MoleditPy-linux 2.4.1__py3-none-any.whl

moleditpy_linux/modules/main_window_edit_3d.py

@@ -0,0 +1,536 @@
+#!/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
+"""
+
+"""
+main_window_edit_3d.py
+MainWindow (main_window.py) から分離されたモジュール
+機能クラス: MainWindowEdit3d
+"""
+
+
+import numpy as np
+
+
+# RDKit imports (explicit to satisfy flake8 and used features)
+try:
+    from . import sip_isdeleted_safe
+except Exception:
+    from modules import sip_isdeleted_safe
+
+# PyQt6 Modules
+from PyQt6.QtWidgets import (
+    QGraphicsTextItem
+)
+
+from PyQt6.QtGui import (
+    QColor, QFont
+)
+
+
+from PyQt6.QtCore import (
+    QPointF
+)
+
+import pyvista as pv
+
+# Use centralized Open Babel availability from package-level __init__
+# Use per-package modules availability (local __init__).
+try:
+    from . import OBABEL_AVAILABLE
+except Exception:
+    from modules import OBABEL_AVAILABLE
+# Only import pybel on demand — `moleditpy` itself doesn't expose `pybel`.
+if OBABEL_AVAILABLE:
+    try:
+        from openbabel import pybel
+    except Exception:
+        # If import fails here, disable OBABEL locally; avoid raising
+        pybel = None
+        OBABEL_AVAILABLE = False
+        print("Warning: openbabel.pybel not available. Open Babel fallback and OBabel-based options will be disabled.")
+else:
+    pybel = None
+    
+# Optional SIP helper: on some PyQt6 builds sip.isdeleted is available and
+# allows safely detecting C++ wrapper objects that have been deleted. Import
+# it once at module import time and expose a small, robust wrapper so callers
+# can avoid re-importing sip repeatedly and so we centralize exception
+# handling (this reduces crash risk during teardown and deletion operations).
+try:
+    import sip as _sip  # type: ignore
+    _sip_isdeleted = getattr(_sip, 'isdeleted', None)
+except Exception:
+    _sip = None
+    _sip_isdeleted = None
+
+try:
+    # package relative imports (preferred when running as `python -m moleditpy`)
+    from .constants import VDW_RADII
+except Exception:
+    # Fallback to absolute imports for script-style execution
+    from modules.constants import VDW_RADII
+
+
+# --- クラス定義 ---
+class MainWindowEdit3d(object):
+    """ main_window.py から分離された機能クラス """
+
+
+    def toggle_measurement_mode(self, checked):
+        """測定モードのオン/オフを切り替える"""
+        if checked:
+            # 測定モードをオンにする時は、3D Dragモードを無効化
+            if self.is_3d_edit_mode:
+                self.edit_3d_action.setChecked(False)
+                self.toggle_3d_edit_mode(False)
+            
+            # アクティブな3D編集ダイアログを閉じる
+            self.close_all_3d_edit_dialogs()
+        
+        self.measurement_mode = checked
+        
+        if not checked:
+            self.clear_measurement_selection()
+        
+        # ボタンのテキストとステータスメッセージを更新
+        if checked:
+            self.statusBar().showMessage("Measurement mode enabled. Click atoms to measure distances/angles/dihedrals.")
+        else:
+            self.statusBar().showMessage("Measurement mode disabled.")
+    
+
+
+    def close_all_3d_edit_dialogs(self):
+        """すべてのアクティブな3D編集ダイアログを閉じる"""
+        dialogs_to_close = self.active_3d_dialogs.copy()
+        for dialog in dialogs_to_close:
+            try:
+                dialog.close()
+            except Exception:
+                pass
+        self.active_3d_dialogs.clear()
+
+
+
+    def handle_measurement_atom_selection(self, atom_idx):
+        """測定用の原子選択を処理する"""
+        # 既に選択されている原子の場合は除外
+        if atom_idx in self.selected_atoms_for_measurement:
+            return
+        
+        self.selected_atoms_for_measurement.append(atom_idx)
+        
+        '''
+        # 4つ以上選択された場合はクリア
+        if len(self.selected_atoms_for_measurement) > 4:
+            self.clear_measurement_selection()
+            self.selected_atoms_for_measurement.append(atom_idx)
+        '''
+        
+        # 原子にラベルを追加
+        self.add_measurement_label(atom_idx, len(self.selected_atoms_for_measurement))
+        
+        # 測定値を計算して表示
+        self.calculate_and_display_measurements()
+
+
+
+    def add_measurement_label(self, atom_idx, label_number):
+        """原子に数字ラベルを追加する"""
+        if not self.current_mol or atom_idx >= self.current_mol.GetNumAtoms():
+            return
+        
+        # 測定ラベルリストを更新
+        self.measurement_labels.append((atom_idx, str(label_number)))
+        
+        # 3Dビューの測定ラベルを再描画
+        self.update_measurement_labels_display()
+        
+        # 2Dビューの測定ラベルも更新
+        self.update_2d_measurement_labels()
+
+
+
+    def update_measurement_labels_display(self):
+        """測定ラベルを3D表示に描画する（原子中心配置）"""
+        try:
+            # 既存の測定ラベルを削除
+            self.plotter.remove_actor('measurement_labels')
+        except Exception:
+            pass
+        
+        if not self.measurement_labels or not self.current_mol:
+            return
+        
+        # ラベル位置とテキストを準備
+        pts, labels = [], []
+        for atom_idx, label_text in self.measurement_labels:
+            if atom_idx < len(self.atom_positions_3d):
+                coord = self.atom_positions_3d[atom_idx].copy()
+                # オフセットを削除して原子中心に配置
+                pts.append(coord)
+                labels.append(label_text)
+        
+        if pts and labels:
+            # PyVistaのpoint_labelsを使用（赤色固定）
+            self.plotter.add_point_labels(
+                np.array(pts), 
+                labels, 
+                font_size=16,
+                point_size=0,
+                text_color='red',  # 測定時は常に赤色
+                name='measurement_labels',
+                always_visible=True,
+                tolerance=0.01,
+                show_points=False
+            )
+
+
+
+    def clear_measurement_selection(self):
+        """測定選択をクリアする"""
+        self.selected_atoms_for_measurement.clear()
+        
+        # 3Dビューのラベルを削除
+        self.measurement_labels.clear()
+        try:
+            self.plotter.remove_actor('measurement_labels')
+        except Exception:
+            pass
+        
+        # 2Dビューの測定ラベルも削除
+        self.clear_2d_measurement_labels()
+        
+        # 測定結果のテキストを削除
+        if self.measurement_text_actor:
+            try:
+                self.plotter.remove_actor(self.measurement_text_actor)
+                self.measurement_text_actor = None
+            except Exception:
+                pass
+        
+        self.plotter.render()
+
+
+
+    def update_2d_measurement_labels(self):
+        """2Dビューで測定ラベルを更新表示する"""
+        # 既存の2D測定ラベルを削除
+        self.clear_2d_measurement_labels()
+        
+        # 現在の分子から原子-AtomItemマッピングを作成
+        if not self.current_mol or not hasattr(self, 'data') or not self.data.atoms:
+            return
+            
+        # RDKit原子インデックスから2D AtomItemへのマッピングを作成
+        atom_idx_to_item = {}
+        
+        # シーンからAtomItemを取得してマッピング
+        if hasattr(self, 'scene'):
+            for item in self.scene.items():
+                if hasattr(item, 'atom_id') and hasattr(item, 'symbol'):  # AtomItemかチェック
+                    # 原子IDから対応するRDKit原子インデックスを見つける
+                    rdkit_idx = self.find_rdkit_atom_index(item)
+                    if rdkit_idx is not None:
+                        atom_idx_to_item[rdkit_idx] = item
+        
+        # 測定ラベルを2Dビューに追加
+        if not hasattr(self, 'measurement_label_items_2d'):
+            self.measurement_label_items_2d = []
+            
+        for atom_idx, label_text in self.measurement_labels:
+            if atom_idx in atom_idx_to_item:
+                atom_item = atom_idx_to_item[atom_idx]
+                self.add_2d_measurement_label(atom_item, label_text)
+
+
+
+    def add_2d_measurement_label(self, atom_item, label_text):
+        """特定のAtomItemに測定ラベルを追加する"""
+        # ラベルアイテムを作成
+        label_item = QGraphicsTextItem(label_text)
+        label_item.setDefaultTextColor(QColor(255, 0, 0))  # 赤色
+        label_item.setFont(QFont("Arial", 12, QFont.Weight.Bold))
+        
+        # Z値を設定して最前面に表示（原子ラベルより上）
+        label_item.setZValue(2000)  # より高い値で確実に最前面に配置
+        
+        # 原子の右上により近く配置
+        atom_pos = atom_item.pos()
+        atom_rect = atom_item.boundingRect()
+        label_pos = QPointF(
+            atom_pos.x() + atom_rect.width() / 4 + 2,
+            atom_pos.y() - atom_rect.height() / 4 - 8
+        )
+        label_item.setPos(label_pos)
+        
+        # シーンに追加
+        self.scene.addItem(label_item)
+        self.measurement_label_items_2d.append(label_item)
+
+
+
+    def clear_2d_measurement_labels(self):
+        """2Dビューの測定ラベルを全て削除する"""
+        if hasattr(self, 'measurement_label_items_2d'):
+            for label_item in self.measurement_label_items_2d:
+                try:
+                    # Avoid touching partially-deleted wrappers
+                    if sip_isdeleted_safe(label_item):
+                        continue
+                    try:
+                        if label_item.scene():
+                            self.scene.removeItem(label_item)
+                    except Exception:
+                        # Scene access or removal failed; skip
+                        continue
+                except Exception:
+                    # If sip check itself fails, fall back to best-effort removal
+                    try:
+                        if label_item.scene():
+                            self.scene.removeItem(label_item)
+                    except Exception:
+                        continue
+            self.measurement_label_items_2d.clear()
+
+
+
+    def find_rdkit_atom_index(self, atom_item):
+        """AtomItemから対応するRDKit原子インデックスを見つける"""
+        if not self.current_mol or not atom_item:
+            return None
+        
+        # マッピング辞書を使用（最も確実）
+        if hasattr(self, 'atom_id_to_rdkit_idx_map') and atom_item.atom_id in self.atom_id_to_rdkit_idx_map:
+            return self.atom_id_to_rdkit_idx_map[atom_item.atom_id]
+        
+        # マッピングが存在しない場合はNone（外部ファイル読み込み時など）
+        return None
+
+
+
+    def calculate_and_display_measurements(self):
+        """選択された原子に基づいて測定値を計算し表示する"""
+        num_selected = len(self.selected_atoms_for_measurement)
+        if num_selected < 2:
+            return
+        
+        measurement_text = []
+        
+        if num_selected >= 2:
+            # 距離の計算
+            atom1_idx = self.selected_atoms_for_measurement[0]
+            atom2_idx = self.selected_atoms_for_measurement[1]
+            distance = self.calculate_distance(atom1_idx, atom2_idx)
+            measurement_text.append(f"Distance 1-2: {distance:.3f} Å")
+        
+        if num_selected >= 3:
+            # 角度の計算
+            atom1_idx = self.selected_atoms_for_measurement[0]
+            atom2_idx = self.selected_atoms_for_measurement[1] 
+            atom3_idx = self.selected_atoms_for_measurement[2]
+            angle = self.calculate_angle(atom1_idx, atom2_idx, atom3_idx)
+            measurement_text.append(f"Angle 1-2-3: {angle:.2f}°")
+        
+        if num_selected >= 4:
+            # 二面角の計算
+            atom1_idx = self.selected_atoms_for_measurement[0]
+            atom2_idx = self.selected_atoms_for_measurement[1]
+            atom3_idx = self.selected_atoms_for_measurement[2]
+            atom4_idx = self.selected_atoms_for_measurement[3]
+            dihedral = self.calculate_dihedral(atom1_idx, atom2_idx, atom3_idx, atom4_idx)
+            measurement_text.append(f"Dihedral 1-2-3-4: {dihedral:.2f}°")
+        
+        # 測定結果を3D画面の右上に表示
+        self.display_measurement_text(measurement_text)
+
+
+
+    def calculate_distance(self, atom1_idx, atom2_idx):
+        """2原子間の距離を計算する"""
+        pos1 = np.array(self.atom_positions_3d[atom1_idx])
+        pos2 = np.array(self.atom_positions_3d[atom2_idx])
+        return np.linalg.norm(pos2 - pos1)
+
+
+
+    def calculate_angle(self, atom1_idx, atom2_idx, atom3_idx):
+        """3原子の角度を計算する（中央が頂点）"""
+        pos1 = np.array(self.atom_positions_3d[atom1_idx])
+        pos2 = np.array(self.atom_positions_3d[atom2_idx])  # 頂点
+        pos3 = np.array(self.atom_positions_3d[atom3_idx])
+        
+        # ベクトルを計算
+        vec1 = pos1 - pos2
+        vec2 = pos3 - pos2
+        
+        # 角度を計算（ラジアンから度に変換）
+        cos_angle = np.dot(vec1, vec2) / (np.linalg.norm(vec1) * np.linalg.norm(vec2))
+        # 数値誤差による範囲外の値をクリップ
+        cos_angle = np.clip(cos_angle, -1.0, 1.0)
+        angle_rad = np.arccos(cos_angle)
+        return np.degrees(angle_rad)
+
+
+
+    def calculate_dihedral(self, atom1_idx, atom2_idx, atom3_idx, atom4_idx):
+        """4原子の二面角を計算する（正しい公式を使用）"""
+        pos1 = np.array(self.atom_positions_3d[atom1_idx])
+        pos2 = np.array(self.atom_positions_3d[atom2_idx])
+        pos3 = np.array(self.atom_positions_3d[atom3_idx])
+        pos4 = np.array(self.atom_positions_3d[atom4_idx])
+        
+        # Vectors between consecutive atoms
+        v1 = pos2 - pos1  # 1->2
+        v2 = pos3 - pos2  # 2->3 (central bond)
+        v3 = pos4 - pos3  # 3->4
+        
+        # Normalize the central bond vector
+        v2_norm = v2 / np.linalg.norm(v2)
+        
+        # Calculate plane normal vectors
+        n1 = np.cross(v1, v2)  # Normal to plane 1-2-3
+        n2 = np.cross(v2, v3)  # Normal to plane 2-3-4
+        
+        # Normalize the normal vectors
+        n1_norm = np.linalg.norm(n1)
+        n2_norm = np.linalg.norm(n2)
+        
+        if n1_norm == 0 or n2_norm == 0:
+            return 0.0  # Atoms are collinear
+        
+        n1 = n1 / n1_norm
+        n2 = n2 / n2_norm
+        
+        # Calculate the cosine of the dihedral angle
+        cos_angle = np.dot(n1, n2)
+        cos_angle = np.clip(cos_angle, -1.0, 1.0)
+        
+        # Calculate the sine for proper sign determination
+        sin_angle = np.dot(np.cross(n1, n2), v2_norm)
+        
+        # Calculate the dihedral angle with correct sign
+        angle_rad = np.arctan2(sin_angle, cos_angle)
+        return np.degrees(angle_rad)
+
+
+
+    def display_measurement_text(self, measurement_lines):
+        """測定結果のテキストを3D画面の左上に表示する（小さな等幅フォント）"""
+        # 既存のテキストを削除
+        if self.measurement_text_actor:
+            try:
+                self.plotter.remove_actor(self.measurement_text_actor)
+            except Exception:
+                pass
+        
+        if not measurement_lines:
+            self.measurement_text_actor = None
+            return
+        
+        # テキストを結合
+        text = '\n'.join(measurement_lines)
+        
+        # 背景色から適切なテキスト色を決定
+        try:
+            bg_color_hex = self.settings.get('background_color', '#919191')
+            bg_qcolor = QColor(bg_color_hex)
+            if bg_qcolor.isValid():
+                luminance = bg_qcolor.toHsl().lightness()
+                text_color = 'black' if luminance > 128 else 'white'
+            else:
+                text_color = 'white'
+        except Exception:
+            text_color = 'white'
+        
+        # 左上に表示（小さな等幅フォント）
+        self.measurement_text_actor = self.plotter.add_text(
+            text,
+            position='upper_left',
+            font_size=10,  # より小さく
+            color=text_color,  # 背景に合わせた色
+            font='courier',  # 等幅フォント
+            name='measurement_display'
+        )
+        
+        self.plotter.render()
+
+    # --- 3D Drag functionality ---
+    
+
+
+    def toggle_atom_selection_3d(self, atom_idx):
+        """3Dビューで原子の選択状態をトグルする"""
+        if atom_idx in self.selected_atoms_3d:
+            self.selected_atoms_3d.remove(atom_idx)
+        else:
+            self.selected_atoms_3d.add(atom_idx)
+        
+        # 選択状態のビジュアルフィードバックを更新
+        self.update_3d_selection_display()
+    
+
+
+    def clear_3d_selection(self):
+        """3Dビューでの原子選択をクリア"""
+        self.selected_atoms_3d.clear()
+        self.update_3d_selection_display()
+    
+
+
+    def update_3d_selection_display(self):
+        """3Dビューでの選択原子のハイライト表示を更新"""
+        try:
+            # 既存の選択ハイライトを削除
+            self.plotter.remove_actor('selection_highlight')
+        except Exception:
+            pass
+        
+        if not self.selected_atoms_3d or not self.current_mol:
+            self.plotter.render()
+            return
+        
+        # 選択された原子のインデックスリストを作成
+        selected_indices = list(self.selected_atoms_3d)
+        
+        # 選択された原子の位置を取得
+        selected_positions = self.atom_positions_3d[selected_indices]
+        
+        # 原子の半径を少し大きくしてハイライト表示
+        selected_radii = np.array([VDW_RADII.get(
+            self.current_mol.GetAtomWithIdx(i).GetSymbol(), 0.4) * 1.3 
+            for i in selected_indices])
+        
+        # ハイライト用のデータセットを作成
+        highlight_source = pv.PolyData(selected_positions)
+        highlight_source['radii'] = selected_radii
+        
+        # 黄色の半透明球でハイライト
+        highlight_glyphs = highlight_source.glyph(
+            scale='radii', 
+            geom=pv.Sphere(radius=1.0, theta_resolution=16, phi_resolution=16), 
+            orient=False
+        )
+        
+        self.plotter.add_mesh(
+            highlight_glyphs, 
+            color='yellow', 
+            opacity=0.3, 
+            name='selection_highlight'
+        )
+        
+        self.plotter.render()
+    
+    def remove_dialog_from_list(self, dialog):
+        """ダイアログをアクティブリストから削除"""
+        if dialog in self.active_3d_dialogs:
+            self.active_3d_dialogs.remove(dialog)