MoleditPy-linux 2.8.0__tar.gz → 2.8.2__tar.gz

{moleditpy_linux-2.8.0 → moleditpy_linux-2.8.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 2.8.0
+Version: 2.8.2
 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
@@ -711,10 +711,10 @@ This is the Linux version of MoleditPy. The Open Babel fallback is disabled due
 [![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-8.63%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_linux-2.8.0 → moleditpy_linux-2.8.2}/README.md

@@ -8,10 +8,10 @@ This is the Linux version of MoleditPy. The Open Babel fallback is disabled due
 [![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-8.63%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_linux-2.8.0 → moleditpy_linux-2.8.2}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy-linux"
 
-version = "2.8.0"
+version = "2.8.2"
 
 license = {file = "LICENSE"}
 

{moleditpy_linux-2.8.0 → moleditpy_linux-2.8.2}/src/MoleditPy_linux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 2.8.0
+Version: 2.8.2
 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
@@ -711,10 +711,10 @@ This is the Linux version of MoleditPy. The Open Babel fallback is disabled due
 [![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-8.63%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_linux-2.8.0 → moleditpy_linux-2.8.2}/src/moleditpy_linux/modules/angle_dialog.py

@@ -24,10 +24,10 @@ from PyQt6.QtWidgets import (
 
 try:
     from .dialog3_d_picking_mixin import Dialog3DPickingMixin
-    from .mol_geometry import adjust_bond_angle, get_connected_group, rodrigues_rotate
+    from .mol_geometry import adjust_bond_angle, calc_angle_deg, get_connected_group, rodrigues_rotate
 except Exception:
     from modules.dialog3_d_picking_mixin import Dialog3DPickingMixin
-    from modules.mol_geometry import adjust_bond_angle, get_connected_group, rodrigues_rotate
+    from modules.mol_geometry import adjust_bond_angle, calc_angle_deg, get_connected_group, rodrigues_rotate
 
 import numpy as np
 from PyQt6.QtCore import Qt
@@ -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)")
@@ -308,17 +310,10 @@ class AngleDialog(Dialog3DPickingMixin, QDialog):  # pragma: no cover
     def calculate_angle(self):
         """現在の角度を計算"""
         conf = self.mol.GetConformer()
-        pos1 = np.array(conf.GetAtomPosition(self.atom1_idx))
-        pos2 = np.array(conf.GetAtomPosition(self.atom2_idx))  # vertex
-        pos3 = np.array(conf.GetAtomPosition(self.atom3_idx))
-
-        vec1 = pos1 - pos2
-        vec2 = pos3 - pos2
-
-        cos_angle = np.dot(vec1, vec2) / (np.linalg.norm(vec1) * np.linalg.norm(vec2))
-        cos_angle = np.clip(cos_angle, -1.0, 1.0)
-        angle_rad = np.arccos(cos_angle)
-        return np.degrees(angle_rad)
+        pos1 = conf.GetAtomPosition(self.atom1_idx)
+        pos2 = conf.GetAtomPosition(self.atom2_idx)  # vertex
+        pos3 = conf.GetAtomPosition(self.atom3_idx)
+        return calc_angle_deg(pos1, pos2, pos3)
 
     def on_angle_input_changed(self, text):
         """Line edit text changed, update slider."""
@@ -340,7 +335,9 @@ 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 +353,8 @@ 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 +365,11 @@ 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 +471,9 @@ 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_linux-2.8.0 → moleditpy_linux-2.8.2}/src/moleditpy_linux/modules/bond_length_dialog.py

@@ -26,7 +26,7 @@ from PyQt6.QtWidgets import (
 )
 
 from .dialog3_d_picking_mixin import Dialog3DPickingMixin
-from .mol_geometry import get_connected_group
+from .mol_geometry import calc_distance, get_connected_group
 
 
 class BondLengthDialog(Dialog3DPickingMixin, QDialog):  # pragma: no cover
@@ -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()
@@ -248,9 +242,10 @@ class BondLengthDialog(Dialog3DPickingMixin, QDialog):  # pragma: no cover
 
             # Calculate current distance
             conf = self.mol.GetConformer()
-            pos1 = np.array(conf.GetAtomPosition(self.atom1_idx))
-            pos2 = np.array(conf.GetAtomPosition(self.atom2_idx))
-            current_distance = np.linalg.norm(pos2 - pos1)
+            current_distance = calc_distance(
+                conf.GetAtomPosition(self.atom1_idx),
+                conf.GetAtomPosition(self.atom2_idx),
+            )
             self.distance_label.setText(f"Current distance: {current_distance:.3f} Å")
             self.apply_button.setEnabled(True)
             # Update the distance input box to show current distance
@@ -355,7 +350,7 @@ class BondLengthDialog(Dialog3DPickingMixin, QDialog):  # pragma: no cover
 
         # Direction vector from atom1 to atom2
         direction = pos2 - pos1
-        current_distance = np.linalg.norm(direction)
+        current_distance = calc_distance(pos1, pos2)
 
         if current_distance == 0:
             return
@@ -420,6 +415,9 @@ 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: