hbat 2.2.5__tar.gz → 2.2.6.dev24__tar.gz

{hbat-2.2.5 → hbat-2.2.6.dev24}/.github/workflows/release.yml

@@ -116,7 +116,6 @@ jobs:
         retention-days: 30
     
     - name: Publish to PyPI
-      if: needs.generate-version.outputs.is_prerelease == 'false'
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
         attestations: true
@@ -419,21 +418,28 @@ jobs:
             - `hbat_${{ needs.generate-version.outputs.version }}_amd64.deb` - Debian package
           
           ### Conda Package
-          - `hbat-${{ needs.generate-version.outputs.version }}.tar.bz2` or `.conda`
+          - `hbat-${{ needs.generate-version.outputs.version }}-py0.conda`
           
           ### Documentation
           - `hbat-docs-${{ needs.generate-version.outputs.version }}.zip` - Full HTML documentation
           
           ## Installation
           
-          **pip:**
+          **PIP:**
           ```bash
           pip install https://github.com/${{ github.repository }}/releases/download/${{ needs.generate-version.outputs.github_tag }}/hbat-${{ needs.generate-version.outputs.version }}-py3-none-any.whl
           ```
           
-          ${{ needs.generate-version.outputs.is_prerelease == 'false' && '**PyPI:**\n```bash\npip install hbat\n```' || '' }}
+          **PyPI:**
+          ```bash
+          pip install hbat${{ needs.generate-version.outputs.is_prerelease == 'true' && '==' || '' }}${{ needs.generate-version.outputs.is_prerelease == 'true' && needs.generate-version.outputs.version || '' }}
+          ```
           
-          ${{ needs.generate-version.outputs.is_prerelease == 'false' && '**Conda:**\n```bash\nconda install -c ${{ secrets.ANACONDA_ORG }} hbat\n```' || '**Conda:** Download the package and install locally' }}
+          ${{ needs.generate-version.outputs.is_prerelease == 'false' && '**Conda:**
+          ```bash
+          conda install -c ${{ secrets.ANACONDA_ORG }} hbat
+          ```' || '**Conda:**
+          Download the package and install locally' }}
         prerelease: ${{ needs.generate-version.outputs.is_prerelease == 'true' }}
         draft: false
     
@@ -451,6 +457,13 @@ jobs:
           A pre-release has been created for this PR: **${tag}**
           
           ### Quick Install
+          
+          **From PyPI (recommended):**
+          \`\`\`bash
+          pip install hbat==${version}
+          \`\`\`
+          
+          **From GitHub Release:**
           \`\`\`bash
           pip install https://github.com/${{ github.repository }}/releases/download/${tag}/hbat-${version}-py3-none-any.whl
           \`\`\`

{hbat-2.2.5 → hbat-2.2.6.dev24}/.github/workflows/test.yml

@@ -38,11 +38,19 @@ jobs:
     
     - name: Run coverage
       run: make test-coverage
-      if: matrix.python-version == '3.9'
+      if: matrix.python-version == '3.10'
     
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
-      if: matrix.python-version == '3.9'
+      uses: codecov/codecov-action@v5
+      if: matrix.python-version == '3.10'
       with:
-        file: ./tests/htmlcov/coverage.xml
-        fail_ci_if_error: false
+        fail_ci_if_error: false
+        files: ./coverage.xml
+        token: ${{ secrets.CODECOV_TOKEN }}
+
+    - name: Upload test results to Codecov
+      if: ${{ !cancelled() }}
+      uses: codecov/test-results-action@v1
+      with:
+        files: ./junit.xml
+        token: ${{ secrets.CODECOV_TOKEN }}

{hbat-2.2.5 → hbat-2.2.6.dev24}/CLAUDE.md

@@ -33,3 +33,9 @@
     - 1UBI.pdb and 1BHL.pdb lack hydrogen atoms. Add missing hydrogen atoms (i.e. PDB fixing) and then perform hydrogen bond analysis. Test both OpenBabel and PDB fixer for fixing missing hydrogen atoms.
 
 6. Store all debugging and experimental scripts and utilities in `experiments` folder
+
+7. When asked, output planning details into `plan` folder in markdown files. For every feature first plan and then implement. During plan phase, create a new `feature-XYZ` folder under `plan`. Create 3 files (1) `requirements.md`: includes detailed requirements for the feature and acceptance criteria (which can be used for writing tests), (2) `design.md` contains detailed design for the feature including any mermaid and or plantUML diagrams, and (3) `tasks.md` implementation plan for test first development.
+
+9. We will follow test-first development i.e. write tests before the actual code that implements the functionality they verify.
+
+10. Always use existing constants from `constants` package and avoid directly hard coding in the code. If you need new constants define them and import.  

{hbat-2.2.5 → hbat-2.2.6.dev24}/Makefile

@@ -1,6 +1,6 @@
 # HBAT Development Makefile
 
-.PHONY: help install install-dev test test-fast test-legacy test-pytest test-core test-cli test-gui test-coverage test-ccd clean lint format type-check docs generate-ccd-bonds
+.PHONY: help install install-dev test test-all test-fast test-legacy test-pytest test-unit test-integration test-e2e test-performance test-cli test-gui test-coverage test-ccd clean lint format type-check docs generate-ccd-bonds
 
 # Default target
 help:
@@ -9,11 +9,15 @@ help:
 	@echo "  install-dev   Install with development dependencies"
 	@echo ""
 	@echo "Testing:"
-	@echo "  test          Run comprehensive test suite (recommended)"
+	@echo "  test          Run comprehensive test suite (excludes slow tests)"
+	@echo "  test-all      Run ALL tests including slow performance tests"
 	@echo "  test-fast     Run fast tests only (skip slow integration tests)"
 	@echo "  test-legacy   Run legacy test runner"
 	@echo "  test-pytest   Run tests with pytest (if available)"
-	@echo "  test-core     Run core module tests only"
+	@echo "  test-unit     Run unit tests only (fast, isolated)"
+	@echo "  test-integration Run integration tests only (component interactions)"
+	@echo "  test-e2e      Run end-to-end workflow tests only"
+	@echo "  test-performance Run performance benchmark tests only"
 	@echo "  test-cli      Run CLI tests only"
 	@echo "  test-gui      Run GUI tests only (requires display)"
 	@echo "  test-coverage Generate test coverage report"
@@ -32,6 +36,7 @@ help:
 	@echo "Development:"
 	@echo "  clean         Clean build artifacts"
 	@echo "  docs          Build documentation"
+	@echo "  docs-watch    Build docs with auto-reload and open browser"
 	@echo "  run-gui       Launch GUI application"
 	@echo "  run-cli       Run CLI with test file"
 	@echo "  generate-ccd-bonds Generate residue bond constants from CCD files"
@@ -46,36 +51,52 @@ install-dev:
 
 # Testing
 test:
-	@echo "Running additional pytest tests if available..."
-	-pytest tests/ -v
+	@echo "Running all tests except slow ones..."
+	pytest tests/ -v -m "not slow"
 
 test-fast:
 	@echo "Running fast tests only..."
 	cd tests && python run_tests.py --fast
 
+test-all:
+	@echo "Running ALL tests including slow ones..."
+	pytest tests/ -v
+
 test-pytest:
 	@echo "Running tests with pytest..."
 	pytest tests/ -v
 
 test-cli:
 	@echo "Running CLI tests..."
-	cd tests && python run_tests.py --cli --fast
-
-test-core:
-	@echo "Running core tests..."
-	cd tests && python run_tests.py --core --fast
+	pytest tests/cli/ -v -m "cli"
 
 test-coverage:
-	@echo "Running tests with coverage..."
-	cd tests && python run_tests.py --coverage
+	@echo "Running tests with coverage...(excludes slow tests)"
+	pytest tests/ -v -m "not slow" --cov --cov-branch --cov-report=xml --junitxml=junit.xml -o junit_family=legacy 
 
 test-gui:
 	@echo "Running GUI tests..."
-	cd tests && python run_tests.py --gui --fast
+	pytest tests/gui/ -v -m "gui"
+
+test-unit:
+	@echo "Running unit tests..."
+	pytest tests/unit/ -v -m "unit"
+
+test-integration:
+	@echo "Running integration tests..."
+	pytest tests/integration/ -v -m "integration"
+
+test-e2e:
+	@echo "Running end-to-end tests..."
+	pytest tests/e2e/ -v -m "e2e"
+
+test-performance:
+	@echo "Running performance tests..."
+	pytest tests/performance/ -v -m "performance"
 
 test-ccd:
 	@echo "Running CCD performance tests..."
-	pytest tests/core/test_ccd_performance.py -v -m "ccd"
+	pytest tests/performance/test_ccd_performance.py -v -m "ccd"
 
 # Code quality
 lint:
@@ -125,6 +146,10 @@ docs-serve:
 		echo "Documentation not built. Run 'make docs' first."; \
 	fi
 
+docs-watch:
+	@echo "Building and watching documentation with auto-reload (requires sphinx-autobuild)..."
+	sphinx-autobuild docs/source/ docs/build/html/ --open-browser
+
 # Development runners
 run-gui:
 	python hbat_gui.py

{hbat-2.2.5 → hbat-2.2.6.dev24}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: hbat
-Version: 2.2.5
+Version: 2.2.6.dev24
 Summary: Hydrogen Bond Analysis Tool for PDB structures
 Author-email: Abhishek Tiwari <hbat@abhishek-tiwari.com>
 License-Expression: MIT
@@ -87,13 +87,16 @@ A Python package to automate the analysis of potential hydrogen bonds and simila
 ![License](https://img.shields.io/github/license/abhishektiwari/hbat)
 ![GitHub Downloads (all assets, all releases)](https://img.shields.io/github/downloads/abhishektiwari/hbat/total?label=GitHub%20Downloads)
 ![SourceForge Downloads](https://img.shields.io/sourceforge/dt/hbat?label=SourceForge%20Downloads)
-
+![PyPI Downloads](https://img.shields.io/pypi/dm/hbat?label=PyPI%20Downloads)
+[![codecov](https://codecov.io/gh/abhishektiwari/hbat/graph/badge.svg?token=QSKYLB3M1V)](https://codecov.io/gh/abhishektiwari/hbat)
+[![Cited By](https://img.shields.io/badge/dynamic/regex?url=https%3A%2F%2Fscholar.google.com%2Fcitations%3Fview_op%3Dview_citation%26hl%3Den%26user%3DMb7eYKYAAAAJ%26citation_for_view%3DMb7eYKYAAAAJ%3Au-x6o8ySG0sC&search=Cited%20by%20(%5Cd%2B)&replace=%241&style=plastic&logo=googlescholar&label=Cited%20By&cacheSeconds=86400)](https://scholar.google.com/citations?view_op=view_citation&hl=en&user=Mb7eYKYAAAAJ&citation_for_view=Mb7eYKYAAAAJ:u-x6o8ySG0sC)
 
 
 ## Background
 
 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.
 
+
 ## Features
 
 - **Comprehensive Analysis**: Detect and analyze potential hydrogen bonds, halogen bonds, and X-H...π interactions

{hbat-2.2.5 → hbat-2.2.6.dev24}/README.md

@@ -15,13 +15,16 @@ A Python package to automate the analysis of potential hydrogen bonds and simila
 ![License](https://img.shields.io/github/license/abhishektiwari/hbat)
 ![GitHub Downloads (all assets, all releases)](https://img.shields.io/github/downloads/abhishektiwari/hbat/total?label=GitHub%20Downloads)
 ![SourceForge Downloads](https://img.shields.io/sourceforge/dt/hbat?label=SourceForge%20Downloads)
-
+![PyPI Downloads](https://img.shields.io/pypi/dm/hbat?label=PyPI%20Downloads)
+[![codecov](https://codecov.io/gh/abhishektiwari/hbat/graph/badge.svg?token=QSKYLB3M1V)](https://codecov.io/gh/abhishektiwari/hbat)
+[![Cited By](https://img.shields.io/badge/dynamic/regex?url=https%3A%2F%2Fscholar.google.com%2Fcitations%3Fview_op%3Dview_citation%26hl%3Den%26user%3DMb7eYKYAAAAJ%26citation_for_view%3DMb7eYKYAAAAJ%3Au-x6o8ySG0sC&search=Cited%20by%20(%5Cd%2B)&replace=%241&style=plastic&logo=googlescholar&label=Cited%20By&cacheSeconds=86400)](https://scholar.google.com/citations?view_op=view_citation&hl=en&user=Mb7eYKYAAAAJ&citation_for_view=Mb7eYKYAAAAJ:u-x6o8ySG0sC)
 
 
 ## Background
 
 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.
 
+
 ## Features
 
 - **Comprehensive Analysis**: Detect and analyze potential hydrogen bonds, halogen bonds, and X-H...π interactions

{hbat-2.2.5 → hbat-2.2.6.dev24}/build_standalone_linux.py

@@ -38,7 +38,13 @@ def install_dependencies():
 def clean_build():
     """Clean previous build artifacts."""
     print("Cleaning previous builds...")
-    paths_to_clean = ["build", "dist", "__pycache__", "appimagetool-extracted", "squashfs-root"]
+    paths_to_clean = [
+        "build",
+        "dist",
+        "__pycache__",
+        "appimagetool-extracted",
+        "squashfs-root",
+    ]
 
     for path in paths_to_clean:
         if os.path.exists(path):
@@ -129,9 +135,9 @@ def build_cli():
 def create_appimage():
     """Create AppImage for better Linux distribution."""
     print("\nCreating AppImage...")
-    
+
     # Get version from environment or use default
-    version = os.environ.get('HBAT_VERSION', '2.0.0')
+    version = os.environ.get("HBAT_VERSION", "2.0.0")
 
     # Create AppDir structure
     appdir = Path("HBAT.AppDir")
@@ -183,7 +189,7 @@ Terminal=false
 
     with open(appdir / "usr" / "share" / "applications" / "hbat.desktop", "w") as f:
         f.write(desktop_content)
-    
+
     # Also create desktop file at root for appimagetool
     with open(appdir / "hbat.desktop", "w") as f:
         f.write(desktop_content)
@@ -209,7 +215,7 @@ fi
     # Download and extract appimagetool if not present
     appimagetool = "appimagetool-x86_64.AppImage"
     appimagetool_dir = "appimagetool-extracted"
-    
+
     if not os.path.exists(appimagetool_dir):
         if not os.path.exists(appimagetool):
             print("Downloading appimagetool...")
@@ -222,13 +228,16 @@ fi
             except Exception as e:
                 print(f"Failed to download appimagetool: {e}")
                 return False
-        
+
         # Extract appimagetool to avoid FUSE requirement
         print("Extracting appimagetool...")
         try:
             # Extract quietly to avoid verbose output
-            result = subprocess.run([f"./{appimagetool}", "--appimage-extract"], 
-                                  capture_output=True, text=True)
+            result = subprocess.run(
+                [f"./{appimagetool}", "--appimage-extract"],
+                capture_output=True,
+                text=True,
+            )
             if result.returncode != 0 and "squashfs-root" not in result.stdout:
                 print(f"Failed to extract appimagetool: {result.stderr}")
                 return False
@@ -246,13 +255,13 @@ fi
         env = os.environ.copy()
         env["ARCH"] = "x86_64"
         appimage_name = f"dist/HBAT-{version}-x86_64.AppImage"
-        
+
         # Check if desktop file exists at root (required by appimagetool)
         desktop_file = appdir / "hbat.desktop"
         if not desktop_file.exists():
             print(f"Error: Desktop file not found at {desktop_file}")
             return False
-            
+
         # Use the extracted AppRun instead of the AppImage
         print(f"Building AppImage with {appimagetool_dir}/AppRun...")
         result = subprocess.run(
@@ -261,12 +270,12 @@ fi
             text=True,
             env=env,
         )
-        
+
         if result.returncode != 0:
             print(f"AppImage build failed: {result.stderr}")
             print(f"stdout: {result.stdout}")
             return False
-            
+
         shutil.rmtree(appdir)
         print(f"✓ AppImage created successfully: HBAT-{version}-x86_64.AppImage")
         return True
@@ -278,9 +287,9 @@ fi
 def create_deb_package():
     """Create .deb package for Debian/Ubuntu."""
     print("\nCreating .deb package...")
-    
+
     # Get version from environment or use default
-    version = os.environ.get('HBAT_VERSION', '2.0.0')
+    version = os.environ.get("HBAT_VERSION", "2.0.0")
 
     # Create debian package structure
     debdir = Path("hbat-deb")
@@ -349,7 +358,8 @@ Description: Hydrogen Bond Analysis Tool
     # Build .deb package
     try:
         subprocess.run(
-            ["dpkg-deb", "--build", "hbat-deb", f"dist/hbat_{version}_amd64.deb"], check=True
+            ["dpkg-deb", "--build", "hbat-deb", f"dist/hbat_{version}_amd64.deb"],
+            check=True,
         )
         shutil.rmtree(debdir)
         print(f"✓ .deb package created successfully: hbat_{version}_amd64.deb")
@@ -365,9 +375,9 @@ def main():
     """Main build function."""
     print("HBAT Linux Build Script")
     print("=" * 40)
-    
+
     # Get version from environment or use default
-    version = os.environ.get('HBAT_VERSION', '2.0.0')
+    version = os.environ.get("HBAT_VERSION", "2.0.0")
     print(f"Building version: {version}")
 
     # Check we're in the right directory

hbat-2.2.6.dev24/docs/source/_static/custom.css

@@ -0,0 +1,4 @@
+/* Custom styles for HBAT documentation */
+a.image-reference {
+    text-decoration: none;
+}

hbat-2.2.6.dev24/docs/source/_static/light-theme.css

@@ -0,0 +1 @@
+/* Light Theme Override for HBAT Documentation */

{hbat-2.2.5 → hbat-2.2.6.dev24}/docs/source/conf.py

@@ -35,6 +35,7 @@ extensions = [
     'sphinx.ext.githubpages',
     'sphinx_toolbox.shields',
     'sphinx_sitemap',
+    'sphinx_copybutton',
 ]
 
 # Mock imports for modules that might not be available in CI
@@ -56,7 +57,7 @@ master_doc = 'index'
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.
-html_theme = 'sphinx_rtd_theme'
+html_theme = 'sphinx_book_theme'
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -64,9 +65,9 @@ html_theme = 'sphinx_rtd_theme'
 html_static_path = ['_static']
 
 # Custom CSS files
-# html_css_files = [
-#    'custom.css',
-# ]
+html_css_files = [
+    'custom.css',
+]
 
 # -- Extension configuration -------------------------------------------------
 
@@ -107,6 +108,7 @@ intersphinx_mapping = {
 html_theme_options = {
     'canonical_url': '',
     'analytics_id': '',
+    'google_analytics_id': 'G-PLZNCJY1B7',
     'logo_only': False,
     'prev_next_buttons_location': 'bottom',
     'style_external_links': False,
@@ -116,7 +118,39 @@ html_theme_options = {
     'sticky_navigation': True,
     'navigation_depth': 4,
     'includehidden': True,
-    'titles_only': False
+    'titles_only': False,
+    "repository_url": "https://github.com/abhishektiwari/hbat",
+    "repository_provider": "github",
+    "repository_branch": "main",
+    "path_to_docs": "docs/source",
+    "use_issues_button": True,
+    "use_repository_button": True,
+    "use_edit_page_button": True,
+    "use_download_button": False,
+    "use_fullscreen_button": True,
+    "use_search_button": True,
+    "use_sidenotes": True,
+    "icon_links_label": "Quick Links",
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/abhishektiwari/hbat",
+            "icon": "fa-brands fa-square-github",
+            "type": "fontawesome",
+        },
+        {
+            "name": "Abhishek Tiwari",
+            "url": "https://www.abhishek-tiwari.com",
+            "icon": "https://www.abhishek-tiwari.com/images/logo.svg",
+            "type": "local",
+        },
+        {
+            "name": "PyPI",
+            "url": "https://pypi.org/project/hbat/",
+            "icon": "fa-brands fa-python",
+            "type": "fontawesome",
+        },
+   ]
 }
 
 # The version info for the project you're documenting, acts as replacement for

{hbat-2.2.5 → hbat-2.2.6.dev24}/docs/source/index.rst

@@ -3,9 +3,11 @@ HBAT Documentation
 
 .. image:: https://img.shields.io/github/v/release/abhishektiwari/hbat
    :alt: GitHub Release
+   :target: https://github.com/abhishektiwari/hbat/releases
 
 .. image:: https://img.shields.io/github/actions/workflow/status/abhishektiwari/hbat/test.yml?label=tests
    :alt: GitHub Actions Test Workflow Status
+   :target: https://github.com/abhishektiwari/hbat/actions/workflows/test.yml
 
 .. pypi-shield::
    :project: hbat
@@ -36,43 +38,59 @@ HBAT Documentation
 
 .. image:: https://img.shields.io/github/downloads/abhishektiwari/hbat/total?label=GitHub%20Downloads
    :alt: GitHub Downloads (all assets, all releases)
+   :target: https://github.com/abhishektiwari/hbat/releases
 
 .. image:: https://img.shields.io/sourceforge/dt/hbat?label=SourceForge%20Downloads
    :alt: SourceForge Downloads
+   :target: https://sourceforge.net/projects/hbat/files/
+
+.. image:: https://img.shields.io/pypi/dm/hbat?label=PyPI%20Downloads
+   :alt: PyPI Downloads
+   :target: https://pypi.org/project/hbat/
+
+.. image:: https://codecov.io/gh/abhishektiwari/hbat/graph/badge.svg?token=QSKYLB3M1V 
+   :alt: Codecov Coverage
+   :target: https://codecov.io/gh/abhishektiwari/hbat
+
+.. image:: https://img.shields.io/badge/dynamic/regex?url=https%3A%2F%2Fscholar.google.com%2Fcitations%3Fview_op%3Dview_citation%26hl%3Den%26user%3DMb7eYKYAAAAJ%26citation_for_view%3DMb7eYKYAAAAJ%3Au-x6o8ySG0sC&search=Cited%20by%20(%5Cd%2B)&replace=%241&style=plastic&logo=googlescholar&label=Cited%20By&cacheSeconds=86400
+   :alt: Cited by Google Scholar
+   :target: https://scholar.google.com/citations?view_op=view_citation&hl=en&user=Mb7eYKYAAAAJ&citation_for_view=Mb7eYKYAAAAJ:u-x6o8ySG0sC
+
+
 
 Welcome to HBAT (Hydrogen Bond Analysis Tool) documentation!
 
+
+.. raw:: html
+
+   <span class="__dimensions_badge_embed__" data-doi="10.3233/isi-2007-00337" data-legend="always" data-style="small_circle"></span><script async src="https://badge.dimensions.ai/badge.js" charset="utf-8"></script>
+
 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.
 
 .. toctree::
-   :maxdepth: 2
-   :caption: Contents:
+   :maxdepth: 1
+   :caption: User Guide
 
    installation
    quickstart
    cli
    parameters
    pdbfixing
-   api/index
-   development
-   logic
    license
 
-Features
---------
+.. toctree::
+   :maxdepth: 1
+   :caption: Developer Guide
 
-- **Comprehensive Analysis**: Detects hydrogen bonds, halogen bonds, and X-H...π interactions
-- **Cooperativity Detection**: Identifies chains of cooperative molecular interactions
-- **Structure Enhancement**: Automated PDB fixing with OpenBabel and PDBFixer integration
-- **Flexible Parameters**: Customizable analysis parameters for different research needs
-- **Multiple Output Formats**: Support for CSV, JSON, and formatted text output
-- **GUI Interface**: User-friendly graphical interface for interactive analysis
-- **Command Line Tool**: Scriptable CLI for batch processing and automation
+   api/index
+   development
+   logic
 
 Quick Start
 -----------
 
-Install HBAT:
+Install HBAT
+~~~~~~~~~~~~
 
 .. code-block:: bash
 
@@ -80,11 +98,22 @@ Install HBAT:
 
 **Recommended**: For fixing missing Hydrogen Atoms, install PDBFixer (preferred over OpenBabel). See :doc:`pdbfixing` for details.
 
+.. code-block:: bash
+
+   pip install git+https://github.com/abhishektiwari/hbat.git
+
+
+If you installed HBAT from PyPI, you can also install PDBFixer using,
+
 .. code-block:: bash
 
    pip install git+https://github.com/openmm/pdbfixer.git
 
-Basic usage:
+
+See complete installation instructions in :doc:`installation`.
+
+Basic usage
+~~~~~~~~~~~
 
 .. code-block:: bash
 
@@ -93,6 +122,38 @@ Basic usage:
 
 See full CLI options :doc:`cli`.
 
+Features
+--------
+
+- **Comprehensive Analysis**: Detects hydrogen bonds, halogen bonds, and X-H...π interactions
+- **Cooperativity Detection**: Identifies chains of cooperative molecular interactions
+- **Structure Enhancement**: Automated PDB fixing with OpenBabel and PDBFixer integration
+- **Flexible Parameters**: Customizable analysis parameters for different research needs
+- **Multiple Output Formats**: Support for CSV, JSON, and formatted text output
+- **GUI Interface**: User-friendly graphical interface for interactive analysis
+- **Command Line Tool**: Scriptable CLI for batch processing and automation
+
+
+Cite HBAT
+---------
+
+.. code-block:: bash
+
+   @article{tiwari2023hbat,
+       title={HBAT: A Python Package for Automated Hydrogen Bond Analysis in Macromolecular Structures},
+       author={Tiwari, Abhishek and others},
+       journal={Journal of Open Research Software},
+       volume={11},
+       number={1},
+       pages={1-8},
+       year={2023},
+       publisher={Ubiquity Press}
+   }
+
+.. code-block:: bash
+
+   Tiwari, A., & Panigrahi, S. K. (2007). HBAT: A Complete Package for Analysing Strong and Weak Hydrogen Bonds in Macromolecular Crystal Structures. In Silico Biology, 7(6). https://doi.org/10.3233/ISI-2007-00337
+
 Indices and tables
 ==================
 

{hbat-2.2.5 → hbat-2.2.6.dev24}/docs/source/installation.rst

@@ -9,21 +9,33 @@ HBAT requires:
 - **Python**: 3.9 or higher
 - **tkinter**: Included with Python standard library on most systems. On macOS, install Python and tkinter using Homebrew:
   
-  .. code-block:: bash
+.. code-block:: bash
 
-     brew install python python3-tk
+   brew install python python3-tk
 
 Installation Methods
 --------------------
 
-From PyPI (Recommended)
-~~~~~~~~~~~~~~~~~~~~~~~
+From PyPI
+~~~~~~~~~
 
 .. code-block:: bash
 
    pip install hbat
 
-**Recommended**: For fixing missing Hydrogen Atoms, install PDBFixer (preferred over OpenBabel). See :doc:`pdbfixing` for details.
+
+From Github
+~~~~~~~~~~~
+
+**Recommended** for fixing missing Hydrogen Atoms using PDBFixer (preferred over OpenBabel). See :doc:`pdbfixing` for details.
+
+
+.. code-block:: bash
+
+   pip install git+https://github.com/abhishektiwari/hbat.git
+
+
+If you installed HBAT from PyPI, you can also install PDBFixer using,
 
 .. code-block:: bash
 
@@ -38,15 +50,6 @@ From Source
    git clone https://github.com/abhishektiwari/hbat.git
    cd hbat
    pip install -e .
-
-
-Alternatively,  
-
-.. code-block:: bash
-
-   pip install git+https://github.com/abhishektiwari/hbat.git
-
-
 From Conda
 ~~~~~~~~~~