hbat 2.2.10__tar.gz → 2.2.10.dev28__tar.gz

{hbat-2.2.10 → hbat-2.2.10.dev28}/CODE_OF_CONDUCT.md

@@ -60,8 +60,7 @@ representative at an online or offline event.
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported to the community leaders responsible for enforcement at
-``pwessel at hawaii dot edu``, ``leouieda at gmail dot com``, or
-``meghanj at hawaii dot edu``. All complaints will be reviewed and investigated
+``hbat at abhishek-tiwari dot com``. All complaints will be reviewed and investigated
 promptly and fairly.
 
 All community leaders are obligated to respect the privacy and security of the

{hbat-2.2.10 → hbat-2.2.10.dev28}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: hbat
-Version: 2.2.10
+Version: 2.2.10.dev28
 Summary: Hydrogen Bond Analysis Tool for PDB structures
 Author-email: Abhishek Tiwari <hbat@abhishek-tiwari.com>
 License-Expression: MIT
@@ -93,6 +93,7 @@ A Python package to automate the analysis of potential hydrogen bonds and simila
 
 HBAT v2  is a modern Python re-implementation of the original Perl-based tool developed by [Abhishek Tiwari](https://www.abhishek-tiwari.com) and Sunil Kumar Panigrahi.
 
+![HBAT GUI](https://static.abhishek-tiwari.com/hbat/hbat-window-v1.png)
 
 ## Features
 
@@ -109,6 +110,8 @@ HBAT v2  is a modern Python re-implementation of the original Perl-based tool de
 
 Please review [HBAT documentation](https://hbat.abhishek-tiwari.com/) for more details.
 
+![Cooperativity chain visualization](https://static.abhishek-tiwari.com/hbat/6rsa-pdb-chain-6.png)
+
 ### Supported Interactions
 
 1. **Hydrogen Bonds**: O-H...O, N-H...O, N-H...N, and other X-H...Y interactions

{hbat-2.2.10 → hbat-2.2.10.dev28}/README.md

@@ -25,6 +25,7 @@ A Python package to automate the analysis of potential hydrogen bonds and simila
 
 HBAT v2  is a modern Python re-implementation of the original Perl-based tool developed by [Abhishek Tiwari](https://www.abhishek-tiwari.com) and Sunil Kumar Panigrahi.
 
+![HBAT GUI](https://static.abhishek-tiwari.com/hbat/hbat-window-v1.png)
 
 ## Features
 
@@ -41,6 +42,8 @@ HBAT v2  is a modern Python re-implementation of the original Perl-based tool de
 
 Please review [HBAT documentation](https://hbat.abhishek-tiwari.com/) for more details.
 
+![Cooperativity chain visualization](https://static.abhishek-tiwari.com/hbat/6rsa-pdb-chain-6.png)
+
 ### Supported Interactions
 
 1. **Hydrogen Bonds**: O-H...O, N-H...O, N-H...N, and other X-H...Y interactions

{hbat-2.2.10 → hbat-2.2.10.dev28}/docs/source/index.rst

@@ -73,6 +73,10 @@ Welcome to HBAT (Hydrogen Bond Analysis Tool) documentation!
 
 A Python package to automate the analysis of potential hydrogen bonds and similar type of weak interactions like halogen bonds and non-canonical interactions in macromolecular structures, available in Brookhaven Protein Database (PDB) file format. HBAT uses a geometric approach to identify potential hydrogen bonds by analyzing distance and angular criteria between donor-hydrogen-acceptor triplets.
 
+.. image:: https://static.abhishek-tiwari.com/hbat/hbat-window-v1.png
+   :alt: HBAT GUI
+   :align: center
+
 .. toctree::
    :maxdepth: 1
    :caption: User Guide
@@ -141,6 +145,9 @@ Features
 - **GUI Interface**: User-friendly graphical interface for interactive analysis
 - **Command Line Tool**: Scriptable CLI for batch processing and automation
 
+.. image:: https://static.abhishek-tiwari.com/hbat/6rsa-pdb-chain-6.png
+   :alt: Cooperativity chain visualization
+   :align: center
 
 Cite HBAT
 ---------

{hbat-2.2.10 → hbat-2.2.10.dev28}/hbat/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '2.2.10'
-__version_tuple__ = version_tuple = (2, 2, 10)
+__version__ = version = '2.2.10.dev28'
+__version_tuple__ = version_tuple = (2, 2, 10, 'dev28')

{hbat-2.2.10 → hbat-2.2.10.dev28}/hbat/constants/misc.py

@@ -9,11 +9,11 @@ from .app import APP_VERSION
 class GUIDefaults:
     """Default values for GUI interface."""
 
-    # Window settings
-    WINDOW_WIDTH = 1800
-    WINDOW_HEIGHT = 900
-    MIN_WINDOW_WIDTH = 1200
-    MIN_WINDOW_HEIGHT = 800
+    # Window settings - optimized for standard displays (1366x768, 1920x1080)
+    WINDOW_WIDTH = 1280
+    WINDOW_HEIGHT = 720
+    MIN_WINDOW_WIDTH = 1024
+    MIN_WINDOW_HEIGHT = 680
 
     # Layout settings
     LEFT_PANEL_WIDTH = 400  # Initial pane position

{hbat-2.2.10 → hbat-2.2.10.dev28}/hbat/gui/chain_visualization.py

@@ -77,7 +77,7 @@ class ChainVisualizationWindow:
         """Create the visualization window."""
         self.viz_window = tk.Toplevel(self.parent)
         self.viz_window.title(f"Cooperativity Chain Visualization - {self.chain_id}")
-        self.viz_window.geometry("1000x1000")
+        self.viz_window.geometry("900x700")
 
         # Create main container frames
         main_frame = ttk.Frame(self.viz_window)

{hbat-2.2.10 → hbat-2.2.10.dev28}/hbat/gui/graphviz_preferences_dialog.py

@@ -89,7 +89,7 @@ class GraphVizPreferencesDialog:
         """Create the preferences dialog window."""
         self.dialog = tk.Toplevel(self.parent)
         self.dialog.title("GraphViz Preferences")
-        self.dialog.geometry("600x500")
+        self.dialog.geometry("550x450")
         self.dialog.resizable(False, False)
         self.dialog.grab_set()  # Make dialog modal
 

{hbat-2.2.10 → hbat-2.2.10.dev28}/hbat/gui/main_window.py

@@ -179,27 +179,27 @@ class MainWindow:
     def _create_main_content(self) -> None:
         """Create the main content area.
 
-        Sets up the main interface with a paned window containing file content,
-        parameter panels, and results display areas.
+        Sets up the main interface with a vertical paned window containing PDB file
+        content on top (30%) and results display area below (70%).
 
         :returns: None
         :rtype: None
         """
-        # Create main paned window
-        main_paned = ttk.PanedWindow(self.root, orient=tk.HORIZONTAL)
+        # Create main paned window with vertical orientation
+        main_paned = ttk.PanedWindow(self.root, orient=tk.VERTICAL)
         main_paned.pack(fill=tk.BOTH, expand=True, padx=5, pady=5)
 
-        # Left panel - File content and parameters
-        left_frame = ttk.Frame(main_paned)
-        main_paned.add(left_frame, weight=1)
+        # Top panel - PDB File content (30% of height)
+        top_frame = ttk.Frame(main_paned)
+        main_paned.add(top_frame, weight=3)  # 30% weight ratio
 
-        # Create notebook for left panel
-        left_notebook = ttk.Notebook(left_frame)
-        left_notebook.pack(fill=tk.BOTH, expand=True)
+        # Create notebook for PDB file tabs
+        self.left_notebook = ttk.Notebook(top_frame)
+        self.left_notebook.pack(fill=tk.BOTH, expand=True)
 
         # File content tab
-        file_frame = ttk.Frame(left_notebook)
-        left_notebook.add(file_frame, text="PDB File")
+        file_frame = ttk.Frame(self.left_notebook)
+        self.left_notebook.add(file_frame, text="PDB File")
 
         # Create text widget with both vertical and horizontal scrollbars
         text_frame = ttk.Frame(file_frame)
@@ -224,8 +224,8 @@ class MainWindow:
         text_frame.grid_columnconfigure(0, weight=1)
 
         # Fixed PDB content tab
-        fixed_file_frame = ttk.Frame(left_notebook)
-        left_notebook.add(fixed_file_frame, text="Fixed PDB")
+        fixed_file_frame = ttk.Frame(self.left_notebook)
+        self.left_notebook.add(fixed_file_frame, text="Fixed PDB")
 
         # Create text widget with both vertical and horizontal scrollbars
         fixed_text_frame = ttk.Frame(fixed_file_frame)
@@ -254,22 +254,24 @@ class MainWindow:
         # Add context menu for Fixed PDB tab
         self._create_fixed_pdb_context_menu()
 
-        # Store reference to the notebook for later updates
-        self.left_notebook = left_notebook
-
         # Store parameters separately (no longer in tab)
         self.parameter_panel = None
         self.parameters_window = None
         self.session_parameters = None  # Store parameters for session persistence
 
-        # Right panel - Results
-        right_frame = ttk.Frame(main_paned)
-        main_paned.add(right_frame, weight=2)
+        # Bottom panel - Results (70% of height)
+        bottom_frame = ttk.Frame(main_paned)
+        main_paned.add(bottom_frame, weight=7)  # 70% weight ratio
 
-        self.results_panel = ResultsPanel(right_frame)
+        self.results_panel = ResultsPanel(bottom_frame)
 
-        # Set initial pane positions
-        main_paned.sashpos(0, GUIDefaults.LEFT_PANEL_WIDTH)
+        # Set initial pane positions (30% for top, 70% for bottom)
+        # Position the sash at 30% of the total height
+        main_paned.update_idletasks()  # Ensure the window is rendered
+        total_height = self.root.winfo_height() - 60  # Account for padding and menu
+        if total_height > 0:
+            sash_position = int(total_height * 0.3)
+            main_paned.sashpos(0, sash_position)
 
     def _create_status_bar(self) -> None:
         """Create the status bar.
@@ -1138,7 +1140,7 @@ Author: Abhishek Tiwari
         # Create new parameters window
         self.parameters_window = tk.Toplevel(self.root)
         self.parameters_window.title("Analysis Parameters")
-        self.parameters_window.geometry("800x800")
+        self.parameters_window.geometry("700x600")
         self.parameters_window.resizable(True, True)
 
         # Create parameter panel in popup window