MoleditPy 4.10.2__tar.gz → 4.10.3__tar.gz

{moleditpy-4.10.2 → moleditpy-4.10.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 4.10.2
+Version: 4.10.3
 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
@@ -705,9 +705,10 @@ Dynamic: license-file
 # MoleditPy — A Python Molecular Editor
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17268532.svg)](https://doi.org/10.5281/zenodo.17268532)
+![MoleditPy](https://img.shields.io/badge/MoleditPy-v4-3577F7)
 [![Powered by RDKit](https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC)](https://www.rdkit.org/)
 [![PyPI version](https://badge.fury.io/py/MoleditPy.svg)](https://badge.fury.io/py/MoleditPy)
-[![Python Versions](https://img.shields.io/pypi/pyversions/MoleditPy.svg)](https://pypi.org/project/MoleditPy/)
+[![Python Versions](https://img.shields.io/badge/python-3.9--3.14-blue.svg)](https://pypi.org/project/MoleditPy/)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Build Status](https://github.com/HiroYokoyama/python_molecular_editor/actions/workflows/tests.yml/badge.svg)](https://github.com/HiroYokoyama/python_molecular_editor/actions)
 [![codecov](https://codecov.io/gh/HiroYokoyama/python_molecular_editor/graph/badge.svg)](https://codecov.io/gh/HiroYokoyama/python_molecular_editor)
@@ -727,7 +728,10 @@ Dynamic: license-file
 **Repository**: [https://github.com/HiroYokoyama/python\_molecular\_editor](https://github.com/HiroYokoyama/python_molecular_editor)
 
 -----
-![](img/icon.png)
+<p align="center">
+  <img src="img/icon.png" width="500" alt="MoleditPy Icon">
+</p>
+
 ![](img/screenshot.png)
 
 

{moleditpy-4.10.2 → moleditpy-4.10.3}/README.md

@@ -1,9 +1,10 @@
 # MoleditPy — A Python Molecular Editor
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17268532.svg)](https://doi.org/10.5281/zenodo.17268532)
+![MoleditPy](https://img.shields.io/badge/MoleditPy-v4-3577F7)
 [![Powered by RDKit](https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC)](https://www.rdkit.org/)
 [![PyPI version](https://badge.fury.io/py/MoleditPy.svg)](https://badge.fury.io/py/MoleditPy)
-[![Python Versions](https://img.shields.io/pypi/pyversions/MoleditPy.svg)](https://pypi.org/project/MoleditPy/)
+[![Python Versions](https://img.shields.io/badge/python-3.9--3.14-blue.svg)](https://pypi.org/project/MoleditPy/)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Build Status](https://github.com/HiroYokoyama/python_molecular_editor/actions/workflows/tests.yml/badge.svg)](https://github.com/HiroYokoyama/python_molecular_editor/actions)
 [![codecov](https://codecov.io/gh/HiroYokoyama/python_molecular_editor/graph/badge.svg)](https://codecov.io/gh/HiroYokoyama/python_molecular_editor)
@@ -23,7 +24,10 @@
 **Repository**: [https://github.com/HiroYokoyama/python\_molecular\_editor](https://github.com/HiroYokoyama/python_molecular_editor)
 
 -----
-![](img/icon.png)
+<p align="center">
+  <img src="img/icon.png" width="500" alt="MoleditPy Icon">
+</p>
+
 ![](img/screenshot.png)
 
 

{moleditpy-4.10.2 → moleditpy-4.10.3}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "4.10.2"
+version = "4.10.3"
 
 license = {file = "LICENSE"}
 

{moleditpy-4.10.2 → moleditpy-4.10.3}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 4.10.2
+Version: 4.10.3
 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
@@ -705,9 +705,10 @@ Dynamic: license-file
 # MoleditPy — A Python Molecular Editor
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17268532.svg)](https://doi.org/10.5281/zenodo.17268532)
+![MoleditPy](https://img.shields.io/badge/MoleditPy-v4-3577F7)
 [![Powered by RDKit](https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC)](https://www.rdkit.org/)
 [![PyPI version](https://badge.fury.io/py/MoleditPy.svg)](https://badge.fury.io/py/MoleditPy)
-[![Python Versions](https://img.shields.io/pypi/pyversions/MoleditPy.svg)](https://pypi.org/project/MoleditPy/)
+[![Python Versions](https://img.shields.io/badge/python-3.9--3.14-blue.svg)](https://pypi.org/project/MoleditPy/)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Build Status](https://github.com/HiroYokoyama/python_molecular_editor/actions/workflows/tests.yml/badge.svg)](https://github.com/HiroYokoyama/python_molecular_editor/actions)
 [![codecov](https://codecov.io/gh/HiroYokoyama/python_molecular_editor/graph/badge.svg)](https://codecov.io/gh/HiroYokoyama/python_molecular_editor)
@@ -727,7 +728,10 @@ Dynamic: license-file
 **Repository**: [https://github.com/HiroYokoyama/python\_molecular\_editor](https://github.com/HiroYokoyama/python_molecular_editor)
 
 -----
-![](img/icon.png)
+<p align="center">
+  <img src="img/icon.png" width="500" alt="MoleditPy Icon">
+</p>
+
 ![](img/screenshot.png)
 
 

{moleditpy-4.10.2 → moleditpy-4.10.3}/src/MoleditPy.egg-info/SOURCES.txt

@@ -53,6 +53,7 @@ src/moleditpy/ui/main_window_init.py
 src/moleditpy/ui/mirror_dialog.py
 src/moleditpy/ui/molecular_scene_handler.py
 src/moleditpy/ui/molecule_scene.py
+src/moleditpy/ui/move_dialog_mixin.py
 src/moleditpy/ui/move_group_dialog.py
 src/moleditpy/ui/move_selected_atoms_dialog.py
 src/moleditpy/ui/periodic_table_dialog.py

{moleditpy-4.10.2 → moleditpy-4.10.3}/src/moleditpy/main.py

@@ -280,7 +280,9 @@ def main() -> None:
                 metadata_file = init_py
 
         info = (
-            pm.get_plugin_info_safe(metadata_file)
+            pm.get_plugin_info_safe(
+                metadata_file, fallback_name=os.path.basename(plugin_path)
+            )
             if metadata_file.endswith(".py")
             else {}
         )

{moleditpy-4.10.2 → moleditpy-4.10.3}/src/moleditpy/plugins/plugin_manager.py

@@ -348,10 +348,11 @@ class PluginManager:
         self, filepath: str, module_name: str, category: str
     ) -> None:
         """Add a disabled plugin without importing or initializing its code."""
-        info = self.get_plugin_info_safe(filepath)
+        # Same fallback as _load_single_plugin's getattr(..., module_name).
+        info = self.get_plugin_info_safe(filepath, fallback_name=module_name)
         self.plugins.append(
             {
-                "name": info.get("name", module_name),
+                "name": info["name"],
                 "version": info.get("version", "Unknown"),
                 "author": info.get("author", "Unknown"),
                 "description": info.get("description", ""),
@@ -800,10 +801,13 @@ class PluginManager:
             logging.debug("Suppressed non-critical error", exc_info=True)
         return False
 
-    def get_plugin_info_safe(self, file_path: str) -> Dict[str, str]:
-        """Extracts plugin metadata using AST parsing (safe, no execution)."""
+    def get_plugin_info_safe(
+        self, file_path: str, fallback_name: Optional[str] = None
+    ) -> Dict[str, str]:
+        """Extract plugin metadata by AST parsing; ``fallback_name`` stands in
+        for a missing PLUGIN_NAME, defaulting to the file's basename."""
         info = {
-            "name": os.path.basename(file_path),
+            "name": fallback_name or os.path.basename(file_path),
             "version": "Unknown",
             "author": "Unknown",
             "description": "",

{moleditpy-4.10.2 → moleditpy-4.10.3}/src/moleditpy/plugins/plugin_manager_window.py

@@ -115,7 +115,8 @@ class PluginManagerWindow(QDialog):
         btn_layout = QHBoxLayout()
 
         btn_reload = QPushButton("Reload Plugins")
-        btn_reload.clicked.connect(self.on_reload)
+        # Not connect(self.on_reload): clicked(bool) would land in *silent*.
+        btn_reload.clicked.connect(lambda: self.on_reload())
         btn_layout.addWidget(btn_reload)
 
         btn_folder = QPushButton("Open Plugin Folder")
@@ -144,8 +145,8 @@ class PluginManagerWindow(QDialog):
 
     def _create_checkbox_container(
         self, checked: bool, tooltip: str = "Enable or disable this plugin"
-    ) -> tuple[QWidget, QCheckBox]:
-        """Create a centered QCheckBox container widget without custom stylesheets."""
+    ) -> QWidget:
+        """Create a centered QCheckBox container; read it back via _status_checkbox."""
         container = QWidget()
         box_layout = QHBoxLayout(container)
         box_layout.setContentsMargins(0, 0, 0, 0)
@@ -154,7 +155,7 @@ class PluginManagerWindow(QDialog):
         checkbox.setChecked(checked)
         checkbox.setToolTip(tooltip)
         box_layout.addWidget(checkbox)
-        return container, checkbox
+        return container
 
     def refresh_plugin_list(self) -> None:
         """Repopulate the plugin table from the current plugin registry."""
@@ -165,13 +166,12 @@ class PluginManagerWindow(QDialog):
         for row, p in enumerate(plugins):
             # Column 0: Enabled Checkbox (Clean native check, centered)
             is_enabled = not p.get("disabled", False)
-            container, _ = self._create_checkbox_container(is_enabled)
-            self.table.setCellWidget(row, 0, container)
+            self.table.setCellWidget(
+                row, 0, self._create_checkbox_container(is_enabled)
+            )
 
-            # Store the plugin index in the item's UserRole for stable reference during filtering
-            enabled_item = QTableWidgetItem()
-            enabled_item.setData(Qt.ItemDataRole.UserRole, row)
-            self.table.setItem(row, 0, enabled_item)
+            # Empty item behind the widget so the column still selects the row.
+            self.table.setItem(row, 0, QTableWidgetItem())
 
             # Column 1: Status (colored text)
             status = str(p.get("status", "Unknown"))
@@ -254,6 +254,16 @@ class PluginManagerWindow(QDialog):
             )
             self.table.setRowHidden(row, not match)
 
+        self._drop_hidden_selection()
+
+    def _drop_hidden_selection(self) -> None:
+        """Clear the selection when the filter hides the row it points at."""
+        row = self.table.currentRow()
+        if row >= 0 and self.table.isRowHidden(row):
+            self.table.clearSelection()
+            self.table.setCurrentCell(-1, -1)
+            self.update_button_state()
+
     def _status_checkbox(self, row: int) -> Optional[QCheckBox]:
         """Return the visible status checkbox for a plugin table row."""
         container = self.table.cellWidget(row, 0)
@@ -265,22 +275,17 @@ class PluginManagerWindow(QDialog):
         return None
 
     def _save_checkbox_preferences(self) -> set[str]:
-        """Collect and persist checkbox choices."""
+        """Collect and persist checkbox choices, hidden rows included."""
         disabled_paths = set()
         for row in range(self.table.rowCount()):
-            item = self.table.item(row, 0)
-            plugin_idx = item.data(Qt.ItemDataRole.UserRole) if item else row
-            if plugin_idx is not None and 0 <= plugin_idx < len(
-                self.plugin_manager.plugins
-            ):
-                plugin = self.plugin_manager.plugins[plugin_idx]
-                status_checkbox = self._status_checkbox(row)
-                if status_checkbox is not None and not status_checkbox.isChecked():
-                    filepath = plugin.get("filepath")
-                    if filepath:
-                        disabled_paths.add(
-                            self.plugin_manager.plugin_path_key(filepath)
-                        )
+            plugin = self._plugin_for_row(row)
+            if plugin is None:
+                continue
+            status_checkbox = self._status_checkbox(row)
+            if status_checkbox is not None and not status_checkbox.isChecked():
+                filepath = plugin.get("filepath")
+                if filepath:
+                    disabled_paths.add(self.plugin_manager.plugin_path_key(filepath))
 
         self.plugin_manager.save_disabled_plugins(disabled_paths)
         return disabled_paths
@@ -299,9 +304,12 @@ class PluginManagerWindow(QDialog):
             self.plugin_manager.discover_plugins()
 
     def done(self, result: int) -> None:
-        """Apply plugin preferences for every way the dialog can close."""
-        self._apply_plugin_preferences()
+        """Apply plugin preferences for every way the dialog can close.
+
+        Close first: applying them re-runs every plugin's ``initialize()``.
+        """
         super().done(result)
+        self._apply_plugin_preferences()
 
     def update_button_state(self) -> None:
         """Enable or disable the Remove button based on table selection."""
@@ -324,17 +332,15 @@ class PluginManagerWindow(QDialog):
             self.refresh_plugin_list()
 
     def _plugin_for_row(self, row: int) -> Optional[dict[str, Any]]:
-        """Retrieve plugin dict for a table row, accounting for search filtering."""
-        if row < 0 or row >= self.table.rowCount():
+        """Retrieve the plugin dict a table row was built from.
+
+        Row index is the plugin index; filtering hides rows, never reorders.
+        """
+        if row < 0 or row >= min(
+            self.table.rowCount(), len(self.plugin_manager.plugins)
+        ):
             return None
-        item = self.table.item(row, 0)
-        idx = item.data(Qt.ItemDataRole.UserRole) if item else row
-        if idx is not None and 0 <= idx < len(self.plugin_manager.plugins):
-            plugin: dict[str, Any] = cast(
-                dict[str, Any], self.plugin_manager.plugins[idx]
-            )
-            return plugin
-        return None
+        return cast(dict[str, Any], self.plugin_manager.plugins[row])
 
     def on_remove_plugin(self) -> None:
         """Delete the selected plugin file or folder and reload."""
@@ -456,8 +462,14 @@ class PluginManagerWindow(QDialog):
                     # Try to parse __init__.py if it exists
                     init_path = os.path.join(file_path, "__init__.py")
                     if os.path.exists(init_path):
-                        info = self.plugin_manager.get_plugin_info_safe(init_path)
-                        info["description"] += f" (Package: {info['name']})"
+                        folder_note = info["description"]
+                        info = self.plugin_manager.get_plugin_info_safe(
+                            init_path, fallback_name=os.path.basename(file_path)
+                        )
+                        declared = info["description"]
+                        info["description"] = f"{folder_note} (Package: {info['name']})"
+                        if declared:
+                            info["description"] += f" - {declared}"
 
                 elif is_zip:
                     info["description"] = "ZIP Package Plugin"

{moleditpy-4.10.2 → moleditpy-4.10.3}/src/moleditpy/ui/compute_logic.py

@@ -66,12 +66,12 @@ class ComputeManager:
         self._active_calc_threads = []
 
     def _safe_disconnect(self, signal: Any) -> None:
-        """Safely disconnect a signal, silently ignoring RuntimeError."""
+        """Disconnect a signal, tolerating one that has nothing connected."""
         try:
             signal.disconnect()
-        except RuntimeError:
-            # Safe defensive fallback catching RuntimeError
-            logging.debug("Suppressed non-critical error", exc_info=True)
+        except (RuntimeError, TypeError):
+            # PyQt raises TypeError, not RuntimeError, when nothing is attached.
+            logging.debug("Nothing to disconnect from %s", signal, exc_info=True)
 
     def _remove_calculating_text(self) -> None:
         """Safely remove the 'Calculating...' text actor from the plotter."""
@@ -90,14 +90,17 @@ class ComputeManager:
         """Restore the Convert and Optimize buttons to their default state."""
         self._safe_disconnect(self.host.init_manager.convert_button.clicked)  # type: ignore[union-attr]
         self.host.init_manager.convert_button.setText("Convert 2D to 3D")  # type: ignore[union-attr]
-        self.host.init_manager.convert_button.clicked.connect(self.trigger_conversion)  # type: ignore[union-attr]
+        # Wrapped: clicked(bool) would otherwise arrive as conversion_mode.
+        self.host.init_manager.convert_button.clicked.connect(  # type: ignore[union-attr]
+            lambda: self.trigger_conversion()
+        )
         self.host.init_manager.convert_button.setEnabled(True)  # type: ignore[union-attr]
 
         if self.host.init_manager.optimize_3d_button:
             self._safe_disconnect(self.host.init_manager.optimize_3d_button.clicked)
             self.host.init_manager.optimize_3d_button.setText("Optimize 3D")
             self.host.init_manager.optimize_3d_button.clicked.connect(
-                self.optimize_3d_structure
+                lambda: self.optimize_3d_structure()
             )
             self.host.init_manager.optimize_3d_button.setEnabled(True)
 

{moleditpy-4.10.2 → moleditpy-4.10.3}/src/moleditpy/ui/io_logic.py

@@ -16,6 +16,7 @@ import logging
 import os
 import json
 import pickle
+import unicodedata
 from ..utils.suppress_log import suppress_log
 from typing import Any, Callable, List, Optional, Tuple
 
@@ -33,6 +34,8 @@ from PyQt6.QtWidgets import (
     QWidget,
 )
 
+from io import BytesIO
+
 from rdkit import Chem
 from rdkit.Chem import (
     Descriptors,
@@ -143,6 +146,23 @@ class IOManager:
             raw = self._first_sdf_record(raw)
         return self.fix_mol_block(raw)
 
+    def _read_mol_or_sdf(self, file_path: str) -> Optional[Chem.Mol]:
+        """Read the molecule from a .mol or .sdf file, whatever its encoding.
+
+        The SDF goes through a stream, not a path, so both the encoding
+        fallbacks and the record's data fields survive.
+        """
+        if file_path.lower().endswith(".sdf"):
+            raw = "".join(self._read_text_lines_flexible(file_path))
+            stream = BytesIO(self.fix_mol_block(raw).encode("utf-8"))
+            supplier = Chem.ForwardSDMolSupplier(stream, removeHs=False)
+            mol = next(supplier, None)
+            if mol is not None:
+                return mol
+        return Chem.MolFromMolBlock(
+            self._load_mol_block_text(file_path), sanitize=True, removeHs=False
+        )
+
     @staticmethod
     def _read_text_lines_flexible(file_path: str) -> list[str]:
         """Read a text file's lines, tolerating non-UTF-8 encodings.
@@ -159,12 +179,29 @@ class IOManager:
         # some genuinely EUC-JP byte sequences and decodes them to the wrong
         # (mojibake) characters instead of raising, so trying cp932 first
         # would never let euc_jp text reach its correct decoding.
-        for encoding in ("utf-8-sig", "euc_jp", "cp932", "shift_jis"):
+        mojibake: Optional[List[str]] = None
+        cp932_gaiji: Optional[List[str]] = None
+        for encoding in ("utf-8-sig", "euc_jp", "cp932", "shift_jis", "cp1252"):
             try:
                 with open(file_path, "r", encoding=encoding) as f:
-                    return f.readlines()
+                    lines = f.readlines()
             except UnicodeDecodeError:
                 continue
+            # A wrong codec can land bytes in the private-use area. Keep looking,
+            # but preserve CP932's F0-lead gaiji range: CP1252 can otherwise
+            # decode bytes such as F0 40 cleanly while losing U+E000.
+            if any(unicodedata.category(ch) == "Co" for line in lines for ch in line):
+                if encoding == "cp932" and any(
+                    "\ue000" <= ch <= "\ue0bb" for line in lines for ch in line
+                ):
+                    cp932_gaiji = lines
+                mojibake = mojibake if mojibake is not None else lines
+                continue
+            if encoding == "cp1252" and cp932_gaiji is not None:
+                return cp932_gaiji
+            return lines
+        if mojibake is not None:
+            return mojibake
         with open(file_path, "r", encoding="utf-8", errors="replace") as f:
             return f.readlines()
 
@@ -839,13 +876,10 @@ class IOManager:
             return
 
         try:
-            fixed_block = self._load_mol_block_text(file_path)
-            # MolFromMolBlock can come back empty on a malformed file; the
-            # stub does not say so, hence the explicit declaration. The None
-            # check below covers that.
-            mol: Optional[Chem.Mol] = Chem.MolFromMolBlock(
-                fixed_block, sanitize=True, removeHs=False
-            )
+            # Both readers can come back empty on a malformed file; the stubs
+            # do not say so, hence the explicit declaration. The None check
+            # below covers that.
+            mol: Optional[Chem.Mol] = self._read_mol_or_sdf(file_path)
 
             if mol is None:
                 raise ValueError("Failed to read molecule from file.")
@@ -1047,8 +1081,7 @@ class IOManager:
             if not file_path:
                 return
         try:
-            fixed_block = self._load_mol_block_text(file_path)
-            mol = Chem.MolFromMolBlock(fixed_block, sanitize=True, removeHs=False)
+            mol = self._read_mol_or_sdf(file_path)
 
             if mol is None:
                 raise ValueError("Failed to load molecule.")

{moleditpy-4.10.2 → moleditpy-4.10.3}/src/moleditpy/ui/main_window_init.py

@@ -681,8 +681,9 @@ class MainInitManager:
         left_buttons_layout.addWidget(self.cleanup_button)
 
         self.convert_button = QPushButton("Convert 2D to 3D")
+        # Wrapped: clicked(bool) would otherwise arrive as conversion_mode.
         self.convert_button.clicked.connect(
-            self.host.compute_manager.trigger_conversion
+            lambda: self.host.compute_manager.trigger_conversion()
         )
         # Allow right-click to open a temporary conversion-mode menu
         try:
@@ -726,7 +727,7 @@ class MainInitManager:
             QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Fixed
         )
         self.optimize_3d_button.clicked.connect(
-            self.host.compute_manager.optimize_3d_structure
+            lambda: self.host.compute_manager.optimize_3d_structure()
         )
         self.optimize_3d_button.setEnabled(False)
         # Initialized via _enable_3d_features(False)
@@ -979,7 +980,7 @@ class MainInitManager:
             if key == "ball_and_stick":
                 action.setChecked(True)
             action.triggered.connect(
-                lambda checked=False, k=key: (self.host.view_3d_manager.set_3d_style(k))
+                lambda checked=False, k=key: self.host.view_3d_manager.set_3d_style(k)
             )
             style_menu.addAction(action)
             style_group.addAction(action)
@@ -1392,9 +1393,11 @@ class MainInitManager:
         view_menu.addSeparator()
         reset_3d_view_action = QAction("Reset 3D View", self.host)
         reset_3d_view_action.triggered.connect(
-            lambda: self.host.view_3d_manager.plotter.reset_camera()
-            if self.host.view_3d_manager.plotter
-            else None
+            lambda: (
+                self.host.view_3d_manager.plotter.reset_camera()
+                if self.host.view_3d_manager.plotter
+                else None
+            )
         )
         reset_3d_view_action.setShortcut(QKeySequence("Ctrl+Shift+R"))
         view_menu.addAction(reset_3d_view_action)
@@ -1750,8 +1753,9 @@ class MainInitManager:
             if key.endswith("_OBABEL") and not OBABEL_AVAILABLE:
                 action.setEnabled(False)
             action.triggered.connect(
-                lambda checked,
-                m=key: self.host.compute_manager.set_optimization_method(m)
+                lambda checked, m=key: (
+                    self.host.compute_manager.set_optimization_method(m)
+                )
             )
             self.optimization_menu.addAction(action)
             self.opt_group.addAction(action)
@@ -1796,8 +1800,9 @@ class MainInitManager:
         action = QAction(label, self.host)
         action.setCheckable(True)
         action.triggered.connect(
-            lambda checked,
-            m=key_upper: self.host.compute_manager.set_optimization_method(m)
+            lambda checked, m=key_upper: (
+                self.host.compute_manager.set_optimization_method(m)
+            )
         )
 
         self.optimization_menu.insertAction(self.opt3d_separator, action)