hbat 2.2.14.dev32__tar.gz → 2.2.15__tar.gz

{hbat-2.2.14.dev32 → hbat-2.2.15}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: hbat
-Version: 2.2.14.dev32
+Version: 2.2.15
 Summary: Hydrogen Bond Analysis Tool for PDB structures
 Author-email: Abhishek Tiwari <hbat@abhishek-tiwari.com>
 License-Expression: MIT

hbat-2.2.15/docs/source/api/gui/index.rst

@@ -0,0 +1,176 @@
+Graphical User Interface
+------------------------
+
+The GUI module provides graphical interface components for HBAT, including comprehensive parameter management, preset handling, and advanced visualization capabilities with support for both NetworkX/matplotlib and GraphViz renderers.
+
+**Key Features:**
+
+- **Parameter Management**: Comprehensive geometry cutoffs dialog with tabbed interface for different interaction types
+- **Preset System**: Full preset management with Settings → Manage Presets interface
+- **PDB Fixing**: Integrated structure enhancement dialog with OpenBabel and PDBFixer support
+- **Visualization**: Advanced graph rendering with multiple backend support
+
+Core Components
+===============
+
+Main Window
+-----------
+
+The primary GUI window with updated menu structure:
+
+- **File Menu**: PDB file operations and recent files
+- **Settings Menu**: 
+  - **Geometry Cutoffs**: Configure interaction parameters
+  - **Manage Presets**: Access preset management system
+  - **PDB Fixing Options**: Structure enhancement settings
+  - **GraphViz Preferences**: Visualization settings
+- **Analysis Tools**: Run analysis and view results
+- **Visualization**: Integrated graph rendering and export
+
+.. automodule:: hbat.gui.main_window
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Dialog Components
+=================
+
+HBAT provides specialized dialog components for comprehensive parameter management and configuration.
+
+Geometry Cutoffs Dialog
+-----------------------
+
+Provides tabbed interface for configuring molecular interaction parameters including:
+
+- **Hydrogen Bonds**: Classical strong interactions (N/O-H···O/N)
+- **Weak Hydrogen Bonds**: C-H···O interactions for binding analysis
+- **Halogen Bonds**: C-X···A interactions with 150° default angle
+- **π Interactions**: Multiple subtypes including hydrogen-π and halogen-π interactions
+- **General Parameters**: Analysis mode and covalent bond detection
+
+.. automodule:: hbat.gui.geometry_cutoffs_dialog
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Preset Manager Dialog
+---------------------
+
+Manages parameter presets through **Settings → Manage Presets** menu:
+
+- **Load Presets**: Apply built-in or custom parameter sets
+- **Save Presets**: Store current parameter configurations
+- **Delete Presets**: Remove custom presets (built-in presets protected)
+- **Preset Validation**: Automatic parameter validation and error checking
+
+.. automodule:: hbat.gui.preset_manager_dialog
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+PDB Fixing Dialog
+-----------------
+
+Configures structure enhancement options:
+
+- **Method Selection**: OpenBabel vs PDBFixer (default: PDBFixer)
+- **Hydrogen Addition**: Add missing hydrogen atoms
+- **Heavy Atom Completion**: Add missing heavy atoms (PDBFixer only)
+- **Structure Cleaning**: Handle non-standard residues and heterogens
+
+.. automodule:: hbat.gui.pdb_fixing_dialog
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Results Panel
+-------------
+
+Displays comprehensive analysis results with enhanced interaction type support:
+
+- **Hydrogen Bonds**: Classical and weak (C-H···O) interactions
+- **Halogen Bonds**: With updated 150° default angle detection
+- **π Interactions**: All subtypes (C-H···π, N-H···π, O-H···π, S-H···π, C-Cl···π, C-Br···π, C-I···π)
+- **Cooperativity Chains**: Linked interaction networks
+- **Export Options**: CSV, JSON, and formatted text output
+
+.. automodule:: hbat.gui.results_panel
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Chain Visualization
+-------------------
+
+Visualization of cooperativity chains and interaction networks with support for the expanded interaction types.
+
+.. automodule:: hbat.gui.chain_visualization
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Visualization System
+====================
+
+The visualization system provides a flexible renderer architecture with support for multiple backends, enhanced to handle the expanded set of molecular interactions including π interaction subtypes and weak hydrogen bonds.
+
+Visualization Renderer Protocol
+-------------------------------
+
+.. automodule:: hbat.gui.visualization_renderer
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+GraphViz Renderer
+-----------------
+
+Advanced graph rendering with support for all interaction types and enhanced visual styling:
+
+- **Node Styling**: Residue-based coloring and labeling
+- **Edge Types**: Different styles for hydrogen bonds, halogen bonds, π interactions
+- **Interaction Labeling**: Display interaction types (C-H···π, C-Cl···π, etc.)
+- **Export Formats**: PNG, SVG, PDF with configurable DPI
+
+.. automodule:: hbat.gui.graphviz_renderer
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Matplotlib Renderer
+--------------------
+
+.. automodule:: hbat.gui.matplotlib_renderer
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Export Manager
+--------------
+
+Handles export of analysis results and visualizations with support for new interaction types:
+
+- **Data Export**: CSV, JSON formats with all interaction subtypes
+- **Graph Export**: Multiple image formats via GraphViz
+- **Batch Export**: Automatic file generation for each interaction type
+- **Format Options**: Configurable output parameters
+
+.. automodule:: hbat.gui.export_manager
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+GraphViz Preferences Dialog
+---------------------------
+
+Configures GraphViz rendering options accessible via **Settings → GraphViz Preferences**:
+
+- **Engine Selection**: Choose GraphViz layout engine (dot, neato, circo, etc.)
+- **Output Format**: PNG, SVG, PDF export options
+- **DPI Settings**: Configure resolution for image exports
+- **Visual Styling**: Node and edge appearance options
+
+.. automodule:: hbat.gui.graphviz_preferences_dialog
+   :members:
+   :undoc-members:
+   :show-inheritance:

{hbat-2.2.14.dev32 → hbat-2.2.15}/docs/source/development.rst

@@ -359,7 +359,7 @@ To add a new parameter preset:
        },
        "halogen_bonds": {
          "x_a_distance_cutoff": 4.0,
-         "cxa_angle_cutoff": 120.0
+         "dxa_angle_cutoff": 120.0
        },
        "pi_interactions": {
          "h_pi_distance_cutoff": 4.5,

{hbat-2.2.14.dev32 → hbat-2.2.15}/docs/source/index.rst

@@ -85,6 +85,7 @@ A Python package to automate the analysis of potential hydrogen bonds and simila
    quickstart
    cli
    parameters
+   presets
    pdbfixing
    license