MoleditPy-linux 2.4.1__py3-none-any.whl

moleditpy_linux/modules/bond_length_dialog.py

@@ -0,0 +1,380 @@
+#!/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, QHBoxLayout, QPushButton, QLineEdit, QWidget, QRadioButton, QMessageBox
+)
+
+from .dialog3_d_picking_mixin import Dialog3DPickingMixin
+
+from PyQt6.QtCore import Qt
+import numpy as np
+
+class BondLengthDialog(Dialog3DPickingMixin, QDialog):
+    def __init__(self, mol, main_window, preselected_atoms=None, parent=None):
+        QDialog.__init__(self, parent)
+        Dialog3DPickingMixin.__init__(self)
+        self.mol = mol
+        self.main_window = main_window
+        self.atom1_idx = None
+        self.atom2_idx = None
+        
+        # 事前選択された原子を設定
+        if preselected_atoms and len(preselected_atoms) >= 2:
+            self.atom1_idx = preselected_atoms[0]
+            self.atom2_idx = preselected_atoms[1]
+        
+        self.init_ui()
+    
+    def init_ui(self):
+        self.setWindowTitle("Adjust Bond Length")
+        self.setModal(False)  # モードレスにしてクリックを阻害しない
+  # 常に前面表示
+        layout = QVBoxLayout(self)
+        
+        # Instructions
+        instruction_label = QLabel("Click two atoms in the 3D view to select a bond, then specify the new length.")
+        instruction_label.setWordWrap(True)
+        layout.addWidget(instruction_label)
+        
+        # Selected atoms display
+        self.selection_label = QLabel("No atoms selected")
+        layout.addWidget(self.selection_label)
+        
+        # Current distance display
+        self.distance_label = QLabel("")
+        layout.addWidget(self.distance_label)
+        
+        # New distance input
+        distance_layout = QHBoxLayout()
+        distance_layout.addWidget(QLabel("New distance (Å):"))
+        self.distance_input = QLineEdit()
+        self.distance_input.setPlaceholderText("1.54")
+        distance_layout.addWidget(self.distance_input)
+        layout.addLayout(distance_layout)
+        
+        # Movement options
+        group_box = QWidget()
+        group_layout = QVBoxLayout(group_box)
+        group_layout.addWidget(QLabel("Movement Options:"))
+        
+        self.atom1_fix_group_radio = QRadioButton("Atom 1: Fixed, Atom 2: Move connected group")
+        self.atom1_fix_group_radio.setChecked(True)
+        group_layout.addWidget(self.atom1_fix_group_radio)
+
+        self.atom1_fix_radio = QRadioButton("Atom 1: Fixed, Atom 2: Move atom only")
+        group_layout.addWidget(self.atom1_fix_radio)
+        
+        self.both_groups_radio = QRadioButton("Both groups: Move towards center equally")
+        group_layout.addWidget(self.both_groups_radio)
+        
+        layout.addWidget(group_box)
+        
+        # Buttons
+        button_layout = QHBoxLayout()
+        self.clear_button = QPushButton("Clear Selection")
+        self.clear_button.clicked.connect(self.clear_selection)
+        button_layout.addWidget(self.clear_button)
+        
+        button_layout.addStretch()
+        
+        self.apply_button = QPushButton("Apply")
+        self.apply_button.clicked.connect(self.apply_changes)
+        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()
+        
+        # 事前選択された原子がある場合は初期表示を更新
+        if self.atom1_idx is not None:
+            self.show_atom_labels()
+            self.update_display()
+    
+    def on_atom_picked(self, atom_idx):
+        """原子がピックされたときの処理"""
+        if self.atom1_idx is None:
+            self.atom1_idx = atom_idx
+        elif self.atom2_idx is None:
+            self.atom2_idx = atom_idx
+        else:
+            # Reset and start over
+            self.atom1_idx = atom_idx
+            self.atom2_idx = None
+        
+        # 原子ラベルを表示
+        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_changes()
+            event.accept()
+        else:
+            super().keyPressEvent(event)
+    
+    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()
+        super().closeEvent(event)
+    
+    def reject(self):
+        """キャンセル時の処理"""
+        self.clear_atom_labels()
+        self.disable_picking()
+        super().reject()
+    
+    def accept(self):
+        """OK時の処理"""
+        self.clear_atom_labels()
+        self.disable_picking()
+        super().accept()
+    
+    def clear_selection(self):
+        """選択をクリア"""
+        self.atom1_idx = None
+        self.atom2_idx = None
+        self.clear_selection_labels()
+        self.update_display()
+    
+    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()
+        
+        # 新しいラベルを表示
+        if not hasattr(self, 'selection_labels'):
+            self.selection_labels = []
+        
+        selected_atoms = [self.atom1_idx, self.atom2_idx]
+        labels = ["1st", "2nd"]
+        colors = ["yellow", "yellow"]
+        
+        for i, atom_idx in enumerate(selected_atoms):
+            if atom_idx is not None:
+                pos = self.main_window.atom_positions_3d[atom_idx]
+                label_text = f"{labels[i]}"
+                
+                # ラベルを追加
+                label_actor = self.main_window.plotter.add_point_labels(
+                    [pos], [label_text], 
+                    point_size=20, 
+                    font_size=12,
+                    text_color=colors[i],
+                    always_visible=True
+                )
+                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 = []
+    
+    def clear_selection_labels(self):
+        """選択ラベルをクリア"""
+        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 = []
+    
+    def add_selection_label(self, atom_idx, label_text):
+        """選択された原子にラベルを追加"""
+        if not hasattr(self, 'selection_labels'):
+            self.selection_labels = []
+        
+        # 原子の位置を取得
+        pos = self.main_window.atom_positions_3d[atom_idx]
+        
+        # ラベルを追加
+        label_actor = self.main_window.plotter.add_point_labels(
+            [pos], [label_text], 
+            point_size=20, 
+            font_size=12,
+            text_color='yellow',
+            always_visible=True
+        )
+        self.selection_labels.append(label_actor)
+    
+    def update_display(self):
+        """表示を更新"""
+        # 既存のラベルをクリア
+        self.clear_selection_labels()
+        
+        if self.atom1_idx is None:
+            self.selection_label.setText("No atoms selected")
+            self.distance_label.setText("")
+            self.apply_button.setEnabled(False)
+            # Clear distance input when no selection
+            try:
+                self.distance_input.clear()
+            except Exception:
+                pass
+        elif self.atom2_idx is None:
+            symbol1 = self.mol.GetAtomWithIdx(self.atom1_idx).GetSymbol()
+            self.selection_label.setText(f"First atom: {symbol1} (index {self.atom1_idx})")
+            self.distance_label.setText("")
+            self.apply_button.setEnabled(False)
+            # ラベル追加
+            self.add_selection_label(self.atom1_idx, "1")
+            # Clear distance input while selection is incomplete
+            try:
+                self.distance_input.clear()
+            except Exception:
+                pass
+        else:
+            symbol1 = self.mol.GetAtomWithIdx(self.atom1_idx).GetSymbol()
+            symbol2 = self.mol.GetAtomWithIdx(self.atom2_idx).GetSymbol()
+            self.selection_label.setText(f"Bond: {symbol1}({self.atom1_idx}) - {symbol2}({self.atom2_idx})")
+            
+            # Calculate current distance
+            conf = self.mol.GetConformer()
+            pos1 = np.array(conf.GetAtomPosition(self.atom1_idx))
+            pos2 = np.array(conf.GetAtomPosition(self.atom2_idx))
+            current_distance = np.linalg.norm(pos2 - pos1)
+            self.distance_label.setText(f"Current distance: {current_distance:.3f} Å")
+            self.apply_button.setEnabled(True)
+            # Update the distance input box to show current distance
+            try:
+                self.distance_input.setText(f"{current_distance:.3f}")
+            except Exception:
+                pass
+            # ラベル追加
+            self.add_selection_label(self.atom1_idx, "1")
+            self.add_selection_label(self.atom2_idx, "2")
+    
+    def apply_changes(self):
+        """変更を適用"""
+        if self.atom1_idx is None or self.atom2_idx is None:
+            return
+        
+        try:
+            new_distance = float(self.distance_input.text())
+            if new_distance <= 0:
+                QMessageBox.warning(self, "Invalid Input", "Distance must be positive.")
+                return
+        except ValueError:
+            QMessageBox.warning(self, "Invalid Input", "Please enter a valid number.")
+            return
+        
+        # Undo状態を保存
+        self.main_window.push_undo_state()
+        
+        # Apply the bond length change
+        self.adjust_bond_length(new_distance)
+        
+        # キラルラベルを更新
+        self.main_window.update_chiral_labels()
+    
+    def adjust_bond_length(self, new_distance):
+        """結合長を調整"""
+        conf = self.mol.GetConformer()
+        pos1 = np.array(conf.GetAtomPosition(self.atom1_idx))
+        pos2 = np.array(conf.GetAtomPosition(self.atom2_idx))
+        
+        # Direction vector from atom1 to atom2
+        direction = pos2 - pos1
+        current_distance = np.linalg.norm(direction)
+        
+        if current_distance == 0:
+            return
+        
+        direction = direction / current_distance
+        
+        if self.both_groups_radio.isChecked():
+            # Both groups move towards center equally
+            bond_center = (pos1 + pos2) / 2
+            half_distance = new_distance / 2
+            
+            # New positions for both atoms
+            new_pos1 = bond_center - direction * half_distance
+            new_pos2 = bond_center + direction * half_distance
+            
+            # Get both connected groups
+            group1_atoms = self.get_connected_group(self.atom1_idx, exclude=self.atom2_idx)
+            group2_atoms = self.get_connected_group(self.atom2_idx, exclude=self.atom1_idx)
+            
+            # Calculate displacements
+            displacement1 = new_pos1 - pos1
+            displacement2 = new_pos2 - pos2
+            
+            # Move group 1
+            for atom_idx in group1_atoms:
+                current_pos = np.array(conf.GetAtomPosition(atom_idx))
+                new_pos = current_pos + displacement1
+                conf.SetAtomPosition(atom_idx, new_pos.tolist())
+                self.main_window.atom_positions_3d[atom_idx] = new_pos
+            
+            # Move group 2
+            for atom_idx in group2_atoms:
+                current_pos = np.array(conf.GetAtomPosition(atom_idx))
+                new_pos = current_pos + displacement2
+                conf.SetAtomPosition(atom_idx, new_pos.tolist())
+                self.main_window.atom_positions_3d[atom_idx] = new_pos
+                
+        elif self.atom1_fix_radio.isChecked():
+            # Move only the second atom
+            new_pos2 = pos1 + direction * new_distance
+            conf.SetAtomPosition(self.atom2_idx, new_pos2.tolist())
+            self.main_window.atom_positions_3d[self.atom2_idx] = new_pos2
+        else:
+            # Move the connected group (default behavior)
+            new_pos2 = pos1 + direction * new_distance
+            atoms_to_move = self.get_connected_group(self.atom2_idx, exclude=self.atom1_idx)
+            displacement = new_pos2 - pos2
+            
+            for atom_idx in atoms_to_move:
+                current_pos = np.array(conf.GetAtomPosition(atom_idx))
+                new_pos = current_pos + displacement
+                conf.SetAtomPosition(atom_idx, new_pos.tolist())
+                self.main_window.atom_positions_3d[atom_idx] = new_pos
+        
+        # Update the 3D view
+        self.main_window.draw_molecule_3d(self.mol)
+    
+    def get_connected_group(self, start_atom, exclude=None):
+        """指定された原子から連結されているグループを取得"""
+        visited = set()
+        to_visit = [start_atom]
+        
+        while to_visit:
+            current = to_visit.pop()
+            if current in visited or current == exclude:
+                continue
+            
+            visited.add(current)
+            
+            # Get neighboring atoms
+            atom = self.mol.GetAtomWithIdx(current)
+            for bond in atom.GetBonds():
+                other_idx = bond.GetOtherAtomIdx(current)
+                if other_idx not in visited and other_idx != exclude:
+                    to_visit.append(other_idx)
+        
+        return visited