MoleditPy 3.3.0__tar.gz → 3.4.0__tar.gz

{moleditpy-3.3.0 → moleditpy-3.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.3.0
+Version: 3.4.0
 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
@@ -713,8 +713,10 @@ Dynamic: license-file
 ![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage->80%25-green)
 ![Overall Coverage](https://img.shields.io/badge/coverage->75%25-green)
 ![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)
-![Pylint Score](https://img.shields.io/badge/pylint-9%2F10-brightgreen)
+![Pylint Score](https://img.shields.io/badge/pylint->9%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)
+[![PyPI Downloads](https://static.pepy.tech/personalized-badge/moleditpy?period=monthly&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=monthly+downloads)](https://pepy.tech/projects/moleditpy)
+[![Ask DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/HiroYokoyama/python_molecular_editor)
 
 [🇯🇵 日本語 (Japanese)](#japanese)
 
@@ -840,6 +842,14 @@ moleditpy
 
 This project is licensed under the **GNU General Public License v3.0 (GPL-v3)**. See the `LICENSE` file for details.
 
+## Citation
+
+If you use this software in your work, please cite it as follows:
+
+```
+Yokoyama, H. (2026). MoleditPy — A Python-based molecular editing software. Zenodo. https://doi.org/10.5281/zenodo.17268532
+```
+
 -----
 
 <div id="japanese"></div>
@@ -963,3 +973,11 @@ moleditpy
 ## ライセンス
 
 このプロジェクトは **GNU General Public License v3.0 (GPL-v3)** のもとで公開されています。詳細は `LICENSE` ファイルを参照してください。
+
+## 引用
+
+本ソフトウェアを研究で使用される場合は、以下の通り引用を明記してください。
+
+```
+Yokoyama, H. (2026). MoleditPy — A Python-based molecular editing software. Zenodo. https://doi.org/10.5281/zenodo.17268532
+```

{moleditpy-3.3.0 → moleditpy-3.4.0}/README.md

@@ -9,8 +9,10 @@
 ![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage->80%25-green)
 ![Overall Coverage](https://img.shields.io/badge/coverage->75%25-green)
 ![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)
-![Pylint Score](https://img.shields.io/badge/pylint-9%2F10-brightgreen)
+![Pylint Score](https://img.shields.io/badge/pylint->9%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)
+[![PyPI Downloads](https://static.pepy.tech/personalized-badge/moleditpy?period=monthly&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=monthly+downloads)](https://pepy.tech/projects/moleditpy)
+[![Ask DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/HiroYokoyama/python_molecular_editor)
 
 [🇯🇵 日本語 (Japanese)](#japanese)
 
@@ -136,6 +138,14 @@ moleditpy
 
 This project is licensed under the **GNU General Public License v3.0 (GPL-v3)**. See the `LICENSE` file for details.
 
+## Citation
+
+If you use this software in your work, please cite it as follows:
+
+```
+Yokoyama, H. (2026). MoleditPy — A Python-based molecular editing software. Zenodo. https://doi.org/10.5281/zenodo.17268532
+```
+
 -----
 
 <div id="japanese"></div>
@@ -259,3 +269,11 @@ moleditpy
 ## ライセンス
 
 このプロジェクトは **GNU General Public License v3.0 (GPL-v3)** のもとで公開されています。詳細は `LICENSE` ファイルを参照してください。
+
+## 引用
+
+本ソフトウェアを研究で使用される場合は、以下の通り引用を明記してください。
+
+```
+Yokoyama, H. (2026). MoleditPy — A Python-based molecular editing software. Zenodo. https://doi.org/10.5281/zenodo.17268532
+```

{moleditpy-3.3.0 → moleditpy-3.4.0}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "3.3.0"
+version = "3.4.0"
 
 license = {file = "LICENSE"}
 

{moleditpy-3.3.0 → moleditpy-3.4.0}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.3.0
+Version: 3.4.0
 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
@@ -713,8 +713,10 @@ Dynamic: license-file
 ![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage->80%25-green)
 ![Overall Coverage](https://img.shields.io/badge/coverage->75%25-green)
 ![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)
-![Pylint Score](https://img.shields.io/badge/pylint-9%2F10-brightgreen)
+![Pylint Score](https://img.shields.io/badge/pylint->9%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)
+[![PyPI Downloads](https://static.pepy.tech/personalized-badge/moleditpy?period=monthly&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=monthly+downloads)](https://pepy.tech/projects/moleditpy)
+[![Ask DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/HiroYokoyama/python_molecular_editor)
 
 [🇯🇵 日本語 (Japanese)](#japanese)
 
@@ -840,6 +842,14 @@ moleditpy
 
 This project is licensed under the **GNU General Public License v3.0 (GPL-v3)**. See the `LICENSE` file for details.
 
+## Citation
+
+If you use this software in your work, please cite it as follows:
+
+```
+Yokoyama, H. (2026). MoleditPy — A Python-based molecular editing software. Zenodo. https://doi.org/10.5281/zenodo.17268532
+```
+
 -----
 
 <div id="japanese"></div>
@@ -963,3 +973,11 @@ moleditpy
 ## ライセンス
 
 このプロジェクトは **GNU General Public License v3.0 (GPL-v3)** のもとで公開されています。詳細は `LICENSE` ファイルを参照してください。
+
+## 引用
+
+本ソフトウェアを研究で使用される場合は、以下の通り引用を明記してください。
+
+```
+Yokoyama, H. (2026). MoleditPy — A Python-based molecular editing software. Zenodo. https://doi.org/10.5281/zenodo.17268532
+```

{moleditpy-3.3.0 → moleditpy-3.4.0}/src/moleditpy/__init__.py

@@ -18,3 +18,5 @@ try:
     OBABEL_AVAILABLE = importlib.util.find_spec("openbabel") is not None
 except ImportError:
     OBABEL_AVAILABLE = False
+
+from .utils.constants import VERSION as __version__  # noqa: F401

{moleditpy-3.3.0 → moleditpy-3.4.0}/src/moleditpy/main.py

@@ -68,7 +68,8 @@ def main() -> None:
         ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID(myappid)
 
     parser = argparse.ArgumentParser(
-        prog="moleditpy", description="MoleditPy molecular editor"
+        prog="moleditpy",
+        description="MoleditPy — A Python-based molecular editing software",
     )
     parser.add_argument("file", nargs="?", default=None, help="File to open on startup")
     _variant = " (Linux)" if "moleditpy_linux" in (__file__ or "") else ""

{moleditpy-3.3.0 → moleditpy-3.4.0}/src/moleditpy/ui/angle_dialog.py

@@ -189,8 +189,10 @@ class AngleDialog(GeometryBaseDialog):
                 self.atom2_idx = atom_idx
             elif self.atom3_idx is None:
                 self.atom3_idx = atom_idx
-                # Take a fresh snapshot immediately upon completing the triad selection
-                self._snapshot_positions = self.mol.GetConformer().GetPositions().copy()
+                # Capture the ABSOLUTE baseline for this selection session.
+                # This prevents 'direction change' drift during multiple slider drags.
+                self._baseline_positions = self.mol.GetConformer().GetPositions().copy()
+                self._snapshot_positions = self._baseline_positions.copy()
             else:
                 # Reset and start over
                 self.atom1_idx = atom_idx
@@ -205,6 +207,7 @@ class AngleDialog(GeometryBaseDialog):
         self.atom1_idx = None
         self.atom2_idx = None  # vertex atom
         self.atom3_idx = None
+        self._baseline_positions = None
         self._snapshot_positions = None
         self.clear_selection_labels()
         self.update_display()
@@ -212,7 +215,7 @@ class AngleDialog(GeometryBaseDialog):
     def show_atom_labels(self) -> None:
         """Display labels on the selected atoms."""
         selected_atoms = [self.atom1_idx, self.atom2_idx, self.atom3_idx]
-        labels = ["1st", "2nd (vertex)", "3rd"]
+        labels = ["1", "2", "3"]
         pairs = [
             (idx, labels[i]) for i, idx in enumerate(selected_atoms) if idx is not None
         ]
@@ -271,7 +274,7 @@ class AngleDialog(GeometryBaseDialog):
             self._snapshot_positions = None
             # Add labels
             self.add_selection_label(self.atom1_idx, "1")
-            self.add_selection_label(self.atom2_idx, "2(vertex)")
+            self.add_selection_label(self.atom2_idx, "2")
             # Clear angle input while selection is incomplete
             try:
                 self.angle_input.blockSignals(True)
@@ -295,23 +298,35 @@ class AngleDialog(GeometryBaseDialog):
             current_angle = self.calculate_angle()
             self.angle_label.setText(f"Current angle: {current_angle:.2f}°")
             self.apply_button.setEnabled(True)
-            # Update angle input box with current angle
+            # Update angle input box and slider
             try:
-                self.angle_input.blockSignals(True)
-                self.angle_input.setText(f"{current_angle:.2f}")
-                self.angle_input.blockSignals(False)
-                self.angle_slider.blockSignals(True)
-                slider_val = int(round(current_angle))
-                slider_val = max(-180, min(180, slider_val))
-                self.angle_slider.setValue(slider_val)
-                self.angle_slider.setEnabled(True)
-                self.angle_slider.blockSignals(False)
+                # Update input box and slider only if not dragging
+                if not self._slider_dragging:
+                    self.angle_input.blockSignals(True)
+                    self.angle_input.setText(f"{current_angle:.2f}")
+                    self.angle_input.blockSignals(False)
+
+                    # UPDATE SLIDER: Logic to prevent 'jumping' to positive value
+                    slider_val = int(round(current_angle))
+                    current_slider_val = self.angle_slider.value()
+
+                    # If the user is on the negative side of the slider, keep the sign
+                    if current_slider_val < 0:
+                        slider_val = -slider_val
+
+                    if current_slider_val != slider_val:
+                        self.angle_slider.blockSignals(True)
+                        self.angle_slider.setValue(slider_val)
+                        self.angle_slider.blockSignals(False)
+                    self.angle_slider.setEnabled(True)
+                else:
+                    self.angle_slider.setEnabled(True)
             except (AttributeError, RuntimeError, TypeError):
                 pass
 
             # Add labels
             self.add_selection_label(self.atom1_idx, "1")
-            self.add_selection_label(self.atom2_idx, "2(vertex)")
+            self.add_selection_label(self.atom2_idx, "2")
             self.add_selection_label(self.atom3_idx, "3")
 
     def calculate_angle(self) -> float:
@@ -366,10 +381,14 @@ class AngleDialog(GeometryBaseDialog):
         """Adjust the bond angle."""
         conf = self.mol.GetConformer()
 
-        # Use snapshot if available (slider dragging) to keep the rotation axis stable
-        snapshot = self._snapshot_positions
-        if snapshot is not None:
-            positions = snapshot.copy()
+        # Use baseline positions (fixed for dialog session) to keep the rotation axis stable.
+        if (
+            hasattr(self, "_baseline_positions")
+            and self._baseline_positions is not None
+        ):
+            positions = self._baseline_positions.copy()
+        elif self._snapshot_positions is not None:
+            positions = self._snapshot_positions.copy()
         else:
             positions = conf.GetPositions()
 
@@ -379,10 +398,16 @@ class AngleDialog(GeometryBaseDialog):
         idx_b: int = self.atom2_idx  # vertex
         idx_c: int = self.atom3_idx
 
+        # Calculate baseline angle from the POSITIONS we are working on (important for snapshot stability)
+        p_a, p_b, p_c = positions[idx_a], positions[idx_b], positions[idx_c]
+        from moleditpy.core.mol_geometry import calc_angle_deg
+
+        baseline_angle = calc_angle_deg(p_a, p_b, p_c)
+
         if self.both_groups_radio.isChecked():
             # Both arms rotate equally (half angle each)
-            current_angle = self.calculate_angle()
-            half_delta_deg = (new_angle_deg - current_angle) / 2.0
+            # Use baseline_angle from snapshot to avoid drift/jumps
+            half_delta_deg = (new_angle_deg - baseline_angle) / 2.0
 
             group1 = get_connected_group(self.mol, idx_a, exclude=idx_b)
             group3 = get_connected_group(self.mol, idx_c, exclude=idx_b)
@@ -393,7 +418,7 @@ class AngleDialog(GeometryBaseDialog):
                 idx_c,
                 idx_b,
                 idx_a,
-                current_angle + half_delta_deg,
+                baseline_angle + half_delta_deg,
                 group1,
             )
             # Arm 3 rotates to the FINAL angle (relative to the now-moved Arm 1)

{moleditpy-3.3.0 → moleditpy-3.4.0}/src/moleditpy/ui/app_state.py

@@ -17,7 +17,8 @@ import binascii
 import copy
 import logging
 import os
-from typing import Any, Dict, Optional, Tuple, TYPE_CHECKING
+from typing import Any, Dict, Optional, Tuple
+
 
 import numpy as np
 
@@ -45,9 +46,6 @@ try:
 except (AttributeError, RuntimeError, TypeError, ImportError):
     from moleditpy.core.molecular_data import MolecularData
 
-if TYPE_CHECKING:
-    from .main_window import MainWindow
-
 
 # --- Class Definition ---
 class StateManager:
@@ -634,7 +632,7 @@ class StateManager:
             method = json_data.get("last_successful_optimization_method", None)
             if hasattr(self.host, "compute_manager"):
                 self.host.compute_manager.last_successful_optimization_method = method
-            else:  # [REPORT ERROR MISSING ATTRIBUTE]
+            else:
                 logging.error(
                     "REPORT ERROR: Missing attribute 'compute_manager' on self.host"
                 )
@@ -808,7 +806,7 @@ class StateManager:
                                         "update_atom_id_menu_text",
                                     ):
                                         self.host.view_3d_manager.update_atom_id_menu_text()
-                                    else:  # [REPORT ERROR MISSING ATTRIBUTE]
+                                    else:
                                         logging.error(
                                             "REPORT ERROR: Missing attribute 'update_atom_id_menu_text' on object"
                                         )
@@ -817,13 +815,13 @@ class StateManager:
                                         "update_atom_id_menu_state",
                                     ):
                                         self.host.view_3d_manager.update_atom_id_menu_state()
-                                    else:  # [REPORT ERROR MISSING ATTRIBUTE]
+                                    else:
                                         logging.error(
                                             "REPORT ERROR: Missing attribute 'update_atom_id_menu_state' on object"
                                         )
                                 except (RuntimeError, TypeError, AttributeError):
                                     pass
-                            else:  # [REPORT ERROR MISSING ATTRIBUTE]
+                            else:
                                 logging.error(
                                     "REPORT ERROR: Missing attribute 'create_atom_id_mapping' on object"
                                 )
@@ -833,7 +831,7 @@ class StateManager:
                             self.host.view_3d_manager.draw_molecule_3d(
                                 self.host.view_3d_manager.current_mol
                             )
-                        else:  # [REPORT ERROR MISSING ATTRIBUTE]
+                        else:
                             logging.error(
                                 "REPORT ERROR: Missing attribute 'draw_molecule_3d' on object"
                             )

{moleditpy-3.3.0 → moleditpy-3.4.0}/src/moleditpy/ui/atom_item.py

@@ -11,7 +11,7 @@ DOI: 10.5281/zenodo.17268532
 """
 
 from __future__ import annotations
-import logging  # [REPORT ERROR MISSING ATTRIBUTE]
+import logging
 from typing import Any, List, Optional
 
 from PyQt6.QtCore import QPointF, QRectF, Qt
@@ -92,7 +92,7 @@ class AtomItem(QGraphicsItem):
             if hasattr(scene, "get_setting"):
                 font_size = scene.get_setting("atom_font_size_2d", 20)
                 font_family = scene.get_setting("atom_font_family_2d", FONT_FAMILY)
-            else:  # [REPORT ERROR MISSING ATTRIBUTE]
+            else:
                 logging.error(
                     f"REPORT ERROR: Missing attribute 'get_setting' on scene of type {type(scene)}"
                 )
@@ -119,7 +119,7 @@ class AtomItem(QGraphicsItem):
             if hasattr(scene, "get_setting"):
                 font_size = scene.get_setting("atom_font_size_2d", 20)
                 font_family = scene.get_setting("atom_font_family_2d", FONT_FAMILY)
-            else:  # [REPORT ERROR MISSING ATTRIBUTE]
+            else:
                 logging.error(
                     f"REPORT ERROR: Missing attribute 'get_setting' on scene of type {type(scene)}"
                 )
@@ -225,6 +225,77 @@ class AtomItem(QGraphicsItem):
         # 3. Add final margins for selection highlights, etc.
         return full_visual_rect.adjusted(-3, -3, 3, 3)
 
+    def get_bg_ellipse_path(self) -> QPainterPath:
+        path = QPainterPath()
+        if not self.is_visible:
+            return path
+
+        font_size = 20
+        font_family = FONT_FAMILY
+        scene = self.scene()
+        if scene is not None:
+            if hasattr(scene, "get_setting"):
+                font_size = scene.get_setting("atom_font_size_2d", 20)
+                font_family = scene.get_setting("atom_font_family_2d", FONT_FAMILY)
+
+        font = QFont(font_family, font_size, FONT_WEIGHT_BOLD)
+        fm = QFontMetricsF(font)
+
+        hydrogen_part = ""
+        if self.implicit_h_count > 0:
+            is_skeletal_carbon = (
+                self.symbol == "C"
+                and self.charge == 0
+                and self.radical == 0
+                and len(self.bonds) > 0
+            )
+            if not is_skeletal_carbon:
+                hydrogen_part = "H"
+                if self.implicit_h_count > 1:
+                    subscript_map = str.maketrans("0123456789", "₀₁₂₃₄₅₆₇₈₉")
+                    hydrogen_part += str(self.implicit_h_count).translate(subscript_map)
+
+        flip_text = False
+        if hydrogen_part and self.bonds:
+            my_pos_x = self.pos().x()
+            total_dx = 0.0
+            for b in self.bonds:
+                partner = b.atom2 if b.atom1 is self else b.atom1
+                try:
+                    if partner is None or sip_isdeleted_safe(partner):
+                        continue
+                    partner_pos = partner.pos()
+                    if partner_pos is None:
+                        continue
+                    total_dx += partner_pos.x() - my_pos_x
+                except (AttributeError, RuntimeError, TypeError, ValueError):
+                    # Suppress non-critical UI sync errors during atom position retrieval
+                    continue
+            if total_dx > 0:
+                flip_text = True
+
+        if flip_text:
+            display_text = hydrogen_part + self.symbol
+        else:
+            display_text = self.symbol + hydrogen_part
+
+        text_rect = fm.boundingRect(display_text)
+        text_rect.adjust(-2, -2, 2, 2)
+        if hydrogen_part:
+            symbol_rect = fm.boundingRect(self.symbol)
+            if flip_text:
+                offset_x = symbol_rect.width() // 2
+                text_rect.moveTo(offset_x - text_rect.width(), -text_rect.height() / 2)
+            else:
+                offset_x = -symbol_rect.width() // 2
+                text_rect.moveTo(offset_x, -text_rect.height() / 2)
+        else:
+            text_rect.moveCenter(QPointF(0, 0))
+
+        bg_rect = text_rect.adjusted(-5, -8, 5, 8)
+        path.addEllipse(bg_rect)
+        return path
+
     def shape(self) -> QPainterPath:
         """Define the shape of the atom item for collision detection."""
         scene = self.scene()
@@ -360,29 +431,6 @@ class AtomItem(QGraphicsItem):
                 offset_x = -symbol_rect.width() // 2
                 text_rect.moveTo(offset_x, -text_rect.height() // 2)
 
-            # 2. Handle background (fill with white or clear if transparent)
-            if self.scene():
-                bg_brush = self.scene().backgroundBrush()
-                bg_rect = text_rect.adjusted(-5, -8, 5, 8)
-
-                if bg_brush.style() == Qt.BrushStyle.NoBrush:
-                    # Use CompositionMode_Clear to erase overlapping bond lines
-                    painter.save()
-                    painter.setCompositionMode(
-                        QPainter.CompositionMode.CompositionMode_Clear
-                    )
-                    painter.setBrush(
-                        QColor(0, 0, 0, 255)
-                    )  # Color doesn't matter (alpha is key)
-                    painter.setPen(Qt.PenStyle.NoPen)
-                    painter.drawEllipse(bg_rect)
-                    painter.restore()
-                else:
-                    # Fill with background color if it exists
-                    painter.setBrush(bg_brush)
-                    painter.setPen(Qt.PenStyle.NoPen)
-                    painter.drawEllipse(bg_rect)
-
             # 3. Draw the atom symbol itself
             # Color is already determined above
             painter.setPen(QPen(color))
@@ -454,7 +502,9 @@ class AtomItem(QGraphicsItem):
                 for bond in self.bonds:
                     if bond.scene():
                         bond.update_position()
-
+        elif change == QGraphicsItem.GraphicsItemChange.ItemSceneHasChanged:
+            if self.scene() is not None:
+                self.update_style()
         return res
 
     def hoverEnterEvent(self, event: Any) -> None: