MoleditPy-linux 2.2.4__py3-none-any.whl

moleditpy_linux/modules/template_preview_item.py

@@ -0,0 +1,157 @@
+#!/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 PyQt6.QtWidgets import (
+    QGraphicsItem
+)
+
+from PyQt6.QtGui import (
+    QPen, QBrush, QColor, QFont, QPolygonF
+)
+
+
+from PyQt6.QtCore import (
+    Qt, QPointF, QRectF, QLineF
+)
+
+try:
+    from .constants import CPK_COLORS
+except Exception:
+    from modules.constants import CPK_COLORS
+
+class TemplatePreviewItem(QGraphicsItem):
+    def __init__(self):
+        super().__init__()
+        self.setZValue(2)
+        self.pen = QPen(QColor(80, 80, 80, 180), 2)
+        self.polygon = QPolygonF()
+        self.is_aromatic = False
+        self.user_template_points = []
+        self.user_template_bonds = []
+        self.user_template_atoms = []
+        self.is_user_template = False
+
+    def set_geometry(self, points, is_aromatic=False):
+        self.prepareGeometryChange()
+        self.polygon = QPolygonF(points)
+        self.is_aromatic = is_aromatic
+        self.is_user_template = False
+        self.update()
+    
+    def set_user_template_geometry(self, points, bonds_info, atoms_data):
+        self.prepareGeometryChange()
+        self.user_template_points = points
+        self.user_template_bonds = bonds_info
+        self.user_template_atoms = atoms_data
+        self.is_user_template = True
+        self.is_aromatic = False
+        self.polygon = QPolygonF()
+        self.update()
+
+    def boundingRect(self):
+        if self.is_user_template and self.user_template_points:
+            # Calculate bounding rect for user template
+            min_x = min(p.x() for p in self.user_template_points)
+            max_x = max(p.x() for p in self.user_template_points)
+            min_y = min(p.y() for p in self.user_template_points)
+            max_y = max(p.y() for p in self.user_template_points)
+            return QRectF(min_x - 20, min_y - 20, max_x - min_x + 40, max_y - min_y + 40)
+        return self.polygon.boundingRect().adjusted(-5, -5, 5, 5)
+
+    def paint(self, painter, option, widget):
+        if self.is_user_template:
+            self.paint_user_template(painter)
+        else:
+            self.paint_regular_template(painter)
+    
+    def paint_regular_template(self, painter):
+        painter.setPen(self.pen)
+        painter.setBrush(Qt.BrushStyle.NoBrush)
+        if not self.polygon.isEmpty():
+            painter.drawPolygon(self.polygon)
+            if self.is_aromatic:
+                center = self.polygon.boundingRect().center()
+                radius = QLineF(center, self.polygon.first()).length() * 0.6
+                painter.drawEllipse(center, radius, radius)
+    
+    def paint_user_template(self, painter):
+        if not self.user_template_points:
+            return
+        
+        # Draw bonds first with better visibility
+        # Draw bonds first with better visibility
+        # Use gray (ghost) color for template preview to distinguish from real bonds
+        bond_pen = QPen(QColor(80, 80, 80, 180), 2.5)
+        painter.setPen(bond_pen)
+        
+        for bond_info in self.user_template_bonds:
+            if len(bond_info) >= 3:
+                atom1_idx, atom2_idx, order = bond_info[:3]
+            else:
+                atom1_idx, atom2_idx = bond_info[:2]
+                order = 1
+                
+            if atom1_idx < len(self.user_template_points) and atom2_idx < len(self.user_template_points):
+                pos1 = self.user_template_points[atom1_idx]
+                pos2 = self.user_template_points[atom2_idx]
+                
+                if order == 2:
+                    # Double bond - draw two parallel lines
+                    line = QLineF(pos1, pos2)
+                    normal = line.normalVector()
+                    normal.setLength(4)
+                    
+                    line1 = QLineF(pos1 + normal.p2() - normal.p1(), pos2 + normal.p2() - normal.p1())
+                    line2 = QLineF(pos1 - normal.p2() + normal.p1(), pos2 - normal.p2() + normal.p1())
+                    
+                    painter.drawLine(line1)
+                    painter.drawLine(line2)
+                elif order == 3:
+                    # Triple bond - draw three parallel lines
+                    line = QLineF(pos1, pos2)
+                    normal = line.normalVector()
+                    normal.setLength(6)
+                    
+                    painter.drawLine(line)
+                    line1 = QLineF(pos1 + normal.p2() - normal.p1(), pos2 + normal.p2() - normal.p1())
+                    line2 = QLineF(pos1 - normal.p2() + normal.p1(), pos2 - normal.p2() + normal.p1())
+                    
+                    painter.drawLine(line1)
+                    painter.drawLine(line2)
+                else:
+                    # Single bond
+                    painter.drawLine(QLineF(pos1, pos2))
+        
+        # Draw atoms - white ellipse background to hide bonds, then CPK colored text
+        for i, pos in enumerate(self.user_template_points):
+            if i < len(self.user_template_atoms):
+                atom_data = self.user_template_atoms[i]
+                symbol = atom_data.get('symbol', 'C')
+                
+                # Draw all non-carbon atoms including hydrogen with white background ellipse + CPK colored text
+                if symbol != 'C':
+                    # Get CPK color for text
+                    color = CPK_COLORS.get(symbol, CPK_COLORS.get('DEFAULT', QColor('#FF1493')))
+                    
+                    # Draw white background ellipse to hide bonds
+                    painter.setPen(QPen(Qt.GlobalColor.white, 0))  # No border
+                    painter.setBrush(QBrush(Qt.GlobalColor.white))
+                    painter.drawEllipse(int(pos.x() - 12), int(pos.y() - 8), 24, 16)
+                    
+                    # Draw CPK colored text on top
+                    painter.setPen(QPen(color))
+                    font = QFont("Arial", 12, QFont.Weight.Bold)  # Larger font
+                    painter.setFont(font)
+                    metrics = painter.fontMetrics()
+                    text_rect = metrics.boundingRect(symbol)
+                    text_pos = QPointF(pos.x() - text_rect.width()/2, pos.y() + text_rect.height()/3)
+                    painter.drawText(text_pos, symbol)

moleditpy_linux/modules/template_preview_view.py

@@ -0,0 +1,74 @@
+#!/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 PyQt6.QtWidgets import QGraphicsView
+
+from PyQt6.QtCore import Qt, QTimer
+
+class TemplatePreviewView(QGraphicsView):
+    """テンプレートプレビュー用のカスタムビュークラス"""
+    
+    def __init__(self, scene):
+        super().__init__(scene)
+        self.original_scene_rect = None
+        self.template_data = None  # Store template data for dynamic redrawing
+        self.parent_dialog = None  # Reference to parent dialog for redraw access
+    
+    def set_template_data(self, template_data, parent_dialog):
+        """テンプレートデータと親ダイアログの参照を設定"""
+        self.template_data = template_data
+        self.parent_dialog = parent_dialog
+    
+    def resizeEvent(self, event):
+        """リサイズイベントを処理してプレビューを再フィット"""
+        super().resizeEvent(event)
+        if self.original_scene_rect and not self.original_scene_rect.isEmpty():
+            # Delay the fitInView call to ensure proper widget sizing
+            QTimer.singleShot(10, self.refit_view)
+    
+    def refit_view(self):
+        """ビューを再フィット"""
+        try:
+            if self.original_scene_rect and not self.original_scene_rect.isEmpty():
+                self.fitInView(self.original_scene_rect, Qt.AspectRatioMode.KeepAspectRatio)
+        except Exception as e:
+            print(f"Warning: Failed to refit template preview: {e}")
+    
+    def showEvent(self, event):
+        """表示イベントを処理"""
+        super().showEvent(event)
+        # Ensure proper fitting when widget becomes visible
+        if self.original_scene_rect:
+            QTimer.singleShot(50, self.refit_view)
+    
+    def redraw_with_current_size(self):
+        """現在のサイズに合わせてテンプレートを再描画"""
+        if self.template_data and self.parent_dialog:
+            try:
+                # Clear current scene
+                self.scene().clear()
+                
+                # Redraw with current view size for proper fit-based scaling
+                view_size = (self.width(), self.height())
+                self.parent_dialog.draw_template_preview(self.scene(), self.template_data, view_size)
+                
+                # Refit the view
+                bounding_rect = self.scene().itemsBoundingRect()
+                if not bounding_rect.isEmpty() and bounding_rect.width() > 0 and bounding_rect.height() > 0:
+                    content_size = max(bounding_rect.width(), bounding_rect.height())
+                    padding = max(20, content_size * 0.2)
+                    padded_rect = bounding_rect.adjusted(-padding, -padding, padding, padding)
+                    self.scene().setSceneRect(padded_rect)
+                    self.original_scene_rect = padded_rect
+                    QTimer.singleShot(10, lambda: self.fitInView(padded_rect, Qt.AspectRatioMode.KeepAspectRatio))
+            except Exception as e:
+                print(f"Warning: Failed to redraw template preview: {e}")

moleditpy_linux/modules/translation_dialog.py

@@ -0,0 +1,365 @@
+#!/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 PyQt6.QtWidgets import (
+    QDialog, QVBoxLayout, QLabel, QGridLayout, QLineEdit, QCheckBox, QPushButton, QHBoxLayout
+)
+from PyQt6.QtWidgets import QMessageBox
+from PyQt6.QtCore import Qt
+import numpy as np
+
+from .dialog3_d_picking_mixin import Dialog3DPickingMixin
+
+class TranslationDialog(Dialog3DPickingMixin, QDialog):
+    def __init__(self, mol, main_window, parent=None):
+        QDialog.__init__(self, parent)
+        Dialog3DPickingMixin.__init__(self)
+        self.mol = mol
+        self.main_window = main_window
+        self.selected_atoms = set()  # 複数原子選択用
+        self.init_ui()
+    
+    def init_ui(self):
+        self.setWindowTitle("Translation")
+        self.setModal(False)  # モードレスにしてクリックを阻害しない
+        self.setWindowFlags(Qt.WindowType.Window | Qt.WindowType.WindowStaysOnTopHint)  # 常に前面表示
+        layout = QVBoxLayout(self)
+        
+        # Instructions
+        instruction_label = QLabel("Click atoms in the 3D view to select them. The centroid of selected atoms will be moved to the target coordinates, translating the entire molecule.")
+        instruction_label.setWordWrap(True)
+        layout.addWidget(instruction_label)
+        
+        # Selected atoms display
+        self.selection_label = QLabel("No atoms selected")
+        layout.addWidget(self.selection_label)
+        
+        # Coordinate inputs
+        coord_layout = QGridLayout()
+        coord_layout.addWidget(QLabel("Target X:"), 0, 0)
+        self.x_input = QLineEdit("0.0")
+        coord_layout.addWidget(self.x_input, 0, 1)
+        
+        coord_layout.addWidget(QLabel("Target Y:"), 1, 0)
+        self.y_input = QLineEdit("0.0")
+        coord_layout.addWidget(self.y_input, 1, 1)
+        
+        coord_layout.addWidget(QLabel("Target Z:"), 2, 0)
+        self.z_input = QLineEdit("0.0")
+        coord_layout.addWidget(self.z_input, 2, 1)
+        
+        layout.addLayout(coord_layout)
+
+        # Translation target toggle: Entire molecule (default) or Selected atoms only
+        self.translate_selected_only_checkbox = QCheckBox("Translate selected atoms only")
+        self.translate_selected_only_checkbox.setToolTip(
+            "When checked, only the atoms you selected will be moved so their centroid matches the target.\n"
+            "When unchecked (default), the entire molecule will be translated so the selected atoms' centroid moves to the target."
+        )
+        self.translate_selected_only_checkbox.setChecked(False)  # default: entire molecule
+        layout.addWidget(self.translate_selected_only_checkbox)
+        
+        # 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 for translation")
+        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):
+        """原子がピックされたときの処理"""
+        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()
+    
+    def keyPressEvent(self, event):
+        """キーボードイベントを処理"""
+        if event.key() == Qt.Key.Key_Return or event.key() == Qt.Key.Key_Enter:
+            if self.apply_button.isEnabled():
+                self.apply_translation()
+            event.accept()
+        else:
+            super().keyPressEvent(event)
+    
+    def update_display(self):
+        """表示を更新"""
+        if not self.selected_atoms:
+            self.selection_label.setText("No atoms selected")
+            self.apply_button.setEnabled(False)
+        else:
+            # 分子の有効性チェック
+            if not self.mol or self.mol.GetNumConformers() == 0:
+                self.selection_label.setText("Error: No valid molecule or conformer")
+                self.apply_button.setEnabled(False)
+                return
+            
+            try:
+                conf = self.mol.GetConformer()
+                # 選択原子の重心を計算
+                centroid = self.calculate_centroid()
+                
+                # 選択原子の情報を表示
+                atom_info = []
+                for atom_idx in sorted(self.selected_atoms):
+                    symbol = self.mol.GetAtomWithIdx(atom_idx).GetSymbol()
+                    atom_info.append(f"{symbol}({atom_idx})")
+                
+                self.selection_label.setText(
+                    f"Selected atoms: {', '.join(atom_info)}\n"
+                    f"Centroid: ({centroid[0]:.2f}, {centroid[1]:.2f}, {centroid[2]:.2f})"
+                )
+                self.apply_button.setEnabled(True)
+            except Exception as e:
+                self.selection_label.setText(f"Error accessing atom data: {str(e)}")
+                self.apply_button.setEnabled(False)
+
+        # Update the coordinate input fields when selection changes
+        # If there are selected atoms, fill the inputs with the computed centroid (or single atom pos).
+        # If no atoms selected, clear or reset to 0.0.
+        try:
+            if self.selected_atoms:
+                # Use the centroid we just computed if available; otherwise compute now.
+                try:
+                    coords = centroid
+                except NameError:
+                    coords = self.calculate_centroid()
+
+                # Format with reasonable precision
+                self.x_input.setText(f"{coords[0]:.4f}")
+                self.y_input.setText(f"{coords[1]:.4f}")
+                self.z_input.setText(f"{coords[2]:.4f}")
+            else:
+                # No selection: reset fields to default
+                self.x_input.setText("0.0")
+                self.y_input.setText("0.0")
+                self.z_input.setText("0.0")
+        except Exception:
+            # Be tolerant: do not crash the UI if inputs cannot be updated
+            pass
+    
+    def calculate_centroid(self):
+        """選択原子の重心を計算"""
+        if not self.selected_atoms:
+            return np.array([0.0, 0.0, 0.0])
+        
+        conf = self.mol.GetConformer()
+        positions = []
+        for atom_idx in self.selected_atoms:
+            pos = conf.GetAtomPosition(atom_idx)
+            positions.append([pos.x, pos.y, pos.z])
+        
+        return np.mean(positions, axis=0)
+    
+    def apply_translation(self):
+        """平行移動を適用"""
+        if not self.selected_atoms:
+            QMessageBox.warning(self, "Warning", "Please select at least one atom.")
+            return
+
+        # 分子の有効性チェック
+        if not self.mol or self.mol.GetNumConformers() == 0:
+            QMessageBox.warning(self, "Warning", "No valid molecule or conformer available.")
+            return
+
+        try:
+            target_x = float(self.x_input.text())
+            target_y = float(self.y_input.text())
+            target_z = float(self.z_input.text())
+        except ValueError:
+            QMessageBox.warning(self, "Warning", "Please enter valid coordinates.")
+            return
+
+        try:
+            # 選択原子の重心を計算
+            current_centroid = self.calculate_centroid()
+            target_pos = np.array([target_x, target_y, target_z])
+
+            # 移動ベクトルを計算
+            translation_vector = target_pos - current_centroid
+
+            conf = self.mol.GetConformer()
+
+            if self.translate_selected_only_checkbox.isChecked():
+                # Move only the selected atoms: shift selected atoms by translation_vector
+                for i in range(self.mol.GetNumAtoms()):
+                    if i in self.selected_atoms:
+                        atom_pos = np.array(conf.GetAtomPosition(i))
+                        new_pos = atom_pos + translation_vector
+                        conf.SetAtomPosition(i, new_pos.tolist())
+                        # Update 3d positions for this atom only
+                        try:
+                            self.main_window.atom_positions_3d[i] = new_pos
+                        except Exception:
+                            pass
+                    else:
+                        # leave other atoms unchanged
+                        continue
+            else:
+                # Default: translate entire molecule so centroid moves to target
+                for i in range(self.mol.GetNumAtoms()):
+                    atom_pos = np.array(conf.GetAtomPosition(i))
+                    new_pos = atom_pos + translation_vector
+                    conf.SetAtomPosition(i, new_pos.tolist())
+                    self.main_window.atom_positions_3d[i] = new_pos
+
+
+            # 3D表示を更新
+            self.main_window.draw_molecule_3d(self.mol)
+
+            # キラルラベルを更新
+            self.main_window.update_chiral_labels()
+
+            # Apply後に選択解除
+            self.clear_selection()
+
+            # Undo状態を保存
+            self.main_window.push_undo_state()
+
+        except Exception as e:
+            QMessageBox.critical(self, "Error", f"Failed to apply translation: {str(e)}")
+    
+    def clear_selection(self):
+        """選択をクリア"""
+        self.selected_atoms.clear()
+        self.clear_atom_labels()
+        self.update_display()
+    
+    def select_all_atoms(self):
+        """Select all atoms in the current molecule and update labels/UI."""
+        try:
+            # Prefer RDKit molecule if available
+            if hasattr(self, 'mol') and self.mol is not None:
+                try:
+                    n = self.mol.GetNumAtoms()
+                    # create a set of indices [0..n-1]
+                    self.selected_atoms = set(range(n))
+                except Exception:
+                    # fallback to main_window data map
+                    self.selected_atoms = set(self.main_window.data.atoms.keys()) if hasattr(self.main_window, 'data') else set()
+            else:
+                # fallback to main_window data map
+                self.selected_atoms = set(self.main_window.data.atoms.keys()) if hasattr(self.main_window, 'data') else set()
+
+            # Update labels and display
+            self.show_atom_labels()
+            self.update_display()
+
+        except Exception as e:
+            QMessageBox.warning(self, "Warning", f"Failed to select all atoms: {e}")
+    
+    def show_atom_labels(self):
+        """選択された原子にラベルを表示"""
+        # 既存のラベルをクリア
+        self.clear_atom_labels()
+
+        if not hasattr(self, 'selection_labels'):
+            self.selection_labels = []
+
+        if self.selected_atoms:
+            positions = []
+            labels = []
+
+            for i, atom_idx in enumerate(sorted(self.selected_atoms)):
+                pos = self.main_window.atom_positions_3d[atom_idx]
+                positions.append(pos)
+                labels.append(f"S{i+1}")
+
+            # 重心位置も表示
+            if len(self.selected_atoms) > 1:
+                centroid = self.calculate_centroid()
+                positions.append(centroid)
+                labels.append("CEN")
+
+            # ラベルを追加
+            if positions:
+                label_actor = self.main_window.plotter.add_point_labels(
+                    positions, labels,
+                    point_size=20,
+                    font_size=12,
+                    text_color='cyan',
+                    always_visible=True
+                )
+                # add_point_labelsがリストを返す場合も考慮
+                if isinstance(label_actor, list):
+                    self.selection_labels.extend(label_actor)
+                else:
+                    self.selection_labels.append(label_actor)
+    
+    def clear_atom_labels(self):
+        """原子ラベルをクリア"""
+        if hasattr(self, 'selection_labels'):
+            for label_actor in self.selection_labels:
+                try:
+                    self.main_window.plotter.remove_actor(label_actor)
+                except Exception:
+                    pass
+            self.selection_labels = []
+        # ラベル消去後に再描画を強制
+        try:
+            self.main_window.plotter.render()
+        except Exception:
+            pass
+    
+    def closeEvent(self, event):
+        """ダイアログが閉じられる時の処理"""
+        self.clear_atom_labels()
+        self.disable_picking()
+        try:
+            self.main_window.draw_molecule_3d(self.mol)
+        except Exception:
+            pass
+        super().closeEvent(event)
+    
+    def reject(self):
+        """キャンセル時の処理"""
+        self.clear_atom_labels()
+        self.disable_picking()
+        try:
+            self.main_window.draw_molecule_3d(self.mol)
+        except Exception:
+            pass
+        super().reject()
+    
+    def accept(self):
+        """OK時の処理"""
+        self.clear_atom_labels()
+        self.disable_picking()
+        try:
+            self.main_window.draw_molecule_3d(self.mol)
+        except Exception:
+            pass
+        super().accept()