MoleditPy-linux 3.0.2__tar.gz → 3.0.3__tar.gz

{moleditpy_linux-3.0.2 → moleditpy_linux-3.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 3.0.2
+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-3.0.2 → moleditpy_linux-3.0.3}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy-linux"
 
-version = "3.0.2"
+version = "3.0.3"
 
 license = {file = "LICENSE"}
 

{moleditpy_linux-3.0.2 → moleditpy_linux-3.0.3}/src/MoleditPy_linux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 3.0.2
+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-3.0.3/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-3.0.2 → 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 = "3.0.2"
+VERSION = "3.0.3"
 
 ATOM_RADIUS = 18
 BOND_OFFSET = 3.5

moleditpy_linux-3.0.2/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()