MoleditPy-linux 1.17.0__py3-none-any.whl → 1.18.0__py3-none-any.whl

moleditpy_linux/modules/molecule_scene.py

@@ -7,7 +7,7 @@ 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
+DOI: 10.5281/zenodo.17268532
 """
 
 import traceback
@@ -1712,7 +1712,11 @@ class MoleculeScene(QGraphicsScene):
                 return
                     
         # --- 3. Atomに対する操作 (原子の追加 - マージされた機能) ---
-        if key == Qt.Key.Key_1:
+        if key in [Qt.Key.Key_1, Qt.Key.Key_2, Qt.Key.Key_3]:
+            target_order = 1
+            if key == Qt.Key.Key_2: target_order = 2
+            elif key == Qt.Key.Key_3: target_order = 3
+
             start_atom = None
             if isinstance(item_at_cursor, AtomItem):
                 start_atom = item_at_cursor
@@ -1802,12 +1806,12 @@ class MoleculeScene(QGraphicsScene):
                 
                 if near_atom and near_atom is not start_atom:
                     # 近くに既存原子があれば結合
-                    self.create_bond(start_atom, near_atom)
+                    self.create_bond(start_atom, near_atom, bond_order=target_order, bond_stereo=0)
                 else:
                     # 新規原子を作成し結合
                     new_atom_id = self.create_atom('C', target_pos)
                     new_atom_item = self.data.atoms[new_atom_id]['item']
-                    self.create_bond(start_atom, new_atom_item)
+                    self.create_bond(start_atom, new_atom_item, bond_order=target_order, bond_stereo=0)
 
                 self.clearSelection()
                 self.window.push_undo_state()

moleditpy_linux/modules/move_group_dialog.py

@@ -7,7 +7,7 @@ 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
+DOI: 10.5281/zenodo.17268532
 """
 
 from PyQt6.QtWidgets import (

moleditpy_linux/modules/periodic_table_dialog.py

@@ -7,7 +7,7 @@ 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
+DOI: 10.5281/zenodo.17268532
 """
 
 from PyQt6.QtWidgets import QDialog, QGridLayout, QPushButton

moleditpy_linux/modules/planarize_dialog.py

@@ -7,7 +7,7 @@ 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
+DOI: 10.5281/zenodo.17268532
 """
 
 from PyQt6.QtWidgets import (

moleditpy_linux/modules/settings_dialog.py

@@ -7,7 +7,7 @@ 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
+DOI: 10.5281/zenodo.17268532
 """
 
 from PyQt6.QtWidgets import (
@@ -69,6 +69,9 @@ class SettingsDialog(QDialog):
             'stick_triple_bond_offset_factor': 1.0,
             'stick_double_bond_radius_factor': 0.6,
             'stick_triple_bond_radius_factor': 0.4,
+            'aromatic_torus_thickness_factor': 0.6,
+            # Whether to draw an aromatic circle inside rings in 3D
+            'display_aromatic_circles_3d': False,
             # If True, attempts to be permissive when RDKit raises chemical/sanitization errors
             # during file import (useful for viewing malformed XYZ/MOL files). When enabled,
             # element symbol recognition will be coerced where possible and Chem.SanitizeMol
@@ -86,6 +89,7 @@ class SettingsDialog(QDialog):
             # If True, RDKit will attempt to kekulize aromatic systems for 3D display
             # (shows alternating single/double bonds rather than aromatic circles)
             'display_kekule_3d': False,
+            'ball_stick_use_cpk_bond_color': False,
         }
         
         # --- 選択された色を管理する専用のインスタンス変数 ---
@@ -118,6 +122,13 @@ class SettingsDialog(QDialog):
 
         # 渡された設定でUIと内部変数を初期化
         self.update_ui_from_settings(current_settings)
+        
+        # Initialize aromatic circle checkbox and torus thickness from settings
+        self.aromatic_circle_checkbox.setChecked(current_settings.get('display_aromatic_circles_3d', self.default_settings.get('display_aromatic_circles_3d', False)))
+        # Thickness factor is stored as a multiplier (e.g., 1.0), slider uses integer 0-300 representing 0.1x-3.0x
+        thickness_factor = current_settings.get('aromatic_torus_thickness_factor', self.default_settings.get('aromatic_torus_thickness_factor', 1.0))
+        self.aromatic_torus_thickness_slider.setValue(int(thickness_factor * 100))
+        self.aromatic_torus_thickness_label.setText(f"{thickness_factor:.1f}")
 
         # --- ボタンの配置 ---
         buttons = QHBoxLayout()
@@ -243,11 +254,42 @@ class SettingsDialog(QDialog):
         except Exception:
             pass
 
+        # Add separator after Kekule bonds option
+        separator = QFrame()
+        separator.setFrameShape(QFrame.Shape.HLine)
+        separator.setFrameShadow(QFrame.Shadow.Sunken)
+        self.other_form_layout.addRow(separator)
+
         # Place the Kekulé option after the always-ask-charge option
         try:
             self.other_form_layout.addRow("Display Kekulé bonds in 3D:", self.kekule_3d_checkbox)
         except Exception:
             pass
+        
+
+        # Aromatic ring circle display option
+        self.aromatic_circle_checkbox = QCheckBox()
+        self.aromatic_circle_checkbox.setToolTip("When enabled, aromatic rings will be displayed with a circle inside the ring in 3D view.")
+        try:
+            self.other_form_layout.addRow("Display aromatic rings as circles in 3D:", self.aromatic_circle_checkbox)
+        except Exception:
+            pass
+        
+        # Aromatic torus thickness factor
+        self.aromatic_torus_thickness_slider = QSlider(Qt.Orientation.Horizontal)
+        self.aromatic_torus_thickness_slider.setRange(10, 300)  # 0.1x to 3.0x
+        self.aromatic_torus_thickness_slider.setValue(100)  # Default 1.0x
+        self.aromatic_torus_thickness_label = QLabel("1.0")
+        self.aromatic_torus_thickness_slider.valueChanged.connect(
+            lambda v: self.aromatic_torus_thickness_label.setText(f"{v/100:.1f}")
+        )
+        thickness_layout = QHBoxLayout()
+        thickness_layout.addWidget(self.aromatic_torus_thickness_slider)
+        thickness_layout.addWidget(self.aromatic_torus_thickness_label)
+        try:
+            self.other_form_layout.addRow("Aromatic torus thickness (× bond radius):", thickness_layout)
+        except Exception:
+            pass
 
         # Add Other tab to the tab widget
         self.tab_widget.addTab(self.other_widget, "Other")
@@ -378,6 +420,12 @@ class SettingsDialog(QDialog):
         resolution_layout.addWidget(self.bs_resolution_label)
         form_layout.addRow("Resolution (Quality):", resolution_layout)
 
+        # --- 区切り線（水平ライン） ---
+        line = QFrame()
+        line.setFrameShape(QFrame.Shape.HLine)
+        line.setFrameShadow(QFrame.Shadow.Sunken)
+        form_layout.addRow(line)
+
         # --- Ball & Stick bond color ---
         self.bs_bond_color_button = QPushButton()
         self.bs_bond_color_button.setFixedSize(36, 24)
@@ -385,6 +433,11 @@ class SettingsDialog(QDialog):
         self.bs_bond_color_button.setToolTip("Choose the uniform bond color for Ball & Stick model (3D)")
         form_layout.addRow("Ball & Stick bond color:", self.bs_bond_color_button)
 
+        # Use CPK colors for bonds option
+        self.bs_use_cpk_bond_checkbox = QCheckBox()
+        self.bs_use_cpk_bond_checkbox.setToolTip("If checked, bonds will be colored using the atom colors (split bonds). If unchecked, a uniform color is used.")
+        form_layout.addRow("Use CPK colors for bonds:", self.bs_use_cpk_bond_checkbox)
+
         self.tab_widget.addTab(ball_stick_widget, "Ball & Stick")
     
     def create_cpk_tab(self):
@@ -619,6 +672,8 @@ class SettingsDialog(QDialog):
                 'skip_chemistry_checks': self.default_settings.get('skip_chemistry_checks', False),
                 'display_kekule_3d': self.default_settings.get('display_kekule_3d', False),
                 'always_ask_charge': self.default_settings.get('always_ask_charge', False),
+                'display_aromatic_circles_3d': self.default_settings.get('display_aromatic_circles_3d', False),
+                'aromatic_torus_thickness_factor': self.default_settings.get('aromatic_torus_thickness_factor', 1.0),
             },
             "Ball & Stick": {
                 'ball_stick_atom_scale': self.default_settings['ball_stick_atom_scale'],
@@ -627,11 +682,14 @@ class SettingsDialog(QDialog):
                 'ball_stick_double_bond_offset_factor': self.default_settings.get('ball_stick_double_bond_offset_factor', 2.0),
                 'ball_stick_triple_bond_offset_factor': self.default_settings.get('ball_stick_triple_bond_offset_factor', 2.0),
                 'ball_stick_double_bond_radius_factor': self.default_settings.get('ball_stick_double_bond_radius_factor', 0.8),
-                'ball_stick_triple_bond_radius_factor': self.default_settings.get('ball_stick_triple_bond_radius_factor', 0.75)
+                'ball_stick_triple_bond_radius_factor': self.default_settings.get('ball_stick_triple_bond_radius_factor', 0.75),
+                'ball_stick_use_cpk_bond_color': self.default_settings['ball_stick_use_cpk_bond_color'],
+                'ball_stick_bond_color': self.default_settings.get('ball_stick_bond_color', '#7F7F7F')
             },
             "CPK (Space-filling)": {
                 'cpk_atom_scale': self.default_settings['cpk_atom_scale'],
                 'cpk_resolution': self.default_settings['cpk_resolution'],
+                'cpk_colors': {}
             },
             "Wireframe": {
                 'wireframe_bond_radius': self.default_settings['wireframe_bond_radius'],
@@ -665,6 +723,7 @@ class SettingsDialog(QDialog):
             
             # UIを更新
             self.update_ui_from_settings(updated_settings)
+            # CPK tab: do not change parent/settings immediately; let Apply/OK persist any changes
             
             # ユーザーへのフィードバック
             QMessageBox.information(self, "Reset Complete", f"Settings for '{tab_name}' tab have been reset to defaults.")
@@ -801,6 +860,17 @@ class SettingsDialog(QDialog):
             'stick_triple_bond_offset_factor': self.stick_triple_offset_slider.value() / 100.0,
             'stick_double_bond_radius_factor': self.stick_double_radius_slider.value() / 100.0,
             'stick_triple_bond_radius_factor': self.stick_triple_radius_slider.value() / 100.0,
+            # Projection mode
+            'projection_mode': self.projection_combo.currentText(),
+            # Kekule / aromatic / torus settings
+            'display_kekule_3d': self.kekule_3d_checkbox.isChecked(),
+            'display_aromatic_circles_3d': self.aromatic_circle_checkbox.isChecked(),
+            'aromatic_torus_thickness_factor': self.aromatic_torus_thickness_slider.value() / 100.0,
+            'skip_chemistry_checks': self.skip_chem_checks_checkbox.isChecked(),
+            'always_ask_charge': self.always_ask_charge_checkbox.isChecked(),
+            # Ball & Stick bond color and use-cpk option
+            'ball_stick_bond_color': getattr(self, 'bs_bond_color', self.default_settings.get('ball_stick_bond_color')),
+            'ball_stick_use_cpk_bond_color': self.bs_use_cpk_bond_checkbox.isChecked(),
         }
     
     def reset_to_defaults(self):
@@ -854,6 +924,9 @@ class SettingsDialog(QDialog):
         except Exception:
             pass
         
+        # Ball & Stick CPK bond color option
+        self.bs_use_cpk_bond_checkbox.setChecked(settings_dict.get('ball_stick_use_cpk_bond_color', self.default_settings['ball_stick_use_cpk_bond_color']))
+        
         # CPK設定
         cpk_atom_scale = int(settings_dict.get('cpk_atom_scale', self.default_settings['cpk_atom_scale']) * 100)
         self.cpk_atom_scale_slider.setValue(cpk_atom_scale)
@@ -944,6 +1017,14 @@ class SettingsDialog(QDialog):
         self.kekule_3d_checkbox.setChecked(settings_dict.get('display_kekule_3d', self.default_settings.get('display_kekule_3d', False)))
         # always ask for charge on XYZ imports
         self.always_ask_charge_checkbox.setChecked(settings_dict.get('always_ask_charge', self.default_settings.get('always_ask_charge', False)))
+        # Aromatic ring circle display and torus thickness factor
+        self.aromatic_circle_checkbox.setChecked(settings_dict.get('display_aromatic_circles_3d', self.default_settings.get('display_aromatic_circles_3d', False)))
+        thickness_factor = float(settings_dict.get('aromatic_torus_thickness_factor', self.default_settings.get('aromatic_torus_thickness_factor', 1.0)))
+        try:
+            self.aromatic_torus_thickness_slider.setValue(int(thickness_factor * 100))
+            self.aromatic_torus_thickness_label.setText(f"{thickness_factor:.1f}")
+        except Exception:
+            pass
       
     def select_color(self):
         """カラーピッカーを開き、選択された色を内部変数とUIに反映させる"""
@@ -996,10 +1077,13 @@ class SettingsDialog(QDialog):
             'stick_double_bond_radius_factor': self.stick_double_radius_slider.value() / 100.0,
             'stick_triple_bond_radius_factor': self.stick_triple_radius_slider.value() / 100.0,
             'display_kekule_3d': self.kekule_3d_checkbox.isChecked(),
+            'display_aromatic_circles_3d': self.aromatic_circle_checkbox.isChecked(),
+            'aromatic_torus_thickness_factor': self.aromatic_torus_thickness_slider.value() / 100.0,
             'skip_chemistry_checks': self.skip_chem_checks_checkbox.isChecked(),
             'always_ask_charge': self.always_ask_charge_checkbox.isChecked(),
             # Ball & Stick bond color (3D grey/uniform color)
             'ball_stick_bond_color': getattr(self, 'bs_bond_color', self.default_settings.get('ball_stick_bond_color', '#7F7F7F')),
+            'ball_stick_use_cpk_bond_color': self.bs_use_cpk_bond_checkbox.isChecked(),
         }
 
     def pick_bs_bond_color(self):

moleditpy_linux/modules/template_preview_item.py

@@ -7,7 +7,7 @@ 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
+DOI: 10.5281/zenodo.17268532
 """
 
 from PyQt6.QtWidgets import (

moleditpy_linux/modules/template_preview_view.py

@@ -7,7 +7,7 @@ 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
+DOI: 10.5281/zenodo.17268532
 """
 
 from PyQt6.QtWidgets import QGraphicsView

moleditpy_linux/modules/translation_dialog.py

@@ -7,7 +7,7 @@ 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
+DOI: 10.5281/zenodo.17268532
 """
 
 from PyQt6.QtWidgets import (

moleditpy_linux/modules/user_template_dialog.py

@@ -7,7 +7,7 @@ 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
+DOI: 10.5281/zenodo.17268532
 """
 
 from PyQt6.QtWidgets import (

moleditpy_linux/modules/zoomable_view.py

@@ -7,7 +7,7 @@ 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
+DOI: 10.5281/zenodo.17268532
 """
 
 from PyQt6.QtWidgets import (
@@ -16,7 +16,7 @@ from PyQt6.QtWidgets import (
 
 
 from PyQt6.QtCore import (
-    Qt, QPointF
+    Qt, QPointF, QEvent
 )
 
 class ZoomableView(QGraphicsView):
@@ -107,3 +107,23 @@ class ZoomableView(QGraphicsView):
             event.accept()
         else:
             super().mouseReleaseEvent(event)
+
+    def viewportEvent(self, event):
+        """ Macのトラックパッドなどのネイティブジェスチャー（ピンチ）に対応 """
+        if event.type() == QEvent.Type.NativeGesture:
+            # ピンチズーム（ZoomNativeGesture）の場合
+            if event.gestureType() == Qt.NativeGestureType.ZoomNativeGesture:
+                # event.value() は拡大縮小の倍率差分を返します
+                # 例: 拡大時は正の値、縮小時は負の値
+                factor = 1.0 + event.value()
+                
+                # 既存の最大・最小スケール制限を考慮する場合（オプション）
+                current_scale = self.transform().m11()
+                min_scale, max_scale = 0.05, 20.0
+                
+                # 制限内であればスケールを適用
+                # (厳密に制限を守るならif文でガードしますが、最小実装としては以下で動作します)
+                self.scale(factor, factor)
+                return True
+                
+        return super().viewportEvent(event)

{moleditpy_linux-1.17.0.dist-info → moleditpy_linux-1.18.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 1.17.0
+Version: 1.18.0
 Summary: A cross-platform, simple, and intuitive molecular structure editor built in Python. It allows 2D molecular drawing and 3D structure visualization. It supports exporting structure files for input to DFT calculation software.
 Author-email: HiroYokoyama <titech.yoko.hiro@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE

moleditpy_linux-1.18.0.dist-info/RECORD

@@ -0,0 +1,55 @@
+moleditpy_linux/__init__.py,sha256=OWErYK0DbSMVsHrTs7rxzzziUalidJfWPYUaSWm2lLY,317
+moleditpy_linux/__main__.py,sha256=bYu_h7lhc6PIl1-I_VI4_Q5MdBHmVrMiO4DYsy9jbiY,829
+moleditpy_linux/main.py,sha256=0D8_CXe4xdgqlu2TWoT2pi35K9y2b4ilFj6LWD9Qk7w,1178
+moleditpy_linux/modules/__init__.py,sha256=PFwvuEKXsgQlHTYL8oT5sTeo22gR0XmQcySp7kOTtqk,1396
+moleditpy_linux/modules/about_dialog.py,sha256=zkR-w0vtqLH1Y0baQaoTb0tYmVamT4ztEMBdIANKKvc,3693
+moleditpy_linux/modules/align_plane_dialog.py,sha256=ULqc0Ik1ju0HSnkkr0f-VLQw7TJbV9PdjDirYYpBXL0,11934
+moleditpy_linux/modules/alignment_dialog.py,sha256=Oikb5lzTxrRX2MJXoeziYqBc9hckVR0PbuBb4KJUCCc,11409
+moleditpy_linux/modules/analysis_window.py,sha256=zjP5ipSTpKw8oLr1eKdoxW8Bk1SslGlPqsVucD-x_5w,9403
+moleditpy_linux/modules/angle_dialog.py,sha256=e06-Bw2E9khyjC3209HuGc5FDS3Pj0StV8u5bO1gKFw,17817
+moleditpy_linux/modules/atom_item.py,sha256=u8ge6B1M9sOGobfzg3tp1-EGXtEUmvdee7Fx6msg8Wk,15566
+moleditpy_linux/modules/bond_item.py,sha256=eVkEeKvM4igYI67DYxpey3FllqDyt_iWDo4VPYMhaPk,19137
+moleditpy_linux/modules/bond_length_dialog.py,sha256=Gaiu4XN3CmMXl-hHl_C5_-ADEA_0VhL5GlAmIKYGRLw,14848
+moleditpy_linux/modules/calculation_worker.py,sha256=KiGQY7i-QCQofEoE0r65KoQgpEGFcbhmxWv6egfkUdc,42324
+moleditpy_linux/modules/color_settings_dialog.py,sha256=Ow44BhCOLo0AFb6klO001k6B4drOgKX9DeNBQhZLp5o,15474
+moleditpy_linux/modules/constants.py,sha256=lbPijXuicncVftXmGiESbdbJ0Ufq_NvziOxOQTEwq50,4703
+moleditpy_linux/modules/constrained_optimization_dialog.py,sha256=OFWJ715N92XLKlJwEnvCa-y01GHst_VoiyzURS9WGvM,30130
+moleditpy_linux/modules/custom_interactor_style.py,sha256=NjsXE2a43IDNEanZBlcG9eR4ZIERT1MsQC6lbfesapQ,38453
+moleditpy_linux/modules/custom_qt_interactor.py,sha256=MFaTuDh-FPeFBS4303CqxsxmsOIOW4QXUz6USwI8PHQ,2451
+moleditpy_linux/modules/dialog3_d_picking_mixin.py,sha256=2Sut0J5ltXMtrUJ9R3o1oZ4ysed27mdSIqLpWxmGdyM,5037
+moleditpy_linux/modules/dihedral_dialog.py,sha256=J_Ri71gkqYzBWK3MFaQv9Uq_iN6caTsEtFCTz4hr4Mk,18078
+moleditpy_linux/modules/main_window.py,sha256=bWgYP3EMOAcy1fnjg5DTXHb2d7Xm6zKQtFcleYjg7Ac,35789
+moleditpy_linux/modules/main_window_app_state.py,sha256=4iwmnaiKu7uJ98r1KpdWgZ1_GBCGsM38hf7DNTFXEZE,33592
+moleditpy_linux/modules/main_window_compute.py,sha256=DsyMvGD2gnB-9XC6SU-ICuScyyQxubfaDYAk8hkY-vk,51911
+moleditpy_linux/modules/main_window_dialog_manager.py,sha256=S1ROCWqzB2uVSKHY4o5CbTtJAEjSyEXGPC1AgmdVgK4,20065
+moleditpy_linux/modules/main_window_edit_3d.py,sha256=xBZxqzkTSUFqY2-WrTGEpTNIgzHdT_oMK5NcHaU2XVQ,19771
+moleditpy_linux/modules/main_window_edit_actions.py,sha256=lUFxNFTUQzeXN8CNlb4_4S9j4M1EEq8kpJmh9dCzM3M,64818
+moleditpy_linux/modules/main_window_export.py,sha256=piWCXSdC2Qfd1BgNvSlAOgCrce7n8YH99GexuTifhlg,34683
+moleditpy_linux/modules/main_window_main_init.py,sha256=rgPCUGB6yto0wTaMvWw721wNurGQ5hHpg0rpa3a1fPI,75595
+moleditpy_linux/modules/main_window_molecular_parsers.py,sha256=yac8DMa4zL35o7fCZFz_qwqLUvkzpzZBITheNO8PM8A,48394
+moleditpy_linux/modules/main_window_project_io.py,sha256=mj6rqLMziNb8YDEBtlt2FLJ3eylmz1pTokjaQ3F1r8k,17239
+moleditpy_linux/modules/main_window_string_importers.py,sha256=mQVDv2Dj4MwnPgMRe2IqdAAKnB_quE6QfYeAgCjfv28,10892
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