MoleditPy-linux 3.2.0__tar.gz → 3.3.1__tar.gz

{moleditpy_linux-3.2.0 → moleditpy_linux-3.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 3.2.0
+Version: 3.3.1
 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
@@ -703,19 +703,19 @@ Dynamic: license-file
 
 # MoleditPy — A Python Molecular Editor
 
-This is the Linux version of MoleditPy. The Open Babel fallback is disabled due to compatibility reasons.
-
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17268532.svg)](https://doi.org/10.5281/zenodo.17268532)
 [![Powered by RDKit](https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC)](https://www.rdkit.org/)
 [![PyPI version](https://badge.fury.io/py/MoleditPy.svg)](https://badge.fury.io/py/MoleditPy)
 [![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-75%25-green)
-![Overall Coverage](https://img.shields.io/badge/coverage-67%25-green)
+![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage->80%25-green)
+![Overall Coverage](https://img.shields.io/badge/coverage->75%25-green)
 ![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)
-![Pylint Score](https://img.shields.io/badge/pylint-9%2F10-brightgreen)
+![Pylint Score](https://img.shields.io/badge/pylint->9%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)
+[![PyPI Downloads](https://static.pepy.tech/personalized-badge/moleditpy?period=monthly&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=monthly+downloads)](https://pepy.tech/projects/moleditpy)
+[![Ask DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/HiroYokoyama/python_molecular_editor)
 
 [🇯🇵 日本語 (Japanese)](#japanese)
 
@@ -841,6 +841,14 @@ moleditpy
 
 This project is licensed under the **GNU General Public License v3.0 (GPL-v3)**. See the `LICENSE` file for details.
 
+## Citation
+
+If you use this software in your work, please cite it as follows:
+
+```
+Yokoyama, H. (2026). MoleditPy — A Python-based molecular editing software. Zenodo. https://doi.org/10.5281/zenodo.17268532
+```
+
 -----
 
 <div id="japanese"></div>
@@ -964,3 +972,11 @@ moleditpy
 ## ライセンス
 
 このプロジェクトは **GNU General Public License v3.0 (GPL-v3)** のもとで公開されています。詳細は `LICENSE` ファイルを参照してください。
+
+## 引用
+
+本ソフトウェアを研究で使用される場合は、以下の通り引用を明記してください。
+
+```
+Yokoyama, H. (2026). MoleditPy — A Python-based molecular editing software. Zenodo. https://doi.org/10.5281/zenodo.17268532
+```

{moleditpy_linux-3.2.0 → moleditpy_linux-3.3.1}/README.md

@@ -1,18 +1,18 @@
 # MoleditPy — A Python Molecular Editor
 
-This is the Linux version of MoleditPy. The Open Babel fallback is disabled due to compatibility reasons.
-
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17268532.svg)](https://doi.org/10.5281/zenodo.17268532)
 [![Powered by RDKit](https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC)](https://www.rdkit.org/)
 [![PyPI version](https://badge.fury.io/py/MoleditPy.svg)](https://badge.fury.io/py/MoleditPy)
 [![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-75%25-green)
-![Overall Coverage](https://img.shields.io/badge/coverage-67%25-green)
+![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage->80%25-green)
+![Overall Coverage](https://img.shields.io/badge/coverage->75%25-green)
 ![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)
-![Pylint Score](https://img.shields.io/badge/pylint-9%2F10-brightgreen)
+![Pylint Score](https://img.shields.io/badge/pylint->9%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)
+[![PyPI Downloads](https://static.pepy.tech/personalized-badge/moleditpy?period=monthly&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=monthly+downloads)](https://pepy.tech/projects/moleditpy)
+[![Ask DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/HiroYokoyama/python_molecular_editor)
 
 [🇯🇵 日本語 (Japanese)](#japanese)
 
@@ -138,6 +138,14 @@ moleditpy
 
 This project is licensed under the **GNU General Public License v3.0 (GPL-v3)**. See the `LICENSE` file for details.
 
+## Citation
+
+If you use this software in your work, please cite it as follows:
+
+```
+Yokoyama, H. (2026). MoleditPy — A Python-based molecular editing software. Zenodo. https://doi.org/10.5281/zenodo.17268532
+```
+
 -----
 
 <div id="japanese"></div>
@@ -261,3 +269,11 @@ moleditpy
 ## ライセンス
 
 このプロジェクトは **GNU General Public License v3.0 (GPL-v3)** のもとで公開されています。詳細は `LICENSE` ファイルを参照してください。
+
+## 引用
+
+本ソフトウェアを研究で使用される場合は、以下の通り引用を明記してください。
+
+```
+Yokoyama, H. (2026). MoleditPy — A Python-based molecular editing software. Zenodo. https://doi.org/10.5281/zenodo.17268532
+```

{moleditpy_linux-3.2.0 → moleditpy_linux-3.3.1}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy-linux"
 
-version = "3.2.0"
+version = "3.3.1"
 
 license = {file = "LICENSE"}
 

{moleditpy_linux-3.2.0 → moleditpy_linux-3.3.1}/src/MoleditPy_linux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 3.2.0
+Version: 3.3.1
 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
@@ -703,19 +703,19 @@ Dynamic: license-file
 
 # MoleditPy — A Python Molecular Editor
 
-This is the Linux version of MoleditPy. The Open Babel fallback is disabled due to compatibility reasons.
-
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17268532.svg)](https://doi.org/10.5281/zenodo.17268532)
 [![Powered by RDKit](https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC)](https://www.rdkit.org/)
 [![PyPI version](https://badge.fury.io/py/MoleditPy.svg)](https://badge.fury.io/py/MoleditPy)
 [![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-75%25-green)
-![Overall Coverage](https://img.shields.io/badge/coverage-67%25-green)
+![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage->80%25-green)
+![Overall Coverage](https://img.shields.io/badge/coverage->75%25-green)
 ![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)
-![Pylint Score](https://img.shields.io/badge/pylint-9%2F10-brightgreen)
+![Pylint Score](https://img.shields.io/badge/pylint->9%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)
+[![PyPI Downloads](https://static.pepy.tech/personalized-badge/moleditpy?period=monthly&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=monthly+downloads)](https://pepy.tech/projects/moleditpy)
+[![Ask DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/HiroYokoyama/python_molecular_editor)
 
 [🇯🇵 日本語 (Japanese)](#japanese)
 
@@ -841,6 +841,14 @@ moleditpy
 
 This project is licensed under the **GNU General Public License v3.0 (GPL-v3)**. See the `LICENSE` file for details.
 
+## Citation
+
+If you use this software in your work, please cite it as follows:
+
+```
+Yokoyama, H. (2026). MoleditPy — A Python-based molecular editing software. Zenodo. https://doi.org/10.5281/zenodo.17268532
+```
+
 -----
 
 <div id="japanese"></div>
@@ -964,3 +972,11 @@ moleditpy
 ## ライセンス
 
 このプロジェクトは **GNU General Public License v3.0 (GPL-v3)** のもとで公開されています。詳細は `LICENSE` ファイルを参照してください。
+
+## 引用
+
+本ソフトウェアを研究で使用される場合は、以下の通り引用を明記してください。
+
+```
+Yokoyama, H. (2026). MoleditPy — A Python-based molecular editing software. Zenodo. https://doi.org/10.5281/zenodo.17268532
+```

{moleditpy_linux-3.2.0 → moleditpy_linux-3.3.1}/src/MoleditPy_linux.egg-info/SOURCES.txt

@@ -29,6 +29,7 @@ src/moleditpy_linux/ui/analysis_window.py
 src/moleditpy_linux/ui/angle_dialog.py
 src/moleditpy_linux/ui/app_state.py
 src/moleditpy_linux/ui/atom_item.py
+src/moleditpy_linux/ui/atom_picking.py
 src/moleditpy_linux/ui/base_picking_dialog.py
 src/moleditpy_linux/ui/bond_item.py
 src/moleditpy_linux/ui/bond_length_dialog.py

{moleditpy_linux-3.2.0 → moleditpy_linux-3.3.1}/src/moleditpy_linux/__init__.py

@@ -18,3 +18,5 @@ try:
     OBABEL_AVAILABLE = False
 except ImportError:
     OBABEL_AVAILABLE = False
+
+from .utils.constants import VERSION as __version__

{moleditpy_linux-3.2.0 → moleditpy_linux-3.3.1}/src/moleditpy_linux/ui/angle_dialog.py

@@ -168,20 +168,35 @@ class AngleDialog(GeometryBaseDialog):
 
     def on_atom_picked(self, atom_idx: int) -> None:
         """Handle atom picking event in the 3D view."""
-        if self.atom1_idx is None:
-            self.atom1_idx = atom_idx
-        elif self.atom2_idx is None:
-            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
-            self._snapshot_positions = self.mol.GetConformer().GetPositions().copy()
-        else:
-            # Reset and start over
-            self.atom1_idx = atom_idx
-            self.atom2_idx = None
+        # Deselection logic: if already selected, remove and shift down
+        if atom_idx == self.atom1_idx:
+            self.atom1_idx = self.atom2_idx
+            self.atom2_idx = self.atom3_idx
             self.atom3_idx = None
             self._snapshot_positions = None
+        elif atom_idx == self.atom2_idx:
+            self.atom2_idx = self.atom3_idx
+            self.atom3_idx = None
+            self._snapshot_positions = None
+        elif atom_idx == self.atom3_idx:
+            self.atom3_idx = None
+            self._snapshot_positions = None
+        else:
+            # Selection logic
+            if self.atom1_idx is None:
+                self.atom1_idx = atom_idx
+            elif self.atom2_idx is None:
+                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
+                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
 
         self.update_display()
 

moleditpy_linux-3.3.1/src/moleditpy_linux/ui/atom_picking.py

@@ -0,0 +1,163 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+MoleditPy — A Python-based molecular editing software
+
+Author: Hiromichi Yokoyama
+License: GPL-3.0 license
+Repo: https://github.com/HiroYokoyama/python_molecular_editor
+DOI: 10.5281/zenodo.17268532
+"""
+
+from __future__ import annotations
+
+from typing import Any, Optional
+
+import numpy as np
+
+try:
+    from ..utils.constants import VDW_RADII, pt
+except ImportError:
+    from moleditpy_linux.utils.constants import VDW_RADII, pt
+
+
+def _world_to_display(renderer: Any, pos: Any) -> Optional[tuple[float, float, float]]:
+    try:
+        renderer.SetWorldPoint(float(pos[0]), float(pos[1]), float(pos[2]), 1.0)
+        renderer.WorldToDisplay()
+        display = renderer.GetDisplayPoint()
+        return (float(display[0]), float(display[1]), float(display[2]))
+    except (AttributeError, RuntimeError, TypeError, ValueError, IndexError):
+        return None
+
+
+def _atom_world_radius(view_3d_manager: Any, mol: Any, atom_idx: int) -> float:
+    try:
+        atom = mol.GetAtomWithIdx(int(atom_idx))
+        symbol = atom.GetSymbol()
+    except (AttributeError, RuntimeError, TypeError, ValueError):
+        symbol = "C"
+
+    settings = {}
+    try:
+        settings = view_3d_manager.host.init_manager.settings
+    except (AttributeError, RuntimeError, TypeError):
+        pass
+
+    style = str(getattr(view_3d_manager, "current_3d_style", "ball_and_stick"))
+    style = style.lower().replace(" ", "_")
+
+    if style == "cpk":
+        scale = settings.get("cpk_atom_scale", 1.0)
+        try:
+            radius = pt.GetRvdw(pt.GetAtomicNumber(symbol))
+            return float(radius if radius > 0.1 else 1.5) * float(scale)
+        except (AttributeError, RuntimeError, TypeError, ValueError):
+            return 1.5 * float(scale)
+
+    if style == "stick":
+        return float(settings.get("stick_bond_radius", 0.15))
+
+    if style == "wireframe":
+        return 0.01
+
+    scale = settings.get("ball_stick_atom_scale", 1.0)
+    return float(VDW_RADII.get(symbol, 0.4)) * float(scale)
+
+
+def _projected_radius_px(
+    renderer: Any, center: Any, world_radius: float
+) -> Optional[float]:
+    center_display = _world_to_display(renderer, center)
+    if center_display is None:
+        return None
+
+    offsets = (
+        (world_radius, 0.0, 0.0),
+        (0.0, world_radius, 0.0),
+        (0.0, 0.0, world_radius),
+    )
+    radius_px = 0.0
+    for offset in offsets:
+        edge = (
+            float(center[0]) + offset[0],
+            float(center[1]) + offset[1],
+            float(center[2]) + offset[2],
+        )
+        edge_display = _world_to_display(renderer, edge)
+        if edge_display is None:
+            continue
+        radius_px = max(
+            radius_px,
+            float(
+                np.hypot(
+                    edge_display[0] - center_display[0],
+                    edge_display[1] - center_display[1],
+                )
+            ),
+        )
+
+    return radius_px
+
+
+def pick_atom_index_from_screen(
+    view_3d_manager: Any,
+    click_pos: tuple[int, int],
+    mol: Optional[Any] = None,
+    padding_px: float = 8.0,
+    min_radius_px: float = 14.0,
+    max_radius_px: float = 96.0,
+) -> Optional[int]:
+    """Return the atom nearest a screen click without invoking VTK cell picking."""
+    try:
+        plotter = view_3d_manager.plotter
+        renderer = plotter.renderer
+        positions = view_3d_manager.atom_positions_3d
+    except (AttributeError, RuntimeError, TypeError):
+        return None
+
+    if positions is None:
+        return None
+
+    try:
+        positions_array = np.asarray(positions, dtype=float)
+    except (TypeError, ValueError):
+        return None
+
+    if positions_array.ndim != 2 or positions_array.shape[1] < 3:
+        return None
+
+    if mol is None:
+        mol = getattr(view_3d_manager, "current_mol", None)
+
+    try:
+        atom_count = int(mol.GetNumAtoms()) if mol is not None else len(positions_array)
+    except (AttributeError, RuntimeError, TypeError, ValueError):
+        atom_count = len(positions_array)
+
+    best_idx: Optional[int] = None
+    best_score: Optional[tuple[float, float]] = None
+
+    for atom_idx in range(min(atom_count, len(positions_array))):
+        center = positions_array[atom_idx]
+        display = _world_to_display(renderer, center)
+        if display is None or not np.all(np.isfinite(display[:2])):
+            continue
+
+        world_radius = _atom_world_radius(view_3d_manager, mol, atom_idx)
+        projected_radius = _projected_radius_px(renderer, center, world_radius)
+        hit_radius = max(
+            float(min_radius_px),
+            min(float(max_radius_px), float(projected_radius or 0.0) + padding_px),
+        )
+        distance = float(np.hypot(display[0] - click_pos[0], display[1] - click_pos[1]))
+        if distance > hit_radius:
+            continue
+
+        score = (distance / hit_radius, distance)
+        if best_score is None or score < best_score:
+            best_idx = atom_idx
+            best_score = score
+
+    return best_idx

{moleditpy_linux-3.2.0 → moleditpy_linux-3.3.1}/src/moleditpy_linux/ui/bond_length_dialog.py

@@ -160,14 +160,20 @@ class BondLengthDialog(GeometryBaseDialog):
 
     def on_atom_picked(self, atom_idx: int) -> None:
         """Handle atom picking event in the 3D view."""
-        if self.atom1_idx is None:
-            self.atom1_idx = atom_idx
-        elif self.atom2_idx is None:
-            self.atom2_idx = atom_idx
-        else:
-            # Reset and start over
-            self.atom1_idx = atom_idx
+        if atom_idx == self.atom1_idx:
+            self.atom1_idx = self.atom2_idx
             self.atom2_idx = None
+        elif atom_idx == self.atom2_idx:
+            self.atom2_idx = None
+        else:
+            if self.atom1_idx is None:
+                self.atom1_idx = atom_idx
+            elif self.atom2_idx is None:
+                self.atom2_idx = atom_idx
+            else:
+                # Reset and start over
+                self.atom1_idx = atom_idx
+                self.atom2_idx = None
 
         self.update_display()
 

{moleditpy_linux-3.2.0 → moleditpy_linux-3.3.1}/src/moleditpy_linux/ui/calculation_worker.py

@@ -16,6 +16,7 @@ import re
 import numpy as np
 import sys
 import subprocess
+import time
 from typing import Any, Callable, Dict, List, Optional, Set, Tuple, Union
 
 from PyQt6.QtCore import QObject, pyqtSignal, pyqtSlot
@@ -250,6 +251,8 @@ def _iterative_optimize(
             chunk = min(chunk_size, max_iters - iters_done)
             res = ff.Minimize(maxIts=chunk)
             iters_done += chunk
+            time.sleep(0.001)
+
             if res == 0:
                 break
         return True
@@ -286,8 +289,6 @@ def _iterative_optimize_obabel(
             if check_halted_cb():
                 raise WorkerHaltError("Halted")
             ff.ConjugateGradients(chunk_size)
-            import time
-
             time.sleep(0.001)
 
         ff.GetCoordinates(ob_mol.OBMol)

{moleditpy_linux-3.2.0 → moleditpy_linux-3.3.1}/src/moleditpy_linux/ui/constrained_optimization_dialog.py

@@ -13,7 +13,7 @@ DOI: 10.5281/zenodo.17268532
 import logging
 from typing import Any
 
-from PyQt6.QtCore import Qt
+from PyQt6.QtCore import Qt, QThread, pyqtSignal
 from PyQt6.QtWidgets import (
     QAbstractItemView,
     QComboBox,
@@ -33,6 +33,23 @@ from rdkit.Chem import AllChem, rdMolTransforms
 from .dialog_3d_picking_mixin import Dialog3DPickingMixin
 
 
+class ConstrainedOptimizationThread(QThread):
+    optimization_finished = pyqtSignal()
+    error_occurred = pyqtSignal(str)
+
+    def __init__(self, ff: Any, max_iters: int = 20000, parent: Any = None) -> None:
+        super().__init__(parent)
+        self.ff = ff
+        self.max_iters = max_iters
+
+    def run(self) -> None:
+        try:
+            self.ff.Minimize(maxIts=self.max_iters)
+            self.optimization_finished.emit()
+        except Exception as e:
+            self.error_occurred.emit(str(e))
+
+
 class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
     """Dialog for constrained optimization."""
 
@@ -427,16 +444,34 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
         if positions:
             plotter = self.main_window.view_3d_manager.plotter
             if plotter is not None:
+                # Save camera position to prevent reset
+                try:
+                    cam = plotter.camera_position
+                except (AttributeError, RuntimeError, TypeError) as e:
+                    logging.debug(f"Could not save camera position: {e}")
+                    cam = None
+
                 label_actor = plotter.add_point_labels(
                     positions,
                     texts,
-                    point_size=20,
+                    point_size=0,
                     font_size=12,
                     text_color="cyan",
                     always_visible=True,
+                    show_points=False,
+                    shape="rect",
+                    shape_color="gray",
+                    shape_opacity=0.5,
                 )
                 self.constraint_labels.append(label_actor)
 
+                # Restore camera position
+                if cam is not None:
+                    try:
+                        plotter.camera_position = cam
+                    except (AttributeError, RuntimeError, TypeError) as e:
+                        logging.debug(f"Could not restore camera position: {e}")
+
     def clear_constraint_labels(self) -> None:
         for label_actor in self.constraint_labels:
             try:
@@ -541,8 +576,30 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
             status_bar = self.main_window.statusBar()
             if status_bar is not None:
                 status_bar.showMessage(f"Running constrained {ff_name} optimization...")
-            ff.Minimize(maxIts=20000)
 
+            self.optimize_button.setEnabled(False)
+
+            self._opt_thread = ConstrainedOptimizationThread(ff, 20000, self)
+            self._opt_thread.optimization_finished.connect(
+                lambda: self._on_optimization_finished(ff_name, conf)
+            )
+            self._opt_thread.error_occurred.connect(self._on_optimization_error)
+            self._opt_thread.start()
+
+        except Exception as e:
+            QMessageBox.critical(self, "Error", f"Failed to start optimization: {e}")
+            self.optimize_button.setEnabled(True)
+
+    def _on_optimization_error(self, err_msg: str) -> None:
+        self.optimize_button.setEnabled(True)
+        status_bar = self.main_window.statusBar()
+        if status_bar is not None:
+            status_bar.showMessage(f"Optimization failed: {err_msg}")
+        QMessageBox.critical(self, "Error", f"Optimization error: {err_msg}")
+
+    def _on_optimization_finished(self, ff_name: str, conf: Any) -> None:
+        self.optimize_button.setEnabled(True)
+        try:
             # Apply optimized coordinates to the main window's numpy array
             cache = self.main_window.view_3d_manager.atom_positions_3d
             for i in range(self.mol.GetNumAtoms()):
@@ -558,6 +615,7 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
             self.main_window.view_3d_manager.draw_molecule_3d(self.mol)
             self.main_window.view_3d_manager.update_chiral_labels()
             self.main_window.edit_actions_manager.push_undo_state()
+            status_bar = self.main_window.statusBar()
             if status_bar is not None:
                 status_bar.showMessage("Constrained optimization finished.")
 
@@ -680,13 +738,24 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
         if positions:
             plotter = self.main_window.view_3d_manager.plotter
             if plotter is not None:
+                # Save camera position to prevent reset
+                try:
+                    cam = plotter.camera_position
+                except (AttributeError, RuntimeError, TypeError) as e:
+                    logging.debug(f"Could not save camera position: {e}")
+                    cam = None
+
                 label_actor = plotter.add_point_labels(
                     positions,
                     texts,
-                    point_size=20,
+                    point_size=0,
                     font_size=12,
                     text_color="yellow",
                     always_visible=True,
+                    show_points=False,
+                    shape="rect",
+                    shape_color="gray",
+                    shape_opacity=0.5,
                 )
                 # Consider case where add_point_labels returns a list
                 if isinstance(label_actor, list):
@@ -694,6 +763,13 @@ class ConstrainedOptimizationDialog(Dialog3DPickingMixin, QDialog):
                 else:
                     self.selection_labels.append(label_actor)
 
+                # Restore camera position
+                if cam is not None:
+                    try:
+                        plotter.camera_position = cam
+                    except (AttributeError, RuntimeError, TypeError) as e:
+                        logging.debug(f"Could not restore camera position: {e}")
+
     def on_cell_changed(self, row: int, column: int) -> None:
         """Update internal data when a table cell is edited."""