MoleditPy 3.0.0a1__tar.gz → 3.0.0a2__tar.gz

{moleditpy-3.0.0a1 → moleditpy-3.0.0a2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.0.0a1
+Version: 3.0.0a2
 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
@@ -710,10 +710,10 @@ Dynamic: license-file
 [![Python Versions](https://img.shields.io/pypi/pyversions/MoleditPy.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)
-![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-72%25-green)
-![Overall Coverage](https://img.shields.io/badge/coverage-50%25-orange)
+![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-80%25-green)
+![Overall Coverage](https://img.shields.io/badge/coverage-63.83%25-green)
 ![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)
-![Pylint Score](https://img.shields.io/badge/pylint-8.64%2F10-brightgreen)
+![Pylint Score](https://img.shields.io/badge/pylint-8.93%2F10-brightgreen)
 [![PyPI Downloads](https://static.pepy.tech/personalized-badge/moleditpy?period=total&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=downloads)](https://pepy.tech/projects/moleditpy)
 
 [🇯🇵 日本語 (Japanese)](#japanese)

{moleditpy-3.0.0a1 → moleditpy-3.0.0a2}/README.md

@@ -6,10 +6,10 @@
 [![Python Versions](https://img.shields.io/pypi/pyversions/MoleditPy.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)
-![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-72%25-green)
-![Overall Coverage](https://img.shields.io/badge/coverage-50%25-orange)
+![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-80%25-green)
+![Overall Coverage](https://img.shields.io/badge/coverage-63.83%25-green)
 ![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)
-![Pylint Score](https://img.shields.io/badge/pylint-8.64%2F10-brightgreen)
+![Pylint Score](https://img.shields.io/badge/pylint-8.93%2F10-brightgreen)
 [![PyPI Downloads](https://static.pepy.tech/personalized-badge/moleditpy?period=total&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=downloads)](https://pepy.tech/projects/moleditpy)
 
 [🇯🇵 日本語 (Japanese)](#japanese)

{moleditpy-3.0.0a1 → moleditpy-3.0.0a2}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "3.0.0a1"
+version = "3.0.0a2"
 
 license = {file = "LICENSE"}
 

{moleditpy-3.0.0a1 → moleditpy-3.0.0a2}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.0.0a1
+Version: 3.0.0a2
 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
@@ -710,10 +710,10 @@ Dynamic: license-file
 [![Python Versions](https://img.shields.io/pypi/pyversions/MoleditPy.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)
-![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-72%25-green)
-![Overall Coverage](https://img.shields.io/badge/coverage-50%25-orange)
+![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-80%25-green)
+![Overall Coverage](https://img.shields.io/badge/coverage-63.83%25-green)
 ![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)
-![Pylint Score](https://img.shields.io/badge/pylint-8.64%2F10-brightgreen)
+![Pylint Score](https://img.shields.io/badge/pylint-8.93%2F10-brightgreen)
 [![PyPI Downloads](https://static.pepy.tech/personalized-badge/moleditpy?period=total&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=downloads)](https://pepy.tech/projects/moleditpy)
 
 [🇯🇵 日本語 (Japanese)](#japanese)

moleditpy-3.0.0a2/src/moleditpy/main.py

@@ -0,0 +1,60 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+MoleditPy — A Python-based molecular editing software
+
+Author: Hiromichi Yokoyama
+License: GPL-3.0 license
+Repo: https://github.com/HiroYokoyama/python_molecular_editor
+DOI: 10.5281/zenodo.17268532
+"""
+
+import ctypes
+import sys
+import argparse
+import logging
+
+from PyQt6.QtWidgets import QApplication
+
+try:
+    from .modules.main_window import MainWindow
+except ImportError:
+    from modules.main_window import MainWindow
+
+
+def setup_logging():
+    """Configure global logging to standard output."""
+    logging.basicConfig(
+        level=logging.INFO,
+        format="%(asctime)s [%(levelname)s] %(name)s: %(message)s",
+        stream=sys.stdout,
+    )
+
+
+def main():
+    # Setup logging as early as possible
+    setup_logging()
+
+    # --- Additional handling for Windows taskbar icon ---
+    if sys.platform == "win32":
+        myappid = "hyoko.moleditpy.1.0"  # Application-specific ID (arbitrary)
+        ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID(myappid)
+
+    parser = argparse.ArgumentParser(
+        prog="moleditpy", description="MoleditPy molecular editor"
+    )
+    parser.add_argument("file", nargs="?", default=None, help="File to open on startup")
+    parser.add_argument(
+        "--safe",
+        action="store_true",
+        default=False,
+        help="Start in safe mode: skip loading all plugins",
+    )
+    # parse_known_args so Qt's own argv flags (e.g. -platform) are passed through
+    args, remaining = parser.parse_known_args()
+
+    app = QApplication([sys.argv[0]] + remaining)
+    window = MainWindow(initial_file=args.file, safe_mode=args.safe)
+    window.show()
+    sys.exit(app.exec())

{moleditpy-3.0.0a1 → moleditpy-3.0.0a2}/src/moleditpy/modules/__init__.py

@@ -12,12 +12,14 @@ DOI: 10.5281/zenodo.17268532
 
 try:
     import importlib.util
+
     OBABEL_AVAILABLE = importlib.util.find_spec("openbabel") is not None
 except ImportError:
     OBABEL_AVAILABLE = False
 
 try:
     from PyQt6 import sip as _sip  # type: ignore
+
     _sip_isdeleted = getattr(_sip, "isdeleted", None)
 except ImportError:
     _sip = None

{moleditpy-3.0.0a1 → moleditpy-3.0.0a2}/src/moleditpy/modules/about_dialog.py

@@ -1,110 +1,115 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-"""
-MoleditPy — A Python-based molecular editing software
-
-Author: Hiromichi Yokoyama
-License: GPL-3.0 license
-Repo: https://github.com/HiroYokoyama/python_molecular_editor
-DOI: 10.5281/zenodo.17268532
-"""
-
-import os
-
-from PyQt6.QtCore import Qt
-from PyQt6.QtGui import QCursor, QPainter, QPen, QPixmap
-from PyQt6.QtWidgets import QDialog, QHBoxLayout, QLabel, QPushButton, QVBoxLayout
-
-try:
-    from .constants import VERSION
-except ImportError:
-    from modules.constants import VERSION
-
-
-class AboutDialog(QDialog):  
-    def __init__(self, main_window, parent=None):
-        super().__init__(parent)
-        self.main_window = main_window
-        self.setWindowTitle("About MoleditPy")
-        self.setFixedSize(250, 300)
-        self.init_ui()
-
-    def init_ui(self):
-        layout = QVBoxLayout(self)
-
-        # Create a clickable image label
-        self.image_label = QLabel()
-        self.image_label.setAlignment(Qt.AlignmentFlag.AlignCenter)
-
-        # Load the original icon image
-        icon_path = os.path.join(os.path.dirname(__file__), "..", "assets", "icon.png")
-        if os.path.exists(icon_path):
-            original_pixmap = QPixmap(icon_path)
-            # Scale to 2x size (160x160)
-            pixmap = original_pixmap.scaled(
-                160,
-                160,
-                Qt.AspectRatioMode.KeepAspectRatio,
-                Qt.TransformationMode.SmoothTransformation,
-            )
-        else:
-            # Fallback: create a simple placeholder if icon.png not found
-            pixmap = QPixmap(160, 160)
-            pixmap.fill(Qt.GlobalColor.lightGray)
-            painter = QPainter(pixmap)
-            painter.setPen(QPen(Qt.GlobalColor.black, 2))
-            painter.drawText(pixmap.rect(), Qt.AlignmentFlag.AlignCenter, "MoleditPy")
-            painter.end()
-
-        self.image_label.setPixmap(pixmap)
-        try:
-            self.image_label.setCursor(QCursor(Qt.CursorShape.ArrowCursor))
-        except (AttributeError, RuntimeError, ValueError, TypeError):  
-            pass  # Suppress cursor setting errors on about image
-
-        self.image_label.mousePressEvent = self.image_mouse_press_event
-
-        layout.addWidget(self.image_label)
-
-        # Add text information
-        info_text = f"MoleditPy Ver. {VERSION}\nAuthor: Hiromichi Yokoyama\nLicense: GPL-3.0 license"
-        info_label = QLabel(info_text)
-        info_label.setAlignment(Qt.AlignmentFlag.AlignCenter)
-        layout.addWidget(info_label)
-
-        # Add OK button
-        ok_button = QPushButton("OK")
-        ok_button.setFixedSize(80, 30)  # Fixed small size
-        ok_button.clicked.connect(self.accept)
-
-        # Center the button
-        button_layout = QHBoxLayout()
-        button_layout.addStretch()
-        button_layout.addWidget(ok_button)
-        button_layout.addStretch()
-        layout.addLayout(button_layout)
-
-    def image_clicked(self, event):
-        """Easter egg: Clear all and load bipyrimidine from SMILES"""
-        # Clear the current scene
-        self.main_window.clear_all()
-
-        bipyrimidine_smiles = "C1=CN=C(N=C1)C2=NC=CC=N2"
-        self.main_window.load_from_smiles(bipyrimidine_smiles)
-
-        # Close the dialog
-        self.accept()
-
-    def image_mouse_press_event(self, event):
-        """Handle mouse press on the image: trigger easter egg only for right-click."""
-        try:
-            if event.button() == Qt.MouseButton.RightButton:
-                self.image_clicked(event)
-            else:
-                event.ignore()
-        except (AttributeError, RuntimeError, ValueError, TypeError):
-            try:
-                event.ignore()
-            except (AttributeError, RuntimeError, ValueError, TypeError):  
-                pass  # Suppress nested event errors
+import logging
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+MoleditPy — A Python-based molecular editing software
+
+Author: Hiromichi Yokoyama
+License: GPL-3.0 license
+Repo: https://github.com/HiroYokoyama/python_molecular_editor
+DOI: 10.5281/zenodo.17268532
+"""
+
+import os
+
+from PyQt6.QtCore import Qt
+from PyQt6.QtGui import QCursor, QPainter, QPen, QPixmap
+from PyQt6.QtWidgets import QDialog, QHBoxLayout, QLabel, QPushButton, QVBoxLayout
+
+try:
+    from .constants import VERSION
+except ImportError:
+    from modules.constants import VERSION
+
+
+class AboutDialog(QDialog):
+    def __init__(self, main_window, parent=None):
+        super().__init__(parent)
+        self.main_window = main_window
+        self.setWindowTitle("About MoleditPy")
+        self.setFixedSize(250, 300)
+        self.init_ui()
+
+    def init_ui(self):
+        layout = QVBoxLayout(self)
+
+        # Create a clickable image label
+        self.image_label = QLabel()
+        self.image_label.setAlignment(Qt.AlignmentFlag.AlignCenter)
+
+        # Load the original icon image
+        icon_path = os.path.join(os.path.dirname(__file__), "..", "assets", "icon.png")
+        if os.path.exists(icon_path):
+            original_pixmap = QPixmap(icon_path)
+            # Scale to 2x size (160x160)
+            pixmap = original_pixmap.scaled(
+                160,
+                160,
+                Qt.AspectRatioMode.KeepAspectRatio,
+                Qt.TransformationMode.SmoothTransformation,
+            )
+        else:
+            # Fallback: create a simple placeholder if icon.png not found
+            pixmap = QPixmap(160, 160)
+            pixmap.fill(Qt.GlobalColor.lightGray)
+            painter = QPainter(pixmap)
+            painter.setPen(QPen(Qt.GlobalColor.black, 2))
+            painter.drawText(pixmap.rect(), Qt.AlignmentFlag.AlignCenter, "MoleditPy")
+            painter.end()
+
+        self.image_label.setPixmap(pixmap)
+        try:
+            self.image_label.setCursor(QCursor(Qt.CursorShape.ArrowCursor))
+        except (AttributeError, RuntimeError, ValueError, TypeError) as e:
+            logging.debug(
+                f"Suppressed exception: {e}"
+            )  # Suppress cursor setting errors on about image
+
+        self.image_label.mousePressEvent = self.image_mouse_press_event
+
+        layout.addWidget(self.image_label)
+
+        # Add text information
+        info_text = f"MoleditPy Ver. {VERSION}\nAuthor: Hiromichi Yokoyama\nLicense: GPL-3.0 license"
+        info_label = QLabel(info_text)
+        info_label.setAlignment(Qt.AlignmentFlag.AlignCenter)
+        layout.addWidget(info_label)
+
+        # Add OK button
+        ok_button = QPushButton("OK")
+        ok_button.setFixedSize(80, 30)  # Fixed small size
+        ok_button.clicked.connect(self.accept)
+
+        # Center the button
+        button_layout = QHBoxLayout()
+        button_layout.addStretch()
+        button_layout.addWidget(ok_button)
+        button_layout.addStretch()
+        layout.addLayout(button_layout)
+
+    def image_clicked(self, event):
+        """Easter egg: Clear all and load bipyrimidine from SMILES"""
+        # Clear the current scene
+        self.main_window.clear_all()
+
+        bipyrimidine_smiles = "C1=CN=C(N=C1)C2=NC=CC=N2"
+        self.main_window.load_from_smiles(bipyrimidine_smiles)
+
+        # Close the dialog
+        self.accept()
+
+    def image_mouse_press_event(self, event):
+        """Handle mouse press on the image: trigger easter egg only for right-click."""
+        try:
+            if event.button() == Qt.MouseButton.RightButton:
+                self.image_clicked(event)
+            else:
+                event.ignore()
+        except (AttributeError, RuntimeError, ValueError, TypeError):
+            try:
+                event.ignore()
+            except (AttributeError, RuntimeError, ValueError, TypeError) as e:
+                logging.debug(
+                    f"Suppressed exception: {e}"
+                )  # Suppress nested event errors

{moleditpy-3.0.0a1 → moleditpy-3.0.0a2}/src/moleditpy/modules/align_plane_dialog.py

@@ -20,6 +20,7 @@ from PyQt6.QtWidgets import (
     QPushButton,
     QVBoxLayout,
 )
+from rdkit import Geometry
 
 try:
     from .dialog_3d_picking_mixin import Dialog3DPickingMixin
@@ -27,7 +28,7 @@ except ImportError:
     from modules.dialog_3d_picking_mixin import Dialog3DPickingMixin
 
 
-class AlignPlaneDialog(Dialog3DPickingMixin, QDialog):  
+class AlignPlaneDialog(Dialog3DPickingMixin, QDialog):
     def __init__(self, mol, main_window, plane, preselected_atoms=None, parent=None):
         QDialog.__init__(self, parent)
         Dialog3DPickingMixin.__init__(self)
@@ -218,7 +219,9 @@ class AlignPlaneDialog(Dialog3DPickingMixin, QDialog):
             eigenvalues, eigenvectors = np.linalg.eigh(cov_matrix)
 
             # Normal vector of the plane corresponds to the smallest eigenvalue
-            normal_vector = eigenvectors[:, 0]  # Normal vector of the plane corresponds to the smallest eigenvalue
+            normal_vector = eigenvectors[
+                :, 0
+            ]  # Normal vector of the plane corresponds to the smallest eigenvalue
 
             # Define target plane normal vector
             if self.plane == "xy":
@@ -264,7 +267,12 @@ class AlignPlaneDialog(Dialog3DPickingMixin, QDialog):
                         centered_pos, rotation_axis, rotation_angle
                     )
                     new_pos = rotated_pos + centroid
-                    conf.SetAtomPosition(i, new_pos.tolist())
+                    conf.SetAtomPosition(
+                        i,
+                        Geometry.Point3D(
+                            float(new_pos[0]), float(new_pos[1]), float(new_pos[2])
+                        ),
+                    )
                     self.main_window.atom_positions_3d[i] = new_pos
 
             # Update 3D visualization

{moleditpy-3.0.0a1 → moleditpy-3.0.0a2}/src/moleditpy/modules/alignment_dialog.py

@@ -19,6 +19,7 @@ from PyQt6.QtWidgets import (
     QPushButton,
     QVBoxLayout,
 )
+from rdkit import Geometry
 
 try:
     from .dialog_3d_picking_mixin import Dialog3DPickingMixin
@@ -26,7 +27,7 @@ except ImportError:
     from modules.dialog_3d_picking_mixin import Dialog3DPickingMixin
 
 
-class AlignmentDialog(Dialog3DPickingMixin, QDialog):  
+class AlignmentDialog(Dialog3DPickingMixin, QDialog):
     def __init__(self, mol, main_window, axis, preselected_atoms=None, parent=None):
         QDialog.__init__(self, parent)
         Dialog3DPickingMixin.__init__(self)
@@ -221,7 +222,14 @@ class AlignmentDialog(Dialog3DPickingMixin, QDialog):
                         rotated_pos = rodrigues_rotation(
                             current_pos, rotation_axis, rotation_angle
                         )
-                        conf.SetAtomPosition(i, rotated_pos.tolist())
+                        conf.SetAtomPosition(
+                            i,
+                            Geometry.Point3D(
+                                float(rotated_pos[0]),
+                                float(rotated_pos[1]),
+                                float(rotated_pos[2]),
+                            ),
+                        )
 
             # Update 3D positions
             self.main_window.atom_positions_3d = np.array(