moleditpy 2.8.0__tar.gz → 2.8.0a1__tar.gz

{moleditpy-2.8.0 → moleditpy-2.8.0a1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 2.8.0
+Version: 2.8.0a1
 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
@@ -694,8 +694,7 @@ Requires-Python: <3.15,>=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
-Requires-Dist: pyqt6<6.10; sys_platform == "darwin"
-Requires-Dist: pyqt6<6.11; sys_platform != "darwin"
+Requires-Dist: pyqt6<6.11
 Requires-Dist: pyvista<0.48
 Requires-Dist: pyvistaqt<0.12
 Requires-Dist: rdkit<2025.10
@@ -713,7 +712,7 @@ Dynamic: license-file
 ![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-73%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-8.63%2F10-brightgreen)
+![Pylint Score](https://img.shields.io/badge/pylint-8.67%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-2.8.0 → moleditpy-2.8.0a1}/README.md

@@ -9,7 +9,7 @@
 ![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-73%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-8.63%2F10-brightgreen)
+![Pylint Score](https://img.shields.io/badge/pylint-8.67%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-2.8.0 → moleditpy-2.8.0a1}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "2.8.0"
+version = "2.8.0a1"
 
 license = {file = "LICENSE"}
 
@@ -34,8 +34,7 @@ classifiers = [
 
 dependencies = [
   "numpy",
-  "pyqt6 < 6.10; sys_platform == 'darwin'",
-  "pyqt6 < 6.11; sys_platform != 'darwin'",
+  "pyqt6 < 6.11",
   "pyvista < 0.48",
   "pyvistaqt < 0.12",
   "rdkit < 2025.10",

{moleditpy-2.8.0 → moleditpy-2.8.0a1}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 2.8.0
+Version: 2.8.0a1
 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
@@ -694,8 +694,7 @@ Requires-Python: <3.15,>=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
-Requires-Dist: pyqt6<6.10; sys_platform == "darwin"
-Requires-Dist: pyqt6<6.11; sys_platform != "darwin"
+Requires-Dist: pyqt6<6.11
 Requires-Dist: pyvista<0.48
 Requires-Dist: pyvistaqt<0.12
 Requires-Dist: rdkit<2025.10
@@ -713,7 +712,7 @@ Dynamic: license-file
 ![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-73%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-8.63%2F10-brightgreen)
+![Pylint Score](https://img.shields.io/badge/pylint-8.67%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-2.8.0 → moleditpy-2.8.0a1}/src/MoleditPy.egg-info/requires.txt

@@ -1,11 +1,6 @@
 numpy
+pyqt6<6.11
 pyvista<0.48
 pyvistaqt<0.12
 rdkit<2025.10
 openbabel-wheel<3.2
-
-[:sys_platform != "darwin"]
-pyqt6<6.11
-
-[:sys_platform == "darwin"]
-pyqt6<6.10

{moleditpy-2.8.0 → moleditpy-2.8.0a1}/src/moleditpy/modules/calculation_worker.py

@@ -21,40 +21,21 @@ from rdkit import Chem
 from rdkit.Chem import AllChem, rdGeometry
 from rdkit.DistanceGeometry import DoTriangleSmoothing
 
-try: # pragma: no cover
+try:
     from . import OBABEL_AVAILABLE
-except Exception: # pragma: no cover
+except Exception:
     from modules import OBABEL_AVAILABLE
 # Only import pybel on demand — `moleditpy` itself doesn't expose `pybel`.
-if OBABEL_AVAILABLE: # pragma: no cover
+if OBABEL_AVAILABLE:
     try:
         import os
-        import glob
         import openbabel
         from openbabel import pybel
         
         # The python wheel often misses setting up the data directory.
-        # Check multiple potential locations for BABEL_DATADIR.
-        ob_base = os.path.dirname(openbabel.__file__)
-        data_candidates = [
-            os.path.join(ob_base, "bin", "data"), # Typical for Windows wheel
-            os.path.join(ob_base, "share", "openbabel", "*") # Typical for macOS/Linux
-        ]
-        
-        found_datadir = None
-        for pattern in data_candidates:
-            matches = glob.glob(pattern)
-            for m in matches:
-                if os.path.isdir(m):
-                    found_datadir = m
-                    break
-            if found_datadir:
-                break
-        
-        if found_datadir:
-            os.environ["BABEL_DATADIR"] = found_datadir
-        
-        os.environ["BABEL_LIBDIR"] = ob_base
+        # It typically places parameter files in openbabel/bin/data.
+        os.environ["BABEL_DATADIR"] = os.path.join(os.path.dirname(openbabel.__file__), "bin", "data")
+        os.environ["BABEL_LIBDIR"] = os.path.dirname(openbabel.__file__)
     except Exception:
         # If import fails here, disable OBABEL locally; avoid raising
         pybel = None
@@ -62,7 +43,7 @@ if OBABEL_AVAILABLE: # pragma: no cover
         print(
             "Warning: openbabel.pybel not available. Open Babel fallback and OBabel-based options will be disabled."
         )
-else: # pragma: no cover
+else:
     pybel = None
 
 
@@ -191,7 +172,7 @@ def _adjust_collision_avoidance(rd_mol, check_halted_cb, safe_status_cb):
         safe_status_cb("Collision avoidance completed.")
     except WorkerHaltError:
         raise
-    except Exception as e: # pragma: no cover
+    except Exception as e:
         import traceback
         traceback.print_exc()
         safe_status_cb(f"Collision avoidance warning: {e}")
@@ -295,11 +276,11 @@ class CalculationWorker(QObject):
     error = pyqtSignal(object)
     start_work = pyqtSignal(str, object)
 
-    def __init__(self, parent=None): # pragma: no cover
+    def __init__(self, parent=None):
         super().__init__(parent)
         try:
             self.start_work.connect(self.run_calculation)
-        except Exception:
+        except Exception:  # pragma: no cover
             import traceback
             traceback.print_exc()
 
@@ -327,7 +308,7 @@ class CalculationWorker(QObject):
                 return False
 
         # Safe-emission helpers: do nothing if this worker has been halted.
-        def _safe_status(msg): # pragma: no cover
+        def _safe_status(msg):
             try:
                 if _check_halted():
                     raise WorkerHaltError("Halted")
@@ -393,13 +374,13 @@ class CalculationWorker(QObject):
                 worker_id = None
 
             _warned_no_worker_id = False
-            if worker_id is None: # pragma: no cover
+            if worker_id is None:
                 try:
                     # best-effort, swallow any errors (signals may not be connected)
                     self.status_update.emit(
                         "Warning: worker started without 'worker_id'; will listen for global halt signals."
                     )
-                except Exception:
+                except Exception:  # pragma: no cover
                     import traceback
                     traceback.print_exc()
                 _warned_no_worker_id = True
@@ -505,16 +486,8 @@ class CalculationWorker(QObject):
                     method_key = "GHEMICAL"
 
                 if backend == "OBABEL":
-                    try:
-                        mol.SetProp("_pme_optimization_method", opt_method)
-                    except Exception:
-                        pass
                     opt_success = _iterative_optimize_obabel(mol, method_key, _check_halted, _safe_status)
                 else:
-                    try:
-                        mol.SetProp("_pme_optimization_method", opt_method)
-                    except Exception:
-                        pass
                     opt_success = _iterative_optimize(mol, method_key, _check_halted, _safe_status)
                 
                 if not opt_success:
@@ -1108,7 +1081,7 @@ class CalculationWorker(QObject):
                         conf_id = AllChem.EmbedMolecule(mol, basic_params)
                     else:
                         conf_id = -1
-                except Exception: # pragma: no cover
+                except Exception:  # pragma: no cover
                     import traceback
                     traceback.print_exc()
             """

{moleditpy-2.8.0 → moleditpy-2.8.0a1}/src/moleditpy/modules/constants.py

@@ -16,7 +16,7 @@ from PyQt6.QtGui import QColor, QFont
 from rdkit import Chem
 
 # Version
-VERSION = "2.8.0"
+VERSION = "2.8.0a1"
 
 ATOM_RADIUS = 18
 BOND_OFFSET = 3.5

{moleditpy-2.8.0 → moleditpy-2.8.0a1}/src/moleditpy/modules/main_window_compute.py

@@ -1024,14 +1024,17 @@ class MainWindowCompute(object):
                 traceback.print_exc()
             if not opt_method:
                 opt_method = getattr(self, "optimization_method", None)
-            # Store the optimization method using its user-friendly UI label if available.
+            # normalize common forms
             if opt_method:
-                try:
-                    # Look up the UI label (e.g. "MMFF94s (RDKit)") from the internal ID (e.g. "MMFF_RDKIT")
-                    method_key = str(opt_method).upper()
-                    label = self.opt3d_method_labels.get(method_key, opt_method)
-                    self.last_successful_optimization_method = label
-                except Exception:
+                om = str(opt_method).upper()
+                if "MMFF94S" in om or "MMFF_RDKIT" in om:
+                    self.last_successful_optimization_method = "MMFF94s"
+                elif "MMFF94" in om:
+                    self.last_successful_optimization_method = "MMFF94"
+                elif "UFF" in om:
+                    self.last_successful_optimization_method = "UFF"
+                else:
+                    # store raw value otherwise
                     self.last_successful_optimization_method = opt_method
         except Exception:
             # non-fatal
@@ -1119,10 +1122,7 @@ class MainWindowCompute(object):
             import traceback
             traceback.print_exc()
 
-        if self.last_successful_optimization_method:
-            self.statusBar().showMessage(f"3D calculation ({self.last_successful_optimization_method}) successful.")
-        else:
-            self.statusBar().showMessage("3D calculation successful.")
+        # self.statusBar().showMessage("3D conversion successful.")
         self.convert_button.setEnabled(True)
         # Restore button text/handlers in case they were changed to Halt
         try:
@@ -1203,18 +1203,11 @@ class MainWindowCompute(object):
             return
 
         # Clear temporary plotter content and remove calculating text if present
-        # Only clear the entire plotter if we don't have an existing molecule to fall back to.
         try:
-            if self.current_mol is None:
-                self.plotter.clear()
-            else:
-                # If we have a molecule, just re-render to make sure it's drawn correctly
-                # (in case partial actors were added during 'calculating' phase)
-                self.plotter.render()
+            self.plotter.clear()
         except Exception:  # pragma: no cover
             import traceback
             traceback.print_exc()
-            traceback.print_exc()
 
         # Also attempt to explicitly remove the calculating text actor if it was stored
         try:
@@ -1289,7 +1282,7 @@ class MainWindowCompute(object):
                     QMessageBox.StandardButton.Yes,
                 )
                 if reply == QMessageBox.StandardButton.Yes:
-                    self._temp_optimization_method = "UFF_RDKIT"
+                    self.set_optimization_method("UFF_RDKIT")
                     self.optimize_3d_structure()
                     # Return immediately so the rest of the error cleanup doesn't disable buttons permanently
                     return
@@ -1332,70 +1325,51 @@ class MainWindowCompute(object):
             import traceback
             traceback.print_exc()
 
-        # On calculation error we should NOT enable 3D-only features IF we have no molecule.
-        # However, if we ALREADY had a molecule (e.g. optimization failed but previous 3D was valid),
-        # we should keep them enabled.
-        if self.current_mol is None:
-            try:
-                if hasattr(self, "optimize_3d_button"):
-                    self.optimize_3d_button.setEnabled(False)
-            except Exception:  # pragma: no cover
-                import traceback
-                traceback.print_exc()
+        # On calculation error we should NOT enable 3D-only features.
+        # Explicitly disable Optimize and Export so the user can't try to operate
+        # on an invalid or missing 3D molecule.
+        try:
+            if hasattr(self, "optimize_3d_button"):
+                self.optimize_3d_button.setEnabled(False)
+        except Exception:  # pragma: no cover
+            import traceback
+            traceback.print_exc()
 
-            try:
-                if hasattr(self, "export_button"):
-                    self.export_button.setEnabled(False)
-            except Exception:  # pragma: no cover
-                import traceback
-                traceback.print_exc()
+        try:
+            if hasattr(self, "export_button"):
+                self.export_button.setEnabled(False)
+        except Exception:  # pragma: no cover
+            import traceback
+            traceback.print_exc()
 
-            # Keep 3D feature buttons disabled to avoid inconsistent UI state
-            try:
-                self._enable_3d_features(False)
-            except Exception:  # pragma: no cover
-                import traceback
-                traceback.print_exc()
+        # Keep 3D feature buttons disabled to avoid inconsistent UI state
+        try:
+            self._enable_3d_features(False)
+        except Exception:  # pragma: no cover
+            import traceback
+            traceback.print_exc()
 
-            # Keep 3D edit actions disabled (no molecule to edit)
-            try:
-                self._enable_3d_edit_actions(False)
-            except Exception:  # pragma: no cover
-                import traceback
-                traceback.print_exc()
-        else:
-            # We HAVE a molecule, ensure features are enabled
-            try:
-                self._enable_3d_features(True)
-            except Exception:  # pragma: no cover
-                import traceback
-                traceback.print_exc()
+        # Keep 3D edit actions disabled (no molecule to edit)
+        try:
+            self._enable_3d_edit_actions(False)
+        except Exception:  # pragma: no cover
+            import traceback
+            traceback.print_exc()
 
-        # Some menu items are explicitly disabled on error IF no molecule exists
-        if self.current_mol is None:
-            try:
-                if hasattr(self, "analysis_action"):
-                    self.analysis_action.setEnabled(False)
-            except Exception:  # pragma: no cover
-                import traceback
-                traceback.print_exc()
+        # Some menu items are explicitly disabled on error
+        try:
+            if hasattr(self, "analysis_action"):
+                self.analysis_action.setEnabled(False)
+        except Exception:  # pragma: no cover
+            import traceback
+            traceback.print_exc()
 
-            try:
-                if hasattr(self, "edit_3d_action"):
-                    self.edit_3d_action.setEnabled(False)
-            except Exception:  # pragma: no cover
-                import traceback
-                traceback.print_exc()
-        else:
-            # Ensure they are enabled if we have a molecule
-            try:
-                if hasattr(self, "analysis_action"):
-                    self.analysis_action.setEnabled(True)
-                if hasattr(self, "edit_3d_action"):
-                    self.edit_3d_action.setEnabled(True)
-            except Exception:  # pragma: no cover
-                import traceback
-                traceback.print_exc()
+        try:
+            if hasattr(self, "edit_3d_action"):
+                self.edit_3d_action.setEnabled(False)
+        except Exception:  # pragma: no cover
+            import traceback
+            traceback.print_exc()
 
         # Force a UI refresh
         try:

{moleditpy-2.8.0 → moleditpy-2.8.0a1}/src/moleditpy/modules/main_window_main_init.py

@@ -1484,9 +1484,6 @@ 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)
             )