moleditpy 2.8.0a4__tar.gz → 2.8.1__tar.gz

{moleditpy-2.8.0a4 → moleditpy-2.8.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 2.8.0a4
+Version: 2.8.1
 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
@@ -710,10 +710,10 @@ Dynamic: license-file
 [![Python Versions](https://img.shields.io/pypi/pyversions/MoleditPy.svg)](https://pypi.org/project/MoleditPy/)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Build Status](https://github.com/HiroYokoyama/python_molecular_editor/actions/workflows/tests.yml/badge.svg)](https://github.com/HiroYokoyama/python_molecular_editor/actions)
-![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-73%25-green)
+![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-72%25-green)
 ![Overall Coverage](https://img.shields.io/badge/coverage-50%25-orange)
 ![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)
-![Pylint Score](https://img.shields.io/badge/pylint-8.67%2F10-brightgreen)
+![Pylint Score](https://img.shields.io/badge/pylint-8.64%2F10-brightgreen)
 [![PyPI Downloads](https://static.pepy.tech/personalized-badge/moleditpy?period=total&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=downloads)](https://pepy.tech/projects/moleditpy)
 
 [🇯🇵 日本語 (Japanese)](#japanese)

{moleditpy-2.8.0a4 → moleditpy-2.8.1}/README.md

@@ -6,10 +6,10 @@
 [![Python Versions](https://img.shields.io/pypi/pyversions/MoleditPy.svg)](https://pypi.org/project/MoleditPy/)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Build Status](https://github.com/HiroYokoyama/python_molecular_editor/actions/workflows/tests.yml/badge.svg)](https://github.com/HiroYokoyama/python_molecular_editor/actions)
-![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-73%25-green)
+![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-72%25-green)
 ![Overall Coverage](https://img.shields.io/badge/coverage-50%25-orange)
 ![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)
-![Pylint Score](https://img.shields.io/badge/pylint-8.67%2F10-brightgreen)
+![Pylint Score](https://img.shields.io/badge/pylint-8.64%2F10-brightgreen)
 [![PyPI Downloads](https://static.pepy.tech/personalized-badge/moleditpy?period=total&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=downloads)](https://pepy.tech/projects/moleditpy)
 
 [🇯🇵 日本語 (Japanese)](#japanese)

{moleditpy-2.8.0a4 → moleditpy-2.8.1}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "2.8.0a4"
+version = "2.8.1"
 
 license = {file = "LICENSE"}
 

{moleditpy-2.8.0a4 → moleditpy-2.8.1}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 2.8.0a4
+Version: 2.8.1
 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
@@ -710,10 +710,10 @@ Dynamic: license-file
 [![Python Versions](https://img.shields.io/pypi/pyversions/MoleditPy.svg)](https://pypi.org/project/MoleditPy/)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Build Status](https://github.com/HiroYokoyama/python_molecular_editor/actions/workflows/tests.yml/badge.svg)](https://github.com/HiroYokoyama/python_molecular_editor/actions)
-![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-73%25-green)
+![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-72%25-green)
 ![Overall Coverage](https://img.shields.io/badge/coverage-50%25-orange)
 ![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)
-![Pylint Score](https://img.shields.io/badge/pylint-8.67%2F10-brightgreen)
+![Pylint Score](https://img.shields.io/badge/pylint-8.64%2F10-brightgreen)
 [![PyPI Downloads](https://static.pepy.tech/personalized-badge/moleditpy?period=total&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=downloads)](https://pepy.tech/projects/moleditpy)
 
 [🇯🇵 日本語 (Japanese)](#japanese)

{moleditpy-2.8.0a4 → moleditpy-2.8.1}/src/moleditpy/modules/angle_dialog.py

@@ -152,11 +152,15 @@ class AngleDialog(Dialog3DPickingMixin, QDialog):  # pragma: no cover
             self.atom2_idx = atom_idx
         elif self.atom3_idx is None:
             self.atom3_idx = atom_idx
+            # Take a fresh snapshot immediately upon completing the triad selection
+            # This locks in the "original" initial geometry the user started modifying from
+            self._snapshot_positions = self.mol.GetConformer().GetPositions().copy()
         else:
             # Reset and start over
             self.atom1_idx = atom_idx
             self.atom2_idx = None
             self.atom3_idx = None
+            self._snapshot_positions = None
 
         # 原子ラベルを表示
         self.show_atom_labels()
@@ -177,12 +181,6 @@ class AngleDialog(Dialog3DPickingMixin, QDialog):  # pragma: no cover
         self.disable_picking()
         super().closeEvent(event)
 
-    def reject(self):
-        """キャンセル時の処理"""
-        self.clear_atom_labels()
-        self.disable_picking()
-        super().reject()
-
     def accept(self):
         """OK時の処理"""
         self.clear_atom_labels()
@@ -194,6 +192,7 @@ class AngleDialog(Dialog3DPickingMixin, QDialog):  # pragma: no cover
         self.atom1_idx = None
         self.atom2_idx = None  # vertex atom
         self.atom3_idx = None
+        self._snapshot_positions = None
         self.clear_selection_labels()
         self.update_display()
 
@@ -215,6 +214,7 @@ class AngleDialog(Dialog3DPickingMixin, QDialog):  # pragma: no cover
             self.selection_label.setText("No atoms selected")
             self.angle_label.setText("")
             self.apply_button.setEnabled(False)
+            self._snapshot_positions = None
             # Clear angle input when no selection
             try:
                 self.angle_input.blockSignals(True)
@@ -235,6 +235,7 @@ class AngleDialog(Dialog3DPickingMixin, QDialog):  # pragma: no cover
             )
             self.angle_label.setText("")
             self.apply_button.setEnabled(False)
+            self._snapshot_positions = None
             # ラベル追加
             self.add_selection_label(self.atom1_idx, "1")
             # Clear angle input while selection is incomplete
@@ -258,6 +259,7 @@ class AngleDialog(Dialog3DPickingMixin, QDialog):  # pragma: no cover
             )
             self.angle_label.setText("")
             self.apply_button.setEnabled(False)
+            self._snapshot_positions = None
             # ラベル追加
             self.add_selection_label(self.atom1_idx, "1")
             self.add_selection_label(self.atom2_idx, "2(vertex)")
@@ -340,7 +342,9 @@ class AngleDialog(Dialog3DPickingMixin, QDialog):  # pragma: no cover
         self._slider_dragging = True
         self.main_window.push_undo_state()
         # Snapshot positions so the rotation axis stays stable during drag
-        self._snapshot_positions = self.mol.GetConformer().GetPositions().copy()
+        # Only take snapshot if one doesn't exist to preserve directional info
+        if getattr(self, '_snapshot_positions', None) is None:
+            self._snapshot_positions = self.mol.GetConformer().GetPositions().copy()
 
     def on_slider_moved(self, value):
         """Update geometry in real-time while dragging."""
@@ -356,7 +360,8 @@ class AngleDialog(Dialog3DPickingMixin, QDialog):  # pragma: no cover
     def on_slider_released(self):
         """Finalize slider dragging."""
         self._slider_dragging = False
-        self._snapshot_positions = None
+        # Do NOT clear snapshot here. Keep it to preserve the turning direction
+        # even if they approach ±180°. It gets cleared when selection is changed.
         self.main_window.draw_molecule_3d(self.mol)
         self.main_window.update_chiral_labels()
 
@@ -367,6 +372,11 @@ class AngleDialog(Dialog3DPickingMixin, QDialog):  # pragma: no cover
         if self.atom1_idx is None or self.atom2_idx is None or self.atom3_idx is None:
             return
         self.main_window.push_undo_state()
+        
+        # Ensure we have a snapshot for click-to-position as well to maintain direction
+        if getattr(self, '_snapshot_positions', None) is None:
+            self._snapshot_positions = self.mol.GetConformer().GetPositions().copy()
+            
         self.angle_input.blockSignals(True)
         self.angle_input.setText(f"{value}")
         self.angle_input.blockSignals(False)
@@ -468,6 +478,9 @@ class AngleDialog(Dialog3DPickingMixin, QDialog):  # pragma: no cover
         self.main_window.draw_molecule_3d(self.mol)
 
     def reject(self):
+        """キャンセル時の処理"""
+        self.clear_atom_labels()
+        self.disable_picking()
         super().reject()
         try:
             if self.main_window.current_mol:

{moleditpy-2.8.0a4 → moleditpy-2.8.1}/src/moleditpy/modules/bond_length_dialog.py

@@ -168,12 +168,6 @@ class BondLengthDialog(Dialog3DPickingMixin, QDialog):  # pragma: no cover
         self.disable_picking()
         super().closeEvent(event)
 
-    def reject(self):
-        """キャンセル時の処理"""
-        self.clear_atom_labels()
-        self.disable_picking()
-        super().reject()
-
     def accept(self):
         """OK時の処理"""
         self.clear_atom_labels()
@@ -420,6 +414,9 @@ class BondLengthDialog(Dialog3DPickingMixin, QDialog):  # pragma: no cover
         self.main_window.draw_molecule_3d(self.mol)
 
     def reject(self):
+        """キャンセル時の処理"""
+        self.clear_atom_labels()
+        self.disable_picking()
         super().reject()
         try:
             if self.main_window.current_mol:

{moleditpy-2.8.0a4 → moleditpy-2.8.1}/src/moleditpy/modules/calculation_worker.py

@@ -204,15 +204,15 @@ def _iterative_optimize(mol, method, check_halted_cb, safe_status_cb, max_iters=
             mmff_variant = "MMFF94" if method == "MMFF94" else "MMFF94s"
             props = AllChem.MMFFGetMoleculeProperties(mol, mmffVariant=mmff_variant)
             if props is None:
-                return False
+                raise ValueError(f"Failed to generate MMFF properties for variant {mmff_variant}.")
             ff = AllChem.MMFFGetMoleculeForceField(mol, props, confId=0)
         elif method == "UFF":
             ff = AllChem.UFFGetMoleculeForceField(mol, confId=0)
         else:
-            return False
+            raise ValueError(f"Unknown optimization method: {method}")
 
         if ff is None:
-            return False
+            raise ValueError(f"Failed to setup force field for method: {method}")
 
         ff.Initialize()
         iters_done = 0
@@ -238,8 +238,7 @@ def _iterative_optimize_obabel(mol, method, check_halted_cb, safe_status_cb, max
     """Perform force field optimization using OpenBabel in chunks to avoid UI freezing."""
     try:
         if not OBABEL_AVAILABLE or pybel is None:
-            safe_status_cb("OpenBabel is not available.")
-            return False
+            raise RuntimeError("OpenBabel is not available.")
             
         ff_name = method.lower()
         
@@ -250,8 +249,7 @@ def _iterative_optimize_obabel(mol, method, check_halted_cb, safe_status_cb, max
         # Set up forcefield
         ff = pybel.ob.OBForceField.FindForceField(ff_name)
         if not ff:
-            safe_status_cb(f"Forcefield '{ff_name}' not found in OpenBabel.")
-            return False
+            raise ValueError(f"Forcefield '{ff_name}' not found in OpenBabel.")
             
         if not ff.Setup(ob_mol.OBMol):
             error_msg = f"Failed to load parameters for '{ff_name}'."
@@ -960,7 +958,11 @@ class CalculationWorker(QObject):
                             _safe_status(f"Applying force field optimization ({method_key} / OpenBabel)...")
                             opt_success = _iterative_optimize_obabel(mol, method_key, _check_halted, _safe_status)
                             if not opt_success:
-                                raise Exception(f"Optimization with {opt_method} failed. You can change the method in the settings.")
+                                _safe_status(f"Warning: Optimization with {opt_method} failed. Using unoptimized structure.")
+                                try:
+                                    mol.ClearProp("_pme_optimization_method")
+                                except Exception:
+                                    pass
                         else: # RDKit backend
                             try:
                                 # Add property for UI feedback
@@ -970,7 +972,11 @@ class CalculationWorker(QObject):
                             _safe_status(f"Applying force field optimization ({method_key} / RDKit)...")
                             opt_success = _iterative_optimize(mol, method_key, _check_halted, _safe_status)
                             if not opt_success:
-                                raise Exception(f"Optimization with {opt_method} failed. You can change the method in the settings.")
+                                _safe_status(f"Warning: Optimization with {opt_method} failed. Using unoptimized structure.")
+                                try:
+                                    mol.ClearProp("_pme_optimization_method")
+                                except Exception:
+                                    pass
 
                     if _check_halted():
                         raise WorkerHaltError("Halted")
@@ -1163,14 +1169,14 @@ class CalculationWorker(QObject):
                     if backend == "OBABEL":
                         try:
                             mol.SetProp("_pme_optimization_method", opt_method_raw)
-                        except Exception:
+                        except Exception:  # pragma: no cover
                             pass
                         _safe_status(f"Optimizing with OpenBabel ({method_key})...")
                         opt_success = _iterative_optimize_obabel(mol, method_key, _check_halted, _safe_status)
                     else:
                         try:
                             mol.SetProp("_pme_optimization_method", opt_method_raw)
-                        except Exception:
+                        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)
@@ -1180,31 +1186,39 @@ class CalculationWorker(QObject):
                 except WorkerHaltError:
                     raise
                 except Exception as opt_err:
-                    _safe_status(f"Optimization failed: {opt_err}")
-                    raise
+                    if conversion_mode == "rdkit":
+                        raise Exception(f"Optimization with {opt_method_raw} failed: {opt_err}")
+                    _safe_status(f"Optimization failed: {opt_err}. Falling back...")  # pragma: no cover
+                    try:  # pragma: no cover
+                        mol.ClearProp("_pme_optimization_method")
+                    except Exception:  # pragma: no cover
+                        pass
+                    # Allow fallback to proceed instead of crashing
+                    conf_id = -1  # pragma: no cover
                 
                 # CRITICAL: Restore stereochemistry again after optimization (explicit labels priority)
-                for bond_idx, stereo, stereo_atoms in original_stereo_info:
-                    bond = mol.GetBondWithIdx(bond_idx)
-                    if len(stereo_atoms) == 2:
-                        bond.SetStereoAtoms(stereo_atoms[0], stereo_atoms[1])
-                    bond.SetStereo(stereo)
+                if conf_id != -1:
+                    for bond_idx, stereo, stereo_atoms in original_stereo_info:
+                        bond = mol.GetBondWithIdx(bond_idx)
+                        if len(stereo_atoms) == 2:
+                            bond.SetStereoAtoms(stereo_atoms[0], stereo_atoms[1])
+                        bond.SetStereo(stereo)
 
-                # CRITICAL: Check for halt *before* emitting finished signal
-                if _check_halted():
-                    raise WorkerHaltError("Halted")
+                    # CRITICAL: Check for halt *before* emitting finished signal
+                    if _check_halted():
+                        raise WorkerHaltError("Halted")
 
-                # Collision avoidance
-                _adjust_collision_avoidance(mol, _check_halted, _safe_status)
+                    # Collision avoidance
+                    _adjust_collision_avoidance(mol, _check_halted, _safe_status)
 
-                try:
-                    _safe_finished((worker_id, mol))
-                except WorkerHaltError:
-                    raise
-                except Exception:
-                    _safe_finished(mol)
-                _safe_status("RDKit 3D conversion succeeded.")
-                return
+                    try:
+                        _safe_finished((worker_id, mol))
+                    except WorkerHaltError:
+                        raise
+                    except Exception:
+                        _safe_finished(mol)
+                    _safe_status("RDKit 3D conversion succeeded.")
+                    return
 
             # If RDKit did not produce a conf and OBabel is allowed, try Open Babel
             if conf_id == -1 and conversion_mode in ("fallback", "obabel"):
@@ -1260,12 +1274,19 @@ class CalculationWorker(QObject):
                             opt_success = _iterative_optimize(rd_mol, method_key, _check_halted, _safe_status)
 
                         if not opt_success:
-                            raise Exception(f"Optimization with {opt_method_raw} failed. You can change the method in the settings.")
+                            _safe_status(f"Warning: Optimization with {opt_method_raw} failed. Using unoptimized structure.")
+                            try:
+                                rd_mol.ClearProp("_pme_optimization_method")
+                            except Exception:
+                                pass
                     except WorkerHaltError:
                         raise
                     except Exception as opt_err:
-                        _safe_status(f"Optimization failed: {opt_err}")
-                        raise
+                        _safe_status(f"Warning: Optimization failed: {opt_err}. Using unoptimized structure.")
+                        try:
+                            rd_mol.ClearProp("_pme_optimization_method")
+                        except Exception:
+                            pass
 
                     _safe_status(
                         "Open Babel embedding succeeded. Warning: Conformation accuracy may be limited."

{moleditpy-2.8.0a4 → moleditpy-2.8.1}/src/moleditpy/modules/constants.py

@@ -16,7 +16,7 @@ from PyQt6.QtGui import QColor, QFont
 from rdkit import Chem
 
 # Version
-VERSION = "2.8.0a4"
+VERSION = "2.8.1"
 
 ATOM_RADIUS = 18
 BOND_OFFSET = 3.5

{moleditpy-2.8.0a4 → moleditpy-2.8.1}/src/moleditpy/modules/dihedral_dialog.py

@@ -182,12 +182,6 @@ class DihedralDialog(Dialog3DPickingMixin, QDialog):  # pragma: no cover
         self.disable_picking()
         super().closeEvent(event)
 
-    def reject(self):
-        """キャンセル時の処理"""
-        self.clear_atom_labels()
-        self.disable_picking()
-        super().reject()
-
     def accept(self):
         """OK時の処理"""
         self.clear_atom_labels()
@@ -511,6 +505,9 @@ class DihedralDialog(Dialog3DPickingMixin, QDialog):  # pragma: no cover
         self.main_window.draw_molecule_3d(self.mol)
 
     def reject(self):
+        """キャンセル時の処理"""
+        self.clear_atom_labels()
+        self.disable_picking()
         super().reject()
         try:
             if self.main_window.current_mol:

{moleditpy-2.8.0a4 → moleditpy-2.8.1}/src/moleditpy/modules/main_window_compute.py

@@ -51,6 +51,9 @@ except Exception:
 # --- クラス定義 ---
 class MainWindowCompute(object):
     """main_window.py から分離された機能クラス"""
+    
+    # Default initial state 
+    last_successful_optimization_method = None
 
     def set_optimization_method(self, method_name):  # pragma: no cover
         """Set preferred 3D optimization method and persist to settings.
@@ -67,6 +70,7 @@ class MainWindowCompute(object):
             "UFF_RDKIT",
             "UFF_OBABEL",
             "GAFF_OBABEL",
+            "MMFF94s_OBABEL",
             "MMFF94_OBABEL",
             "GHEMICAL_OBABEL",
         )
@@ -166,6 +170,7 @@ class MainWindowCompute(object):
                 ("MMFF94s (RDKit)", "MMFF_RDKIT"),
                 ("MMFF94 (RDKit)", "MMFF94_RDKIT"),
                 ("UFF (RDKit)", "UFF_RDKIT"),
+                ("MMFF94s (Open Babel)", "MMFF94s_OBABEL"),
                 ("MMFF94 (Open Babel)", "MMFF94_OBABEL"),
                 ("UFF (Open Babel)", "UFF_OBABEL"),
                 ("GAFF (Open Babel)", "GAFF_OBABEL"),
@@ -1022,8 +1027,8 @@ class MainWindowCompute(object):
             except Exception:  # pragma: no cover
                 import traceback
                 traceback.print_exc()
-            if not opt_method:
-                opt_method = getattr(self, "optimization_method", None)
+            # If the property is not on the molecule, it means optimization failed or was bypassed.
+            # We explicitly do not fall back to self.optimization_method.
             # Store the optimization method using its user-friendly UI label if available.
             if opt_method:
                 try:
@@ -1033,6 +1038,8 @@ class MainWindowCompute(object):
                     self.last_successful_optimization_method = label
                 except Exception:
                     self.last_successful_optimization_method = opt_method
+            else:
+                self.last_successful_optimization_method = None
         except Exception:
             # non-fatal
             pass

{moleditpy-2.8.0a4 → moleditpy-2.8.1}/src/moleditpy/modules/main_window_main_init.py

@@ -1458,6 +1458,7 @@ class MainWindowMainInit(object):
             ("MMFF94s (RDKit)", "MMFF_RDKIT"),
             ("MMFF94 (RDKit)", "MMFF94_RDKIT"),
             ("UFF (RDKit)", "UFF_RDKIT"),
+            ("MMFF94s (Open Babel)", "MMFF94s_OBABEL"),
             ("MMFF94 (Open Babel)", "MMFF94_OBABEL"),
             ("UFF (Open Babel)", "UFF_OBABEL"),
             ("GAFF (Open Babel)", "GAFF_OBABEL"),
@@ -1484,6 +1485,9 @@ class MainWindowMainInit(object):
                 import traceback
                 traceback.print_exc()
 
+            # If Open Babel is not available, disable Open Babel-based optimization methods
+            if key.endswith("_OBABEL") and not OBABEL_AVAILABLE:
+                action.setEnabled(False)
             action.triggered.connect(
                 lambda checked, m=key: self.set_optimization_method(m)
             )