MoleditPy-linux 2.4.7__py3-none-any.whl → 2.4.9__py3-none-any.whl

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@@ -16,7 +16,7 @@ from PyQt6.QtGui import QFont, QColor
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  from rdkit import Chem
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  #Version
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- VERSION = '2.4.7'
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+ VERSION = '2.4.9'
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  ATOM_RADIUS = 18
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  BOND_OFFSET = 3.5
@@ -109,7 +109,21 @@ class MainWindowAppState(object):
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  state['version'] = VERSION
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- if self.current_mol: state['mol_3d'] = self.current_mol.ToBinary()
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+ if self.current_mol:
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+ state['mol_3d'] = self.current_mol.ToBinary()
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+ # RDKit binary serialization does not preserve custom properties like _original_atom_id.
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+ # We store them separately to ensure we can restore the 2D-3D link after undo/redo.
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+ mol_3d_atom_ids = []
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+ for i in range(self.current_mol.GetNumAtoms()):
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+ atom = self.current_mol.GetAtomWithIdx(i)
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+ try:
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+ if atom.HasProp("_original_atom_id"):
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+ mol_3d_atom_ids.append(atom.GetIntProp("_original_atom_id"))
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+ else:
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+ mol_3d_atom_ids.append(None)
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+ except Exception:
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+ mol_3d_atom_ids.append(None)
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+ state['mol_3d_atom_ids'] = mol_3d_atom_ids
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  state['is_3d_viewer_mode'] = not self.is_2d_editable
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@@ -204,6 +218,27 @@ class MainWindowAppState(object):
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  self.current_mol = Chem.Mol(loaded_data['mol_3d'])
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  # デバッグ:3D構造が有効かチェック
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  if self.current_mol and self.current_mol.GetNumAtoms() > 0:
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+ # Restore _original_atom_id if present in saved state
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+ if 'mol_3d_atom_ids' in loaded_data:
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+ atom_ids = loaded_data['mol_3d_atom_ids']
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+ if len(atom_ids) == self.current_mol.GetNumAtoms():
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+ for i, aid in enumerate(atom_ids):
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+ if aid is not None:
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+ try:
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+ self.current_mol.GetAtomWithIdx(i).SetIntProp("_original_atom_id", int(aid))
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+ except Exception:
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+ pass
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+
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+ # Re-create atom ID mapping to synchronize 2D atoms with 3D actors
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+ # This MUST be done before draw_molecule_3d for labels to be correct.
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+ try:
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+ self.create_atom_id_mapping()
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+ self.update_atom_id_menu_text()
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+ self.update_atom_id_menu_state()
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+ except Exception:
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+ pass
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+
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+ # draw_molecule_3d will use the restored IDs for labels/picking if show_all_atom_info is called.
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  self.draw_molecule_3d(self.current_mol)
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  self.plotter.reset_camera()
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  # 3D関連機能を統一的に有効化
@@ -254,7 +289,11 @@ class MainWindowAppState(object):
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  'atoms': {k: (v['symbol'], v['item'].pos().x(), v['item'].pos().y(), v.get('charge', 0), v.get('radical', 0)) for k, v in self.data.atoms.items()},
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  'bonds': {k: (v['order'], v.get('stereo', 0)) for k, v in self.data.bonds.items()},
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  '_next_atom_id': self.data._next_atom_id,
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- 'mol_3d': self.current_mol.ToBinary() if self.current_mol else None
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+ 'mol_3d': self.current_mol.ToBinary() if self.current_mol else None,
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+ 'mol_3d_atom_ids': [
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+ (a.GetIntProp("_original_atom_id") if a.HasProp("_original_atom_id") else None)
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+ for a in self.current_mol.GetAtoms()
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+ ] if self.current_mol else None
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  }
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  last_state_for_comparison = None
@@ -266,7 +305,8 @@ class MainWindowAppState(object):
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  'atoms': {k: (v['symbol'], v['pos'][0], v['pos'][1], v.get('charge', 0), v.get('radical', 0)) for k, v in last_atoms.items()},
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  'bonds': {k: (v['order'], v.get('stereo', 0)) for k, v in last_bonds.items()},
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  '_next_atom_id': last_state.get('_next_atom_id'),
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- 'mol_3d': last_state.get('mol_3d', None)
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+ 'mol_3d': last_state.get('mol_3d', None),
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+ 'mol_3d_atom_ids': last_state.get('mol_3d_atom_ids', None)
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  }
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  if not last_state_for_comparison or current_state_for_comparison != last_state_for_comparison:
@@ -1838,6 +1838,39 @@ class MainWindowMainInit(object):
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  # Add dynamic plugin actions (Legacy + New Registration)
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  plugins = self.plugin_manager.discover_plugins(self)
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+ # --- Update 3D Style Menu with discovered styles ---
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+ # This menu is built in init_ui (before plugins are discovered), so we must update it here.
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+ if hasattr(self, 'style_button') and self.style_button.menu():
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+ style_menu = self.style_button.menu()
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+
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+ # Find the exclusive ActionGroup from an existing action (e.g. Ball & Stick)
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+ style_group = None
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+ for action in style_menu.actions():
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+ if action.actionGroup():
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+ style_group = action.actionGroup()
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+ break
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+
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+ if style_group and self.plugin_manager.custom_3d_styles:
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+ # Add separator if not present at end
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+ actions = style_menu.actions()
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+ if actions and not actions[-1].isSeparator():
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+ style_menu.addSeparator()
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+
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+ for style_name in self.plugin_manager.custom_3d_styles:
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+ # Check if already added to avoid duplicates
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+ exists = False
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+ for act in style_menu.actions():
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+ if act.text() == style_name:
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+ exists = True
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+ break
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+
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+ if not exists:
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+ action = QAction(style_name, self, checkable=True)
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+ # Use default arg to capture loop variable
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+ action.triggered.connect(lambda checked=False, s=style_name: self.set_3d_style(s))
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+ style_menu.addAction(action)
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+ style_group.addAction(action)
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+
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  # 1. Add Registered Menu Actions (New System)
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  if self.plugin_manager.menu_actions:
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  for action_def in self.plugin_manager.menu_actions:
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: MoleditPy-linux
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- Version: 2.4.7
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+ Version: 2.4.9
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  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.
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  Author-email: HiroYokoyama <titech.yoko.hiro@gmail.com>
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  License: GNU GENERAL PUBLIC LICENSE
@@ -12,20 +12,20 @@ moleditpy_linux/modules/bond_item.py,sha256=21oX1sR5kpY-MlfUsmekkV6XATVwIAhmsH1U
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  moleditpy_linux/modules/bond_length_dialog.py,sha256=6bFPGssnqlgINuqpxLv-OhjMH3_hspnaH8QtorAyu2M,14782
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  moleditpy_linux/modules/calculation_worker.py,sha256=KiGQY7i-QCQofEoE0r65KoQgpEGFcbhmxWv6egfkUdc,42324
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  moleditpy_linux/modules/color_settings_dialog.py,sha256=Ow44BhCOLo0AFb6klO001k6B4drOgKX9DeNBQhZLp5o,15474
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- moleditpy_linux/modules/constants.py,sha256=cJBVJ8ESdrhJ3CVXNEWjf8jAUcw9bjzBIm80BxT3CFw,4702
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+ moleditpy_linux/modules/constants.py,sha256=6Q8jR5TnrGM7OnB2cCyDHvTN8XZyg2kH7-Ioz5nsW8s,4702
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  moleditpy_linux/modules/constrained_optimization_dialog.py,sha256=REsk4ePsqNmAGPMTS_jckeM7jexrU3krwun8sKqKUCs,30062
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  moleditpy_linux/modules/custom_interactor_style.py,sha256=LDNODMJoNHGe1AUSrvqv6PdeJm-hpPmSpWINppnJLt0,38942
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  moleditpy_linux/modules/custom_qt_interactor.py,sha256=vCZsDfRO-FtphD5cTP7Ps-5rpHZMIGloaoe6EaKzrsw,4139
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  moleditpy_linux/modules/dialog3_d_picking_mixin.py,sha256=z4udbkiX9PYmIGazPXsbftkk_oRRwZhcvlCqbyJzr24,6493
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  moleditpy_linux/modules/dihedral_dialog.py,sha256=bOTDO6-b74vEDn_z6OyuBr5cRz3RnRj83PiaEBUyWJA,18002
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  moleditpy_linux/modules/main_window.py,sha256=w52L0F7V3b0BiNhQImbulZ9N8cRKolYy06szfoMOIcg,36830
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- moleditpy_linux/modules/main_window_app_state.py,sha256=8YDcGNCSpLTO1NGL9tEvNkXpUcS7JW-uK7TdUGvEqnk,35189
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+ moleditpy_linux/modules/main_window_app_state.py,sha256=Civ28scAuIPXdD1qix5IkUAgEgl4Wy3wCqblomF3EY4,37493
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  moleditpy_linux/modules/main_window_compute.py,sha256=ipIkhH_DONXDnPzh7xeym9X-Yfx8EhsvXYOdyxsAj4c,53347
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  moleditpy_linux/modules/main_window_dialog_manager.py,sha256=QR96LqHAPSOShXbc9cK-Ffq8a16JrXAoMKB0pHjESrQ,20072
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  moleditpy_linux/modules/main_window_edit_3d.py,sha256=CUArB5wcsgq1C7LygAEC6URlbnn4RhRYDa5n-Y-etWI,19731
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  moleditpy_linux/modules/main_window_edit_actions.py,sha256=drVXRFpSOhILYfApcSro9zssnDw-a8F7wNcfQ3xQukw,69412
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  moleditpy_linux/modules/main_window_export.py,sha256=_Vd7MeP_xaLWDYDm3-ZIZiPuAXhP-AvrQbi7Yx3Jy3c,43020
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- moleditpy_linux/modules/main_window_main_init.py,sha256=SNgsnovYEbe_5lkpon3Wgh-v5SawI0xsb26DE5-W7ic,94882
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+ moleditpy_linux/modules/main_window_main_init.py,sha256=s51xvG0vsZnVfLfB6GaidW1axflWWQp8ssPCF63TCUM,96573
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  moleditpy_linux/modules/main_window_molecular_parsers.py,sha256=KR6vzuqc3nutOcorpYr0QOyX3MFBcxTwDhZX96VgJ9Q,48291
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  moleditpy_linux/modules/main_window_project_io.py,sha256=TWwtuKDuvgcvPZ9IGmW8r1EJJOrgxrIJRnxe_f4C1oM,17149
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  moleditpy_linux/modules/main_window_string_importers.py,sha256=v47wOd4RtjKYcF-aLP-mogGGdYTpTEo3dDyAu79_5MM,10782
@@ -51,9 +51,9 @@ moleditpy_linux/modules/assets/file_icon.ico,sha256=yyVj084A7HuMNbV073cE_Ag3Ne40
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  moleditpy_linux/modules/assets/icon.icns,sha256=wD5R6-Vw7K662tVKhu2E1ImN0oUuyAP4youesEQsn9c,139863
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  moleditpy_linux/modules/assets/icon.ico,sha256=RfgFcx7-dHY_2STdsOQCQziY5SNhDr3gPnjO6jzEDPI,147975
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  moleditpy_linux/modules/assets/icon.png,sha256=kCFN1WacYIdy0GN6SFEbNA00ef39pCczBnFdkkBI8Bs,147110
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- moleditpy_linux-2.4.7.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
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- moleditpy_linux-2.4.7.dist-info/METADATA,sha256=iFu5Ov9NUgyr0c5AUzscJqZKGQ0pkIpk8g-yOEgHMXo,60708
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- moleditpy_linux-2.4.7.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
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- moleditpy_linux-2.4.7.dist-info/entry_points.txt,sha256=-OzipSi__yVwlimNtu3eiRP5t5UMg55Cs0udyhXYiyw,60
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- moleditpy_linux-2.4.7.dist-info/top_level.txt,sha256=qyqe-hDYL6CXyin9E5Me5rVl3PG84VqiOjf9bQvfJLs,16
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- moleditpy_linux-2.4.7.dist-info/RECORD,,
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+ moleditpy_linux-2.4.9.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
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+ moleditpy_linux-2.4.9.dist-info/METADATA,sha256=49bF-GvDF51aSUq2w99a2XPGFRFiXY6nDPwfRPDnK2c,60708
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+ moleditpy_linux-2.4.9.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
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+ moleditpy_linux-2.4.9.dist-info/entry_points.txt,sha256=-OzipSi__yVwlimNtu3eiRP5t5UMg55Cs0udyhXYiyw,60
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+ moleditpy_linux-2.4.9.dist-info/top_level.txt,sha256=qyqe-hDYL6CXyin9E5Me5rVl3PG84VqiOjf9bQvfJLs,16
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+ moleditpy_linux-2.4.9.dist-info/RECORD,,