MoleditPy-linux 2.8.1__tar.gz → 2.8.3__tar.gz

{moleditpy_linux-2.8.1 → moleditpy_linux-2.8.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 2.8.1
+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-2.8.1 → moleditpy_linux-2.8.3}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy-linux"
 
-version = "2.8.1"
+version = "2.8.3"
 
 license = {file = "LICENSE"}
 

{moleditpy_linux-2.8.1 → moleditpy_linux-2.8.3}/src/MoleditPy_linux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 2.8.1
+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-2.8.1 → moleditpy_linux-2.8.3}/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
@@ -310,17 +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."""

{moleditpy_linux-2.8.1 → moleditpy_linux-2.8.3}/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
@@ -242,9 +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
@@ -349,7 +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