MoleditPy-linux 3.0.5__tar.gz → 3.1.0__tar.gz

{moleditpy_linux-3.0.5 → moleditpy_linux-3.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 3.0.5
+Version: 3.1.0
 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-3.0.5 → moleditpy_linux-3.1.0}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy-linux"
 
-version = "3.0.5"
+version = "3.1.0"
 
 license = {file = "LICENSE"}
 

{moleditpy_linux-3.0.5 → moleditpy_linux-3.1.0}/src/MoleditPy_linux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy-linux
-Version: 3.0.5
+Version: 3.1.0
 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-3.0.5 → moleditpy_linux-3.1.0}/src/moleditpy_linux/__main__.py

@@ -11,7 +11,7 @@ DOI: 10.5281/zenodo.17268532
 """
 
 print("-----------------------------------------------------")
-print("MoleditPy — A Python-based molecular editing software")
+print("MoleditPy - A Python-based molecular editing software")
 print("-----------------------------------------------------\n")
 
 try:

{moleditpy_linux-3.0.5 → moleditpy_linux-3.1.0}/src/moleditpy_linux/main.py

@@ -80,9 +80,69 @@ def main():
         default=False,
         help="Start in safe mode: skip loading all plugins",
     )
+    parser.add_argument(
+        "--install-plugin",
+        metavar="PATH",
+        help="Install a plugin from a .py file, .zip, or folder (Headless)",
+    )
     # parse_known_args so Qt's own argv flags (e.g. -platform) are passed through
     args, remaining = parser.parse_known_args()
 
+    # --- Headless Plugin Installation ---
+    if args.install_plugin:
+        plugin_path = os.path.abspath(args.install_plugin)
+        if not os.path.exists(plugin_path):
+            print(f"Error: Plugin path not found: {plugin_path}")
+            sys.exit(1)
+
+        try:
+            from moleditpy_linux.plugins.plugin_manager import PluginManager
+        except ImportError:
+            from .plugins.plugin_manager import PluginManager
+
+        pm = PluginManager()
+        sha256 = pm._compute_sha256(plugin_path)
+
+        # Extract metadata
+        metadata_file = plugin_path
+        if os.path.isdir(plugin_path):
+            init_py = os.path.join(plugin_path, "__init__.py")
+            if os.path.exists(init_py):
+                metadata_file = init_py
+
+        info = (
+            pm.get_plugin_info_safe(metadata_file)
+            if metadata_file.endswith(".py")
+            else {}
+        )
+
+        print("\n" + "=" * 40)
+        print("      PLUGIN INSTALLATION (HEADLESS)")
+        print("=" * 40)
+        print(f" Name:        {info.get('name', os.path.basename(plugin_path))}")
+        print(f" Author:      {info.get('author', 'Unknown')}")
+        print(f" Version:     {info.get('version', 'Unknown')}")
+        print(f" Description: {info.get('description', 'No description')}")
+        print("-" * 40)
+        print(f" Path:        {plugin_path}")
+        print(f" SHA-256:     {sha256}")
+        print("=" * 40)
+
+        confirm = (
+            input("\nDo you want to proceed with installation? (y/N): ").strip().lower()
+        )
+        if confirm == "y":
+            success, msg = pm.install_plugin(plugin_path)
+            if success:
+                print(f"Success: {msg}")
+                sys.exit(0)
+            else:
+                print(f"Error: {msg}")
+                sys.exit(1)
+        else:
+            print("Installation aborted.")
+            sys.exit(0)
+
     app = QApplication([sys.argv[0]] + remaining)
     window = MainWindow(initial_file=args.file, safe_mode=args.safe)
     window.show()

{moleditpy_linux-3.0.5 → moleditpy_linux-3.1.0}/src/moleditpy_linux/plugins/plugin_manager.py

@@ -12,6 +12,7 @@ DOI: 10.5281/zenodo.17268532
 
 from __future__ import annotations
 import ast
+import hashlib
 import importlib.util
 import logging
 import os
@@ -32,6 +33,46 @@ except ImportError:
 
 
 class PluginManager:
+    def _compute_sha256(self, path: str) -> str:
+        """Computes SHA-256 for a file or a directory (concatenated hashes of all files)."""
+        if os.path.isfile(path):
+            return self._sha256_for_file(path)
+        if os.path.isdir(path):
+            return self._sha256_for_directory(path)
+        return "N/A"
+
+    def _sha256_for_file(self, path: str) -> str:
+        """Computes SHA-256 for a single file."""
+        hasher = hashlib.sha256()
+        try:
+            with open(path, "rb") as f:
+                for chunk in iter(lambda: f.read(8192), b""):
+                    hasher.update(chunk)
+            return hasher.hexdigest()
+        except (AttributeError, OSError, RuntimeError, ValueError, TypeError):
+            return "N/A"
+
+    def _sha256_for_directory(self, dir_path: str) -> str:
+        """Computes SHA-256 for a directory by hashing all files in sorted order."""
+        hasher = hashlib.sha256()
+        try:
+            root = os.path.abspath(dir_path)
+            for current_root, _dirs, files in os.walk(root):
+                rel_root = os.path.relpath(current_root, root)
+                for filename in sorted(files):
+                    file_path = os.path.join(current_root, filename)
+                    rel_path = os.path.normpath(os.path.join(rel_root, filename))
+                    # Hash the path to ensure directory structure is captured
+                    hasher.update(rel_path.encode("utf-8", errors="replace"))
+                    hasher.update(b"\0")
+                    with open(file_path, "rb") as f:
+                        for chunk in iter(lambda: f.read(8192), b""):
+                            hasher.update(chunk)
+                    hasher.update(b"\0")
+            return hasher.hexdigest()
+        except (AttributeError, OSError, RuntimeError, ValueError, TypeError):
+            return "N/A"
+
     def __init__(self, main_window: Any = None) -> None:
         self.plugin_dir: str = os.path.join(
             os.path.expanduser("~"), ".moleditpy", "plugins"
@@ -265,6 +306,7 @@ class PluginManager:
                     parent_name = ".".join(parts[:i])
                     if parent_name not in sys.modules:
                         import types as _types
+
                         stub = _types.ModuleType(parent_name)
                         stub.__path__ = []
                         stub.__package__ = parent_name

{moleditpy_linux-3.0.5 → moleditpy_linux-3.1.0}/src/moleditpy_linux/plugins/plugin_manager_window.py

@@ -12,7 +12,7 @@ DOI: 10.5281/zenodo.17268532
 
 import os
 import shutil
-import hashlib
+
 
 from PyQt6.QtCore import Qt, QUrl
 from PyQt6.QtGui import QDesktopServices, QDragEnterEvent, QDropEvent
@@ -259,7 +259,7 @@ class PluginManagerWindow(QDialog):
                 is_folder = True
 
             if is_valid:
-                sha256_value = self._compute_sha256(file_path)
+                sha256_value = self.plugin_manager._compute_sha256(file_path)
                 # Extract info and confirm
                 info = {
                     "name": os.path.basename(file_path),
@@ -314,39 +314,3 @@ class PluginManagerWindow(QDialog):
                 summary += "Errors:\n" + "\n".join(errors)
 
             QMessageBox.information(self, "Plugin Installation", summary)
-
-    def _compute_sha256(self, path):
-        if os.path.isfile(path):
-            return self._sha256_for_file(path)
-        if os.path.isdir(path):
-            return self._sha256_for_directory(path)
-        return "N/A"
-
-    def _sha256_for_file(self, path):
-        hasher = hashlib.sha256()
-        try:
-            with open(path, "rb") as f:
-                for chunk in iter(lambda: f.read(8192), b""):
-                    hasher.update(chunk)
-            return hasher.hexdigest()
-        except (AttributeError, OSError, RuntimeError, ValueError, TypeError):
-            return "N/A"
-
-    def _sha256_for_directory(self, dir_path):
-        hasher = hashlib.sha256()
-        try:
-            root = os.path.abspath(dir_path)
-            for current_root, _dirs, files in os.walk(root):
-                rel_root = os.path.relpath(current_root, root)
-                for filename in sorted(files):
-                    file_path = os.path.join(current_root, filename)
-                    rel_path = os.path.normpath(os.path.join(rel_root, filename))
-                    hasher.update(rel_path.encode("utf-8", errors="replace"))
-                    hasher.update(b"\0")
-                    with open(file_path, "rb") as f:
-                        for chunk in iter(lambda: f.read(8192), b""):
-                            hasher.update(chunk)
-                    hasher.update(b"\0")
-            return hasher.hexdigest()
-        except (AttributeError, OSError, RuntimeError, ValueError, TypeError):
-            return "N/A"

{moleditpy_linux-3.0.5 → moleditpy_linux-3.1.0}/src/moleditpy_linux/ui/align_plane_dialog.py

@@ -97,8 +97,6 @@ class AlignPlaneDialog(BasePickingDialog):
         else:
             self.selected_atoms.add(atom_idx)
 
-        # Display labels on the atoms
-        self.show_atom_labels()
         self.update_display()
 
     def clear_selection(self):

{moleditpy_linux-3.0.5 → moleditpy_linux-3.1.0}/src/moleditpy_linux/ui/angle_dialog.py

@@ -169,8 +169,6 @@ class AngleDialog(GeometryBaseDialog):
             self.atom3_idx = None
             self._snapshot_positions = None
 
-        # Display atom labels
-        self.show_atom_labels()
         self.update_display()
 
     def clear_selection(self):

{moleditpy_linux-3.0.5 → moleditpy_linux-3.1.0}/src/moleditpy_linux/ui/app_state.py

@@ -364,9 +364,9 @@ class StateManager:
             # 'Save As' if not PMEPRJ
             file_path = self.host.init_manager.current_file_path
             if not file_path or not file_path.lower().endswith(".pmeprj"):
-                self.save_project_as()
+                self.host.io_manager.save_project_as()
             else:
-                self.save_project()
+                self.host.io_manager.save_project()
             return (
                 not self.host.state_manager.has_unsaved_changes
             )  # Return True only if save was successful

{moleditpy_linux-3.0.5 → moleditpy_linux-3.1.0}/src/moleditpy_linux/ui/bond_length_dialog.py

@@ -155,8 +155,6 @@ class BondLengthDialog(GeometryBaseDialog):
             self.atom1_idx = atom_idx
             self.atom2_idx = None
 
-        # Display atom labels
-        self.show_atom_labels()
         self.update_display()
 
     def clear_selection(self):

{moleditpy_linux-3.0.5 → moleditpy_linux-3.1.0}/src/moleditpy_linux/ui/dialog_3d_picking_mixin.py

@@ -192,9 +192,14 @@ class Dialog3DPickingMixin:
         color : str, optional
             Label colour (default ``'yellow'``).
         """
-        pos = self.main_window.view_3d_manager.atom_positions_3d[atom_idx]
+        plotter = self.main_window.view_3d_manager.plotter
+        try:
+            cam = plotter.camera_position
+        except (AttributeError, RuntimeError, TypeError):
+            cam = None
 
-        label_actor = self.main_window.view_3d_manager.plotter.add_point_labels(
+        pos = self.main_window.view_3d_manager.atom_positions_3d[atom_idx]
+        label_actor = plotter.add_point_labels(
             [pos],
             [label_text],
             point_size=20,
@@ -204,6 +209,12 @@ class Dialog3DPickingMixin:
         )
         self.selection_labels.append(label_actor)
 
+        if cam is not None:
+            try:
+                plotter.camera_position = cam
+            except (AttributeError, RuntimeError, TypeError):
+                pass
+
     def show_atom_labels_for(self, atoms_and_labels, color="yellow"):
         """Clear existing labels and add new ones for each *(idx, text)* pair.
 
@@ -214,11 +225,17 @@ class Dialog3DPickingMixin:
         color : str, optional
             Label colour (default ``'yellow'``).
         """
+        plotter = self.main_window.view_3d_manager.plotter
+        try:
+            cam = plotter.camera_position
+        except (AttributeError, RuntimeError, TypeError):
+            cam = None
+
         self.clear_atom_labels()
 
         for atom_idx, label_text in atoms_and_labels:
             pos = self.main_window.view_3d_manager.atom_positions_3d[atom_idx]
-            label_actor = self.main_window.view_3d_manager.plotter.add_point_labels(
+            label_actor = plotter.add_point_labels(
                 [pos],
                 [label_text],
                 point_size=20,
@@ -227,3 +244,9 @@ class Dialog3DPickingMixin:
                 always_visible=True,
             )
             self.selection_labels.append(label_actor)
+
+        if cam is not None:
+            try:
+                plotter.camera_position = cam
+            except (AttributeError, RuntimeError, TypeError):
+                pass

{moleditpy_linux-3.0.5 → moleditpy_linux-3.1.0}/src/moleditpy_linux/ui/dialog_logic.py

@@ -200,10 +200,6 @@ class DialogManager:
             with open(filepath, "w", encoding="utf-8") as f:
                 json.dump(template_data, f, indent=2, ensure_ascii=False)
 
-            # Mark as saved (no unsaved changes for this operation)
-            self.host.state_manager.has_unsaved_changes = False
-            self.host.state_manager.update_window_title()
-
             QMessageBox.information(
                 self.host, "Success", f"Template '{name}' saved successfully."
             )
@@ -215,14 +211,14 @@ class DialogManager:
 
     def open_translation_dialog(self):
         """Open the translation dialog"""
+        # Get preselected atoms
+        preselected_atoms = self._get_preselected_atoms_3d()
+
         # Disable measurement mode
         if self.host.edit_3d_manager.measurement_mode:
             self.host.init_manager.measurement_action.setChecked(False)
             self.host.edit_3d_manager.toggle_measurement_mode(False)
 
-        # Get preselected atoms
-        preselected_atoms = self._get_preselected_atoms_3d()
-
         dialog = TranslationDialog(
             self.host.view_3d_manager.current_mol,
             self.host,
@@ -241,14 +237,14 @@ class DialogManager:
 
     def open_move_group_dialog(self):
         """Open Move Group dialog"""
+        # Get preselected atoms
+        preselected_atoms = self._get_preselected_atoms_3d()
+
         # Disable measurement mode
         if self.host.edit_3d_manager.measurement_mode:
             self.host.init_manager.measurement_action.setChecked(False)
             self.host.edit_3d_manager.toggle_measurement_mode(False)
 
-        # Get preselected atoms
-        preselected_atoms = self._get_preselected_atoms_3d()
-
         dialog = MoveGroupDialog(
             self.host.view_3d_manager.current_mol,
             self.host,

{moleditpy_linux-3.0.5 → moleditpy_linux-3.1.0}/src/moleditpy_linux/ui/dihedral_dialog.py

@@ -176,8 +176,6 @@ class DihedralDialog(GeometryBaseDialog):
             self.atom4_idx = None
             self._snapshot_positions = None
 
-        # Display atom labels
-        self.show_atom_labels()
         self.update_display()
 
     def clear_selection(self):

{moleditpy_linux-3.0.5 → moleditpy_linux-3.1.0}/src/moleditpy_linux/ui/io_logic.py

@@ -564,10 +564,7 @@ class IOManager:
             self.host.statusBar().showMessage(f"Export error: {e}")
 
     def load_mol_file(self, file_path: Optional[str] = None) -> None:
-        """Regular 2D MOL file loading logic."""
-        if not self.host.state_manager.check_unsaved_changes():
-            return
-
+        """Import a MOL/SDF file and add its contents to the 2D editor."""
         if not file_path:
             default_dir = (
                 os.path.dirname(self.host.init_manager.current_file_path)
@@ -601,11 +598,6 @@ class IOManager:
                 raise ValueError("Failed to read molecule from file.")
 
             Chem.Kekulize(mol)
-            self.host.ui_manager.restore_ui_for_editing()
-            self.host.edit_actions_manager.clear_2d_editor(push_to_undo=False)
-            self.host.view_3d_manager.current_mol = None
-            self.host.view_3d_manager.plotter.clear()
-            self.host.init_manager.analysis_action.setEnabled(False)
 
             if mol.GetNumConformers() == 0:
                 AllChem.Compute2DCoords(mol)
@@ -615,9 +607,22 @@ class IOManager:
             AllChem.WedgeMolBonds(mol, conf)
 
             SCALE_FACTOR = 50.0
-            view_center = self.host.init_manager.view_2d.mapToScene(
-                self.host.init_manager.view_2d.viewport().rect().center()
-            )
+            existing_atoms = self.host.state_manager.data.atoms
+            if existing_atoms:
+                max_x = max(
+                    v["pos"].x() if hasattr(v["pos"], "x") else v["pos"][0]
+                    for v in existing_atoms.values()
+                )
+                avg_y = sum(
+                    v["pos"].y() if hasattr(v["pos"], "y") else v["pos"][1]
+                    for v in existing_atoms.values()
+                ) / len(existing_atoms)
+                place_center = QPointF(max_x + 80.0, avg_y)
+            else:
+                place_center = self.host.init_manager.view_2d.mapToScene(
+                    self.host.init_manager.view_2d.viewport().rect().center()
+                )
+
             positions = [conf.GetAtomPosition(i) for i in range(mol.GetNumAtoms())]
             mol_center_x = (
                 sum(p.x for p in positions) / len(positions) if positions else 0.0
@@ -630,8 +635,8 @@ class IOManager:
             for i in range(mol.GetNumAtoms()):
                 atom = mol.GetAtomWithIdx(i)
                 pos = conf.GetAtomPosition(i)
-                scene_x = ((pos.x - mol_center_x) * SCALE_FACTOR) + view_center.x()
-                scene_y = (-(pos.y - mol_center_y) * SCALE_FACTOR) + view_center.y()
+                scene_x = ((pos.x - mol_center_x) * SCALE_FACTOR) + place_center.x()
+                scene_y = (-(pos.y - mol_center_y) * SCALE_FACTOR) + place_center.y()
                 atom_id = self.host.init_manager.scene.create_atom(
                     atom.GetSymbol(),
                     QPointF(scene_x, scene_y),
@@ -662,18 +667,9 @@ class IOManager:
                     bond_stereo=stereo,
                 )
 
-            self.host.statusBar().showMessage(f"Successfully loaded {file_path}")
-            self.host.state_manager.reset_undo_stack()
-            self.host.init_manager.current_file_path = file_path
-            self.host.state_manager.has_unsaved_changes = False
-            self.host.state_manager.update_window_title()
+            self.host.statusBar().showMessage(f"Successfully imported {file_path}")
             self.host.init_manager.scene.update_all_items()
-
-            # Reset camera/zoom after drawing
-            QTimer.singleShot(
-                50, lambda: self.host.view_3d_manager.plotter.view_isometric()
-            )
-            QTimer.singleShot(100, lambda: self.host.view_3d_manager.plotter.render())
+            self.host.edit_actions_manager.push_undo_state()
             QTimer.singleShot(100, self.host.view_3d_manager.fit_to_view)
         except Exception as e:
             self.host.statusBar().showMessage(f"Error loading file: {e}")

{moleditpy_linux-3.0.5 → moleditpy_linux-3.1.0}/src/moleditpy_linux/ui/main_window_init.py

@@ -264,7 +264,10 @@ class MainInitManager:
         file_ext = ext_with_dot.lstrip(".")
 
         # 1. Custom Plugin Openers
-        if self.host.plugin_manager and ext_with_dot in self.host.plugin_manager.file_openers:
+        if (
+            self.host.plugin_manager
+            and ext_with_dot in self.host.plugin_manager.file_openers
+        ):
             openers = self.host.plugin_manager.file_openers[ext_with_dot]
             # Iterate through openers (already sorted by priority)
             for opener_info in openers:
@@ -279,7 +282,8 @@ class MainInitManager:
                 except Exception as e:
                     logging.warning(
                         "Plugin opener failed for '%s': %s",
-                        opener_info.get('plugin', 'Unknown'), e
+                        opener_info.get("plugin", "Unknown"),
+                        e,
                     )
                     # If this opener fails, try the next one or fall through to default
                     continue

{moleditpy_linux-3.0.5 → moleditpy_linux-3.1.0}/src/moleditpy_linux/ui/planarize_dialog.py

@@ -90,7 +90,6 @@ class PlanarizeDialog(BasePickingDialog):
             self.selected_atoms.remove(atom_idx)
         else:
             self.selected_atoms.add(atom_idx)
-        self.show_atom_labels()
         self.update_display()
 
     def clear_selection(self):