MoleditPy-linux 4.6.1__tar.gz → 4.7.1__tar.gz

{moleditpy_linux-4.6.1 → moleditpy_linux-4.7.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 4.6.1
+Version: 4.7.1
 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-4.6.1 → moleditpy_linux-4.7.1}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy-linux"
 
-version = "4.6.1"
+version = "4.7.1"
 
 license = {file = "LICENSE"}
 

{moleditpy_linux-4.6.1 → moleditpy_linux-4.7.1}/src/MoleditPy_linux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 4.6.1
+Version: 4.7.1
 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-4.6.1 → moleditpy_linux-4.7.1}/src/MoleditPy_linux.egg-info/SOURCES.txt

@@ -75,6 +75,7 @@ src/moleditpy_linux/ui/settings_tabs/settings_tab_base.py
 src/moleditpy_linux/utils/__init__.py
 src/moleditpy_linux/utils/constants.py
 src/moleditpy_linux/utils/default_settings.py
+src/moleditpy_linux/utils/hit_radius.py
 src/moleditpy_linux/utils/sip_isdeleted_safe.py
 src/moleditpy_linux/utils/suppress_log.py
 src/moleditpy_linux/utils/system_utils.py

{moleditpy_linux-4.6.1 → moleditpy_linux-4.7.1}/src/moleditpy_linux/plugins/plugin_interface.py

@@ -409,6 +409,43 @@ class PluginContext:
             mw.init_manager.settings[namespaced] = value
             mw.init_manager.settings_dirty = True
 
+    def get_current_file(self) -> Optional[str]:
+        """
+        Path of the file the application currently has open, or None.
+
+        Returns:
+            The path, or None when nothing is open.
+        """
+        mw = self.get_main_window()
+        if mw and hasattr(mw, "init_manager"):
+            path = mw.init_manager.current_file_path
+            return str(path) if path else None
+        return None
+
+    def set_current_file(self, path: Optional[str]) -> None:
+        """
+        Record *path* as the file the application has open and retitle its window.
+
+        Use this after a plugin file opener loads a file, so the window names it
+        the way it names a project. Assigning ``init_manager.current_file_path``
+        directly leaves the title showing the previous file: it is only rebuilt
+        on demand.
+
+        Args:
+            path: File path to show, or None for "Untitled".
+        """
+        mw = self.get_main_window()
+        if mw is None or not hasattr(mw, "init_manager"):
+            return
+        try:
+            mw.init_manager.current_file_path = path
+            if hasattr(mw, "state_manager"):
+                fn = getattr(mw.state_manager, "update_window_title", None)
+                if fn:
+                    fn()
+        except (AttributeError, RuntimeError):
+            logging.debug("set_current_file failed", exc_info=True)
+
     def mark_project_modified(self) -> None:
         """Mark the current project as having unsaved changes and update the window title."""
         mw = self.get_main_window()

{moleditpy_linux-4.6.1 → moleditpy_linux-4.7.1}/src/moleditpy_linux/ui/angle_dialog.py

@@ -487,7 +487,10 @@ class AngleDialog(GeometryBaseDialog):
         if abs(achieved - requested) < 0.5:
             return
         with suppress_log(AttributeError, RuntimeError, TypeError):
-            self.main_window.statusBar().showMessage(
+            status_bar = self.main_window.statusBar()
+            if status_bar is None:
+                return
+            status_bar.showMessage(
                 f"Angle unchanged ({achieved:.2f} deg): the three atoms rotate "
                 "together, which happens for an angle inside a ring.",
                 5000,

{moleditpy_linux-4.6.1 → moleditpy_linux-4.7.1}/src/moleditpy_linux/ui/atom_item.py

@@ -37,6 +37,7 @@ from ..utils.constants import (
     FONT_FAMILY,
     FONT_WEIGHT_BOLD,
 )
+from ..utils.hit_radius import scene_hit_radius
 from ..utils.sip_isdeleted_safe import sip_isdeleted_safe
 
 if TYPE_CHECKING:
@@ -111,8 +112,8 @@ class AtomItem(QGraphicsItem):
         font_italic = False
         font_underline = False
 
-        scene = self.scene()
-        if scene is not None and hasattr(scene, "get_setting"):
+        scene: Any = self.scene()
+        if scene is not None:
             font_size = scene.get_setting("atom_font_size_2d", 20)
             font_family = scene.get_setting("atom_font_family_2d", FONT_FAMILY)
             font_bold = scene.get_setting("atom_font_bold_2d", True)
@@ -133,15 +134,15 @@ class AtomItem(QGraphicsItem):
         )
         self.update()
 
-    def boundingRect(self) -> QRectF:
-        """Calculate the bounding rectangle for the atom item."""
+    def visual_rect(self) -> QRectF:
+        """Return the rectangle the atom draws into; highlights use this."""
         font_size = 20
         font_family = FONT_FAMILY
         font_bold = True
         font_italic = False
         font_underline = False
-        scene = self.scene()
-        if scene is not None and hasattr(scene, "get_setting"):
+        scene: Any = self.scene()
+        if scene is not None:
             font_size = scene.get_setting("atom_font_size_2d", 20)
             font_family = scene.get_setting("atom_font_family_2d", FONT_FAMILY)
             font_bold = scene.get_setting("atom_font_bold_2d", True)
@@ -251,6 +252,13 @@ class AtomItem(QGraphicsItem):
         # 3. Add final margins for selection highlights, etc.
         return full_visual_rect.adjusted(-3, -3, 3, 3)
 
+    def boundingRect(self) -> QRectF:
+        """Return the drawn rect plus the hit shape, which Qt requires it to cover."""
+        hit_r = self.hit_radius()
+        return self.visual_rect().united(
+            QRectF(-hit_r, -hit_r, hit_r * 2.0, hit_r * 2.0)
+        )
+
     def get_bg_ellipse_path(self) -> QPainterPath:
         """Return the elliptical background path used for bond endpoint clipping."""
         path = QPainterPath()
@@ -262,8 +270,8 @@ class AtomItem(QGraphicsItem):
         font_bold = True
         font_italic = False
         font_underline = False
-        scene = self.scene()
-        if scene is not None and hasattr(scene, "get_setting"):
+        scene: Any = self.scene()
+        if scene is not None:
             font_size = scene.get_setting("atom_font_size_2d", 20)
             font_family = scene.get_setting("atom_font_family_2d", FONT_FAMILY)
             font_bold = scene.get_setting("atom_font_bold_2d", True)
@@ -330,33 +338,13 @@ class AtomItem(QGraphicsItem):
         path.addEllipse(bg_rect)
         return path
 
-    def shape(self) -> QPainterPath:
-        """Define the shape of the atom item for collision detection.
-
-        The hit radius is derived from the ``bond_snapping_distance_2d``
-        setting so that hover highlight matches the snapping / keyboard
-        instant-switch zone exactly.  The radius is expressed in screen
-        pixels and divided by the current view scale.
-        """
-        scene = self.scene()
-        if not scene or not scene.views():
-            path = QPainterPath()
-            hit_r = max(4.0, ATOM_RADIUS - 6.0) * 2
-            path.addEllipse(QRectF(-hit_r, -hit_r, hit_r * 2.0, hit_r * 2.0))
-            return path
-
-        view = scene.views()[0]
-        scale = view.transform().m11()
-        if scale <= 0.0:
-            scale = 1.0
+    def hit_radius(self) -> float:
+        """Return the hit/snap radius in scene units for the current zoom."""
+        return scene_hit_radius(self.scene(), fallback=max(4.0, ATOM_RADIUS - 6.0) * 2)
 
-        # Use the same setting that find_atom_near() uses for snapping,
-        # so hover highlight and snap zones are identical.
-        if hasattr(scene, "get_setting"):
-            hit_px = scene.get_setting("bond_snapping_distance_2d", 14.0)
-        else:
-            hit_px = 14.0
-        scene_radius = hit_px / scale
+    def shape(self) -> QPainterPath:
+        """Define the collision area: a fixed pixel radius, never the drawn label."""
+        scene_radius = self.hit_radius()
 
         path = QPainterPath()
         path.addEllipse(QPointF(0, 0), scene_radius, scene_radius)
@@ -374,11 +362,11 @@ class AtomItem(QGraphicsItem):
         # Color logic: check if we should use bond color (uniform) or CPK (element-specific)
         color = CPK_COLORS.get(self.symbol, CPK_COLORS["DEFAULT"])
         # Use bond color if specified in settings
-        scene = self.scene()
-        if hasattr(scene, "get_setting") and (
-            self.symbol == "H" or scene.get_setting("atom_use_bond_color_2d", False)  # type: ignore[union-attr]
+        scene: Any = self.scene()
+        if scene is not None and (
+            self.symbol == "H" or scene.get_setting("atom_use_bond_color_2d", False)
         ):
-            custom_color = scene.get_setting("bond_color_2d", "#222222")  # type: ignore[union-attr]
+            custom_color = scene.get_setting("bond_color_2d", "#222222")
             if isinstance(custom_color, str):
                 color = QColor(custom_color)
 
@@ -533,17 +521,17 @@ class AtomItem(QGraphicsItem):
         if self.has_problem:
             painter.setBrush(Qt.BrushStyle.NoBrush)
             painter.setPen(QPen(QColor(255, 0, 0, 200), 4))
-            painter.drawRect(self.boundingRect())
+            painter.drawRect(self.visual_rect())
         elif self.isSelected():
             painter.setBrush(Qt.BrushStyle.NoBrush)
             painter.setPen(QPen(QColor(0, 100, 255), 3))
-            painter.drawRect(self.boundingRect())
+            painter.drawRect(self.visual_rect())
         if (not self.isSelected()) and getattr(self, "hovered", False):
             pen = QPen(QColor(144, 238, 144, 200), 3)
             pen.setJoinStyle(Qt.PenJoinStyle.RoundJoin)
             painter.setBrush(Qt.BrushStyle.NoBrush)
             painter.setPen(pen)
-            painter.drawRect(self.boundingRect())
+            painter.drawRect(self.visual_rect())
 
     def itemChange(self, change: QGraphicsItem.GraphicsItemChange, value: Any) -> Any:
         """Propagate position and scene changes to connected bond items."""

{moleditpy_linux-4.6.1 → moleditpy_linux-4.7.1}/src/moleditpy_linux/ui/bond_item.py

@@ -13,7 +13,7 @@ DOI: 10.5281/zenodo.17268532
 from __future__ import annotations
 import math
 import logging
-from typing import TYPE_CHECKING, Optional, Tuple, Union
+from typing import TYPE_CHECKING, Any, Optional, Tuple, Union
 
 from PyQt6.QtCore import QLineF, QPointF, QRectF, Qt
 from PyQt6.QtGui import (
@@ -43,6 +43,7 @@ from ..utils.constants import (
     FONT_WEIGHT_BOLD,
     HOVER_PEN_WIDTH,
 )
+from ..utils.hit_radius import scene_hit_radius
 
 if TYPE_CHECKING:
     from .atom_item import AtomItem
@@ -231,6 +232,10 @@ class BondItem(QGraphicsItem):
             # return zero line to prevent downstream crashes.
             return QLineF(0, 0, 0, 0)
 
+    def hit_radius(self) -> float:
+        """Return the click/hover half-width in scene units for the current zoom."""
+        return scene_hit_radius(self.scene())
+
     def boundingRect(self) -> QRectF:
         """Return the bounding rect encompassing all visual bond representations."""
         try:
@@ -239,10 +244,10 @@ class BondItem(QGraphicsItem):
             line = QLineF(0, 0, 0, 0)
 
         # Get dynamic bond offset (spacing)
-        scene = self.scene()
+        scene: Any = self.scene()
         bond_offset = 3.5
         wedge_width = 6.0
-        if scene is not None and hasattr(scene, "get_setting"):
+        if scene is not None:
             key = (
                 "bond_spacing_triple_2d"
                 if getattr(self, "order", 1) == 3
@@ -251,7 +256,9 @@ class BondItem(QGraphicsItem):
             bond_offset = scene.get_setting(key, 3.5)
             wedge_width = scene.get_setting("bond_wedge_width_2d", 6.0)
 
+        # Qt prunes clicks whose shape() escapes boundingRect().
         extra = (getattr(self, "order", 1) - 1) * bond_offset + 50 + wedge_width
+        extra = max(extra, self.hit_radius() + 2.0)
         rect = (
             QRectF(line.p1(), line.p2())
             .normalized()
@@ -262,7 +269,7 @@ class BondItem(QGraphicsItem):
         if self.order == 2 and self.stereo in [3, 4]:
             font_size = 20
             font_family = FONT_FAMILY
-            if scene is not None and hasattr(scene, "get_setting"):
+            if scene is not None:
                 font_size = scene.get_setting("atom_font_size_2d", 20)
                 font_family = scene.get_setting("atom_font_family_2d", FONT_FAMILY)
 
@@ -292,25 +299,9 @@ class BondItem(QGraphicsItem):
             path.moveTo(line.p1())
             path.lineTo(line.p2())
 
-            # Use the exact same setting as atom hover highlight and snapping, zoom-aware.
-            scene = self.scene()
-            if scene and scene.views():
-                view = scene.views()[0]
-                scale = view.transform().m11()
-                if scale <= 0.0:
-                    scale = 1.0
-                if hasattr(scene, "get_setting"):
-                    hit_px = scene.get_setting("bond_snapping_distance_2d", 14.0)
-                else:
-                    hit_px = 14.0
-                # width is diameter, so 2 * radius
-                scene_width = (hit_px * 2) / scale
-            else:
-                scene_width = 28.0
-
-            # Stroke it to give it some width
+            # Stroke it to give it some width (width is a diameter, so 2 * radius)
             stroker = QPainterPathStroker()
-            stroker.setWidth(scene_width)
+            stroker.setWidth(self.hit_radius() * 2.0)
             path = stroker.createStroke(path)
 
             # If there's an E/Z label, add its rect to the selection shape
@@ -362,8 +353,8 @@ class BondItem(QGraphicsItem):
         bond_color = QColor("#222222")
 
         try:
-            scene = self.scene()
-            if scene is not None and hasattr(scene, "get_setting"):
+            scene: Any = self.scene()
+            if scene is not None:
                 # Color
                 if self.isSelected():
                     bond_color = QColor("blue")
@@ -538,8 +529,8 @@ class BondItem(QGraphicsItem):
                         # --- Label Settings ---
                         font_size = 20
                         font_family = FONT_FAMILY
-                        _sc = self.scene()
-                        if _sc is not None and hasattr(_sc, "get_setting"):
+                        _sc: Any = self.scene()
+                        if _sc is not None:
                             font_size = _sc.get_setting("atom_font_size_2d", 20)
                             font_family = _sc.get_setting(
                                 "atom_font_family_2d", FONT_FAMILY

{moleditpy_linux-4.6.1 → moleditpy_linux-4.7.1}/src/moleditpy_linux/ui/bond_length_dialog.py

@@ -441,7 +441,10 @@ class BondLengthDialog(GeometryBaseDialog):
         if abs(worst_delta) < 1e-4:
             return
         with suppress_log(AttributeError, RuntimeError, TypeError):
-            self.main_window.statusBar().showMessage(
+            status_bar = self.main_window.statusBar()
+            if status_bar is None:
+                return
+            status_bar.showMessage(
                 f"Bond {worst_label} also changed by {worst_delta:+.3f} A: a bond "
                 "inside a ring cannot be resized on its own.",
                 5000,

{moleditpy_linux-4.6.1 → moleditpy_linux-4.7.1}/src/moleditpy_linux/ui/custom_interactor_style.py

@@ -51,8 +51,9 @@ _GROUP_ROTATION_RADIANS_PER_PIXEL = 0.008
 def _rodrigues_matrix(axis: np.ndarray, angle: float) -> np.ndarray:
     """Return the rotation matrix for `angle` radians about `axis` (Rodrigues)."""
     norm = float(np.linalg.norm(axis))
+    identity: np.ndarray = np.eye(3)
     if norm < 1e-6 or abs(angle) < 1e-6:
-        return np.eye(3)
+        return identity
     unit = axis / norm
     k_mat = np.array(
         [
@@ -61,7 +62,10 @@ def _rodrigues_matrix(axis: np.ndarray, angle: float) -> np.ndarray:
             [-unit[1], unit[0], 0.0],
         ]
     )
-    return np.eye(3) + np.sin(angle) * k_mat + (1.0 - np.cos(angle)) * (k_mat @ k_mat)
+    rotation: np.ndarray = (
+        identity + np.sin(angle) * k_mat + (1.0 - np.cos(angle)) * (k_mat @ k_mat)
+    )
+    return rotation
 
 
 class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
@@ -944,7 +948,8 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
             speed = _GROUP_ROTATION_RADIANS_PER_PIXEL * self._rotation_sensitivity()
             rot_y = _rodrigues_matrix(view_up, float(dx) * speed)
             rot_x = _rodrigues_matrix(right, -float(dy) * speed)
-            return rot_x @ rot_y
+            combined: np.ndarray = rot_x @ rot_y
+            return combined
         except (AttributeError, RuntimeError, TypeError, ValueError):
             logging.debug("Suppressed non-critical error", exc_info=True)
             return None

{moleditpy_linux-4.6.1 → moleditpy_linux-4.7.1}/src/moleditpy_linux/ui/dihedral_dialog.py

@@ -489,7 +489,10 @@ class DihedralDialog(GeometryBaseDialog):
         if min(difference, 360.0 - difference) < 0.5:
             return
         with suppress_log(AttributeError, RuntimeError, TypeError):
-            self.main_window.statusBar().showMessage(
+            status_bar = self.main_window.statusBar()
+            if status_bar is None:
+                return
+            status_bar.showMessage(
                 f"Dihedral unchanged ({achieved:.2f}°): the four atoms rotate "
                 "together, which happens for a bond inside a ring.",
                 5000,

{moleditpy_linux-4.6.1 → moleditpy_linux-4.7.1}/src/moleditpy_linux/ui/edit_3d_logic.py

@@ -242,7 +242,7 @@ class Edit3DManager:
 
         # Position near top-right of atom
         atom_pos = atom_item.pos()
-        atom_rect = atom_item.boundingRect()
+        atom_rect = atom_item.visual_rect()
         label_pos = QPointF(
             atom_pos.x() + atom_rect.width() / 4 + 2,
             atom_pos.y() - atom_rect.height() / 4 - 8,

{moleditpy_linux-4.6.1 → moleditpy_linux-4.7.1}/src/moleditpy_linux/ui/edit_actions_logic.py

@@ -1045,7 +1045,7 @@ class EditActionsManager:
                 # Only prepare a geometry change if the implicit H count
                 # changes (this may affect the item's bounding rect).
                 need_geometry = current != new_count
-                if need_geometry and hasattr(item, "prepareGeometryChange"):
+                if need_geometry:
                     item.prepareGeometryChange()
                 item.implicit_h_count = new_count
                 item.has_problem = bool(desired_prob)

{moleditpy_linux-4.6.1 → moleditpy_linux-4.7.1}/src/moleditpy_linux/ui/io_logic.py

@@ -495,22 +495,20 @@ class IOManager:
             self.host.statusBar().showMessage("Error: Nothing to save.")
             return
 
-        native_exts = [".pmeprj", ".pmeraw"]
-        if self.host.init_manager.current_file_path and any(
-            self.host.init_manager.current_file_path.lower().endswith(ext)
-            for ext in native_exts
-        ):
+        current_path = self.host.init_manager.current_file_path
+        if current_path and current_path.lower().endswith(".pmeraw"):
+            # Never write the legacy pickle back; Save As only emits .pmeprj.
+            self.host.update_status_message(
+                "Raw (.pmeraw) files are read-only — saving as .pmeprj instead."
+            )
+            self.save_project_as()
+            return
+
+        if current_path and current_path.lower().endswith(".pmeprj"):
             try:
-                if self.host.init_manager.current_file_path.lower().endswith(".pmeraw"):
-                    save_data = self.host.state_manager.get_current_state()
-                    with open(self.host.init_manager.current_file_path, "wb") as f:
-                        pickle.dump(save_data, f)
-                else:
-                    json_data = self.host.state_manager.create_json_data()
-                    with open(
-                        self.host.init_manager.current_file_path, "w", encoding="utf-8"
-                    ) as f:
-                        json.dump(json_data, f, indent=2, ensure_ascii=False)
+                json_data = self.host.state_manager.create_json_data()
+                with open(current_path, "w", encoding="utf-8") as f:
+                    json.dump(json_data, f, indent=2, ensure_ascii=False)
 
                 self.host.set_has_unsaved_changes(False)
                 self.host.state_manager.update_window_title()
@@ -1109,6 +1107,25 @@ class IOManager:
             except (OSError, IOError, ValueError, RuntimeError, AttributeError) as e:
                 self.host.statusBar().showMessage(f"Error saving XYZ: {e}")
 
+    def _confirm_pickle_load(self, file_path: str) -> bool:
+        """Ask before unpickling a .pmeraw file, which can run arbitrary code."""
+        box = QMessageBox(self.host)
+        box.setIcon(QMessageBox.Icon.Warning)
+        box.setWindowTitle("Open Raw Project File?")
+        box.setText("This file is in the legacy raw (pickle) format.")
+        box.setInformativeText(
+            f"{os.path.basename(file_path)}\n\n"
+            "Raw project files can execute arbitrary code when opened. "
+            "Only open .pmeraw files that you created yourself or received "
+            "from a source you trust.\n\n"
+            "The .pmeprj format is safe and is recommended instead."
+        )
+        open_button = box.addButton("Open", QMessageBox.ButtonRole.AcceptRole)
+        cancel_button = box.addButton(QMessageBox.StandardButton.Cancel)
+        box.setDefaultButton(cancel_button)
+        box.exec()
+        return box.clickedButton() is open_button
+
     def load_raw_data(self, file_path: Optional[str] = None) -> None:
         """Open a .pmeraw pickle project file."""
         if not self.host.state_manager.check_unsaved_changes():
@@ -1129,6 +1146,10 @@ class IOManager:
             if not file_path:
                 return
 
+        if not self._confirm_pickle_load(file_path):
+            self.host.update_status_message("Opening raw project file cancelled.")
+            return
+
         if not self.host.edit_actions_manager.clear_all(skip_check=True):
             return
 

{moleditpy_linux-4.6.1 → moleditpy_linux-4.7.1}/src/moleditpy_linux/ui/main_window_init.py

@@ -223,7 +223,7 @@ class MainInitManager:
         """Resolve the atom-label font now, in the user's configured family."""
         scene = getattr(self, "scene", None)
         font = None
-        if scene is not None and hasattr(scene, "get_setting"):
+        if scene is not None:
             family = scene.get_setting("atom_font_family_2d", FONT_FAMILY)
             size = scene.get_setting("atom_font_size_2d", 20)
             bold = scene.get_setting("atom_font_bold_2d", True)

{moleditpy_linux-4.6.1 → moleditpy_linux-4.7.1}/src/moleditpy_linux/ui/molecular_scene_handler.py

@@ -1396,6 +1396,7 @@ class SceneQueryMixin:
     items: Any
     update_all_items: Any
     window: Any
+    views: Any
     addItem: Any
     removeItem: Any
 
@@ -1592,20 +1593,15 @@ class SceneQueryMixin:
     def find_atom_near(self, pos: Any, tol: float = 14.0) -> Any:
         """Return the AtomItem within tolerance distance of pos, or None.
 
-        ``tol`` is specified in **screen pixels**.  It is divided by the
-        current view scale so that the effective snap radius stays constant
-        on screen regardless of zoom level — matching the behaviour of
-        ``AtomItem.shape()`` (hover highlight).
+        ``tol`` is in screen pixels, divided by the view scale to match shape().
         """
         if pos is None:
             return None
         # Convert screen-pixel tolerance to scene units (zoom-aware).
         if self.views():
-            xform = self.views()[0].transform()
-            if xform is not None:
-                scale = xform.m11()
-                if scale > 0:
-                    tol = tol / scale
+            scale = self.views()[0].transform().m11()
+            if scale > 0:
+                tol = tol / scale
         # Create a small search rectangle around the position
         search_rect = QRectF(pos.x() - tol, pos.y() - tol, 2 * tol, 2 * tol)
         nearby_items = self.items(search_rect)

{moleditpy_linux-4.6.1 → moleditpy_linux-4.7.1}/src/moleditpy_linux/ui/settings_tabs/settings_2d_tab.py

@@ -190,10 +190,11 @@ class Settings2DTab(SettingsTabBase):
 
         form_layout.addRow(self._create_separator())
 
-        # --- Bond Snapping Settings ---
-        form_layout.addRow(QLabel("<b>Bond Snapping Settings</b>"))
+        # --- Atom Hit / Snap Settings ---
+        form_layout.addRow(QLabel("<b>Atom Hit / Snap Settings</b>"))
 
-        # Bond Snapping Distance
+        # Atom hit radius (also used for bond snapping) — internal key is
+        # kept as bond_snapping_distance_2d so existing settings files load.
         self.bond_snapping_distance_2d_slider, self.bond_snapping_distance_2d_label = (
             self._create_slider(5, 50, 1.0, is_int=True)
         )
@@ -201,10 +202,10 @@ class Settings2DTab(SettingsTabBase):
             "The distance in screen pixels (zoom-independent) within which:\n"
             "• Drawing a bond snaps to an existing atom\n"
             "• Keyboard shortcuts instantly edit the atom under cursor\n"
-            "• Atoms show hover highlight"
+            "• Atoms and bonds show hover highlight and respond to clicks"
         )
         form_layout.addRow(
-            "Bond Snapping Distance (px):",
+            "Atom Hit / Snap Distance (px):",
             self._wrap_layout(
                 self.bond_snapping_distance_2d_slider,
                 self.bond_snapping_distance_2d_label,

{moleditpy_linux-4.6.1 → moleditpy_linux-4.7.1}/src/moleditpy_linux/ui/zoomable_view.py

@@ -14,7 +14,7 @@ from __future__ import annotations
 
 from typing import Optional, cast
 
-from PyQt6.QtCore import QEvent, QPointF, Qt
+from PyQt6.QtCore import QEvent, QPointF, Qt, QTimer
 from PyQt6.QtGui import QMouseEvent, QWheelEvent, QNativeGestureEvent
 from PyQt6.QtWidgets import QGraphicsScene, QGraphicsView, QWidget
 
@@ -38,6 +38,14 @@ class ZoomableView(QGraphicsView):
         self._pan_start_scroll_h = 0
         self._pan_start_scroll_v = 0
 
+        # Coalesces re-indexing to once per zoom gesture; doing it per wheel
+        # tick dirties every item and costs ~40x the zoom step on a large
+        # structure.
+        self._geometry_timer = QTimer(self)
+        self._geometry_timer.setSingleShot(True)
+        self._geometry_timer.setInterval(50)
+        self._geometry_timer.timeout.connect(self._invalidate_item_geometry)
+
     def wheelEvent(self, event: Optional[QWheelEvent]) -> None:
         """Event handler for mouse wheel rotation"""
         if event is None:
@@ -123,6 +131,28 @@ class ZoomableView(QGraphicsView):
         else:
             super().mouseReleaseEvent(event)
 
+    def _invalidate_item_geometry(self) -> None:
+        """Re-index items: their pixel-sized hit geometry changes with zoom."""
+        scene = self.scene()
+        if scene is None:
+            return
+        for item in scene.items():
+            # A wrapper deleted mid-iteration (scene teardown) raises.
+            try:
+                item.prepareGeometryChange()
+            except RuntimeError:
+                continue
+
+    def scale(self, sx: float, sy: float) -> None:
+        """Scale the view, then re-index items once the gesture settles."""
+        super().scale(sx, sy)
+        self._geometry_timer.start()
+
+    def resetTransform(self) -> None:
+        """Reset the view transform and re-index items for the new scale."""
+        super().resetTransform()
+        self._geometry_timer.start()
+
     def viewportEvent(self, event: Optional[QEvent]) -> bool:
         """Handle native gestures (like pinch zoom on trackpads)"""
         if event is None:

moleditpy_linux-4.7.1/src/moleditpy_linux/utils/hit_radius.py

@@ -0,0 +1,32 @@
+#!/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
+"""
+
+from typing import Any
+
+DEFAULT_HIT_PX = 14.0
+
+
+def scene_hit_radius(scene: Any, fallback: float = DEFAULT_HIT_PX) -> float:
+    """Return the 2D hit/snap radius in scene units for the current zoom.
+
+    bond_snapping_distance_2d is in screen pixels, so it is divided by the view
+    scale; shape() and find_atom_near() share this to stay in step.
+    """
+    if not scene or not scene.views():
+        return fallback
+
+    scale = scene.views()[0].transform().m11()
+    if scale <= 0.0:
+        scale = 1.0
+
+    hit_px = scene.get_setting("bond_snapping_distance_2d", DEFAULT_HIT_PX)
+    return float(hit_px / scale)