MoleditPy-linux 2.4.4__tar.gz → 2.4.6__tar.gz

{moleditpy_linux-2.4.4 → moleditpy_linux-2.4.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 2.4.4
+Version: 2.4.6
 Summary: A cross-platform, simple, and intuitive molecular structure editor built in Python. It allows 2D molecular drawing and 3D structure visualization. It supports exporting structure files for input to DFT calculation software.
 Author-email: HiroYokoyama <titech.yoko.hiro@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE

{moleditpy_linux-2.4.4 → moleditpy_linux-2.4.6}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy-linux"
 
-version = "2.4.4"
+version = "2.4.6"
 
 license = {file = "LICENSE"}
 

{moleditpy_linux-2.4.4 → moleditpy_linux-2.4.6}/src/MoleditPy_linux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 2.4.4
+Version: 2.4.6
 Summary: A cross-platform, simple, and intuitive molecular structure editor built in Python. It allows 2D molecular drawing and 3D structure visualization. It supports exporting structure files for input to DFT calculation software.
 Author-email: HiroYokoyama <titech.yoko.hiro@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE

{moleditpy_linux-2.4.4 → moleditpy_linux-2.4.6}/src/moleditpy_linux/modules/atom_item.py

@@ -60,9 +60,13 @@ class AtomItem(QGraphicsItem):
                 win = self.scene().views()[0].window()
                 if win and hasattr(win, 'settings'):
                     font_size = win.settings.get('atom_font_size_2d', 20)
+                    font_family = win.settings.get('atom_font_family_2d', FONT_FAMILY)
+            else:
+                font_family = FONT_FAMILY
         except Exception:
-            pass
-        self.font = QFont(FONT_FAMILY, font_size, FONT_WEIGHT_BOLD)
+            font_family = FONT_FAMILY
+        
+        self.font = QFont(font_family, font_size, FONT_WEIGHT_BOLD)
         self.prepareGeometryChange()
         
         self.is_visible = not (self.symbol == 'C' and len(self.bonds) > 0 and self.charge == 0 and self.radical == 0)
@@ -70,16 +74,18 @@ class AtomItem(QGraphicsItem):
 
     def boundingRect(self):
         # --- paint()メソッドと完全に同じロジックでテキストの位置とサイズを計算 ---
-        # Get dynamic font size
+        # Get dynamic font size and family
         font_size = 20
+        font_family = FONT_FAMILY
         try:
             if self.scene() and self.scene().views():
                 win = self.scene().views()[0].window()
                 if win and hasattr(win, 'settings'):
                     font_size = win.settings.get('atom_font_size_2d', 20)
+                    font_family = win.settings.get('atom_font_family_2d', FONT_FAMILY)
         except Exception:
             pass
-        font = QFont(FONT_FAMILY, font_size, FONT_WEIGHT_BOLD)
+        font = QFont(font_family, font_size, FONT_WEIGHT_BOLD)
         fm = QFontMetricsF(font)
 
         hydrogen_part = ""
@@ -197,7 +203,9 @@ class AtomItem(QGraphicsItem):
             if self.scene() and self.scene().views():
                 win = self.scene().views()[0].window()
                 if win and hasattr(win, 'settings'):
-                    if win.settings.get('atom_use_bond_color_2d', False):
+                    # Force Hydrogen to use bond color (invisible on white bg otherwise)
+                    # OR if the global setting is checked
+                    if self.symbol == 'H' or win.settings.get('atom_use_bond_color_2d', False):
                         bond_col = win.settings.get('bond_color_2d', '#222222')
                         color = QColor(bond_col)
         except Exception:
@@ -374,11 +382,9 @@ class AtomItem(QGraphicsItem):
         res = super().itemChange(change, value)
         if change == QGraphicsItem.GraphicsItemChange.ItemPositionHasChanged:
             if self.flags() & QGraphicsItem.GraphicsItemFlag.ItemIsMovable:
-                # Prevent cascading updates during batch operations
-                if not getattr(self, '_updating_position', False):
-                    for bond in self.bonds: 
-                        if bond.scene():  # Only update if bond is still in scene
-                            bond.update_position()
+                for bond in self.bonds: 
+                    if bond.scene():
+                        bond.update_position()
             
         return res
 

{moleditpy_linux-2.4.4 → moleditpy_linux-2.4.6}/src/moleditpy_linux/modules/bond_item.py

@@ -94,10 +94,12 @@ class BondItem(QGraphicsItem):
         if self.atom1 is None or self.atom2 is None:
             return QLineF(0, 0, 0, 0)
         try:
-            p2 = self.mapFromItem(self.atom2, 0, 0)
-            return QLineF(QPointF(0, 0), p2)
-        except (RuntimeError, TypeError):
-            # Handle case where atoms are deleted from scene
+            # Use pos() directly - assuming items are in scene coords (no parent)
+            # This is robust and efficient.
+            p1 = self.atom1.pos()
+            p2 = self.atom2.pos()
+            return QLineF(QPointF(0, 0), p2 - p1)
+        except Exception:
             return QLineF(0, 0, 0, 0)
 
     def boundingRect(self):
@@ -120,12 +122,33 @@ class BondItem(QGraphicsItem):
         except Exception:
              bond_offset = globals().get('BOND_OFFSET', 3.5)
 
-        extra = (getattr(self, 'order', 1) - 1) * bond_offset + 20
+        # Get dynamic wedge width
+        wedge_width = 6.0
+        try:
+             if self.scene() and self.scene().views():
+                  win = self.scene().views()[0].window()
+                  if win and hasattr(win, 'settings'):
+                       wedge_width = win.settings.get('bond_wedge_width_2d', 6.0)
+        except Exception:
+             pass
+
+        extra = (getattr(self, 'order', 1) - 1) * bond_offset + 50 + wedge_width
         rect = QRectF(line.p1(), line.p2()).normalized().adjusted(-extra, -extra, extra, extra)
 
         # E/Zラベルの描画範囲も考慮して拡張（QFontMetricsFで正確に）
         if self.order == 2 and self.stereo in [3, 4]:
-            font = QFont(FONT_FAMILY, FONT_SIZE_LARGE, FONT_WEIGHT_BOLD)
+            font_size = 20
+            font_family = FONT_FAMILY
+            try:
+                if self.scene() and self.scene().views():
+                    win = self.scene().views()[0].window()
+                    if win and hasattr(win, 'settings'):
+                        font_size = win.settings.get('atom_font_size_2d', 20)
+                        font_family = win.settings.get('atom_font_family_2d', FONT_FAMILY)
+            except Exception:
+                pass
+            
+            font = QFont(font_family, font_size, FONT_WEIGHT_BOLD)
             font.setItalic(True)
             text = "Z" if self.stereo == 3 else "E"
             fm = QFontMetricsF(font)
@@ -383,7 +406,18 @@ class BondItem(QGraphicsItem):
                         painter.save() # 現在の描画設定を保存
 
                         # --- ラベルの設定 ---
-                        font = QFont(FONT_FAMILY, FONT_SIZE_LARGE, FONT_WEIGHT_BOLD)
+                        font_size = 20
+                        font_family = FONT_FAMILY
+                        try:
+                            if self.scene() and self.scene().views():
+                                win = self.scene().views()[0].window()
+                                if win and hasattr(win, 'settings'):
+                                    font_size = win.settings.get('atom_font_size_2d', 20)
+                                    font_family = win.settings.get('atom_font_family_2d', FONT_FAMILY)
+                        except Exception:
+                            pass
+                        
+                        font = QFont(font_family, font_size, FONT_WEIGHT_BOLD)
                         font.setItalic(True)
                         text_color = QColor("gray")
                         # 輪郭の色を背景色と同じにする（scene()がNoneのときは安全なフォールバックを使う）
@@ -442,9 +476,10 @@ class BondItem(QGraphicsItem):
 
 
 
-    def update_position(self):
+    def update_position(self, notify=True):
         try:
-            self.prepareGeometryChange()
+            if notify:
+                self.prepareGeometryChange()
             if self.atom1:
                 self.setPos(self.atom1.pos())
             self.update()

{moleditpy_linux-2.4.4 → moleditpy_linux-2.4.6}/src/moleditpy_linux/modules/constants.py

@@ -16,7 +16,7 @@ from PyQt6.QtGui import QFont, QColor
 from rdkit import Chem
 
 #Version
-VERSION = '2.4.4'
+VERSION = '2.4.6'
 
 ATOM_RADIUS = 18
 BOND_OFFSET = 3.5

{moleditpy_linux-2.4.4 → moleditpy_linux-2.4.6}/src/moleditpy_linux/modules/main_window_main_init.py

@@ -1253,8 +1253,6 @@ class MainWindowMainInit(object):
         
         plugin_menu.addSeparator()
         
-        # Initial population of plugins
-        self.update_plugin_menu(plugin_menu)
 
         settings_menu = menu_bar.addMenu("&Settings")
         # 1) 3D View settings (existing)
@@ -1420,11 +1418,12 @@ class MainWindowMainInit(object):
         )
         help_menu.addAction(manual_action)
 
-
-
         # 3D関連機能の初期状態を統一的に設定
         self._enable_3d_features(False)
         
+        # Finally, populate plugins now that all menus are created
+        self.update_plugin_menu(plugin_menu)
+        
 
 
     def init_worker_thread(self):

{moleditpy_linux-2.4.4 → moleditpy_linux-2.4.6}/src/moleditpy_linux/modules/settings_dialog.py

@@ -12,11 +12,11 @@ DOI: 10.5281/zenodo.17268532
 
 from PyQt6.QtWidgets import (
     QDialog, QVBoxLayout, QTabWidget, QWidget, QFormLayout, QPushButton, QHBoxLayout,
-    QCheckBox, QComboBox, QLabel, QColorDialog, QSlider, QFrame, QMessageBox
+    QCheckBox, QComboBox, QLabel, QColorDialog, QSlider, QFrame, QMessageBox, QFontComboBox
 )
 from PyQt6.QtWidgets import QApplication
 from PyQt6.QtCore import Qt
-from PyQt6.QtGui import QColor
+from PyQt6.QtGui import QColor, QFont
 try:
     from .constants import CPK_COLORS
 except Exception:
@@ -101,6 +101,7 @@ class SettingsDialog(QDialog):
             'bond_cap_style_2d': 'Round',
             'bond_wedge_width_2d': 6.0,
             'bond_dash_count_2d': 8,
+            'atom_font_family_2d': 'Arial',
         }
         
         # --- 選択された色を管理する専用のインスタンス変数 ---
@@ -275,6 +276,13 @@ class SettingsDialog(QDialog):
         # --- Atom Settings ---
         form_layout.addRow(QLabel("<b>Atom Settings</b>"))
 
+        # Font Family
+        self.atom_font_family_2d_combo = QFontComboBox()
+        self.atom_font_family_2d_combo.setEditable(False) # Force selection from list
+        # Filter mostly for scalable fonts if desired, but default is usually fine
+        self.atom_font_family_2d_combo.setFontFilters(QFontComboBox.FontFilter.ScalableFonts)
+        form_layout.addRow("Atom Label Font Family:", self.atom_font_family_2d_combo)
+
         # Font Size
         self.atom_font_size_2d_slider = QSlider(Qt.Orientation.Horizontal)
         self.atom_font_size_2d_slider.setRange(8, 72)
@@ -813,10 +821,10 @@ class SettingsDialog(QDialog):
                 'background_color_2d': self.default_settings['background_color_2d'],
                 'bond_color_2d': self.default_settings['bond_color_2d'],
                 'atom_use_bond_color_2d': self.default_settings['atom_use_bond_color_2d'],
-                'atom_use_bond_color_2d': self.default_settings['atom_use_bond_color_2d'],
                 'bond_cap_style_2d': self.default_settings['bond_cap_style_2d'],
                 'bond_wedge_width_2d': self.default_settings['bond_wedge_width_2d'],
-                'bond_dash_count_2d': self.default_settings['bond_dash_count_2d']
+                'bond_dash_count_2d': self.default_settings['bond_dash_count_2d'],
+                'atom_font_family_2d': self.default_settings['atom_font_family_2d']
             },
             "3D Scene": {
                 'background_color': self.default_settings['background_color'],
@@ -1258,6 +1266,7 @@ class SettingsDialog(QDialog):
             'bond_cap_style_2d': self.bond_cap_style_2d_combo.currentText(),
             'bond_wedge_width_2d': self.bond_wedge_width_2d_slider.value() / 10.0,
             'bond_dash_count_2d': self.bond_dash_count_2d_slider.value(),
+            'atom_font_family_2d': self.atom_font_family_2d_combo.currentFont().family(),
         }
 
     def pick_bs_bond_color(self):
@@ -1519,6 +1528,10 @@ class SettingsDialog(QDialog):
         self.atom_font_size_2d_slider.setValue(int(fs_2d))
         self.atom_font_size_2d_label.setText(str(fs_2d))
 
+        # Load Font Family
+        font_family = settings_dict.get('atom_font_family_2d', self.default_settings['atom_font_family_2d'])
+        self.atom_font_family_2d_combo.setCurrentFont(QFont(font_family))
+
         self.atom_use_bond_color_2d_checkbox.setChecked(settings_dict.get('atom_use_bond_color_2d', self.default_settings.get('atom_use_bond_color_2d', False)))
 
         self.current_bg_color_2d = settings_dict.get('background_color_2d', self.default_settings['background_color_2d'])