MoleditPy-linux 3.0.1__tar.gz → 3.0.3__tar.gz

{moleditpy_linux-3.0.1 → moleditpy_linux-3.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 3.0.1
+Version: 3.0.3
 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-3.0.1 → moleditpy_linux-3.0.3}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy-linux"
 
-version = "3.0.1"
+version = "3.0.3"
 
 license = {file = "LICENSE"}
 

{moleditpy_linux-3.0.1 → moleditpy_linux-3.0.3}/src/MoleditPy_linux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 3.0.1
+Version: 3.0.3
 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-3.0.1 → moleditpy_linux-3.0.3}/src/moleditpy_linux/plugins/plugin_interface.py

@@ -119,12 +119,6 @@ class PluginContext:
         """
         return Plugin3DController(self._manager.get_main_window())
 
-    def show_status_message(self, message: str, timeout: int = 3000) -> None:
-        """
-        Display a message in the application status bar.
-        """
-        self._manager.show_status_message(message, timeout)
-
     def push_undo_checkpoint(self) -> None:
         """
         Create an undo checkpoint for the current state.
@@ -133,18 +127,6 @@ class PluginContext:
         """
         self._manager.push_undo_checkpoint()
 
-    def refresh_3d_view(self) -> None:
-        """
-        Force a refresh (re-render) of the 3D scene.
-        """
-        self._manager.refresh_3d_view()
-
-    def reset_3d_camera(self) -> None:
-        """
-        Resets the 3D camera to fit the current molecule.
-        """
-        self._manager.reset_3d_camera()
-
     def get_selected_atom_indices(self) -> List[int]:
         """
         Returns a list of RDKit atom indices currently selected in the 2D or 3D view.
@@ -177,9 +159,7 @@ class PluginContext:
         """
         Display a temporary message in the status bar of the main window.
         """
-        mw = self.get_main_window()
-        if mw and hasattr(mw, "ui_manager"):
-            mw.ui_manager.update_status_bar(message)
+        self._manager.show_status_message(message, timeout)
 
     @property
     def current_mol(self) -> Any:
@@ -187,7 +167,11 @@ class PluginContext:
         Get or set the current molecule (RDKit Mol object). Shortcut for current_molecule.
         """
         mw = self.get_main_window()
-        return mw.view_3d_manager.current_mol if mw and hasattr(mw, "view_3d_manager") else None
+        return (
+            mw.view_3d_manager.current_mol
+            if mw and hasattr(mw, "view_3d_manager")
+            else None
+        )
 
     @current_mol.setter
     def current_mol(self, mol: Any):
@@ -211,7 +195,11 @@ class PluginContext:
         Returns the PyVista plotter from the MainWindow.
         """
         mw = self.get_main_window()
-        return mw.view_3d_manager.plotter if mw and hasattr(mw, "view_3d_manager") else None
+        return (
+            mw.view_3d_manager.plotter
+            if mw and hasattr(mw, "view_3d_manager")
+            else None
+        )
 
     @property
     def scene(self) -> Any:
@@ -236,7 +224,10 @@ class PluginContext:
                 mw.view_3d_manager.draw_molecule_3d(mol)
             else:
                 # Also redraw/clear plotter if no molecule
-                if hasattr(mw.view_3d_manager, "plotter") and mw.view_3d_manager.plotter:
+                if (
+                    hasattr(mw.view_3d_manager, "plotter")
+                    and mw.view_3d_manager.plotter
+                ):
                     mw.view_3d_manager.plotter.render()
 
     def reset_3d_camera(self) -> None:

{moleditpy_linux-3.0.1 → moleditpy_linux-3.0.3}/src/moleditpy_linux/plugins/plugin_manager.py

@@ -514,7 +514,6 @@ class PluginManager:
 
         # Check 2D selection
         try:
-            from .plugin_interface import PluginContext
             # We need to access the scene items.
             # In MoleditPy, atoms in the scene are AtomItem objects which have an 'atom_id'.
             # These atom_ids map to entries in state_manager.data.atoms.

{moleditpy_linux-3.0.1 → moleditpy_linux-3.0.3}/src/moleditpy_linux/ui/app_state.py

@@ -752,7 +752,6 @@ class StateManager:
                     if self.host.view_3d_manager.current_mol:
                         # Set 3D coordinates
                         if self.host.view_3d_manager.current_mol.GetNumConformers() > 0:
-                            conf = self.host.view_3d_manager.current_mol.GetConformer()
                             atoms_3d = structure_3d.get("atoms", [])
                             # Ensure numpy array size matches atoms in file
                             num_atoms_file = len(atoms_3d)

{moleditpy_linux-3.0.1 → moleditpy_linux-3.0.3}/src/moleditpy_linux/ui/bond_item.py

@@ -242,7 +242,6 @@ class BondItem(QGraphicsItem):
             center = line.center()
 
             # Logic similar to boundingRect but returning just the label box
-            font_size = 20
             # ... (Simpler logic: just return a box around center)
             # Standard size estimate
             box_size = 30
@@ -265,7 +264,6 @@ class BondItem(QGraphicsItem):
             return
 
         # Default values
-        width_2d = 2.0
         wedge_width_half = 6.0
         num_dashes = 8
         bond_color = QColor("#222222")
@@ -375,9 +373,6 @@ class BondItem(QGraphicsItem):
 
                     if is_in_ring and ring_center:
                         # Ring structure: 1 central line (single bond pos) + 1 short inner line
-                        # Calculate direction from bond center to ring center
-                        bond_center = line.center()
-
                         # Ring center direction in local coords
                         # ring_center may be QPointF (from old/legacy code) or tuple (from new decoupled core)
                         if isinstance(ring_center, (list, tuple)):
@@ -512,8 +507,6 @@ class BondItem(QGraphicsItem):
             # Continue without crashing
 
     def hoverEnterEvent(self, event: Any) -> None:
-        scene = self.scene()
-        mode = getattr(scene, "mode", "")
         self.hovered = True
         self.update()
         if self.scene():

{moleditpy_linux-3.0.1 → moleditpy_linux-3.0.3}/src/moleditpy_linux/ui/custom_interactor_style.py

@@ -182,11 +182,6 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
         )
         is_edit_active = mw.edit_3d_manager.is_3d_edit_mode or is_temp_mode
 
-        # Ctrl+Click for atom selection (3D edit)
-        is_ctrl_click = bool(
-            QApplication.keyboardModifiers() & Qt.KeyboardModifier.ControlModifier
-        )
-
         # Handle measurement mode
         if mw.edit_3d_manager.measurement_mode and mw.view_3d_manager.current_mol:
             click_pos = self.GetInteractor().GetEventPosition()
@@ -419,7 +414,6 @@ class CustomInteractorStyle(vtkInteractorStyleTrackballCamera):
         if self._is_dragging_atom and mw.dragged_atom_info is not None:
             # Custom atom drag
             self.is_dragging = True
-            atom_id = mw.dragged_atom_info["id"]
         else:
             # Delegate camera rotation to parent
             super().OnMouseMove()

{moleditpy_linux-3.0.1 → moleditpy_linux-3.0.3}/src/moleditpy_linux/ui/dialog_logic.py

@@ -16,10 +16,6 @@ import json
 import os
 from PyQt6.QtWidgets import QInputDialog, QMessageBox
 
-try:
-    from . import sip_isdeleted_safe
-except ImportError:
-    pass
 
 try:
     # package relative imports (preferred when running as `python -m moleditpy`)

{moleditpy_linux-3.0.1 → moleditpy_linux-3.0.3}/src/moleditpy_linux/ui/edit_actions_logic.py

@@ -22,7 +22,7 @@ from typing import Any, Dict, List, Optional
 import numpy as np
 
 try:
-    from .mol_geometry import is_problematic_valence, identify_valence_problems
+    from .mol_geometry import identify_valence_problems
 except ImportError:
     from moleditpy_linux.core.mol_geometry import identify_valence_problems
 

{moleditpy_linux-3.0.1 → moleditpy_linux-3.0.3}/src/moleditpy_linux/ui/io_logic.py

@@ -207,7 +207,10 @@ class IOManager:
                             final_mol = _process(charge_val, use_rd_determine=True)
                             break
                         except (RuntimeError, ValueError, TypeError) as e:
-                            if hasattr(self.host, "statusBar") and self.host.statusBar():
+                            if (
+                                hasattr(self.host, "statusBar")
+                                and self.host.statusBar()
+                            ):
                                 self.host.statusBar().showMessage(
                                     f"Chemistry failed for charge {charge_val}: {e}. Try a different charge or skip."
                                 )
@@ -919,8 +922,8 @@ class IOManager:
                         charge = Chem.GetFormalCharge(
                             self.host.view_3d_manager.current_mol
                         )
-                    except:
-                        pass
+                    except Exception as e:
+                        logging.warning("Could not compute formal charge: %s", e)
 
                 multiplicity = 1
                 try:
@@ -930,8 +933,8 @@ class IOManager:
                         )
                         + 1
                     )
-                except:
-                    pass
+                except Exception as e:
+                    logging.warning("Could not compute multiplicity: %s", e)
 
                 xyz_lines.append(
                     f"chrg = {charge}  mult = {multiplicity} | Generated by MoleditPy Ver. {VERSION}"
@@ -1035,4 +1038,3 @@ def _set_mol_prop_safe(mol: Any, key: str, val: Any) -> None:
 
 # Backward-compat aliases
 IOManager = IOManager
-

{moleditpy_linux-3.0.1 → moleditpy_linux-3.0.3}/src/moleditpy_linux/ui/main_window_init.py

@@ -371,30 +371,28 @@ class MainInitManager:
 
                     modules_to_update.append(constants_mod)
 
-            for constants_mod in modules_to_update:
-                constants_mod.CPK_COLORS.clear()
+            for mod in modules_to_update:
+                mod.CPK_COLORS.clear()
                 for k, v in DEFAULT_CPK_COLORS.items():
-                    constants_mod.CPK_COLORS[k] = (
-                        QColor(v) if not isinstance(v, QColor) else v
-                    )
+                    mod.CPK_COLORS[k] = QColor(v) if not isinstance(v, QColor) else v
 
                 # Apply overrides from settings
                 for k, hexv in overrides.items():
                     if isinstance(hexv, str) and hexv:
-                        constants_mod.CPK_COLORS[k] = QColor(hexv)
+                        mod.CPK_COLORS[k] = QColor(hexv)
 
                 # Rebuild the PV representation in-place too
-                if hasattr(constants_mod, "CPK_COLORS_PV"):
-                    constants_mod.CPK_COLORS_PV.clear()
-                    for k, c in constants_mod.CPK_COLORS.items():
-                        constants_mod.CPK_COLORS_PV[k] = [
+                if hasattr(mod, "CPK_COLORS_PV"):
+                    mod.CPK_COLORS_PV.clear()
+                    for k, c in mod.CPK_COLORS.items():
+                        mod.CPK_COLORS_PV[k] = [
                             c.redF(),
                             c.greenF(),
                             c.blueF(),
                         ]
                 else:  # [REPORT ERROR MISSING ATTRIBUTE]
                     logging.error(
-                        "REPORT ERROR: Missing attribute 'CPK_COLORS_PV' on constants_mod"
+                        "REPORT ERROR: Missing attribute 'CPK_COLORS_PV' on constants module"
                     )
         except (AttributeError, RuntimeError, TypeError, ValueError) as e:
             print(f"Failed to update CPK colors from settings: {e}")
@@ -1318,9 +1316,7 @@ class MainInitManager:
             if key == "ball_and_stick":
                 action.setChecked(True)
             action.triggered.connect(
-                lambda checked=False, k=key: (
-                    self.host.view_3d_manager.set_3d_style(k)
-                )
+                lambda checked=False, k=key: (self.host.view_3d_manager.set_3d_style(k))
             )
             style_menu.addAction(action)
             style_group.addAction(action)

{moleditpy_linux-3.0.1 → moleditpy_linux-3.0.3}/src/moleditpy_linux/ui/molecular_scene_handler.py

@@ -733,7 +733,7 @@ class KeyboardMixin:
                 # Case 1: Cursor over atom/bond (one-shot placement)
                 if isinstance(item_at_cursor, (AtomItem, BondItem)):
                     # Set benzene template parameters
-                    n, is_aromatic = 6, True
+                    n = 6
                     points, bonds_info, existing_items = [], [], []
 
                     # Calculate placement like update_template_preview
@@ -903,7 +903,6 @@ class KeyboardMixin:
                             self.data.bonds[new_key] = bond_data
                             bond.atom1, bond.atom2 = bond.atom2, bond.atom1
                             bond.update_position()
-                            was_reversed = True
                         else:
                             bond.order = 1
                             bond.stereo = 1
@@ -915,7 +914,6 @@ class KeyboardMixin:
                             self.data.bonds[new_key] = bond_data
                             bond.atom1, bond.atom2 = bond.atom2, bond.atom1
                             bond.update_position()
-                            was_reversed = True
                         else:
                             bond.order = 1
                             bond.stereo = 2

{moleditpy_linux-3.0.1 → moleditpy_linux-3.0.3}/src/moleditpy_linux/ui/molecule_scene.py

@@ -32,10 +32,6 @@ except ImportError:
     from moleditpy_linux.ui.bond_item import BondItem
     from moleditpy_linux.ui.template_preview_item import TemplatePreviewItem
 
-try:
-    from ..utils.constants import DEFAULT_BOND_LENGTH, SNAP_DISTANCE, SUM_TOLERANCE
-except ImportError:
-    pass
 
 try:
     from PyQt6 import sip as _sip  # type: ignore

{moleditpy_linux-3.0.1 → moleditpy_linux-3.0.3}/src/moleditpy_linux/ui/settings_dialog.py

@@ -27,7 +27,6 @@ from .settings_tabs.settings_3d_tabs import Settings3DSceneTab, SettingsModelTab
 from .settings_tabs.settings_other_tab import SettingsOtherTab
 
 try:
-    from ..utils.constants import CPK_COLORS
     from ..utils.default_settings import DEFAULT_SETTINGS
 except ImportError:
     from moleditpy_linux.utils.default_settings import DEFAULT_SETTINGS

moleditpy_linux-3.0.3/src/moleditpy_linux/ui/translation_dialog.py

@@ -0,0 +1,340 @@
+#!/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 numpy as np
+from PyQt6.QtWidgets import (
+    QCheckBox,
+    QHBoxLayout,
+    QLabel,
+    QLineEdit,
+    QMessageBox,
+    QPushButton,
+    QTabWidget,
+    QVBoxLayout,
+    QWidget,
+)
+
+try:
+    from .base_picking_dialog import BasePickingDialog
+except ImportError:
+    from moleditpy_linux.ui.base_picking_dialog import BasePickingDialog
+
+_TAB_ABSOLUTE = 0
+_TAB_DELTA = 1
+
+
+class TranslationDialog(BasePickingDialog):
+    def __init__(self, mol, main_window, preselected_atoms=None, parent=None):
+        super().__init__(mol, main_window, parent)
+        self.selected_atoms = set()
+
+        if preselected_atoms:
+            self.selected_atoms.update(preselected_atoms)
+
+        self.init_ui()
+
+        if self.selected_atoms:
+            self.show_atom_labels()
+            self.update_display()
+
+    # ------------------------------------------------------------------
+    # UI construction
+    # ------------------------------------------------------------------
+
+    def init_ui(self):
+        self.setWindowTitle("Translate Atoms")
+        self.setModal(False)
+        layout = QVBoxLayout(self)
+
+        self.tabs = QTabWidget()
+        self.tabs.addTab(self._build_absolute_tab(), "Absolute")
+        self.tabs.addTab(self._build_delta_tab(), "Delta")
+        self.tabs.currentChanged.connect(self._on_tab_changed)
+        layout.addWidget(self.tabs)
+
+        # Shared Close button row
+        close_row = QHBoxLayout()
+        close_row.addStretch()
+        close_btn = QPushButton("Close")
+        close_btn.clicked.connect(self.reject)
+        close_row.addWidget(close_btn)
+        layout.addLayout(close_row)
+
+        self.enable_picking()
+
+    def _build_absolute_tab(self):
+        widget = QWidget()
+        layout = QVBoxLayout(widget)
+
+        instr = QLabel(
+            "Click one atom to select it, then specify its target absolute coordinates (Å)."
+        )
+        instr.setWordWrap(True)
+        layout.addWidget(instr)
+
+        self.abs_selection_label = QLabel("No atom selected")
+        layout.addWidget(self.abs_selection_label)
+
+        coord_row = QHBoxLayout()
+        coord_row.addWidget(QLabel("X:"))
+        self.abs_x_input = QLineEdit("0.000")
+        coord_row.addWidget(self.abs_x_input)
+        coord_row.addWidget(QLabel("Y:"))
+        self.abs_y_input = QLineEdit("0.000")
+        coord_row.addWidget(self.abs_y_input)
+        coord_row.addWidget(QLabel("Z:"))
+        self.abs_z_input = QLineEdit("0.000")
+        coord_row.addWidget(self.abs_z_input)
+        layout.addLayout(coord_row)
+
+        self.move_mol_checkbox = QCheckBox("Move entire molecule")
+        self.move_mol_checkbox.setChecked(True)
+        self.move_mol_checkbox.stateChanged.connect(self._on_move_mol_toggled)
+        layout.addWidget(self.move_mol_checkbox)
+
+        btn_row = QHBoxLayout()
+        abs_clear_btn = QPushButton("Clear Selection")
+        abs_clear_btn.clicked.connect(self._abs_clear_selection)
+        btn_row.addWidget(abs_clear_btn)
+        origin_btn = QPushButton("Set to Origin")
+        origin_btn.setToolTip("Set target coordinates to the origin")
+        origin_btn.clicked.connect(self._set_origin)
+        btn_row.addWidget(origin_btn)
+        btn_row.addStretch()
+        self.abs_apply_btn = QPushButton("Move Molecule")
+        self.abs_apply_btn.clicked.connect(self.apply_absolute)
+        self.abs_apply_btn.setEnabled(False)
+        btn_row.addWidget(self.abs_apply_btn)
+        layout.addLayout(btn_row)
+
+        layout.addStretch()
+        return widget
+
+    def _build_delta_tab(self):
+        widget = QWidget()
+        layout = QVBoxLayout(widget)
+
+        instr = QLabel(
+            "Click atoms in the 3D view to select them, then specify the translation vector (Å)."
+        )
+        instr.setWordWrap(True)
+        layout.addWidget(instr)
+
+        self.delta_selection_label = QLabel("No atoms selected")
+        layout.addWidget(self.delta_selection_label)
+
+        vector_row = QHBoxLayout()
+        vector_row.addWidget(QLabel("dX:"))
+        self.dx_input = QLineEdit("0.0")
+        vector_row.addWidget(self.dx_input)
+        vector_row.addWidget(QLabel("dY:"))
+        self.dy_input = QLineEdit("0.0")
+        vector_row.addWidget(self.dy_input)
+        vector_row.addWidget(QLabel("dZ:"))
+        self.dz_input = QLineEdit("0.0")
+        vector_row.addWidget(self.dz_input)
+        layout.addLayout(vector_row)
+
+        btn_row = QHBoxLayout()
+        clear_btn = QPushButton("Clear Selection")
+        clear_btn.clicked.connect(self.clear_selection)
+        btn_row.addWidget(clear_btn)
+
+        select_all_btn = QPushButton("Select All Atoms")
+        select_all_btn.setToolTip("Select all atoms in the molecule")
+        select_all_btn.clicked.connect(self.select_all_atoms)
+        btn_row.addWidget(select_all_btn)
+
+        btn_row.addStretch()
+        self.apply_button = QPushButton("Apply Translation")
+        self.apply_button.clicked.connect(self.apply_translation)
+        self.apply_button.setEnabled(False)
+        btn_row.addWidget(self.apply_button)
+        layout.addLayout(btn_row)
+
+        layout.addStretch()
+        return widget
+
+    # ------------------------------------------------------------------
+    # Tab switching
+    # ------------------------------------------------------------------
+
+    def _on_tab_changed(self, index):
+        self.selected_atoms.clear()
+        self.clear_atom_labels()
+        self.update_display()
+
+    # ------------------------------------------------------------------
+    # Atom picking dispatch
+    # ------------------------------------------------------------------
+
+    def on_atom_picked(self, atom_idx):
+        if self.tabs.currentIndex() == _TAB_ABSOLUTE:
+            self._abs_on_atom_picked(atom_idx)
+        else:
+            self._delta_on_atom_picked(atom_idx)
+
+    def _abs_on_atom_picked(self, atom_idx):
+        # Enforce single selection: replace previous atom
+        self.selected_atoms = {atom_idx}
+        self._populate_abs_inputs_from_atom(atom_idx)
+        self.show_atom_labels()
+        self.update_display()
+
+    def _delta_on_atom_picked(self, atom_idx):
+        if atom_idx in self.selected_atoms:
+            self.selected_atoms.remove(atom_idx)
+        else:
+            self.selected_atoms.add(atom_idx)
+        self.show_atom_labels()
+        self.update_display()
+
+    # ------------------------------------------------------------------
+    # Absolute tab helpers
+    # ------------------------------------------------------------------
+
+    def _populate_abs_inputs_from_atom(self, atom_idx):
+        pos = self.main_window.view_3d_manager.current_mol.GetConformer().GetPositions()[atom_idx]
+        self.abs_x_input.setText(f"{pos[0]:.4f}")
+        self.abs_y_input.setText(f"{pos[1]:.4f}")
+        self.abs_z_input.setText(f"{pos[2]:.4f}")
+
+    def _abs_clear_selection(self):
+        self.selected_atoms.clear()
+        self.clear_atom_labels()
+        self.abs_x_input.setText("0.000")
+        self.abs_y_input.setText("0.000")
+        self.abs_z_input.setText("0.000")
+        self.update_display()
+
+    def _set_origin(self):
+        self.abs_x_input.setText("0.0000")
+        self.abs_y_input.setText("0.0000")
+        self.abs_z_input.setText("0.0000")
+
+    def _on_move_mol_toggled(self, state):
+        label = "Move Molecule" if self.move_mol_checkbox.isChecked() else "Move Atom"
+        self.abs_apply_btn.setText(label)
+
+    def apply_absolute(self):
+        self.mol = self.main_window.view_3d_manager.current_mol
+        if len(self.selected_atoms) != 1:
+            QMessageBox.warning(self, "Warning", "Please select exactly one atom.")
+            return
+
+        try:
+            tx = float(self.abs_x_input.text())
+            ty = float(self.abs_y_input.text())
+            tz = float(self.abs_z_input.text())
+        except ValueError:
+            QMessageBox.warning(self, "Warning", "Please enter valid numbers for X, Y, Z.")
+            return
+
+        atom_idx = next(iter(self.selected_atoms))
+        positions = self.mol.GetConformer().GetPositions()
+        current = positions[atom_idx]
+        delta = np.array([tx, ty, tz]) - current
+
+        if np.allclose(delta, 0):
+            return
+
+        if self.move_mol_checkbox.isChecked():
+            positions += delta
+        else:
+            positions[atom_idx] += delta
+
+        self._update_molecule_geometry(positions)
+        self._push_undo()
+        self.show_atom_labels()
+
+    # ------------------------------------------------------------------
+    # Delta tab methods (unchanged logic)
+    # ------------------------------------------------------------------
+
+    def clear_selection(self):
+        self.selected_atoms.clear()
+        self.clear_atom_labels()
+        self.update_display()
+
+    def select_all_atoms(self):
+        try:
+            if hasattr(self, "mol") and self.mol is not None:
+                self.selected_atoms = set(range(self.mol.GetNumAtoms()))
+            else:
+                self.selected_atoms = (
+                    set(self.main_window.state_manager.data.atoms.keys())
+                    if hasattr(self.main_window.state_manager, "data")
+                    else set()
+                )
+            self.show_atom_labels()
+            self.update_display()
+        except (AttributeError, RuntimeError, TypeError, KeyError) as e:
+            QMessageBox.warning(self, "Warning", f"Failed to select all atoms: {e}")
+
+    def apply_translation(self):
+        self.mol = self.main_window.view_3d_manager.current_mol
+        if not self.selected_atoms:
+            QMessageBox.warning(self, "Warning", "Please select at least one atom.")
+            return
+
+        try:
+            dx = float(self.dx_input.text())
+            dy = float(self.dy_input.text())
+            dz = float(self.dz_input.text())
+        except ValueError:
+            QMessageBox.warning(self, "Warning", "Please enter valid numbers for dx, dy, dz.")
+            return
+
+        if dx == 0 and dy == 0 and dz == 0:
+            return
+
+        translation_vec = np.array([dx, dy, dz])
+        positions = self.mol.GetConformer().GetPositions()
+        for atom_idx in self.selected_atoms:
+            positions[atom_idx] += translation_vec
+
+        self._update_molecule_geometry(positions)
+        self._push_undo()
+        self.show_atom_labels()
+
+    # ------------------------------------------------------------------
+    # Shared display update
+    # ------------------------------------------------------------------
+
+    def update_display(self):
+        tab = self.tabs.currentIndex()
+        count = len(self.selected_atoms)
+
+        if tab == _TAB_ABSOLUTE:
+            if count == 0:
+                self.abs_selection_label.setText("Click one atom to select it")
+                self.abs_apply_btn.setEnabled(False)
+            else:
+                atom_idx = next(iter(self.selected_atoms))
+                sym = self.mol.GetAtomWithIdx(atom_idx).GetSymbol()
+                self.abs_selection_label.setText(f"Selected: atom {atom_idx} ({sym})")
+                self.abs_apply_btn.setEnabled(True)
+        else:
+            if count == 0:
+                self.delta_selection_label.setText("Click atoms to select (minimum 1 required)")
+                self.apply_button.setEnabled(False)
+            else:
+                self.delta_selection_label.setText(f"Selected {count} atom{'s' if count != 1 else ''}")
+                self.apply_button.setEnabled(True)
+
+    def show_atom_labels(self):
+        if self.selected_atoms:
+            sorted_atoms = sorted(self.selected_atoms)
+            pairs = [(idx, str(i + 1)) for i, idx in enumerate(sorted_atoms)]
+            self.show_atom_labels_for(pairs)
+        else:
+            self.clear_atom_labels()

{moleditpy_linux-3.0.1 → moleditpy_linux-3.0.3}/src/moleditpy_linux/ui/ui_manager.py

@@ -319,7 +319,6 @@ class UIManager(QObject):
         self.host.view_3d_manager.plotter.interactor.SetInteractorStyle(style)
         self.host.view_3d_manager.plotter.interactor.Initialize()
 
-
     def handle_drag_enter_event(self, event):
         """Internal handler for drag enter event (bypasses PyQt type checks in tests)."""
         if not event.mimeData().hasUrls():
@@ -344,7 +343,6 @@ class UIManager(QObject):
 
         event.ignore()
 
-
     def handle_drop_event(self, event):
         """Internal handler for file drop event (bypasses PyQt type checks in tests)."""
         urls = event.mimeData().urls()

{moleditpy_linux-3.0.1 → moleditpy_linux-3.0.3}/src/moleditpy_linux/ui/user_template_dialog.py

@@ -508,7 +508,7 @@ class UserTemplateDialog(QDialog):
                     brush = QBrush(Qt.GlobalColor.white)
                     ellipse_x = pos.x() - ellipse_width / 2
                     ellipse_y = pos.y() - ellipse_height / 2
-                    ellipse = scene.addEllipse(
+                    scene.addEllipse(
                         ellipse_x, ellipse_y, ellipse_width, ellipse_height, pen, brush
                     )
 

{moleditpy_linux-3.0.1 → moleditpy_linux-3.0.3}/src/moleditpy_linux/ui/view_3d_logic.py

@@ -37,7 +37,7 @@ except (ImportError, AttributeError, TypeError):
 
 try:
     # package relative imports (preferred when running as `python -m moleditpy`)
-    from .constants import CPK_COLORS_PV, DEFAULT_CPK_COLORS, VDW_RADII, pt
+    from .constants import CPK_COLORS_PV, VDW_RADII, pt
     from .template_preview_item import TemplatePreviewItem
 except ImportError:
     # Fallback to absolute imports for script-style execution

{moleditpy_linux-3.0.1 → moleditpy_linux-3.0.3}/src/moleditpy_linux/ui/zoomable_view.py

@@ -117,9 +117,6 @@ class ZoomableView(QGraphicsView):
                 # (positive for zoom-in, negative for zoom-out)
                 factor = 1.0 + event.value()
 
-                current_scale = self.transform().m11()
-                min_scale, max_scale = 0.05, 20.0
-
                 # Apply scaling if within limits
                 self.scale(factor, factor)
                 return True

{moleditpy_linux-3.0.1 → moleditpy_linux-3.0.3}/src/moleditpy_linux/utils/constants.py

@@ -16,7 +16,7 @@ from PyQt6.QtGui import QColor, QFont
 from rdkit import Chem
 
 # Version
-VERSION = "3.0.1"
+VERSION = "3.0.3"
 
 ATOM_RADIUS = 18
 BOND_OFFSET = 3.5

moleditpy_linux-3.0.1/src/moleditpy_linux/ui/translation_dialog.py

@@ -1,193 +0,0 @@
-#!/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 numpy as np
-from PyQt6.QtWidgets import (
-    QHBoxLayout,
-    QLabel,
-    QLineEdit,
-    QMessageBox,
-    QPushButton,
-    QVBoxLayout,
-)
-
-try:
-    from .base_picking_dialog import BasePickingDialog
-except ImportError:
-    from moleditpy_linux.ui.base_picking_dialog import BasePickingDialog
-
-
-class TranslationDialog(BasePickingDialog):
-    def __init__(self, mol, main_window, preselected_atoms=None, parent=None):
-        super().__init__(mol, main_window, parent)
-        self.selected_atoms = set()
-
-        # Add preselected atoms
-        if preselected_atoms:
-            self.selected_atoms.update(preselected_atoms)
-
-        self.init_ui()
-
-        # Add labels to preselected atoms
-        if self.selected_atoms:
-            self.show_atom_labels()
-            self.update_display()
-
-    def init_ui(self):
-        self.setWindowTitle("Translate Atoms")
-        self.setModal(False)
-        layout = QVBoxLayout(self)
-
-        # Instructions
-        instruction_label = QLabel(
-            "Click atoms in the 3D view to select them for translation. Specify the translation vector in Å."
-        )
-        instruction_label.setWordWrap(True)
-        layout.addWidget(instruction_label)
-
-        # Selected atoms display
-        self.selection_label = QLabel("No atoms selected")
-        layout.addWidget(self.selection_label)
-
-        # Translation vector input
-        vector_layout = QHBoxLayout()
-        vector_layout.addWidget(QLabel("dX:"))
-        self.dx_input = QLineEdit("0.0")
-        vector_layout.addWidget(self.dx_input)
-
-        vector_layout.addWidget(QLabel("dY:"))
-        self.dy_input = QLineEdit("0.0")
-        vector_layout.addWidget(self.dy_input)
-
-        vector_layout.addWidget(QLabel("dZ:"))
-        self.dz_input = QLineEdit("0.0")
-        vector_layout.addWidget(self.dz_input)
-
-        layout.addLayout(vector_layout)
-
-        # Buttons
-        button_layout = QHBoxLayout()
-        self.clear_button = QPushButton("Clear Selection")
-        self.clear_button.clicked.connect(self.clear_selection)
-        button_layout.addWidget(self.clear_button)
-
-        # Select all atoms button
-        self.select_all_button = QPushButton("Select All Atoms")
-        self.select_all_button.setToolTip("Select all atoms in the molecule")
-        self.select_all_button.clicked.connect(self.select_all_atoms)
-        button_layout.addWidget(self.select_all_button)
-
-        button_layout.addStretch()
-
-        self.apply_button = QPushButton("Apply Translation")
-        self.apply_button.clicked.connect(self.apply_translation)
-        self.apply_button.setEnabled(False)
-        button_layout.addWidget(self.apply_button)
-
-        close_button = QPushButton("Close")
-        close_button.clicked.connect(self.reject)
-        button_layout.addWidget(close_button)
-
-        layout.addLayout(button_layout)
-
-        # Connect to main window's picker
-        self.picker_connection = None
-        self.enable_picking()
-
-    def on_atom_picked(self, atom_idx):
-        """Handle the event when an atom is picked in the 3D view."""
-        if atom_idx in self.selected_atoms:
-            self.selected_atoms.remove(atom_idx)
-        else:
-            self.selected_atoms.add(atom_idx)
-
-        # Display labels on the atoms
-        self.show_atom_labels()
-        self.update_display()
-
-    def clear_selection(self):
-        """Clear the current atom selection."""
-        self.selected_atoms.clear()
-        self.clear_atom_labels()
-        self.update_display()
-
-    def select_all_atoms(self):
-        """Select all atoms in the current molecule."""
-        try:
-            if hasattr(self, "mol") and self.mol is not None:
-                n = self.mol.GetNumAtoms()
-                self.selected_atoms = set(range(n))
-            else:
-                self.selected_atoms = (
-                    set(self.main_window.state_manager.data.atoms.keys())
-                    if hasattr(self.main_window.state_manager, "data")
-                    else set()
-                )
-
-            self.show_atom_labels()
-            self.update_display()
-        except (AttributeError, RuntimeError, TypeError, KeyError) as e:
-            QMessageBox.warning(self, "Warning", f"Failed to select all atoms: {e}")
-
-    def update_display(self):
-        """Update the UI display with current selection info."""
-        count = len(self.selected_atoms)
-        if count == 0:
-            self.selection_label.setText("Click atoms to select (minimum 1 required)")
-            self.apply_button.setEnabled(False)
-        else:
-            self.selection_label.setText(f"Selected {count} atoms")
-            self.apply_button.setEnabled(True)
-
-    def show_atom_labels(self):
-        """Show numeric labels for the selected atoms."""
-        if self.selected_atoms:
-            sorted_atoms = sorted(self.selected_atoms)
-            pairs = [(idx, str(i + 1)) for i, idx in enumerate(sorted_atoms)]
-            self.show_atom_labels_for(pairs)
-        else:
-            self.clear_atom_labels()
-
-    def apply_translation(self):
-        """Apply the translation to selected atoms."""
-        if not self.selected_atoms:
-            QMessageBox.warning(self, "Warning", "Please select at least one atom.")
-            return
-
-        try:
-            dx = float(self.dx_input.text())
-            dy = float(self.dy_input.text())
-            dz = float(self.dz_input.text())
-        except ValueError:
-            QMessageBox.warning(
-                self, "Warning", "Please enter valid numbers for dx, dy, dz."
-            )
-            return
-
-        if dx == 0 and dy == 0 and dz == 0:
-            return
-
-        translation_vec = np.array([dx, dy, dz])
-
-        # Update positions
-        positions = self.mol.GetConformer().GetPositions()
-        for atom_idx in self.selected_atoms:
-            positions[atom_idx] += translation_vec
-
-        # Write updated positions back using inherited helper
-        self._update_molecule_geometry(positions)
-
-        # Push Undo state AFTER modification
-        self._push_undo()
-
-        # Update labels
-        self.show_atom_labels()