hbat 2.2.6__tar.gz → 2.2.6.dev24__tar.gz

{hbat-2.2.6 → 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
@@ -431,10 +430,10 @@ jobs:
           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
           ```
           
-          ${{ needs.generate-version.outputs.is_prerelease == 'false' && '**PyPI:**
+          **PyPI:**
           ```bash
-          pip install hbat
-          ```' || '' }}
+          pip install hbat${{ needs.generate-version.outputs.is_prerelease == 'true' && '==' || '' }}${{ needs.generate-version.outputs.is_prerelease == 'true' && needs.generate-version.outputs.version || '' }}
+          ```
           
           ${{ needs.generate-version.outputs.is_prerelease == 'false' && '**Conda:**
           ```bash
@@ -458,6 +457,13 @@ jobs:
           A pre-release has been created for this PR: **${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-2.2.6 → 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-2.2.6 → hbat-2.2.6.dev24}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: hbat
-Version: 2.2.6
+Version: 2.2.6.dev24
 Summary: Hydrogen Bond Analysis Tool for PDB structures
 Author-email: Abhishek Tiwari <hbat@abhishek-tiwari.com>
 License-Expression: MIT
@@ -89,11 +89,14 @@ A Python package to automate the analysis of potential hydrogen bonds and simila
 ![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-2.2.6 → hbat-2.2.6.dev24}/README.md

@@ -17,11 +17,14 @@ A Python package to automate the analysis of potential hydrogen bonds and simila
 ![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-2.2.6.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-2.2.6 → hbat-2.2.6.dev24}/docs/source/conf.py

@@ -65,9 +65,9 @@ html_theme = 'sphinx_book_theme'
 html_static_path = ['_static']
 
 # Custom CSS files
-# html_css_files = [
-#    'custom.css',
-# ]
+html_css_files = [
+    'custom.css',
+]
 
 # -- Extension configuration -------------------------------------------------
 

{hbat-2.2.6 → 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
@@ -36,19 +38,33 @@ 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::
@@ -117,6 +133,27 @@ Features
 - **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-2.2.6 → hbat-2.2.6.dev24}/hbat/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '2.2.6'
-__version_tuple__ = version_tuple = (2, 2, 6)
+__version__ = version = '2.2.6.dev24'
+__version_tuple__ = version_tuple = (2, 2, 6, 'dev24')

{hbat-2.2.6 → hbat-2.2.6.dev24}/requirements.txt

@@ -6,6 +6,10 @@ pdbreader>=0.1.0
 
 # Numerical computing
 numpy>=1.20.0
+scipy >=1.14.0
+
+# Parsing library for selection language
+pyparsing>=3.0.0
 
 # Optional visualization (GUI features)
 networkx>=2.5.0

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

@@ -1,78 +0,0 @@
-/* Custom HBAT Documentation Styling */
-
-/* Sidebar customization */
-.wy-nav-side {
-    background: #2c3e50 !important;  /* Main sidebar background */
-}
-
-/* Sidebar header */
-.wy-side-nav-search {
-    background-color: #34495e !important;  /* Search area background */
-}
-
-/* Sidebar navigation links */
-.wy-menu-vertical a {
-    color: #ecf0f1 !important;  /* Link text color */
-}
-
-.wy-menu-vertical a:hover {
-    background-color: #3498db !important;  /* Hover background */
-    color: #ffffff !important;
-}
-
-/* Current page highlighting */
-.wy-menu-vertical li.current a {
-    background-color: #e74c3c !important;  /* Current page background */
-    color: #ffffff !important;
-}
-
-.wy-menu-vertical li.current > a {
-    background-color: #c0392b !important;  /* Current section background */
-}
-
-/* Nested navigation items */
-.wy-menu-vertical li.toctree-l2 a {
-    color: #bdc3c7 !important;  /* Sub-item text color */
-}
-
-.wy-menu-vertical li.toctree-l2.current a {
-    background-color: #e67e22 !important;  /* Current sub-item */
-}
-
-/* Search box styling */
-.wy-side-nav-search input[type=text] {
-    background-color: #ecf0f1 !important;
-    border: 1px solid #bdc3c7 !important;
-    color: #2c3e50 !important;
-}
-
-/* Logo area */
-.wy-side-nav-search > a {
-    color: #ecf0f1 !important;
-    font-weight: bold;
-}
-
-/* Scrollbar customization for webkit browsers */
-.wy-nav-side::-webkit-scrollbar {
-    width: 8px;
-}
-
-.wy-nav-side::-webkit-scrollbar-track {
-    background: #34495e;
-}
-
-.wy-nav-side::-webkit-scrollbar-thumb {
-    background: #3498db;
-    border-radius: 4px;
-}
-
-.wy-nav-side::-webkit-scrollbar-thumb:hover {
-    background: #2980b9;
-}
-
-/* Mobile responsive adjustments */
-@media screen and (max-width: 768px) {
-    .wy-nav-side {
-        background: #2c3e50 !important;
-    }
-}

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

@@ -1,39 +0,0 @@
-/* Light Theme Alternative for HBAT Documentation */
-
-/* Sidebar customization - Light theme */
-.wy-nav-side {
-    background: #f8f9fa !important;  /* Light gray sidebar */
-    border-right: 2px solid #e9ecef !important;
-}
-
-/* Sidebar header */
-.wy-side-nav-search {
-    background-color: #ffffff !important;  /* White search area */
-    border-bottom: 1px solid #dee2e6 !important;
-}
-
-/* Sidebar navigation links */
-.wy-menu-vertical a {
-    color: #495057 !important;  /* Dark gray text */
-}
-
-.wy-menu-vertical a:hover {
-    background-color: #e3f2fd !important;  /* Light blue hover */
-    color: #1976d2 !important;
-}
-
-/* Current page highlighting */
-.wy-menu-vertical li.current a {
-    background-color: #2196f3 !important;  /* Blue current page */
-    color: #ffffff !important;
-}
-
-.wy-menu-vertical li.current > a {
-    background-color: #1976d2 !important;  /* Darker blue current section */
-}
-
-/* Logo area */
-.wy-side-nav-search > a {
-    color: #212529 !important;
-    font-weight: bold;
-}