MoleditPy-linux 2.4.1__py3-none-any.whl

moleditpy_linux/modules/atom_item.py

@@ -0,0 +1,395 @@
+#!/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, QPainterPath, QFontMetricsF, QPainter
+)
+
+from PyQt6.QtCore import (
+    Qt, QPointF, QRectF
+)
+
+try:
+    from .constants import (
+        ATOM_RADIUS, DESIRED_ATOM_PIXEL_RADIUS,
+        FONT_FAMILY, FONT_SIZE_LARGE, FONT_WEIGHT_BOLD,
+        CPK_COLORS,
+    )
+except Exception:
+    from modules.constants import (
+        ATOM_RADIUS, DESIRED_ATOM_PIXEL_RADIUS,
+        FONT_FAMILY, FONT_SIZE_LARGE, FONT_WEIGHT_BOLD,
+        CPK_COLORS,
+    )
+    
+try:
+    from . import sip_isdeleted_safe
+except Exception:
+    from modules import sip_isdeleted_safe
+
+class AtomItem(QGraphicsItem):
+    def __init__(self, atom_id, symbol, pos, charge=0, radical=0):
+        super().__init__()
+        self.atom_id, self.symbol, self.charge, self.radical, self.bonds, self.chiral_label = atom_id, symbol, charge, radical, [], None
+        self.setPos(pos)
+        self.implicit_h_count = 0 
+        self.setFlags(QGraphicsItem.GraphicsItemFlag.ItemIsMovable | QGraphicsItem.GraphicsItemFlag.ItemIsSelectable)
+        self.setZValue(1)
+        self.update_style()
+        self.setAcceptHoverEvents(True)
+        self.hovered = False
+        self.has_problem = False 
+
+
+    def update_style(self):
+        # Allow updating font preference dynamically
+        font_size = 20
+        try:
+            if self.scene() and self.scene().views():
+                win = self.scene().views()[0].window()
+                if win and hasattr(win, 'settings'):
+                    font_size = win.settings.get('atom_font_size_2d', 20)
+        except Exception:
+            pass
+        self.font = QFont(FONT_FAMILY, font_size, FONT_WEIGHT_BOLD)
+        self.prepareGeometryChange()
+        
+        self.is_visible = not (self.symbol == 'C' and len(self.bonds) > 0 and self.charge == 0 and self.radical == 0)
+        self.update()
+
+    def boundingRect(self):
+        # --- paint()メソッドと完全に同じロジックでテキストの位置とサイズを計算 ---
+        # Get dynamic font size
+        font_size = 20
+        try:
+            if self.scene() and self.scene().views():
+                win = self.scene().views()[0].window()
+                if win and hasattr(win, 'settings'):
+                    font_size = win.settings.get('atom_font_size_2d', 20)
+        except Exception:
+            pass
+        font = QFont(FONT_FAMILY, font_size, FONT_WEIGHT_BOLD)
+        fm = QFontMetricsF(font)
+
+        hydrogen_part = ""
+        if self.implicit_h_count > 0:
+            is_skeletal_carbon = (self.symbol == 'C' and 
+                                      self.charge == 0 and 
+                                      self.radical == 0 and 
+                                      len(self.bonds) > 0)
+            if not is_skeletal_carbon:
+                hydrogen_part = "H"
+                if self.implicit_h_count > 1:
+                    subscript_map = str.maketrans("0123456789", "₀₁₂₃₄₅₆₇₈₉")
+                    hydrogen_part += str(self.implicit_h_count).translate(subscript_map)
+
+        flip_text = False
+        if hydrogen_part and self.bonds:
+            my_pos_x = self.pos().x()
+            total_dx = 0.0
+            # Defensive: some bonds may have missing atom references (None) or C++ wrappers
+            # that have been deleted. Iterate and accumulate only valid partner positions.
+            for b in self.bonds:
+                # partner is the atom at the other end of the bond
+                partner = b.atom2 if b.atom1 is self else b.atom1
+                try:
+                    if partner is None:
+                        continue
+                    # If SIP reports the wrapper as deleted, skip it
+                    if sip_isdeleted_safe(partner):
+                        continue
+                    partner_pos = partner.pos()
+                    if partner_pos is None:
+                        continue
+                    total_dx += partner_pos.x() - my_pos_x
+                except Exception:
+                    # Skip any bond that raises while inspecting; keep UI tolerant
+                    continue
+
+            if total_dx > 0:
+                flip_text = True
+        
+        if flip_text:
+            display_text = hydrogen_part + self.symbol
+        else:
+            display_text = self.symbol + hydrogen_part
+
+        text_rect = fm.boundingRect(display_text)
+        text_rect.adjust(-2, -2, 2, 2)
+        if hydrogen_part:
+            symbol_rect = fm.boundingRect(self.symbol)
+            if flip_text:
+                offset_x = symbol_rect.width() // 2
+                text_rect.moveTo(offset_x - text_rect.width(), -text_rect.height() / 2)
+            else:
+                offset_x = -symbol_rect.width() // 2
+                text_rect.moveTo(offset_x, -text_rect.height() / 2)
+        else:
+            text_rect.moveCenter(QPointF(0, 0))
+
+        # 1. paint()で描画される背景の矩形(bg_rect)を計算する
+        bg_rect = text_rect.adjusted(-5, -8, 5, 8)
+        
+        # 2. このbg_rectを基準として全体の描画領域を構築する
+        full_visual_rect = QRectF(bg_rect)
+
+        # 電荷記号の領域を計算に含める
+        if self.charge != 0:
+            # Chemical convention: single charge as "+"/"-", multiple as "2+"/"2-"
+            if self.charge == 1:
+                charge_str = "+"
+            elif self.charge == -1:
+                charge_str = "-"
+            else:
+                sign = '+' if self.charge > 0 else '-'
+                charge_str = f"{abs(self.charge)}{sign}"
+            charge_font = QFont("Arial", 12, QFont.Weight.Bold)
+            charge_fm = QFontMetricsF(charge_font)
+            charge_rect = charge_fm.boundingRect(charge_str)
+
+            if flip_text:
+                charge_pos = QPointF(text_rect.left() - charge_rect.width() - 2, text_rect.top())
+            else:
+                charge_pos = QPointF(text_rect.right() + 2, text_rect.top())
+            charge_rect.moveTopLeft(charge_pos)
+            full_visual_rect = full_visual_rect.united(charge_rect)
+
+        # ラジカル記号の領域を計算に含める
+        if self.radical > 0:
+            radical_area = QRectF(text_rect.center().x() - 8, text_rect.top() - 8, 16, 8)
+            full_visual_rect = full_visual_rect.united(radical_area)
+
+        # 3. 選択ハイライト等のための最終的なマージンを追加する
+        return full_visual_rect.adjusted(-3, -3, 3, 3)
+
+    def shape(self):
+        scene = self.scene()
+        if not scene or not scene.views():
+            path = QPainterPath()
+            hit_r = max(4.0, ATOM_RADIUS - 6.0) * 2
+            path.addEllipse(QRectF(-hit_r, -hit_r, hit_r * 2.0, hit_r * 2.0))
+            return path
+
+        view = scene.views()[0]
+        scale = view.transform().m11()
+
+        scene_radius = DESIRED_ATOM_PIXEL_RADIUS / scale
+
+        path = QPainterPath()
+        path.addEllipse(QPointF(0, 0), scene_radius, scene_radius)
+        return path
+
+    def paint(self, painter, option, widget):
+        # Color logic: check if we should use bond color (uniform) or CPK (element-specific)
+        color = CPK_COLORS.get(self.symbol, CPK_COLORS['DEFAULT'])
+        try:
+            if self.scene() and self.scene().views():
+                win = self.scene().views()[0].window()
+                if win and hasattr(win, 'settings'):
+                    if win.settings.get('atom_use_bond_color_2d', False):
+                        bond_col = win.settings.get('bond_color_2d', '#222222')
+                        color = QColor(bond_col)
+        except Exception:
+            pass
+
+        if self.is_visible:
+            # 1. 描画の準備
+            # Ensure correct font is used (self.font should be updated by update_style)
+            painter.setFont(self.font)
+            fm = painter.fontMetrics()
+
+            # --- 水素部分のテキストを作成 ---
+            hydrogen_part = ""
+            if self.implicit_h_count > 0:
+                is_skeletal_carbon = (self.symbol == 'C' and 
+                                      self.charge == 0 and 
+                                      self.radical == 0 and 
+                                      len(self.bonds) > 0)
+                if not is_skeletal_carbon:
+                    hydrogen_part = "H"
+                    if self.implicit_h_count > 1:
+                        subscript_map = str.maketrans("0123456789", "₀₁₂₃₄₅₆₇₈₉")
+                        hydrogen_part += str(self.implicit_h_count).translate(subscript_map)
+
+            # --- テキストを反転させるか決定 ---
+            flip_text = False
+            # 水素ラベルがあり、結合が1本以上ある場合のみ反転を考慮
+            if hydrogen_part and self.bonds:
+
+                    # 相対的なX座標で、結合が左右どちらに偏っているか判定
+                    my_pos_x = self.pos().x()
+                    total_dx = 0.0
+                    # Defensive: some bonds may have missing atom references (None) or
+                    # wrappers that were deleted by SIP. Only accumulate valid partner positions.
+                    for bond in self.bonds:
+                        try:
+                            other_atom = bond.atom1 if bond.atom2 is self else bond.atom2
+                            if other_atom is None:
+                                continue
+                            # If SIP reports the wrapper as deleted, skip it
+                            try:
+                                if sip_isdeleted_safe(other_atom):
+                                    continue
+                            except Exception:
+                                # If sip check fails, continue defensively
+                                pass
+
+                            other_pos = None
+                            try:
+                                other_pos = other_atom.pos()
+                            except Exception:
+                                # Accessing .pos() may raise if the C++ object was destroyed
+                                other_pos = None
+
+                            if other_pos is None:
+                                continue
+
+                            total_dx += (other_pos.x() - my_pos_x)
+                        except Exception:
+                            # Skip any problematic bond/partner rather than crashing the paint
+                            continue
+
+                    # 結合が主に右側にある場合はテキストを反転させる
+                    if total_dx > 0:
+                        flip_text = True
+
+            # --- 表示テキストとアライメントを最終決定 ---
+            if flip_text:
+                display_text = hydrogen_part + self.symbol
+                alignment_flag = Qt.AlignmentFlag.AlignRight | Qt.AlignmentFlag.AlignVCenter
+            else:
+                display_text = self.symbol + hydrogen_part
+                alignment_flag = Qt.AlignmentFlag.AlignLeft | Qt.AlignmentFlag.AlignVCenter
+
+            text_rect = fm.boundingRect(display_text)
+            text_rect.adjust(-2, -2, 2, 2)
+            symbol_rect = fm.boundingRect(self.symbol) # 主元素のみの幅を計算
+
+            # --- テキストの描画位置を決定 ---
+            # 水素ラベルがない場合 (従来通り中央揃え)
+            if not hydrogen_part:
+                alignment_flag = Qt.AlignmentFlag.AlignCenter
+                text_rect.moveCenter(QPointF(0, 0).toPoint())
+            # 水素ラベルがあり、反転する場合 (右揃え)
+            elif flip_text:
+                # 主元素の中心が原子の中心に来るように、矩形の右端を調整
+                offset_x = symbol_rect.width() // 2
+                text_rect.moveTo(offset_x - text_rect.width(), -text_rect.height() // 2)
+            # 水素ラベルがあり、反転しない場合 (左揃え)
+            else:
+                # 主元素の中心が原子の中心に来るように、矩形の左端を調整
+                offset_x = -symbol_rect.width() // 2
+                text_rect.moveTo(offset_x, -text_rect.height() // 2)
+
+            # 2. 原子記号の背景を処理（白で塗りつぶす か 透明なら切り抜く）
+            if self.scene():
+                bg_brush = self.scene().backgroundBrush()
+                bg_rect = text_rect.adjusted(-5, -8, 5, 8)
+                
+                if bg_brush.style() == Qt.BrushStyle.NoBrush:
+                    # 背景が透明の場合は、CompositionMode_Clearを使って
+                    # 重なっている結合の線を「消しゴム」のように消す
+                    painter.save()
+                    painter.setCompositionMode(QPainter.CompositionMode.CompositionMode_Clear)
+                    painter.setBrush(QColor(0, 0, 0, 255)) # 色は何でも良い（アルファが重要）
+                    painter.setPen(Qt.PenStyle.NoPen)
+                    painter.drawEllipse(bg_rect)
+                    painter.restore()
+                else:
+                    # 背景がある場合は、その背景色で塗りつぶす（従来通り）
+                    painter.setBrush(bg_brush)
+                    painter.setPen(Qt.PenStyle.NoPen)
+                    painter.drawEllipse(bg_rect)
+            
+            # 3. 原子記号自体を描画
+            # Color is already determined above
+            painter.setPen(QPen(color))
+            painter.drawText(text_rect, int(alignment_flag), display_text)
+            
+            # --- 電荷とラジカルの描画  ---
+            if self.charge != 0:
+                # Chemical convention: single charge as "+"/"-", multiple as "2+"/"2-"
+                if self.charge == 1:
+                    charge_str = "+"
+                elif self.charge == -1:
+                    charge_str = "-"
+                else:
+                    sign = '+' if self.charge > 0 else '-'
+                    charge_str = f"{abs(self.charge)}{sign}"
+                charge_font = QFont("Arial", 12, QFont.Weight.Bold)
+                painter.setFont(charge_font)
+                charge_rect = painter.fontMetrics().boundingRect(charge_str)
+                # 電荷の位置も反転に対応
+                if flip_text:
+                    charge_pos = QPointF(text_rect.left() - charge_rect.width() -2, text_rect.top() + charge_rect.height() - 2)
+                else:
+                    charge_pos = QPointF(text_rect.right() + 2, text_rect.top() + charge_rect.height() - 2)
+                painter.setPen(Qt.GlobalColor.black)
+                painter.drawText(charge_pos, charge_str)
+            
+            if self.radical > 0:
+                painter.setBrush(QBrush(Qt.GlobalColor.black))
+                painter.setPen(Qt.PenStyle.NoPen)
+                radical_pos_y = text_rect.top() - 5
+                if self.radical == 1:
+                    painter.drawEllipse(QPointF(text_rect.center().x(), radical_pos_y), 3, 3)
+                elif self.radical == 2:
+                    painter.drawEllipse(QPointF(text_rect.center().x() - 5, radical_pos_y), 3, 3)
+                    painter.drawEllipse(QPointF(text_rect.center().x() + 5, radical_pos_y), 3, 3)
+
+
+        # --- 選択時のハイライトなど ---
+        if self.has_problem:
+            painter.setBrush(Qt.BrushStyle.NoBrush)
+            painter.setPen(QPen(QColor(255, 0, 0, 200), 4))
+            painter.drawRect(self.boundingRect())
+        elif self.isSelected():
+            painter.setBrush(Qt.BrushStyle.NoBrush)
+            painter.setPen(QPen(QColor(0, 100, 255), 3))
+            painter.drawRect(self.boundingRect())
+        if (not self.isSelected()) and getattr(self, 'hovered', False):
+            pen = QPen(QColor(144, 238, 144, 200), 3)
+            pen.setJoinStyle(Qt.PenJoinStyle.RoundJoin)
+            painter.setBrush(Qt.BrushStyle.NoBrush)
+            painter.setPen(pen)
+            painter.drawRect(self.boundingRect())
+
+
+
+
+    # 約203行目 AtomItem クラス内
+
+    def itemChange(self, change, value):
+        res = super().itemChange(change, value)
+        if change == QGraphicsItem.GraphicsItemChange.ItemPositionHasChanged:
+            if self.flags() & QGraphicsItem.GraphicsItemFlag.ItemIsMovable:
+                # Prevent cascading updates during batch operations
+                if not getattr(self, '_updating_position', False):
+                    for bond in self.bonds: 
+                        if bond.scene():  # Only update if bond is still in scene
+                            bond.update_position()
+            
+        return res
+
+    def hoverEnterEvent(self, event):
+        # シーンのモードにかかわらず、ホバー時にハイライトを有効にする
+        self.hovered = True
+        self.update()
+        super().hoverEnterEvent(event)
+
+    def hoverLeaveEvent(self, event):
+        if self.hovered:
+            self.hovered = False
+            self.update()
+        super().hoverLeaveEvent(event)