MoleditPy-linux 3.5.0__tar.gz → 3.5.2__tar.gz

{moleditpy_linux-3.5.0 → moleditpy_linux-3.5.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 3.5.0
+Version: 3.5.2
 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-3.5.0 → moleditpy_linux-3.5.2}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy-linux"
 
-version = "3.5.0"
+version = "3.5.2"
 
 license = {file = "LICENSE"}
 

{moleditpy_linux-3.5.0 → moleditpy_linux-3.5.2}/src/MoleditPy_linux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 3.5.0
+Version: 3.5.2
 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-3.5.0 → moleditpy_linux-3.5.2}/src/moleditpy_linux/ui/main_window_init.py

@@ -613,12 +613,18 @@ class MainInitManager:
             )
 
     def save_settings(self) -> None:
+        if (
+            not self.host.init_manager.settings_dirty
+            or self.host.init_manager.settings == self.host.initial_settings
+        ):
+            return
         try:
             if not os.path.exists(self.host.init_manager.settings_dir):
                 os.makedirs(self.host.init_manager.settings_dir)
             with open(self.host.init_manager.settings_file, "w", encoding="utf-8") as f:
                 json.dump(self.host.init_manager.settings, f, indent=4)
             self.host.init_manager.settings_dirty = False
+            self.host.initial_settings = self.host.init_manager.settings.copy()
         except (AttributeError, RuntimeError, ValueError) as e:
             print(f"Error saving settings: {e}")
 

{moleditpy_linux-3.5.0 → moleditpy_linux-3.5.2}/src/moleditpy_linux/ui/molecular_scene_handler.py

@@ -258,8 +258,8 @@ class TemplateMixin:
 
         # --- 2) Enumerate existing atoms in the scene from self.data.atoms and map them ---
         mapped_atoms = {it for it in atom_items if it is not None}
-        if self.get_setting("atom_fusing_enabled_2d", True):
-            map_threshold = self.get_setting("atom_fusing_distance_2d", 14.0)
+        if self.get_setting("template_fusing_enabled_2d", True):
+            map_threshold = self.get_setting("template_fusing_distance_2d", 14.0)
             for i, p in enumerate(points):
                 if atom_items[i] is not None:
                     continue
@@ -739,8 +739,8 @@ class KeyboardMixin:
         if key == Qt.Key.Key_4:
             snap_dist = self.get_setting("template_snapping_distance_2d", 14.0)
             item_at_cursor = self.find_atom_near(cursor_pos, tol=snap_dist)
-        elif self.get_setting("atom_fusing_enabled_2d", True):
-            fuse_dist = self.get_setting("atom_fusing_distance_2d", 14.0)
+        elif self.get_setting("template_fusing_enabled_2d", True):
+            fuse_dist = self.get_setting("template_fusing_distance_2d", 14.0)
             item_at_cursor = self.find_atom_near(cursor_pos, tol=fuse_dist)
         if item_at_cursor is None:
             item_at_cursor = self.itemAt(cursor_pos, transform)
@@ -1084,9 +1084,9 @@ class KeyboardMixin:
 
                     # Find nearby atom
                     near_atom = None
-                    if self.get_setting("atom_fusing_enabled_2d", True):
+                    if self.get_setting("template_fusing_enabled_2d", True):
                         fuse_dist = self.get_setting(
-                            "atom_fusing_distance_2d", SNAP_DISTANCE
+                            "template_fusing_distance_2d", SNAP_DISTANCE
                         )
                         near_atom = self.find_atom_near(target_pos, tol=fuse_dist)
 

{moleditpy_linux-3.5.0 → moleditpy_linux-3.5.2}/src/moleditpy_linux/ui/molecule_scene.py

@@ -308,10 +308,10 @@ class MoleculeScene(TemplateMixin, KeyboardMixin, SceneQueryMixin, QGraphicsScen
         item = None
         if (
             self.mode.startswith("bond")
-            and self.get_setting("atom_fusing_enabled_2d", True)
+            and self.get_setting("template_fusing_enabled_2d", True)
             and self.press_pos
         ):
-            fuse_dist = self.get_setting("atom_fusing_distance_2d", 14.0)
+            fuse_dist = self.get_setting("template_fusing_distance_2d", 14.0)
             item = self.find_atom_near(self.press_pos, tol=fuse_dist)
         if item is None:
             item = self.itemAt(self.press_pos, self.views()[0].transform())
@@ -360,8 +360,8 @@ class MoleculeScene(TemplateMixin, KeyboardMixin, SceneQueryMixin, QGraphicsScen
             end_point = current_pos
 
             target_atom = None
-            if self.get_setting("atom_fusing_enabled_2d", True) and current_pos:
-                fuse_dist = self.get_setting("atom_fusing_distance_2d", 14.0)
+            if self.get_setting("template_fusing_enabled_2d", True) and current_pos:
+                fuse_dist = self.get_setting("template_fusing_distance_2d", 14.0)
                 target_atom = self.find_atom_near(current_pos, tol=fuse_dist)
             else:
                 for item in self.items(current_pos):
@@ -557,8 +557,8 @@ class MoleculeScene(TemplateMixin, KeyboardMixin, SceneQueryMixin, QGraphicsScen
         ):
             line = QLineF(self.start_atom.pos(), end_pos)
             end_item = None
-            if self.get_setting("atom_fusing_enabled_2d", True) and end_pos:
-                fuse_dist = self.get_setting("atom_fusing_distance_2d", 14.0)
+            if self.get_setting("template_fusing_enabled_2d", True) and end_pos:
+                fuse_dist = self.get_setting("template_fusing_distance_2d", 14.0)
                 end_item = self.find_atom_near(end_pos, tol=fuse_dist)
             if end_item is None:
                 end_item = self.itemAt(end_pos, self.views()[0].transform())
@@ -611,8 +611,8 @@ class MoleculeScene(TemplateMixin, KeyboardMixin, SceneQueryMixin, QGraphicsScen
                 self.data_changed_in_event = True
             else:
                 end_item = None
-                if self.get_setting("atom_fusing_enabled_2d", True) and end_pos:
-                    fuse_dist = self.get_setting("atom_fusing_distance_2d", 14.0)
+                if self.get_setting("template_fusing_enabled_2d", True) and end_pos:
+                    fuse_dist = self.get_setting("template_fusing_distance_2d", 14.0)
                     end_item = self.find_atom_near(end_pos, tol=fuse_dist)
                 if end_item is None:
                     end_item = self.itemAt(end_pos, self.views()[0].transform())

{moleditpy_linux-3.5.0 → moleditpy_linux-3.5.2}/src/moleditpy_linux/ui/settings_tabs/settings_2d_tab.py

@@ -147,45 +147,59 @@ class Settings2DTab(SettingsTabBase):
 
         form_layout.addRow(self._create_separator())
 
-        # --- Atom Fusing Settings ---
-        form_layout.addRow(QLabel("<b>Atom Fusing Settings</b>"))
+        # --- Template Settings ---
+        form_layout.addRow(QLabel("<b>Template Settings</b>"))
 
-        self.atom_fusing_enabled_2d_checkbox = QCheckBox()
-        self.atom_fusing_enabled_2d_checkbox.setToolTip(
-            "If checked, drawing or placing templates near an existing atom "
-            "will connect to it rather than creating a new one."
-        )
-        form_layout.addRow("Enable Atom Fusing:", self.atom_fusing_enabled_2d_checkbox)
-
-        # Fusing Distance
-        self.atom_fusing_distance_2d_slider, self.atom_fusing_distance_2d_label = (
-            self._create_slider(5, 50, 1.0, is_int=True)
+        # Template Snapping Distance
+        (
+            self.template_snapping_distance_2d_slider,
+            self.template_snapping_distance_2d_label,
+        ) = self._create_slider(5, 50, 1.0, is_int=True)
+        self.template_snapping_distance_2d_slider.setToolTip(
+            "The distance in pixels within which a template will snap to existing atoms or bonds."
         )
         form_layout.addRow(
-            "Fusing Distance (px):",
+            "Snapping Distance (px):",
             self._wrap_layout(
-                self.atom_fusing_distance_2d_slider, self.atom_fusing_distance_2d_label
+                self.template_snapping_distance_2d_slider,
+                self.template_snapping_distance_2d_label,
             ),
         )
 
-        form_layout.addRow(self._create_separator())
-
-        # --- Template Snapping Settings ---
-        form_layout.addRow(QLabel("<b>Template Snapping Settings</b>"))
+        self.template_fusing_enabled_2d_checkbox = QCheckBox()
+        self.template_fusing_enabled_2d_checkbox.setToolTip(
+            "If checked, drawing or placing templates near an existing atom "
+            "will connect to it rather than creating a new one."
+        )
+        form_layout.addRow(
+            "Enable Atom Fusing:", self.template_fusing_enabled_2d_checkbox
+        )
 
-        # Template Snapping Distance
+        # Fusing Distance
         (
-            self.template_snapping_distance_2d_slider,
-            self.template_snapping_distance_2d_label,
+            self.template_fusing_distance_2d_slider,
+            self.template_fusing_distance_2d_label,
         ) = self._create_slider(5, 50, 1.0, is_int=True)
+        self.template_fusing_distance_2d_slider.setToolTip(
+            "The distance in pixels within which a template atom "
+            "will be fused with an existing atom."
+        )
         form_layout.addRow(
-            "Snapping Distance (px):",
+            "Fusing Distance (px):",
             self._wrap_layout(
-                self.template_snapping_distance_2d_slider,
-                self.template_snapping_distance_2d_label,
+                self.template_fusing_distance_2d_slider,
+                self.template_fusing_distance_2d_label,
             ),
         )
 
+        # Connect checkbox toggled to enable/disable fusing distance components
+        self.template_fusing_enabled_2d_checkbox.toggled.connect(
+            self.template_fusing_distance_2d_slider.setEnabled
+        )
+        self.template_fusing_enabled_2d_checkbox.toggled.connect(
+            self.template_fusing_distance_2d_label.setEnabled
+        )
+
     def _pick_bg_color_2d(self) -> None:
         color = QColorDialog.getColor(
             QColor(self.current_bg_color_2d), self, "Select 2D Background Color"
@@ -250,11 +264,14 @@ class Settings2DTab(SettingsTabBase):
         self.atom_use_bond_color_2d_checkbox.setChecked(
             settings_dict.get("atom_use_bond_color_2d", False)
         )
-        self.atom_fusing_enabled_2d_checkbox.setChecked(
-            settings_dict.get("atom_fusing_enabled_2d", True)
-        )
-        self.atom_fusing_distance_2d_slider.setValue(
-            int(settings_dict.get("atom_fusing_distance_2d", 14.0))
+
+        fusing_enabled = settings_dict.get("template_fusing_enabled_2d", True)
+        self.template_fusing_enabled_2d_checkbox.setChecked(fusing_enabled)
+        self.template_fusing_distance_2d_slider.setEnabled(fusing_enabled)
+        self.template_fusing_distance_2d_label.setEnabled(fusing_enabled)
+
+        self.template_fusing_distance_2d_slider.setValue(
+            int(settings_dict.get("template_fusing_distance_2d", 14.0))
         )
         self.template_snapping_distance_2d_slider.setValue(
             int(settings_dict.get("template_snapping_distance_2d", 14.0))
@@ -273,9 +290,9 @@ class Settings2DTab(SettingsTabBase):
             "atom_font_family_2d": self.atom_font_family_2d_combo.currentFont().family(),
             "atom_font_size_2d": self.atom_font_size_2d_slider.value(),
             "atom_use_bond_color_2d": self.atom_use_bond_color_2d_checkbox.isChecked(),
-            "atom_fusing_enabled_2d": self.atom_fusing_enabled_2d_checkbox.isChecked(),
-            "atom_fusing_distance_2d": float(
-                self.atom_fusing_distance_2d_slider.value()
+            "template_fusing_enabled_2d": self.template_fusing_enabled_2d_checkbox.isChecked(),
+            "template_fusing_distance_2d": float(
+                self.template_fusing_distance_2d_slider.value()
             ),
             "template_snapping_distance_2d": float(
                 self.template_snapping_distance_2d_slider.value()

{moleditpy_linux-3.5.0 → moleditpy_linux-3.5.2}/src/moleditpy_linux/utils/default_settings.py

@@ -19,7 +19,6 @@ DEFAULT_SETTINGS = {
     "specular_power": 20,
     "light_intensity": 1.0,
     "show_3d_axes": True,
-    "show_chiral_labels": False,
     # --- 3D Model Parameters (Ball and Stick) ---
     "ball_stick_atom_scale": 1.0,
     "ball_stick_bond_radius": 0.1,
@@ -33,7 +32,6 @@ DEFAULT_SETTINGS = {
     # --- 3D Model Parameters (CPK) ---
     "cpk_atom_scale": 1.0,
     "cpk_resolution": 32,
-    "cpk_colors": {},
     # --- 3D Model Parameters (Wireframe) ---
     "wireframe_bond_radius": 0.02,
     "wireframe_resolution": 6,
@@ -58,12 +56,9 @@ DEFAULT_SETTINGS = {
     "optimize_intermolecular_interaction_rdkit": True,
     "skip_chemistry_checks": False,
     "always_ask_charge": False,
-    # --- Interaction and Selection ---
-    "use_high_fidelity_selection": True,
-    "selection_color": "#FFD700",
-    "high_quality_meshing": True,
-    "atom_label_color": "#000000",
+    # --- Color ---
     "bond_color": "#808080",
+    "cpk_colors": {},
     # --- 2D Settings ---
     "bond_width_2d": 2.0,
     "bond_spacing_double_2d": 3.5,
@@ -76,13 +71,7 @@ DEFAULT_SETTINGS = {
     "bond_wedge_width_2d": 6.0,
     "bond_dash_count_2d": 8,
     "atom_font_family_2d": "Arial",
-    "atom_fusing_enabled_2d": True,
-    "atom_fusing_distance_2d": 14.0,
+    "template_fusing_enabled_2d": True,
+    "template_fusing_distance_2d": 14.0,
     "template_snapping_distance_2d": 14.0,
-    # --- Application Session / UI State ---
-    "theme": "light",
-    "window_size": [1200, 800],
-    "window_position": [100, 100],
-    "splitter_sizes": [600, 600],
-    "last_dir": "",
 }