MoleditPy 3.3.0__tar.gz → 3.3.1__tar.gz

{moleditpy-3.3.0 → moleditpy-3.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.3.0
+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
@@ -713,8 +713,10 @@ Dynamic: license-file
 ![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)
 
@@ -840,6 +842,14 @@ 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>
@@ -963,3 +973,11 @@ 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-3.3.0 → moleditpy-3.3.1}/README.md

@@ -9,8 +9,10 @@
 ![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)
 
@@ -136,6 +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>
@@ -259,3 +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-3.3.0 → moleditpy-3.3.1}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "3.3.0"
+version = "3.3.1"
 
 license = {file = "LICENSE"}
 

{moleditpy-3.3.0 → moleditpy-3.3.1}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.3.0
+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
@@ -713,8 +713,10 @@ Dynamic: license-file
 ![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)
 
@@ -840,6 +842,14 @@ 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>
@@ -963,3 +973,11 @@ 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-3.3.0 → moleditpy-3.3.1}/src/moleditpy/__init__.py

@@ -18,3 +18,5 @@ try:
     OBABEL_AVAILABLE = importlib.util.find_spec("openbabel") is not None
 except ImportError:
     OBABEL_AVAILABLE = False
+
+from .utils.constants import VERSION as __version__

{moleditpy-3.3.0 → moleditpy-3.3.1}/src/moleditpy/ui/atom_picking.py

@@ -1,163 +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.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
+#!/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.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-3.3.0 → moleditpy-3.3.1}/src/moleditpy/ui/view_3d_logic.py

@@ -1632,7 +1632,7 @@ class View3DManager:
 
         # Color definitions (dark blue/green/red)
         rdkit_color = "#003366"  # Dark blue
-        id_color = "#006400"  # Dark green
+        id_color = "#009000"  # Green
         xyz_color = "#8B0000"  # Dark red
         other_color = "black"
 

{moleditpy-3.3.0 → moleditpy-3.3.1}/src/moleditpy/utils/constants.py

@@ -12,11 +12,41 @@ DOI: 10.5281/zenodo.17268532
 
 # --- Constants ---
 
+import os
 from PyQt6.QtGui import QColor, QFont
 from rdkit import Chem
 
+
+def _get_version():
+    try:
+        from importlib.metadata import version, PackageNotFoundError
+
+        try:
+            return version("MoleditPy")
+        except PackageNotFoundError:
+            pass
+    except ImportError:
+        pass
+
+    try:
+        # Fallback: Parse pyproject.toml directly
+        current_dir = os.path.abspath(os.path.dirname(__file__))
+        for _ in range(5):
+            pyproject_path = os.path.join(current_dir, "pyproject.toml")
+            if os.path.exists(pyproject_path):
+                with open(pyproject_path, "r", encoding="utf-8") as f:
+                    for line in f:
+                        if line.strip().startswith("version ="):
+                            return line.split("=")[1].strip().strip('"').strip("'")
+            current_dir = os.path.dirname(current_dir)
+    except Exception:
+        pass
+
+    return "Unknown"
+
+
 # Version
-VERSION = "3.3.0"
+VERSION = _get_version()
 
 ATOM_RADIUS = 18
 BOND_OFFSET = 3.5