MoleditPy-linux 2.8.2__tar.gz → 2.8.3__tar.gz

{moleditpy_linux-2.8.2 → moleditpy_linux-2.8.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 2.8.2
+Version: 2.8.3
 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-2.8.2 → moleditpy_linux-2.8.3}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy-linux"
 
-version = "2.8.2"
+version = "2.8.3"
 
 license = {file = "LICENSE"}
 

{moleditpy_linux-2.8.2 → moleditpy_linux-2.8.3}/src/MoleditPy_linux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 2.8.2
+Version: 2.8.3
 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-2.8.2 → moleditpy_linux-2.8.3}/src/moleditpy_linux/modules/calculation_worker.py

@@ -210,17 +210,20 @@ def _adjust_collision_avoidance(rd_mol, check_halted_cb, safe_status_cb):
         safe_status_cb(f"Collision avoidance warning: {e}")
 
 
-def _iterative_optimize(mol, method, check_halted_cb, safe_status_cb, max_iters=4000, chunk_size=100):
+def _iterative_optimize(mol, method, check_halted_cb, safe_status_cb, max_iters=4000, chunk_size=100, options=None):
     """Perform force field optimization in small chunks to avoid UI freezing and allow halts."""
     try:
+        # Respect the "Consider Intermolecular Interaction for RDKit" setting
+        ignore_interfrag = not options.get("optimize_intermolecular_interaction_rdkit", True) if options else False
+
         if method in ("MMFF", "MMFF94", "MMFF94S", "MMFF94s"):
             mmff_variant = "MMFF94" if method == "MMFF94" else "MMFF94s"
             props = AllChem.MMFFGetMoleculeProperties(mol, mmffVariant=mmff_variant)
             if props is None:
                 raise ValueError(f"Failed to generate MMFF properties for variant {mmff_variant}.")
-            ff = AllChem.MMFFGetMoleculeForceField(mol, props, confId=0)
+            ff = AllChem.MMFFGetMoleculeForceField(mol, props, confId=0, ignoreInterfragInteractions=ignore_interfrag)
         elif method == "UFF":
-            ff = AllChem.UFFGetMoleculeForceField(mol, confId=0)
+            ff = AllChem.UFFGetMoleculeForceField(mol, confId=0, ignoreInterfragInteractions=ignore_interfrag)
         else:
             raise ValueError(f"Unknown optimization method: {method}")
 
@@ -714,6 +717,8 @@ def _perform_direct_conversion(mol_block, mol, options, _check_halted, _safe_sta
     # Optimization (respects do_optimize flag)
     do_optimize = options.get("do_optimize", True) if options else True
     if do_optimize:
+        # Collision avoidance before optimization
+        _adjust_collision_avoidance(mol, _check_halted, _safe_status)
         _safe_status("Direct conversion: optimizing geometry...")
         if _check_halted():
             raise WorkerHaltError("Halted")
@@ -755,7 +760,7 @@ def _perform_direct_conversion(mol_block, mol, options, _check_halted, _safe_sta
             except Exception:
                 pass
             _safe_status(f"Applying force field optimization ({method_key} / RDKit)...")
-            opt_success = _iterative_optimize(mol, method_key, _check_halted, _safe_status)
+            opt_success = _iterative_optimize(mol, method_key, _check_halted, _safe_status, options=options)
             if not opt_success:
                 _safe_status(f"Warning: Optimization with {opt_method} failed. Using unoptimized structure.")
                 try:
@@ -765,8 +770,6 @@ def _perform_direct_conversion(mol_block, mol, options, _check_halted, _safe_sta
 
     if _check_halted():
         raise WorkerHaltError("Halted")
-    if do_optimize:
-        _adjust_collision_avoidance(mol, _check_halted, _safe_status)
     return mol
 
 
@@ -800,7 +803,7 @@ def _perform_optimize_only(mol, options, worker_id, _check_halted, _safe_status,
             mol.SetProp("_pme_optimization_method", opt_method)
         except Exception:
             pass
-        opt_success = _iterative_optimize(mol, method_key, _check_halted, _safe_status)
+        opt_success = _iterative_optimize(mol, method_key, _check_halted, _safe_status, options=options)
     
     if not opt_success:
         raise Exception(f"Optimization with {opt_method} failed. You can change the method in the settings.")
@@ -843,6 +846,8 @@ def _perform_obabel_conversion(mol_block, conversion_mode, opt_method, worker_id
         if rd_mol is None:
             raise ValueError("Open Babel produced invalid MOL block.")
         rd_mol = Chem.AddHs(rd_mol)
+        # Collision avoidance before optimization
+        _adjust_collision_avoidance(rd_mol, _check_halted, _safe_status)
         try:
             opt_method_raw = opt_method or "MMFF94s_RDKIT"
             backend = "OBABEL" if "OBABEL" in opt_method_raw.upper() else "RDKIT"
@@ -870,7 +875,7 @@ def _perform_obabel_conversion(mol_block, conversion_mode, opt_method, worker_id
                 except Exception:
                     pass
                 _safe_status(f"Optimizing with RDKit ({method_key})...")
-                opt_success = _iterative_optimize(rd_mol, method_key, _check_halted, _safe_status)
+                opt_success = _iterative_optimize(rd_mol, method_key, _check_halted, _safe_status, options=options)
 
             if not opt_success:
                 _safe_status(f"Warning: Optimization with {opt_method_raw} failed. Using unoptimized structure.")
@@ -894,8 +899,6 @@ def _perform_obabel_conversion(mol_block, conversion_mode, opt_method, worker_id
         if _check_halted():
             raise WorkerHaltError("Halted")
 
-        # Collision avoidance
-        _adjust_collision_avoidance(rd_mol, _check_halted, _safe_status)
         try:
             _safe_finished((worker_id, rd_mol))
         except Exception:
@@ -1226,6 +1229,9 @@ class CalculationWorker(QObject):
                         bond.SetStereoAtoms(stereo_atoms[0], stereo_atoms[1])
                     bond.SetStereo(stereo)
 
+                # Collision avoidance before optimization
+                _adjust_collision_avoidance(mol, _check_halted, _safe_status)
+
                 try:
                     opt_method_raw = opt_method or "MMFF94s_RDKIT"
                     backend = "OBABEL" if "OBABEL" in opt_method_raw.upper() else "RDKIT"
@@ -1253,7 +1259,7 @@ class CalculationWorker(QObject):
                         except Exception:  # pragma: no cover
                             pass
                         _safe_status(f"Optimizing with RDKit ({method_key})...")
-                        opt_success = _iterative_optimize(mol, method_key, _check_halted, _safe_status)
+                        opt_success = _iterative_optimize(mol, method_key, _check_halted, _safe_status, options=options)
 
                     if not opt_success:
                         raise Exception(f"Optimization with {opt_method_raw} failed. You can change the method in the settings.")
@@ -1282,9 +1288,6 @@ class CalculationWorker(QObject):
                     if _check_halted():
                         raise WorkerHaltError("Halted")
 
-                    # Collision avoidance
-                    _adjust_collision_avoidance(mol, _check_halted, _safe_status)
-
                     try:
                         _safe_finished((worker_id, mol))
                     except WorkerHaltError:

{moleditpy_linux-2.8.2 → moleditpy_linux-2.8.3}/src/moleditpy_linux/modules/constants.py

@@ -16,7 +16,7 @@ from PyQt6.QtGui import QColor, QFont
 from rdkit import Chem
 
 # Version
-VERSION = "2.8.2"
+VERSION = "2.8.3"
 
 ATOM_RADIUS = 18
 BOND_OFFSET = 3.5

{moleditpy_linux-2.8.2 → moleditpy_linux-2.8.3}/src/moleditpy_linux/modules/constrained_optimization_dialog.py

@@ -445,14 +445,15 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):  # pragma: n
         conf = self.mol.GetConformer()
 
         try:
+            ignore_interfrag = not self.main_window.settings.get("optimize_intermolecular_interaction_rdkit", True)
             if ff_name.startswith("MMFF"):
                 props = AllChem.MMFFGetMoleculeProperties(self.mol, mmffVariant=ff_name)
-                ff = AllChem.MMFFGetMoleculeForceField(self.mol, props, confId=0)
+                ff = AllChem.MMFFGetMoleculeForceField(self.mol, props, confId=0, ignoreInterfragInteractions=ignore_interfrag)
                 add_dist_constraint = ff.MMFFAddDistanceConstraint
                 add_angle_constraint = ff.MMFFAddAngleConstraint
                 add_torsion_constraint = ff.MMFFAddTorsionConstraint
             else:  # UFF
-                ff = AllChem.UFFGetMoleculeForceField(self.mol, confId=0)
+                ff = AllChem.UFFGetMoleculeForceField(self.mol, confId=0, ignoreInterfragInteractions=ignore_interfrag)
                 add_dist_constraint = ff.UFFAddDistanceConstraint
                 add_angle_constraint = ff.UFFAddAngleConstraint
                 add_torsion_constraint = ff.UFFAddTorsionConstraint

{moleditpy_linux-2.8.2 → moleditpy_linux-2.8.3}/src/moleditpy_linux/modules/main_window.py

@@ -178,6 +178,10 @@ class MainWindow(QMainWindow):
         # --- MOVED TO main_window_compute.py ---
         return self.main_window_compute.set_optimization_method(method_name)
 
+    def toggle_intermolecular_interaction_rdkit(self, checked):
+        # --- MOVED TO main_window_compute.py ---
+        return self.main_window_compute.toggle_intermolecular_interaction_rdkit(checked)
+
     def copy_selection(self):
         # --- MOVED TO main_window_edit_actions.py ---
         return self.main_window_edit_actions.copy_selection()

{moleditpy_linux-2.8.2 → moleditpy_linux-2.8.3}/src/moleditpy_linux/modules/main_window_compute.py

@@ -119,6 +119,20 @@ class MainWindowCompute(object):
             label = self.optimization_method
         self.statusBar().showMessage(f"3D optimization method set to: {label}")
 
+    def toggle_intermolecular_interaction_rdkit(self, checked):  # pragma: no cover
+        """Toggle whether intermolecular interactions are considered for RDKit optimization."""
+        try:
+            self.settings["optimize_intermolecular_interaction_rdkit"] = checked
+            try:
+                self.settings_dirty = True
+            except Exception:
+                pass
+            state_str = "Enabled" if checked else "Disabled"
+            self.statusBar().showMessage(f"Intermolecular interaction for RDKit: {state_str}")
+        except Exception:
+            import traceback
+            traceback.print_exc()
+
     def show_convert_menu(self, pos):  # pragma: no cover
         """右クリックで表示する一時的な3D変換メニュー。
         選択したモードは一時フラグとして保持され、その後の変換で使用されます（永続化しません）。
@@ -442,7 +456,11 @@ class MainWindowCompute(object):
                     import traceback
                     traceback.print_exc()
 
-        options = {"conversion_mode": conv_mode, "optimization_method": opt_method}
+        options = {
+            "conversion_mode": conv_mode,
+            "optimization_method": opt_method,
+            "optimize_intermolecular_interaction_rdkit": self.settings.get("optimize_intermolecular_interaction_rdkit", True)
+        }
         # Attach the run id so the worker and main thread can correlate
         try:
             # Attach the concrete run id rather than the single waiting id
@@ -800,7 +818,8 @@ class MainWindowCompute(object):
                 
                 options = {
                     "conversion_mode": "optimize_only",
-                    "optimization_method": method
+                    "optimization_method": method,
+                    "optimize_intermolecular_interaction_rdkit": self.settings.get("optimize_intermolecular_interaction_rdkit", True)
                 }
                 
                 # Assign a unique ID for this optimization run

{moleditpy_linux-2.8.2 → moleditpy_linux-2.8.3}/src/moleditpy_linux/modules/main_window_main_init.py

@@ -1494,6 +1494,13 @@ class MainWindowMainInit(object):
             optimization_menu.addAction(action)
             opt_group.addAction(action)
             opt_actions[key] = action
+        
+        optimization_menu.addSeparator()
+        self.intermolecular_rdkit_action = QAction("Consider Intermolecular Interaction for RDKit", self)
+        self.intermolecular_rdkit_action.setCheckable(True)
+        self.intermolecular_rdkit_action.setChecked(self.settings.get("optimize_intermolecular_interaction_rdkit", True))
+        self.intermolecular_rdkit_action.triggered.connect(self.toggle_intermolecular_interaction_rdkit)
+        optimization_menu.addAction(self.intermolecular_rdkit_action)
 
         # Persist the actions mapping so other methods can update the checked state
         self.opt3d_actions = opt_actions
@@ -1723,6 +1730,11 @@ class MainWindowMainInit(object):
                         except Exception:  # pragma: no cover
                             import traceback
                             traceback.print_exc()
+                    
+                    # update intermolecular rdkit setting
+                    if hasattr(self, "intermolecular_rdkit_action"):
+                        self.intermolecular_rdkit_action.setChecked(self.settings.get("optimize_intermolecular_interaction_rdkit", True))
+
                     # 3Dビューの設定を適用
                     self.apply_3d_settings()
                     # 現在の分子を再描画（設定変更を反映）
@@ -1850,6 +1862,7 @@ class MainWindowMainInit(object):
             "bond_color_2d": "#222222",  # Almost black
             "atom_use_bond_color_2d": False,
             "bond_cap_style_2d": "Round",
+            "optimize_intermolecular_interaction_rdkit": True,
         }
 
         try:

{moleditpy_linux-2.8.2 → moleditpy_linux-2.8.3}/src/moleditpy_linux/modules/move_group_dialog.py

@@ -654,22 +654,10 @@ class MoveGroupDialog(Dialog3DPickingMixin, QDialog):  # pragma: no cover
         """ダイアログが閉じられる時の処理"""
         self.clear_atom_labels()
         self.disable_picking()
-        try:
-            self.main_window.draw_molecule_3d(self.mol)
-        except Exception:  # pragma: no cover
-            import traceback
-            traceback.print_exc()
-
         super().closeEvent(event)
 
     def reject(self):
         """キャンセル時の処理"""
         self.clear_atom_labels()
         self.disable_picking()
-        try:
-            self.main_window.draw_molecule_3d(self.mol)
-        except Exception:  # pragma: no cover
-            import traceback
-            traceback.print_exc()
-
         super().reject()

{moleditpy_linux-2.8.2 → moleditpy_linux-2.8.3}/src/moleditpy_linux/modules/translation_dialog.py

@@ -358,34 +358,16 @@ class TranslationDialog(Dialog3DPickingMixin, QDialog):  # pragma: no cover
         """ダイアログが閉じられる時の処理"""
         self.clear_atom_labels()
         self.disable_picking()
-        try:
-            self.main_window.draw_molecule_3d(self.mol)
-        except Exception:  # pragma: no cover
-            import traceback
-            traceback.print_exc()
-
         super().closeEvent(event)
 
     def reject(self):
         """キャンセル時の処理"""
         self.clear_atom_labels()
         self.disable_picking()
-        try:
-            self.main_window.draw_molecule_3d(self.mol)
-        except Exception:  # pragma: no cover
-            import traceback
-            traceback.print_exc()
-
         super().reject()
 
     def accept(self):
         """OK時の処理"""
         self.clear_atom_labels()
         self.disable_picking()
-        try:
-            self.main_window.draw_molecule_3d(self.mol)
-        except Exception:  # pragma: no cover
-            import traceback
-            traceback.print_exc()
-
         super().accept()