MoleditPy-linux 2.4.1__py3-none-any.whl

moleditpy_linux/modules/color_settings_dialog.py

@@ -0,0 +1,321 @@
+#!/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, QGridLayout, QPushButton, QHBoxLayout, QLabel,
+    QApplication, QColorDialog
+)
+from PyQt6.QtGui import QColor
+try:
+    from .constants import CPK_COLORS, DEFAULT_CPK_COLORS
+except Exception:
+    from modules.constants import CPK_COLORS, DEFAULT_CPK_COLORS
+
+class ColorSettingsDialog(QDialog):
+    """Dialog to customize CPK element colors.
+
+    - Click an element to pick a new color for the element (CPK colors).
+    - Reset All button to restore defaults for everything.
+    """
+    def __init__(self, current_settings, parent=None):
+        super().__init__(parent)
+        self.setWindowTitle("CPK Colors")
+        self.parent_window = parent
+        self.current_settings = current_settings or {}
+
+        self.changed_cpk = {}  # symbol -> hex
+        self._reset_all_flag = False
+
+        layout = QVBoxLayout(self)
+
+        # Color picking for CPK is available in the periodic table and CPK dialog
+
+        # Periodic table grid (buttons like PeriodicTableDialog)
+        grid = QGridLayout()
+        self.element_buttons = {}
+        elements = [
+            ('H',1,1), ('He',1,18),
+            ('Li',2,1), ('Be',2,2), ('B',2,13), ('C',2,14), ('N',2,15), ('O',2,16), ('F',2,17), ('Ne',2,18),
+            ('Na',3,1), ('Mg',3,2), ('Al',3,13), ('Si',3,14), ('P',3,15), ('S',3,16), ('Cl',3,17), ('Ar',3,18),
+            ('K',4,1), ('Ca',4,2), ('Sc',4,3), ('Ti',4,4), ('V',4,5), ('Cr',4,6), ('Mn',4,7), ('Fe',4,8),
+            ('Co',4,9), ('Ni',4,10), ('Cu',4,11), ('Zn',4,12), ('Ga',4,13), ('Ge',4,14), ('As',4,15), ('Se',4,16),
+            ('Br',4,17), ('Kr',4,18),
+            ('Rb',5,1), ('Sr',5,2), ('Y',5,3), ('Zr',5,4), ('Nb',5,5), ('Mo',5,6), ('Tc',5,7), ('Ru',5,8),
+            ('Rh',5,9), ('Pd',5,10), ('Ag',5,11), ('Cd',5,12), ('In',5,13), ('Sn',5,14), ('Sb',5,15), ('Te',5,16),
+            ('I',5,17), ('Xe',5,18),
+            ('Cs',6,1), ('Ba',6,2), ('Hf',6,4), ('Ta',6,5), ('W',6,6), ('Re',6,7), ('Os',6,8),
+            ('Ir',6,9), ('Pt',6,10), ('Au',6,11), ('Hg',6,12), ('Tl',6,13), ('Pb',6,14), ('Bi',6,15), ('Po',6,16),
+            ('At',6,17), ('Rn',6,18),
+            ('Fr',7,1), ('Ra',7,2), ('Rf',7,4), ('Db',7,5), ('Sg',7,6), ('Bh',7,7), ('Hs',7,8),
+            ('Mt',7,9), ('Ds',7,10), ('Rg',7,11), ('Cn',7,12), ('Nh',7,13), ('Fl',7,14), ('Mc',7,15), ('Lv',7,16),
+            ('Ts',7,17), ('Og',7,18),
+            ('La',8,3), ('Ce',8,4), ('Pr',8,5), ('Nd',8,6), ('Pm',8,7), ('Sm',8,8), ('Eu',8,9), ('Gd',8,10), ('Tb',8,11),
+            ('Dy',8,12), ('Ho',8,13), ('Er',8,14), ('Tm',8,15), ('Yb',8,16), ('Lu',8,17),
+            ('Ac',9,3), ('Th',9,4), ('Pa',9,5), ('U',9,6), ('Np',9,7), ('Pu',9,8), ('Am',9,9), ('Cm',9,10), ('Bk',9,11),
+            ('Cf',9,12), ('Es',9,13), ('Fm',9,14), ('Md',9,15), ('No',9,16), ('Lr',9,17),
+        ]
+
+        for symbol, row, col in elements:
+            b = QPushButton(symbol)
+            b.setFixedSize(40, 40)
+            # Choose override color (if present) else default CPK color
+            override = self.current_settings.get('cpk_colors', {}).get(symbol)
+            if override:
+                q_color = QColor(override)
+            else:
+                q_color = CPK_COLORS.get(symbol, CPK_COLORS['DEFAULT'])
+
+            brightness = (q_color.red() * 299 + q_color.green() * 587 + q_color.blue() * 114) / 1000
+            text_color = 'white' if brightness < 128 else 'black'
+            b.setStyleSheet(f"background-color: {q_color.name()}; color: {text_color}; border: 1px solid #555; font-weight: bold;")
+            b.clicked.connect(self.on_element_clicked)
+            grid.addWidget(b, row, col)
+            self.element_buttons[symbol] = b
+
+        layout.addLayout(grid)
+
+        # Ball & Stick bond color (3D) picker - placed near the periodic table for CPK settings
+        self.changed_bs_color = None
+        try:
+            bs_h = QHBoxLayout()
+            bs_label = QLabel("Ball & Stick bond color:")
+            self.bs_button = QPushButton()
+            self.bs_button.setFixedSize(36, 24)
+            # initialize from current settings (if provided)
+            try:
+                cur_bs = self.current_settings.get('ball_stick_bond_color') if self.current_settings else None
+            except Exception:
+                cur_bs = None
+            if not cur_bs and self.parent_window and hasattr(self.parent_window, 'settings'):
+                cur_bs = self.parent_window.settings.get('ball_stick_bond_color', '#7F7F7F')
+            try:
+                self.bs_button.setStyleSheet(f"background-color: {cur_bs}; border: 1px solid #888;")
+                self.bs_button.setToolTip(cur_bs)
+            except Exception:
+                pass
+            self.bs_button.clicked.connect(self.pick_bs_bond_color)
+            bs_h.addWidget(bs_label)
+            bs_h.addWidget(self.bs_button)
+            bs_h.addStretch(1)
+            layout.addLayout(bs_h)
+        except Exception:
+            pass
+
+        # Reset button and action buttons
+        h = QHBoxLayout()
+        reset_button = QPushButton("Reset All")
+        reset_button.clicked.connect(self.reset_all)
+        h.addWidget(reset_button)
+        h.addStretch(1)
+        apply_button = QPushButton("Apply")
+        apply_button.clicked.connect(self.apply_changes)
+        ok_button = QPushButton("OK")
+        ok_button.clicked.connect(self.accept)
+        cancel_button = QPushButton("Cancel")
+        cancel_button.clicked.connect(self.reject)
+
+        h.addWidget(apply_button); h.addWidget(ok_button); h.addWidget(cancel_button)
+        layout.addLayout(h)
+
+        # initialize
+        # No 2D bond color control here
+
+    # 2D bond color picker removed — 2D bond color is fixed and not configurable here
+
+    def on_element_clicked(self):
+        b = self.sender()
+        symbol = b.text()
+        # get current color (override if exists else default)
+        cur = self.current_settings.get('cpk_colors', {}).get(symbol)
+        if not cur:
+            cur = CPK_COLORS.get(symbol, CPK_COLORS['DEFAULT']).name()
+        color = QColorDialog.getColor(QColor(cur), self)
+        if color.isValid():
+            self.changed_cpk[symbol] = color.name()
+            # Update button appearance
+            brightness = (color.red() * 299 + color.green() * 587 + color.blue() * 114) / 1000
+            text_color = 'white' if brightness < 128 else 'black'
+            b.setStyleSheet(f"background-color: {color.name()}; color: {text_color}; border: 1px solid #555; font-weight: bold;")
+
+    def reset_all(self):
+        # Clear overrides
+        self.changed_cpk = {}
+        self._reset_all_flag = True
+        
+        # 1. B&S結合色もリセット対象（デフォルト値）に設定
+        try:
+            self.changed_bs_color = self.parent_window.default_settings.get('ball_stick_bond_color', '#7F7F7F') if hasattr(self.parent_window, 'default_settings') else '#7F7F7F'
+        except Exception:
+            self.changed_bs_color = '#7F7F7F'
+            
+        # 2. ダイアログ内のCPKボタンの表示をデフォルトに戻す
+        for s, btn in self.element_buttons.items():
+            q_color = DEFAULT_CPK_COLORS.get(s, DEFAULT_CPK_COLORS['DEFAULT'])
+            brightness = (q_color.red() * 299 + q_color.green() * 587 + q_color.blue() * 114) / 1000
+            text_color = 'white' if brightness < 128 else 'black'
+            btn.setStyleSheet(f"background-color: {q_color.name()}; color: {text_color}; border: 1px solid #555; font-weight: bold;")
+        
+        # 3. 3Dプレビューを更新する L.3337〜L.3386 の try...finally ブロックは削除
+
+        # 4. ダイアログ内のB&S結合色ボタンの表示をデフォルトに戻す
+        try:
+            if hasattr(self, 'bs_button'):
+                # self.changed_bs_color に設定したデフォルト値を反映
+                hexv = self.changed_bs_color
+                self.bs_button.setStyleSheet(f"background-color: {hexv}; border: 1px solid #888;")
+                self.bs_button.setToolTip(hexv)
+        except Exception:
+            pass
+
+    def apply_changes(self):
+        # Persist only changed keys
+        if self.parent_window:
+            if self._reset_all_flag:
+                # Remove any cpk overrides
+                try:
+                    if 'cpk_colors' in self.parent_window.settings:
+                        del self.parent_window.settings['cpk_colors']
+                except Exception:
+                    pass
+            if self.changed_cpk:
+                # Merge with existing overrides
+                cdict = self.parent_window.settings.get('cpk_colors', {}).copy()
+                cdict.update(self.changed_cpk)
+                self.parent_window.settings['cpk_colors'] = cdict
+                self.parent_window.settings_dirty = True
+            # After changing settings, update global CPK color map and refresh views
+            try:
+                self.parent_window.update_cpk_colors_from_settings()
+            except Exception:
+                pass
+            try:
+                self.parent_window.apply_3d_settings(redraw=False)
+            except Exception:
+                pass
+            try:
+                if hasattr(self.parent_window, 'current_mol') and self.parent_window.current_mol:
+                    self.parent_window.draw_molecule_3d(self.parent_window.current_mol)
+            except Exception:
+                pass
+            # update 2D scene objects
+            try:
+                if hasattr(self.parent_window, 'scene'):
+                    for it in self.parent_window.scene.items():
+                        try:
+                            if hasattr(it, 'update_style'):
+                                it.update_style()
+                        except Exception:
+                            pass
+            except Exception:
+                pass
+            # update periodic table button styles in the dialog to reflect any overrides
+            try:
+                for s, btn in self.element_buttons.items():
+                    try:
+                        q_color = QColor(self.parent_window.settings.get('cpk_colors', {}).get(s, CPK_COLORS.get(s, CPK_COLORS['DEFAULT']).name()))
+                        brightness = (q_color.red() * 299 + q_color.green() * 587 + q_color.blue() * 114) / 1000
+                        text_color = 'white' if brightness < 128 else 'black'
+                        btn.setStyleSheet(f"background-color: {q_color.name()}; color: {text_color}; border: 1px solid #555; font-weight: bold;")
+                    except Exception:
+                        pass
+            except Exception:
+                pass
+            # Refresh any open SettingsDialog instances so the ball & stick color preview updates
+            try:
+                # Avoid circular import at module level; import SettingsDialog on demand
+                try:
+                    from .settings_dialog import SettingsDialog
+                except Exception:
+                    from modules.settings_dialog import SettingsDialog
+
+                for w in QApplication.topLevelWidgets():
+                    try:
+                        if isinstance(w, SettingsDialog):
+                            try:
+                                w.update_ui_from_settings(self.parent_window.settings)
+                            except Exception:
+                                pass
+                    except Exception:
+                        pass
+            except Exception:
+                pass
+            # Persist changed Ball & Stick color if the user changed it from the CPK dialog
+            if getattr(self, 'changed_bs_color', None):
+                try:
+                    self.parent_window.settings['ball_stick_bond_color'] = self.changed_bs_color
+                    try:
+                        self.parent_window.settings_dirty = True
+                    except Exception:
+                        pass
+                    # After changing ball-stick color, ensure 3D view updates
+                    try:
+                        self.parent_window.apply_3d_settings()
+                    except Exception:
+                        pass
+                    try:
+                        if hasattr(self.parent_window, 'current_mol') and self.parent_window.current_mol:
+                            self.parent_window.draw_molecule_3d(self.parent_window.current_mol)
+                    except Exception:
+                        pass
+                except Exception:
+                    pass
+            # Removed 2D bond color control — nothing to persist here
+            elif self._reset_all_flag:
+                # Reset Ball & Stick 3D bond color to default
+                try:
+                    # Use a stable default instead of relying on parent_window.default_settings
+                    self.parent_window.settings['ball_stick_bond_color'] = '#7F7F7F'
+                    try:
+                        self.parent_window.settings_dirty = True
+                    except Exception:
+                        pass
+                except Exception:
+                    pass
+                self.parent_window.update_cpk_colors_from_settings()
+                self.parent_window.apply_3d_settings()
+                if hasattr(self.parent_window, 'current_mol') and self.parent_window.current_mol:
+                    self.parent_window.draw_molecule_3d(self.parent_window.current_mol)
+
+            # update 2D scene
+            try:
+                if hasattr(self.parent_window, 'scene'):
+                    for it in self.parent_window.scene.items():
+                        try:
+                            # AtomItem.update_style uses CPK_COLORS map
+                            if hasattr(it, 'update_style'):
+                                it.update_style()
+                        except Exception:
+                            pass
+            except Exception:
+                pass
+
+    def accept(self):
+        self.apply_changes()
+        super().accept()
+
+    def pick_bs_bond_color(self):
+        """Pick Ball & Stick 3D bond color from the CPK dialog and update preview immediately."""
+        try:
+            cur = getattr(self, 'changed_bs_color', None) or (self.current_settings.get('ball_stick_bond_color') if self.current_settings else None)
+        except Exception:
+            cur = None
+        if not cur and self.parent_window and hasattr(self.parent_window, 'settings'):
+            cur = self.parent_window.settings.get('ball_stick_bond_color', '#7F7F7F')
+        color = QColorDialog.getColor(QColor(cur), self)
+        if color.isValid():
+            hexv = color.name()
+            self.changed_bs_color = hexv
+            try:
+                self.bs_button.setStyleSheet(f"background-color: {hexv}; border: 1px solid #888;")
+                self.bs_button.setToolTip(hexv)
+            except Exception:
+                pass

moleditpy_linux/modules/constants.py

@@ -0,0 +1,88 @@
+#!/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
+"""
+
+# --- Constants ---
+
+from PyQt6.QtGui import QFont, QColor
+from rdkit import Chem
+
+#Version
+VERSION = '2.4.1'
+
+ATOM_RADIUS = 18
+BOND_OFFSET = 3.5
+DEFAULT_BOND_LENGTH = 75 # テンプレートで使用する標準結合長
+CLIPBOARD_MIME_TYPE = "application/x-moleditpy-fragment"
+
+# Physical bond length (approximate) used to convert scene pixels to angstroms.
+# DEFAULT_BOND_LENGTH is the length in pixels used in the editor UI for a typical bond.
+# Many molecular file formats expect coordinates in angstroms; use ~1.5 Å as a typical single-bond length.
+DEFAULT_BOND_LENGTH_ANGSTROM = 1.5
+# Multiply pixel coordinates by this to get angstroms: ANGSTROM_PER_PIXEL = 1.5Å / DEFAULT_BOND_LENGTH(px)
+ANGSTROM_PER_PIXEL = DEFAULT_BOND_LENGTH_ANGSTROM / DEFAULT_BOND_LENGTH
+
+# UI / drawing / behavior constants (centralized for maintainability)
+FONT_FAMILY = "Arial"
+FONT_SIZE_LARGE = 20
+FONT_SIZE_SMALL = 12
+FONT_WEIGHT_BOLD = QFont.Weight.Bold
+
+# Hit / visual sizes (in pixels at scale=1)
+DESIRED_ATOM_PIXEL_RADIUS = 15.0
+DESIRED_BOND_PIXEL_WIDTH = 18.0
+
+# Bond/EZ label
+EZ_LABEL_TEXT_OUTLINE = 2.5
+EZ_LABEL_MARGIN = 16
+EZ_LABEL_BOX_SIZE = 28
+
+# Interaction thresholds
+SNAP_DISTANCE = 14.0
+SUM_TOLERANCE = 5.0
+
+# Misc drawing
+NUM_DASHES = 8
+HOVER_PEN_WIDTH = 8
+
+CPK_COLORS = {
+    'H': QColor('#FFFFFF'), 'C': QColor('#222222'), 'N': QColor('#3377FF'), 'O': QColor('#FF3333'), 'F': QColor('#99E6E6'),
+    'Cl': QColor('#33FF33'), 'Br': QColor('#A52A2A'), 'I': QColor('#9400D3'), 'S': QColor('#FFC000'), 'P': QColor('#FF8000'),
+    'Si': QColor('#DAA520'), 'B': QColor('#FA8072'), 'He': QColor('#D9FFFF'), 'Ne': QColor('#B3E3F5'), 'Ar': QColor('#80D1E3'),
+    'Kr': QColor('#5CACC8'), 'Xe': QColor('#429EB0'), 'Rn': QColor('#298FA2'), 'Li': QColor('#CC80FF'), 'Na': QColor('#AB5CF2'),
+    'K': QColor('#8F44D7'), 'Rb': QColor('#702EBC'), 'Cs': QColor('#561B9E'), 'Fr': QColor('#421384'), 'Be': QColor('#C2FF00'),
+    'Mg': QColor('#8AFF00'), 'Ca': QColor('#3DFF00'), 'Sr': QColor('#00FF00'), 'Ba': QColor('#00E600'), 'Ra': QColor('#00B800'),
+    'Sc': QColor('#E6E6E6'), 'Ti': QColor('#BFC2C7'), 'V': QColor('#A6A6AB'), 'Cr': QColor('#8A99C7'), 'Mn': QColor('#9C7AC7'),
+    'Fe': QColor('#E06633'), 'Co': QColor('#F090A0'), 'Ni': QColor('#50D050'), 'Cu': QColor('#C88033'), 'Zn': QColor('#7D80B0'),
+    'Ga': QColor('#C28F8F'), 'Ge': QColor('#668F8F'), 'As': QColor('#BD80E3'), 'Se': QColor('#FFA100'), 'Tc': QColor('#3B9E9E'),
+    'Ru': QColor('#248F8F'), 'Rh': QColor('#0A7D8F'), 'Pd': QColor('#006985'), 'Ag': QColor('#C0C0C0'), 'Cd': QColor('#FFD700'),
+    'In': QColor('#A67573'), 'Sn': QColor('#668080'), 'Sb': QColor('#9E63B5'), 'Te': QColor('#D47A00'), 'La': QColor('#70D4FF'),
+    'Ce': QColor('#FFFFC7'), 'Pr': QColor('#D9FFC7'), 'Nd': QColor('#C7FFC7'), 'Pm': QColor('#A3FFC7'), 'Sm': QColor('#8FFFC7'),
+    'Eu': QColor('#61FFC7'), 'Gd': QColor('#45FFC7'), 'Tb': QColor('#30FFC7'), 'Dy': QColor('#1FFFC7'), 'Ho': QColor('#00FF9C'),
+    'Er': QColor('#00E675'), 'Tm': QColor('#00D452'), 'Yb': QColor('#00BF38'), 'Lu': QColor('#00AB24'), 'Hf': QColor('#4DC2FF'),
+    'Ta': QColor('#4DA6FF'), 'W': QColor('#2194D6'), 'Re': QColor('#267DAB'), 'Os': QColor('#266696'), 'Ir': QColor('#175487'),
+    'Pt': QColor('#D0D0E0'), 'Au': QColor('#FFD123'), 'Hg': QColor('#B8B8D0'), 'Tl': QColor('#A6544D'), 'Pb': QColor('#575961'),
+    'Bi': QColor('#9E4FB5'), 'Po': QColor('#AB5C00'), 'At': QColor('#754F45'), 'Ac': QColor('#70ABFA'), 'Th': QColor('#00BAFF'),
+    'Pa': QColor('#00A1FF'), 'U': QColor('#008FFF'), 'Np': QColor('#0080FF'), 'Pu': QColor('#006BFF'), 'Am': QColor('#545CF2'),
+    'Cm': QColor('#785CE3'), 'Bk': QColor('#8A4FE3'), 'Cf': QColor('#A136D4'), 'Es': QColor('#B31FD4'), 'Fm': QColor('#B31FBA'),
+    'Md': QColor('#B30DA6'), 'No': QColor('#BD0D87'), 'Lr': QColor('#C70066'), 'Al': QColor('#B3A68F'), 'Y': QColor('#99FFFF'), 
+    'Zr': QColor('#7EE7E7'), 'Nb': QColor('#68CFCE'), 'Mo': QColor('#52B7B7'), 'DEFAULT': QColor('#FF1493') # Pink fallback
+}
+CPK_COLORS_PV = {
+    k: [c.redF(), c.greenF(), c.blueF()] for k, c in CPK_COLORS.items()
+}
+
+# Keep a copy of the original default map so we can restore it when user resets
+DEFAULT_CPK_COLORS = {k: QColor(v) if not isinstance(v, QColor) else v for k, v in CPK_COLORS.items()}
+
+pt = Chem.GetPeriodicTable()
+VDW_RADII = {pt.GetElementSymbol(i): pt.GetRvdw(i) * 0.3 for i in range(1, 119)}
+