hbat 2.2.13__tar.gz → 2.2.13.dev31__tar.gz

{hbat-2.2.13 → hbat-2.2.13.dev31}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: hbat
-Version: 2.2.13
+Version: 2.2.13.dev31
 Summary: Hydrogen Bond Analysis Tool for PDB structures
 Author-email: Abhishek Tiwari <hbat@abhishek-tiwari.com>
 License-Expression: MIT
@@ -29,6 +29,7 @@ Requires-Dist: networkx>=2.5.0
 Requires-Dist: graphviz>=0.20.0
 Requires-Dist: Pillow>=8.0.0
 Requires-Dist: matplotlib>=3.3.0
+Requires-Dist: pdbfixer-wheel>=1.11.0
 Requires-Dist: openbabel-wheel>=3.1.1.22
 Requires-Dist: pybel>=0.15.5
 Requires-Dist: mmcif-pdbx>=2.0.1
@@ -130,18 +131,6 @@ pip install hbat
 
 Run HBAT Command-Line Interface (CLI) using `hbat` or launch HBAT GUI using `hbat-gui`.
 
-**Recommended:** For [fixing missing Hydrogen Atoms](https://hbat.abhishek-tiwari.com/pdbfixing), using PDBFixer (preferred over OpenBabel).
-
-```bash
-pip install git+https://github.com/abhishektiwari/hbat.git
-```
-
-If you installed HBAT from PyPI, you can also install PDBFixer using,
-
-```bash
-pip install git+https://github.com/openmm/pdbfixer.git
-```
-
 ### Option 2: Install from Source
 
 ```bash

{hbat-2.2.13 → hbat-2.2.13.dev31}/README.md

@@ -62,18 +62,6 @@ pip install hbat
 
 Run HBAT Command-Line Interface (CLI) using `hbat` or launch HBAT GUI using `hbat-gui`.
 
-**Recommended:** For [fixing missing Hydrogen Atoms](https://hbat.abhishek-tiwari.com/pdbfixing), using PDBFixer (preferred over OpenBabel).
-
-```bash
-pip install git+https://github.com/abhishektiwari/hbat.git
-```
-
-If you installed HBAT from PyPI, you can also install PDBFixer using,
-
-```bash
-pip install git+https://github.com/openmm/pdbfixer.git
-```
-
 ### Option 2: Install from Source
 
 ```bash

{hbat-2.2.13 → hbat-2.2.13.dev31}/docs/source/cli.rst

@@ -110,6 +110,35 @@ These options allow fine-tuning of the interaction detection criteria:
    - ``complete``: Analyze all interactions (default)
    - ``local``: Analyze only intra-residue interactions
 
+PDB Fixing Options
+~~~~~~~~~~~~~~~~~~~
+
+HBAT can automatically fix common PDB file issues before analysis:
+
+.. option:: --fix-pdb
+
+   Enable automatic PDB fixing to resolve common structural issues like:
+   
+   - Missing hydrogen atoms
+   - Incomplete residues
+   - Chain breaks
+   - Non-standard residues
+
+.. option:: --fix-method {pdbfixer,openbabel}
+
+   Choose the method for PDB fixing (default: pdbfixer):
+   
+   - ``pdbfixer``: Use PDBFixer (default method, recommended for protein structures)
+   - ``openbabel``: Use OpenBabel (alternative method)
+
+.. option:: --save-fixed PATH
+
+   Save the fixed PDB structure to the specified file path. Useful for:
+   
+   - Inspecting the fixed structure
+   - Reusing the fixed structure in other analyses
+   - Quality control of the fixing process
+
 Preset Management
 ~~~~~~~~~~~~~~~~~
 
@@ -187,9 +216,9 @@ Save results to different formats (auto-detected from extension):
 
 .. code-block:: bash
 
-   hbat protein.pdb -o results.txt   # Text format
-   hbat protein.pdb -o results.csv   # CSV format (single file)
-   hbat protein.pdb -o results.json  # JSON format (single file)
+   hbat input.pdb                                    # Show results in terminal
+   hbat input.pdb -o results.csv                     # Save results to CSV file
+   hbat input.pdb -o results.json                    # Save results to JSON file
 
 Multiple File Outputs
 ~~~~~~~~~~~~~~~~~~~~~~
@@ -207,6 +236,31 @@ This creates files like:
 - ``results_pi_interactions.csv``
 - ``results_cooperativity_chains.csv``
 
+PDB Fixing Examples
+~~~~~~~~~~~~~~~~~~~~
+
+Fix PDB structure automatically before analysis:
+
+.. code-block:: bash
+
+   hbat input.pdb --fix-pdb                                    # Auto-fix using PDBFixer (default)
+   hbat input.pdb --fix-pdb --fix-method=pdbfixer              # Explicitly use PDBFixer
+   hbat input.pdb --fix-pdb --fix-method=openbabel             # Use OpenBabel for fixing
+
+Save the fixed structure for inspection:
+
+.. code-block:: bash
+
+   hbat input.pdb --fix-pdb --save-fixed input_fixed.pdb       # Save fixed structure
+   hbat input.pdb --fix-pdb --save-fixed input_fixed.pdb -o results.json  # Fix, save, and analyze
+
+For structures missing hydrogen atoms:
+
+.. code-block:: bash
+
+   hbat no_hydrogens.pdb --fix-pdb -o results.csv              # Fix and analyze
+   hbat crystal.pdb --fix-pdb --fix-method=pdbfixer --verbose  # Detailed fixing process
+
 Custom Analysis Parameters
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -337,10 +391,18 @@ The CLI is designed for easy integration with shell scripts and workflow systems
 .. code-block:: bash
 
    #!/bin/bash
-   # Process multiple PDB files
+   # Process multiple PDB files with automatic fixing
    for pdb in *.pdb; do
        echo "Processing $pdb..."
-       hbat "$pdb" --json "${pdb%.pdb}_results.json" --quiet
+       hbat "$pdb" --fix-pdb --json "${pdb%.pdb}_results.json" --quiet
+   done
+   
+   # Process crystallographic structures (likely missing hydrogens)
+   for pdb in crystal_*.pdb; do
+       echo "Processing crystal structure $pdb..."
+       hbat "$pdb" --fix-pdb --fix-method=pdbfixer \
+            --save-fixed "${pdb%.pdb}_fixed.pdb" \
+            --csv "${pdb%.pdb}_analysis" --verbose
    done
 
 .. code-block:: python

{hbat-2.2.13 → hbat-2.2.13.dev31}/docs/source/index.rst

@@ -108,20 +108,6 @@ Install HBAT
 
 Run HBAT Command-Line Interface (CLI) using :code:`hbat` or launch HBAT GUI using :code:`hbat-gui`.
 
-**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
-
-   pip install git+https://github.com/openmm/pdbfixer.git
-
-
 See complete installation instructions in :doc:`installation`.
 
 Basic usage
@@ -129,8 +115,10 @@ Basic usage
 
 .. code-block:: bash
 
-   hbat input.pdb                          # Basic analysis
-   hbat input.pdb -o results.csv           # Save results to CSV file (default)
+   hbat input.pdb                                                   # Show results in terminal
+   hbat input.pdb -o results.csv                                    # Save results to CSV file (default)
+   hbat input.pdb -o results.json  --fix-pdb                        # Apply PDB fixing and Save results to JSON file
+   hbat input.pdb -o results.json  --fix-pdb  --fix-method=pdbfixer # Apply PDB fixing using PdbFixer and Save results to JSON file
 
 See full CLI options :doc:`cli`.
 

{hbat-2.2.13 → hbat-2.2.13.dev31}/docs/source/installation.rst

@@ -56,21 +56,11 @@ Run HBAT Command-Line Interface (CLI) using :code:`hbat` or launch HBAT GUI usin
 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
-
-   pip install git+https://github.com/openmm/pdbfixer.git
-
-
 From Source
 ~~~~~~~~~~~
 

{hbat-2.2.13 → hbat-2.2.13.dev31}/example_presets/high_resolution.hbat

@@ -23,7 +23,7 @@
     },
     "pdb_fixing": {
       "enabled": false,
-      "method": "openbabel",
+      "method": "pdbfixer",
       "add_hydrogens": true,
       "add_heavy_atoms": false,
       "replace_nonstandard": false,

{hbat-2.2.13 → hbat-2.2.13.dev31}/example_presets/standard_resolution.hbat

@@ -23,7 +23,7 @@
     },
     "pdb_fixing": {
       "enabled": false,
-      "method": "openbabel",
+      "method": "pdbfixer",
       "add_hydrogens": true,
       "add_heavy_atoms": false,
       "replace_nonstandard": false,

{hbat-2.2.13 → hbat-2.2.13.dev31}/example_presets/strong_interactions_only.hbat

@@ -23,7 +23,7 @@
     },
     "pdb_fixing": {
       "enabled": false,
-      "method": "openbabel",
+      "method": "pdbfixer",
       "add_hydrogens": true,
       "add_heavy_atoms": false,
       "replace_nonstandard": false,

{hbat-2.2.13 → hbat-2.2.13.dev31}/example_presets/weak_interactions_permissive.hbat

@@ -23,7 +23,7 @@
     },
     "pdb_fixing": {
       "enabled": true,
-      "method": "openbabel",
+      "method": "pdbfixer",
       "add_hydrogens": true,
       "add_heavy_atoms": false,
       "replace_nonstandard": false,

{hbat-2.2.13 → hbat-2.2.13.dev31}/hbat/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '2.2.13'
-__version_tuple__ = version_tuple = (2, 2, 13)
+__version__ = version = '2.2.13.dev31'
+__version_tuple__ = version_tuple = (2, 2, 13, 'dev31')

{hbat-2.2.13 → hbat-2.2.13.dev31}/hbat/constants/parameters.py

@@ -35,7 +35,7 @@ class ParametersDefault:
 
     # PDB structure fixing parameters
     FIX_PDB_ENABLED = True  # Enable PDB structure fixing
-    FIX_PDB_METHOD = "openbabel"  # Method: "openbabel" or "pdbfixer"
+    FIX_PDB_METHOD = "pdbfixer"  # Method: "openbabel" or "pdbfixer"
 
     # Fixing operations (explicit control)
     FIX_PDB_ADD_HYDROGENS = (

{hbat-2.2.13 → hbat-2.2.13.dev31}/pyproject.toml

@@ -33,6 +33,7 @@ dependencies = [
     "graphviz>=0.20.0",
     "Pillow>=8.0.0",
     "matplotlib>=3.3.0",
+    "pdbfixer-wheel>=1.11.0",
     "openbabel-wheel>=3.1.1.22",
     "pybel>=0.15.5",
     "mmcif-pdbx>=2.0.1",

{hbat-2.2.13 → hbat-2.2.13.dev31}/requirements.txt

@@ -14,7 +14,7 @@ graphviz>=0.20.0
 Pillow>=8.0.0
 
 # PDB structure fixing and chemical informatics
-pdbfixer @ git+https://github.com/openmm/pdbfixer.git
+pdbfixer-wheel>=1.11.0
 openbabel-wheel>=3.1.1.22
 pybel>=0.15.5