MoleditPy 2.2.0__py3-none-any.whl → 2.2.0a1__py3-none-any.whl

moleditpy/plugins/Utility/vdw_radii_overlay.py

@@ -0,0 +1,303 @@
+
+import os
+import json
+import traceback
+import pyvista as pv
+import numpy as np
+import functools
+import types
+from PyQt6.QtWidgets import (QDialog, QVBoxLayout, QLabel, 
+                             QSlider, QHBoxLayout, QPushButton)
+from PyQt6.QtGui import QAction
+from PyQt6.QtCore import Qt, QTimer
+
+# Try to import VDW radii from constants, fallback if needed
+try:
+    from moleditpy.modules.constants import pt, CPK_COLORS_PV
+except ImportError:
+    try:
+        from modules.constants import pt, CPK_COLORS_PV
+    except ImportError:
+        try:
+            from rdkit import Chem
+            pt = Chem.GetPeriodicTable()
+        except Exception:
+            pt = None
+        CPK_COLORS_PV = {} # Last resort fallback
+
+
+# Plugin Metadata
+__version__="2025.12.17"
+__author__="HiroYokoyama"
+PLUGIN_NAME = "VDW Radii Overlay"
+SETTINGS_FILE = os.path.join(os.path.dirname(os.path.abspath(__file__)), "vdw_radii_overlay.json")
+
+# Global State
+_config_window = None
+_vdw_settings = {
+    "occupancy": 0.3  # Opacity (0.0 - 1.0)
+}
+
+def load_settings():
+    global _vdw_settings
+    try:
+        if os.path.exists(SETTINGS_FILE):
+            with open(SETTINGS_FILE, 'r') as f:
+                saved = json.load(f)
+                # Filter to only keep occupancy
+                if "occupancy" in saved:
+                    _vdw_settings["occupancy"] = float(saved["occupancy"])
+    except Exception as e:
+        print(f"Error loading VDW settings: {e}")
+
+def save_settings():
+    try:
+        with open(SETTINGS_FILE, 'w') as f:
+            json.dump(_vdw_settings, f, indent=4)
+    except Exception as e:
+        print(f"Error saving VDW settings: {e}")
+
+class VDWConfigWindow(QDialog):
+    def __init__(self, main_window):
+        super().__init__(parent=main_window)
+        self.mw = main_window
+        self.setWindowTitle("VDW Overlay Settings")
+        self.setModal(False)
+        self.resize(300, 100)
+        self.init_ui()
+
+    def init_ui(self):
+        layout = QVBoxLayout()
+        
+        # Occupancy Slider
+        occ_layout = QHBoxLayout()
+        occ_layout.addWidget(QLabel("Occupancy:"))
+        self.slider_occ = QSlider(Qt.Orientation.Horizontal)
+        self.slider_occ.setRange(0, 100)
+        current_occ = int(_vdw_settings.get("occupancy", 0.3) * 100)
+        self.slider_occ.setValue(current_occ)
+        self.slider_occ.valueChanged.connect(self.on_occupancy_changed)
+        occ_layout.addWidget(self.slider_occ)
+        self.lbl_occ_val = QLabel(f"{current_occ}%")
+        occ_layout.addWidget(self.lbl_occ_val)
+        layout.addLayout(occ_layout)
+        
+        # Close Button
+        btn_close = QPushButton("Close")
+        btn_close.clicked.connect(self.close)
+        layout.addWidget(btn_close)
+        
+        self.setLayout(layout)
+
+    def on_occupancy_changed(self, value):
+        opacity = value / 100.0
+        _vdw_settings["occupancy"] = opacity
+        self.lbl_occ_val.setText(f"{value}%")
+        save_settings()
+        self.update_view()
+
+    def update_view(self):
+        # Trigger redraw if we are in the correct mode
+        if hasattr(self.mw, 'current_3d_style') and self.mw.current_3d_style == "vdw_overlay":
+            if getattr(self.mw, 'current_mol', None):
+                # Trigger redraw
+                if hasattr(self.mw, 'draw_molecule_3d'):
+                    self.mw.draw_molecule_3d(self.mw.current_mol)
+
+def draw_vdw_overlay(mw, mol):
+    """
+    Callback for drawing the VDW overlay style.
+    Registered via context.register_3d_style.
+    """
+    # 1. Draw standard Ball & Stick
+    # Attempt to locate the standard draw method
+    draw_std = None
+    if hasattr(mw, 'main_window_view_3d') and hasattr(mw.main_window_view_3d, 'draw_standard_3d_style'):
+        draw_std = mw.main_window_view_3d.draw_standard_3d_style
+    elif hasattr(mw, 'view3d') and hasattr(mw.view3d, 'draw_standard_3d_style'):
+        draw_std = mw.view3d.draw_standard_3d_style
+    
+    if draw_std:
+        draw_std(mol, style_override='ball_and_stick')
+    else:
+        print("VDW Plugin Error: could not find draw_standard_3d_style")
+        return
+
+    # 2. Draw VDW Surface Overlay
+    if mol and mol.GetNumAtoms() > 0:
+        try:
+            positions = []
+            radii = []
+            atom_colors = []
+            
+            # Use custom colors if available, otherwise CPK
+            custom_map = getattr(mw, 'custom_atom_colors', {})
+            
+            if mol.GetNumConformers() > 0:
+                conf = mol.GetConformer()
+                for i in range(mol.GetNumAtoms()):
+                    atom = mol.GetAtomWithIdx(i)
+                    pos = conf.GetAtomPosition(i)
+                    positions.append([pos.x, pos.y, pos.z])
+                    
+                    sym = atom.GetSymbol()
+                    # GetRvdw returns standard VDW radius. 
+                    r = 1.5 # Default
+                    if pt:
+                        r = pt.GetRvdw(atom.GetAtomicNum())
+                    radii.append(r)
+                    
+                    # Color handling
+                    if i in custom_map:
+                        c = custom_map[i]
+                        # Normalize 0-255 to 0-1 if needed
+                        if any(x > 1.0 for x in c):
+                            c = [x/255.0 for x in c]
+                    else:
+                        c = CPK_COLORS_PV.get(sym, [0.8, 0.8, 0.8]) # Default grey if missing
+                    atom_colors.append(c)
+            
+            if positions:
+                positions = np.array(positions)
+                radii = np.array(radii)
+                atom_colors = np.array(atom_colors)
+
+                # --- Generate Merged Surface (SDF) ---
+                
+                # 1. Define Grid Bounds
+                padding = radii.max() + 1.0
+                min_bounds = positions.min(axis=0) - padding
+                max_bounds = positions.max(axis=0) + padding
+                
+                # Resolution (voxel size in Angstroms)
+                spacing = (0.125, 0.125, 0.125) 
+                
+                dims = np.ceil((max_bounds - min_bounds) / spacing).astype(int)
+                
+                grid = pv.ImageData()
+                grid.dimensions = dims
+                grid.origin = min_bounds
+                grid.spacing = spacing
+                
+                grid_points = grid.points
+                n_points = grid_points.shape[0]
+                values = np.empty(n_points)
+                
+                # Process in chunks of 100k points
+                chunk_size = 100000 
+                for start_idx in range(0, n_points, chunk_size):
+                    end_idx = min(start_idx + chunk_size, n_points)
+                    chunk_pts = grid_points[start_idx:end_idx]
+                    
+                    d = np.linalg.norm(chunk_pts[:, np.newaxis, :] - positions[np.newaxis, :, :], axis=2)
+                    d_surface = d - radii[np.newaxis, :]
+                    values[start_idx:end_idx] = d_surface.min(axis=1)
+
+                grid.point_data["values"] = values
+                
+                # 3. Contour at iso-value 0 to get the surface
+                mesh = grid.contour([0], scalars="values")
+                
+                # 4. Map Colors to Surface Vertices
+                mesh_points = mesh.points
+                if mesh_points.shape[0] > 0:
+                    n_mesh_pts = mesh_points.shape[0]
+                    mesh_colors = np.zeros((n_mesh_pts, 3))
+                    
+                    chunk_size = 50000
+                    for start_idx in range(0, n_mesh_pts, chunk_size):
+                        end_idx = min(start_idx + chunk_size, n_mesh_pts)
+                        chunk_pts = mesh_points[start_idx:end_idx]
+                        
+                        d_center = np.linalg.norm(chunk_pts[:, np.newaxis, :] - positions[np.newaxis, :, :], axis=2)
+                        d_surface = d_center - radii[np.newaxis, :]
+                        nearest_atom_indices = np.argmin(d_surface, axis=1)
+                        mesh_colors[start_idx:end_idx] = atom_colors[nearest_atom_indices]
+                    
+                    mesh.point_data["AtomColors"] = mesh_colors
+                
+                    opacity = _vdw_settings.get("occupancy", 0.3)
+                    
+                    # Assume mw.plotter is available
+                    if hasattr(mw, 'plotter'):
+                        mw.plotter.add_mesh(
+                            mesh,
+                            scalars="AtomColors", 
+                            rgb=True,
+                            opacity=opacity,
+                            smooth_shading=True,
+                            specular=0.2, 
+                            name="vdw_overlay_mesh"
+                        )
+
+        except Exception as e:
+            print(f"VDW Overlay Error: {e}")
+            traceback.print_exc()
+
+def run(mw):
+    global _config_window
+    load_settings()
+    
+    if _config_window is None:
+        _config_window = VDWConfigWindow(mw)
+        _config_window.finished.connect(lambda: _cleanup_config())
+    
+    _config_window.show()
+    _config_window.raise_()
+    _config_window.activateWindow()
+
+def initialize(context):
+    """
+    New Plugin System Entry Point
+    """
+    mw = context.get_main_window()
+    load_settings()
+    
+    # Register 3D Style
+    if hasattr(context, 'register_3d_style'):
+        context.register_3d_style("vdw_overlay", draw_vdw_overlay)
+    else:
+        print("Error: PluginContext does not support register_3d_style")
+
+    # 1. Register Configuration Menu - REMOVED in favor of run()
+    # (Managed by run() function now)
+
+    # 2. Inject into Style Menu (Legacy behavior preserved via mw access)
+    def add_menu_item():
+        # Locate the "3D Style" tool button on the main toolbar
+        style_button = getattr(mw, 'style_button', None)
+        
+        if style_button and style_button.menu():
+            style_menu = style_button.menu()
+            
+            # Check if already added
+            exists = False
+            for a in style_menu.actions():
+                if a.text() == "VDW Overlay":
+                    exists = True
+                    break
+            
+            if not exists:
+                # Add to action group for mutual exclusion
+                existing_actions = style_menu.actions()
+                group = None
+                if existing_actions:
+                    group = existing_actions[0].actionGroup()
+                
+                action = QAction("VDW Overlay", mw)
+                action.setCheckable(True)
+                
+                if group:
+                    group.addAction(action)
+                
+                # Connect to set_3d_style
+                action.triggered.connect(lambda: mw.set_3d_style("vdw_overlay"))
+                
+                style_menu.addAction(action)
+    
+    # Run after 2000ms to ensure UI is ready
+    QTimer.singleShot(2000, add_menu_item)
+
+def _cleanup_config():
+    global _config_window
+    _config_window = None

{moleditpy-2.2.0.dist-info → moleditpy-2.2.0a1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 2.2.0
+Version: 2.2.0a1
 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

{moleditpy-2.2.0.dist-info → moleditpy-2.2.0a1.dist-info}/RECORD

@@ -12,7 +12,7 @@ moleditpy/modules/bond_item.py,sha256=eVkEeKvM4igYI67DYxpey3FllqDyt_iWDo4VPYMhaP
 moleditpy/modules/bond_length_dialog.py,sha256=k5x_DhK9Q8CSwouKhEo_kLRRdaYHDaK84KDNmuDNLvY,14868
 moleditpy/modules/calculation_worker.py,sha256=KiGQY7i-QCQofEoE0r65KoQgpEGFcbhmxWv6egfkUdc,42324
 moleditpy/modules/color_settings_dialog.py,sha256=Ow44BhCOLo0AFb6klO001k6B4drOgKX9DeNBQhZLp5o,15474
-moleditpy/modules/constants.py,sha256=hdfz_yUW2nYenApAz_N45ia1Qo8bZKhuYC0lw9WOozM,4702
+moleditpy/modules/constants.py,sha256=FeDinXswiCE3mVvn04ts1K8_wT2lsxft6PqIEAGHnSA,4704
 moleditpy/modules/constrained_optimization_dialog.py,sha256=IEdNVhFoNSEMeA5ABpUH9Q88-YzDXFloQM2gwnPwnHY,30150
 moleditpy/modules/custom_interactor_style.py,sha256=NjsXE2a43IDNEanZBlcG9eR4ZIERT1MsQC6lbfesapQ,38453
 moleditpy/modules/custom_qt_interactor.py,sha256=MFaTuDh-FPeFBS4303CqxsxmsOIOW4QXUz6USwI8PHQ,2451
@@ -25,11 +25,11 @@ moleditpy/modules/main_window_dialog_manager.py,sha256=S1ROCWqzB2uVSKHY4o5CbTtJA
 moleditpy/modules/main_window_edit_3d.py,sha256=uY203adPg3CLyAdbG2NCThG2Am0WduzPDan9rXAlc14,19841
 moleditpy/modules/main_window_edit_actions.py,sha256=lUFxNFTUQzeXN8CNlb4_4S9j4M1EEq8kpJmh9dCzM3M,64818
 moleditpy/modules/main_window_export.py,sha256=e0HA_jeaokIOBunQqGxUn5QKdniCmE8GrsE1Igy6zm8,38351
-moleditpy/modules/main_window_main_init.py,sha256=AZb2GZmvUYsVBhV2c54FEoWmFXRPkdSMlsshKraOGPs,89315
+moleditpy/modules/main_window_main_init.py,sha256=2MWBLY_u4UoSC4orjhDh1WcfR8FoWEnhR9ibUeA_fnE,88438
 moleditpy/modules/main_window_molecular_parsers.py,sha256=Ex4-urYsKf6PyHp4XToOhgXzuYWa_n7q--QmHci4OCU,48401
 moleditpy/modules/main_window_project_io.py,sha256=q1vEmWQDqla32HVkmk8-j0OY9ut5TI5NJ4ikahewkEo,17259
 moleditpy/modules/main_window_string_importers.py,sha256=mQVDv2Dj4MwnPgMRe2IqdAAKnB_quE6QfYeAgCjfv28,10892
-moleditpy/modules/main_window_ui_manager.py,sha256=HofI6T9EvcSSzPbsdPqkYEEDoB6Hui1Uj2Ll-wwczGA,24016
+moleditpy/modules/main_window_ui_manager.py,sha256=dqnBzvYZdE5Da6x4IAeGYSgwHp4EUO13THudf2hUePo,22843
 moleditpy/modules/main_window_view_3d.py,sha256=TKRerktpCTYxX9HU-dSOnIhx4OyZaVrRYj4pEOUXmGc,74088
 moleditpy/modules/main_window_view_loaders.py,sha256=Dbdgv4TY_ZkX8Qyaevwr-mBJYJ59CBzRTEks-U1FiGw,14462
 moleditpy/modules/mirror_dialog.py,sha256=c3v4qY6R4FAljzk4EPaDjL9ZdZMjLQSFLqDMXz2fBUk,4696
@@ -38,8 +38,8 @@ moleditpy/modules/molecule_scene.py,sha256=khdt7h9Mk_D1cMbYeHGtq7P9aFXo0xG-hcShU
 moleditpy/modules/move_group_dialog.py,sha256=65HVXTJSaQ9lp03XFhI1l7OzUsXmH_aqd8OgwjpjfGg,27174
 moleditpy/modules/periodic_table_dialog.py,sha256=ItEZUts1XCietz9paY-spvbzxh6SXak3GnikwqkHZCw,4006
 moleditpy/modules/planarize_dialog.py,sha256=yY8o-SxT8vGEHVWnjDTXecRv5NUaEejEsXH-836Xk8g,8681
-moleditpy/modules/plugin_interface.py,sha256=W6Hw1OLqMkcg8XU-S347v2sDBMEoo6iiCSbmL6MjZrA,7639
-moleditpy/modules/plugin_manager.py,sha256=cxbqIE7Rb_KeBd-cG1vF2ySY2qNx8IJVRXjVPyQMFDc,13457
+moleditpy/modules/plugin_interface.py,sha256=54zMHkjf9TCyXyAqYeYvnG-R4mWhTaSZ8oIQt3lHqvQ,8082
+moleditpy/modules/plugin_manager.py,sha256=ghIKOBsWlTmzsQJXtncH9nyfQJUF_dwBOKrU4iBlNo0,13576
 moleditpy/modules/plugin_manager_window.py,sha256=m2lJ-UltwoXQ2SYA1im6Q0v-5SfqWL2HcOBCTzUmiBw,9963
 moleditpy/modules/settings_dialog.py,sha256=Nr7yE8UmYRi3VObWvRlrnv0DnjSjmYXbvqryZ02O12k,65348
 moleditpy/modules/template_preview_item.py,sha256=djdq3tz73d_fJGOvai3E-V9Hk9q9ZW7skx7BV59mooA,6556
@@ -50,9 +50,26 @@ moleditpy/modules/zoomable_view.py,sha256=hjwljui13QpvjvxJHY4Evot4jMQvxRBQUNH5HU
 moleditpy/modules/assets/icon.icns,sha256=wD5R6-Vw7K662tVKhu2E1ImN0oUuyAP4youesEQsn9c,139863
 moleditpy/modules/assets/icon.ico,sha256=RfgFcx7-dHY_2STdsOQCQziY5SNhDr3gPnjO6jzEDPI,147975
 moleditpy/modules/assets/icon.png,sha256=kCFN1WacYIdy0GN6SFEbNA00ef39pCczBnFdkkBI8Bs,147110
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-moleditpy-2.2.0.dist-info/top_level.txt,sha256=ARICrS4ihlPXqywlKl6o-oJa3Qz3gZRWu_VZsQ3_c44,10
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