager:
                     # Smart Extraction: Check if ZIP has a single top-level folder
                     # Fix for paths with backslashes on Windows if zip was created on Windows
                     roots = set()
+                    root_is_dir = False
                     for name in zf.namelist():
                         # Normalize path separators to forward slash for consistent check
                         name = name.replace("\\", "/")
                         parts = name.split("/")
                         if parts[0]:
                             roots.add(parts[0])
+                            # Sub-entries prove the root is a folder
+                            if len(parts) > 1:
+                                root_is_dir = True
 
-                    is_nested = len(roots) == 1
+                    is_nested = len(roots) == 1 and root_is_dir
 
                     if is_nested:
                         # Case A: ZIP contains a single folder (e.g. MyPlugin/init.py)
                         top_folder = list(roots)[0]
 
-                        # Guard: If the single item is __init__.py, we MUST create a wrapper folder
-                        # otherwise we pollute the plugin_dir root.
+                        # A root named __init__.py always needs a wrapper folder
                         if top_folder == "__init__.py":
                             is_nested = False
 
@@ -249,8 +252,10 @@ class PluginManager:
             return []
 
         for root, dirs, files in os.walk(self.plugin_dir):
-            # Exclude hidden directories
-            dirs[:] = [d for d in dirs if not d.startswith("__") and d != "__pycache__"]
+            # Exclude hidden and dunder directories (e.g. .git, __pycache__)
+            dirs[:] = [
+                d for d in dirs if not d.startswith("__") and not d.startswith(".")
+            ]
 
             # [Check] Is current dir a package (plugin body)?
             if "__init__.py" in files:
@@ -333,7 +338,7 @@ class PluginManager:
                 sys.modules[spec.name] = module
 
                 # Inject category info
-                module.PLUGIN_CATEGORY = category
+                module.PLUGIN_CATEGORY = category  # type: ignore[attr-defined]
 
                 spec.loader.exec_module(module)
 
@@ -480,12 +485,18 @@ class PluginManager:
         self, plugin_name: str, method_name: str, callback: Callable
     ) -> None:
         """Register a named 3D optimization method provided by a plugin."""
-        # Key by upper-case method name for consistency
-        self.optimization_methods[method_name.upper()] = {
+        method_key = method_name.upper()
+        self.optimization_methods[method_key] = {
             "plugin": plugin_name,
             "callback": callback,
             "label": method_name,
         }
+        if hasattr(self.main_window, "init_manager") and hasattr(
+            self.main_window.init_manager, "add_optimization_method"
+        ):
+            self.main_window.init_manager.add_optimization_method(
+                method_name, method_key
+            )
 
     def register_file_opener(
         self, plugin_name: str, extension: str, callback: Callable, priority: int = 0
@@ -608,10 +619,6 @@ class PluginManager:
                                     selected_indices.append(i)
                             except (RuntimeError, ValueError, TypeError):
                                 continue
-        except (
-            ImportError
-        ):  # [OPTIONAL DEP] importlib.metadata unavailable (<3.8); silently skip.
-            pass
         except (RuntimeError, AttributeError) as e:
             logging.error(f"Error retrieving selected atom indices: {e}")
 
@@ -660,15 +667,15 @@ class PluginManager:
                     if isinstance(target, ast.Name):
                         # Helper to extract value
                         val = None
-                        if node.value:  # AnnAssign might presumably not have value? (though usually does for module globals)
-                            if isinstance(node.value, ast.Constant):  # Py3.8+
-                                val = node.value.value
-                            elif isinstance(node.value, ast.Tuple):
+                        if node.value:  # type: ignore[attr-defined]  # AnnAssign might presumably not have value? (though usually does for module globals)
+                            if isinstance(node.value, ast.Constant):  # type: ignore[attr-defined]  # Py3.8+
+                                val = node.value.value  # type: ignore[attr-defined]
+                            elif isinstance(node.value, ast.Tuple):  # type: ignore[attr-defined]
                                 # Handle version tuples e.g. (1, 0, 0)
                                 try:
                                     # Extract simple constants from tuple
                                     elts = []
-                                    for elt in node.value.elts:
+                                    for elt in node.value.elts:  # type: ignore[attr-defined]
                                         if isinstance(elt, ast.Constant):
                                             elts.append(elt.value)
                                     val = ".".join(map(str, elts))
@@ -678,7 +685,9 @@ class PluginManager:
                                     ValueError,
                                     TypeError,
                                 ):  # [AST PARSE] Complex/unexpected AST node shapes during metadata extraction; skip gracefully.
-                                    pass
+                                    logging.debug(
+                                        "Suppressed non-critical error", exc_info=True
+                                    )
 
                         if val is not None:
                             if target.id == "PLUGIN_NAME":
@@ -712,7 +721,7 @@ class PluginManager:
                     elif hasattr(ast, "Str") and isinstance(
                         node.value, getattr(ast, "Str", type(None))
                     ):
-                        val = node.value.s
+                        val = node.value.s  # type: ignore[attr-defined]
 
                     if val and not info["description"]:
                         info["description"] = val.strip().split("\n")[0]

moleditpy_linux/plugins/plugin_manager_window.py

@@ -37,8 +37,8 @@ class PluginManagerWindow(QDialog):
 
     def __init__(self, plugin_manager: Any, parent: Optional[QWidget] = None) -> None:
         super().__init__(parent)
-        self.btn_remove = None
-        self.table = None
+        self.btn_remove: Any = None
+        self.table: Any = None
         self.plugin_manager = plugin_manager
         self.setWindowTitle("Plugin Manager")
         self.resize(800, 500)
@@ -241,7 +241,7 @@ class PluginManagerWindow(QDialog):
         """Accept drag events carrying file URLs."""
         if event is None:
             return
-        if event.mimeData().hasUrls():
+        if event.mimeData().hasUrls():  # type: ignore[union-attr]
             event.accept()
         else:
             event.ignore()
@@ -252,7 +252,7 @@ class PluginManagerWindow(QDialog):
             return
         files_installed = []
         errors = []
-        for url in event.mimeData().urls():
+        for url in event.mimeData().urls():  # type: ignore[union-attr]
             file_path = url.toLocalFile()
 
             is_valid = False

moleditpy_linux/ui/about_dialog.py

@@ -34,7 +34,7 @@ class AboutDialog(QDialog):
 
     def __init__(self, main_window: Any, parent: Optional[QWidget] = None) -> None:
         super().__init__(parent)
-        self.image_label = None
+        self.image_label: Any = None
         self.main_window = main_window
         self.setWindowTitle("About MoleditPy")
         self.setFixedSize(250, 300)

moleditpy_linux/ui/align_plane_dialog.py

@@ -11,7 +11,7 @@ DOI: 10.5281/zenodo.17268532
 """
 
 import logging
-from typing import TYPE_CHECKING, Literal, Optional, Sequence
+from typing import TYPE_CHECKING, Any, Literal, Optional, Sequence
 
 import numpy as np
 
@@ -66,9 +66,9 @@ class AlignPlaneDialog(BasePickingDialog):
         return self._selected_atoms
 
     @selected_atoms.setter
-    def selected_atoms(self, val: object) -> None:
+    def selected_atoms(self, val: Any) -> None:
         """Replace the selection with a new SelectionList built from val."""
-        self._selected_atoms = SelectionList(val)  # type: ignore[arg-type]
+        self._selected_atoms = SelectionList(val)
 
     def init_ui(self) -> None:
         """Build and lay out all widgets for the plane-alignment dialog."""

moleditpy_linux/ui/alignment_dialog.py

@@ -11,7 +11,7 @@ DOI: 10.5281/zenodo.17268532
 """
 
 import logging
-from typing import TYPE_CHECKING, Literal, Optional, Sequence
+from typing import TYPE_CHECKING, Any, Literal, Optional, Sequence
 
 import numpy as np
 
@@ -74,9 +74,9 @@ class AlignmentDialog(Dialog3DPickingMixin, QDialog):
         return self._selected_atoms
 
     @selected_atoms.setter
-    def selected_atoms(self, val: object) -> None:
+    def selected_atoms(self, val: Any) -> None:
         """Replace the selection with a new SelectionList built from val."""
-        self._selected_atoms = SelectionList(val)  # type: ignore[arg-type]
+        self._selected_atoms = SelectionList(val)
 
     def init_ui(self) -> None:
         """Build and lay out all widgets for the alignment dialog."""

moleditpy_linux/ui/analysis_window.py

@@ -235,8 +235,8 @@ class AnalysisWindow(QDialog):
     def copy_to_clipboard(self, text: str) -> None:
         """Copy text to the system clipboard and show a status bar message."""
         clipboard = QApplication.clipboard()
-        clipboard.setText(text)
+        clipboard.setText(text)  # type: ignore[union-attr]
         if self.parent() and hasattr(self.parent(), "statusBar"):
-            self.parent().statusBar().showMessage(
+            self.parent().statusBar().showMessage(  # type: ignore[union-attr]
                 f"Copied '{text}' to clipboard.", 2000
             )

moleditpy_linux/ui/angle_dialog.py

@@ -11,8 +11,9 @@ DOI: 10.5281/zenodo.17268532
 """
 
 from __future__ import annotations
+import logging
 
-from typing import TYPE_CHECKING, Optional, Sequence
+from typing import Any, TYPE_CHECKING, Optional, Sequence
 
 from PyQt6.QtCore import Qt
 from PyQt6.QtWidgets import (
@@ -50,18 +51,18 @@ class AngleDialog(GeometryBaseDialog):
         parent: Optional[QWidget] = None,
     ) -> None:
         super().__init__(mol, main_window, parent)
-        self._baseline_positions = None
+        self._baseline_positions: Any = None
         self._snapshot_positions = None
-        self.angle_input = None
-        self.angle_label = None
-        self.angle_slider = None
-        self.apply_button = None
-        self.both_groups_radio = None
-        self.clear_button = None
+        self.angle_input: Any = None
+        self.angle_label: Any = None
+        self.angle_slider: Any = None
+        self.apply_button: Any = None
+        self.both_groups_radio: Any = None
+        self.clear_button: Any = None
         self.picker_connection = None
-        self.rotate_atom_radio = None
-        self.rotate_group_radio = None
-        self.selection_label = None
+        self.rotate_atom_radio: Any = None
+        self.rotate_group_radio: Any = None
+        self.selection_label: Any = None
         self.atom1_idx: Optional[int] = None
         self.atom2_idx: Optional[int] = None  # vertex atom
         self.atom3_idx: Optional[int] = None
@@ -249,7 +250,7 @@ class AngleDialog(GeometryBaseDialog):
                 self.angle_slider.blockSignals(False)
             except (AttributeError, RuntimeError, ValueError, TypeError):
                 # Safe defensive fallback catching AttributeError, RuntimeError, ValueError, TypeError
-                pass
+                logging.debug("Suppressed non-critical error", exc_info=True)
         elif self.atom2_idx is None:
             symbol1 = self.mol.GetAtomWithIdx(self.atom1_idx).GetSymbol()
             self.selection_label.setText(
@@ -271,7 +272,7 @@ class AngleDialog(GeometryBaseDialog):
                 self.angle_slider.blockSignals(False)
             except (AttributeError, RuntimeError, ValueError, TypeError):
                 # Safe defensive fallback catching AttributeError, RuntimeError, ValueError, TypeError
-                pass
+                logging.debug("Suppressed non-critical error", exc_info=True)
         elif self.atom3_idx is None:
             symbol1 = self.mol.GetAtomWithIdx(self.atom1_idx).GetSymbol()
             symbol2 = self.mol.GetAtomWithIdx(self.atom2_idx).GetSymbol()
@@ -295,7 +296,7 @@ class AngleDialog(GeometryBaseDialog):
                 self.angle_slider.blockSignals(False)
             except (AttributeError, RuntimeError, ValueError, TypeError):
                 # Safe defensive fallback catching AttributeError, RuntimeError, ValueError, TypeError
-                pass
+                logging.debug("Suppressed non-critical error", exc_info=True)
         else:
             symbol1 = self.mol.GetAtomWithIdx(self.atom1_idx).GetSymbol()
             symbol2 = self.mol.GetAtomWithIdx(self.atom2_idx).GetSymbol()
@@ -333,7 +334,7 @@ class AngleDialog(GeometryBaseDialog):
                     self.angle_slider.setEnabled(True)
             except (AttributeError, RuntimeError, TypeError):
                 # Safe defensive fallback catching AttributeError, RuntimeError, TypeError
-                pass
+                logging.debug("Suppressed non-critical error", exc_info=True)
 
             # Add labels
             self.add_selection_label(self.atom1_idx, "1")

moleditpy_linux/ui/app_state.py

@@ -18,7 +18,7 @@ import binascii
 import copy
 import logging
 import os
-import contextlib
+from ..utils.suppress_log import suppress_log
 from typing import Any, Dict, Optional, Tuple
 
 
@@ -203,7 +203,10 @@ class StateManager:
                                         )
                                     except (RuntimeError, ValueError, TypeError):
                                         # Safe defensive fallback catching RuntimeError, ValueError, TypeError
-                                        pass
+                                        logging.debug(
+                                            "Suppressed non-critical error",
+                                            exc_info=True,
+                                        )
 
                     # Sync 2D atoms with 3D actors
                     if self.host.compute_manager:
@@ -237,7 +240,7 @@ class StateManager:
         else:
             self.host.clear_3d_view()
             self.host.init_manager.analysis_action.setEnabled(False)
-            self.host.init_manager.optimize_3d_button.setEnabled(False)
+            self.host.init_manager.optimize_3d_button.setEnabled(False)  # type: ignore[union-attr]
             # Disable 3D features
             self.host.ui_manager.enable_3d_features(False)
 
@@ -246,7 +249,7 @@ class StateManager:
 
         if loaded_data.get("is_3d_viewer_mode", False):
             self.host.ui_manager.enter_3d_viewer_mode()
-            self.host.statusBar().showMessage("Project loaded in 3D Viewer Mode.")
+            self.host.statusBar().showMessage("Project loaded in 3D Viewer Mode.")  # type: ignore[union-attr]
         else:
             self.host.ui_manager.restore_ui_for_editing()
             # Enable 3D edit features even in 2D editor mode if 3D molecule exists
@@ -489,7 +492,7 @@ class StateManager:
                     except (AttributeError, RuntimeError, TypeError, ValueError):
                         # Suppress InChI generation errors during project save if RDKit lacks InChI support
                         # Safe defensive fallback catching AttributeError, RuntimeError, TypeError, ValueError
-                        pass
+                        logging.debug("Suppressed non-critical error", exc_info=True)
 
                 except (AttributeError, RuntimeError, ValueError, TypeError) as e:
                     logging.warning("Could not generate molecular identifiers: %s", e)
@@ -543,7 +546,7 @@ class StateManager:
         is_3d_mode = json_data.get("is_3d_viewer_mode", False)
         # Restore last successful optimization method if present in file
         method = json_data.get("last_successful_optimization_method", None)
-        with contextlib.suppress(AttributeError, RuntimeError, TypeError):
+        with suppress_log(AttributeError, RuntimeError, TypeError):
             self.host.set_last_successful_optimization_method(method)
 
         # Plugin State Restoration (Phase 3)
@@ -627,7 +630,10 @@ class StateManager:
                                                 TypeError,
                                                 IndexError,
                                             ):  # [RDKIT GUARD] RDKit atom property assignment may fail on invalid ids; skip silently.
-                                                pass
+                                                logging.debug(
+                                                    "Suppressed non-critical error",
+                                                    exc_info=True,
+                                                )
                                 self.host.set_3d_atom_positions(positions_3d)
 
                             # Build mapping
@@ -637,7 +643,9 @@ class StateManager:
                                 self.host.view_3d_manager.update_atom_id_menu_state()
                             except (RuntimeError, TypeError, AttributeError):
                                 # Safe defensive fallback catching RuntimeError, TypeError, AttributeError
-                                pass
+                                logging.debug(
+                                    "Suppressed non-critical error", exc_info=True
+                                )
 
                         # Always show 3D if 3D molecule exists
                         self.host.view_3d_manager.draw_molecule_3d(
@@ -659,7 +667,9 @@ class StateManager:
                             self.host.ui_manager.enable_3d_features(True)
                         except (RuntimeError, TypeError, AttributeError):
                             # Safe defensive fallback catching RuntimeError, TypeError, AttributeError
-                            pass
+                            logging.debug(
+                                "Suppressed non-critical error", exc_info=True
+                            )
             except (RuntimeError, ValueError, TypeError, binascii.Error) as e:
                 logging.error(f"Could not restore 3D molecular data: {e}")
                 self.host.set_current_molecule(None)