hbat 2.2.13.dev31__tar.gz → 2.2.14__tar.gz

{hbat-2.2.13.dev31 → hbat-2.2.14}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: hbat
-Version: 2.2.13.dev31
+Version: 2.2.14
 Summary: Hydrogen Bond Analysis Tool for PDB structures
 Author-email: Abhishek Tiwari <hbat@abhishek-tiwari.com>
 License-Expression: MIT

{hbat-2.2.13.dev31 → hbat-2.2.14}/docs/source/parameters.rst

@@ -5,7 +5,7 @@ This document provides comprehensive explanations of all analysis parameters use
 
 .. contents:: Table of Contents
    :local:
-   :depth: 2
+   :depth: 1
 
 Overview
 --------
@@ -321,7 +321,7 @@ fix_pdb_enabled (Default: True)
 - **Disable for**: Pre-processed structures, performance-critical workflows
 - **Default disabled**: Preserves original analysis behavior
 
-fix_pdb_method (Default: "openbabel")
+fix_pdb_method (Default: "pdbfixer")
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 **Definition**: Choose the method for structure fixing operations.
@@ -331,33 +331,7 @@ fix_pdb_method (Default: "openbabel")
 - **"openbabel"**: Fast hydrogen addition, good for routine analysis
 - **"pdbfixer"**: Comprehensive fixing with advanced capabilities
 
-**Method comparison**:
-
-.. list-table::
-   :header-rows: 1
-   :widths: 25 35 40
-
-   * - Capability
-     - OpenBabel
-     - PDBFixer
-   * - Add hydrogens
-     - ✓ Fast and reliable
-     - ✓ pH-dependent protonation
-   * - Add heavy atoms
-     - ✗ Not supported
-     - ✓ Complete missing atoms
-   * - Convert residues
-     - ✗ Limited
-     - ✓ Comprehensive database
-   * - Remove heterogens
-     - ✗ Not supported
-     - ✓ Selective removal
-   * - Speed
-     - Very fast
-     - Moderate
-   * - Dependencies
-     - Lightweight
-     - Requires OpenMM
+See :doc:`pdbfixing` for more details on each method.
 
 fix_pdb_add_hydrogens (Default: True)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -472,39 +446,10 @@ fix_pdb_keep_water (Default: True, PDBFixer only)
 - **With water**: More comprehensive interaction networks, water-mediated bonds
 - **Without water**: Direct protein interactions only, simplified patterns
 
-Advanced PDB Fixing Parameters
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-pH Parameter (PDBFixer method)
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-**Definition**: pH value for determining protonation states (default: 7.0).
-
-**Affected residues**:
-
-- **Histidine**: Protonation of ND1/NE2 based on pH
-- **Aspartic acid**: Protonation state of carboxyl group
-- **Glutamic acid**: Protonation state of carboxyl group
-- **Lysine**: Amino group protonation
-- **Arginine**: Guanidinium group state
-- **Cysteine**: Potential disulfide bond formation
-
-**pH ranges and effects**:
-
-- **Low pH (< 4)**: More protonated states, positively charged
-- **Physiological pH (7.0)**: Standard protonation patterns
-- **High pH (> 10)**: More deprotonated states, negatively charged
-
-**Setting guidelines**:
-
-- **pH 7.0**: Standard for most protein analyses
-- **pH 6.0**: Slightly acidic conditions (some enzymes)
-- **pH 8.0**: Slightly basic conditions (alkaline phosphatases)
-
 General Analysis Parameters
 ----------------------------
 
-Covalent Bond Detection Factor (Default: 0.85)
+Covalent Bond Detection Factor (Default: 0.6)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 **Definition**: Multiplier applied to Van der Waals radii sum for covalent bond detection.
@@ -525,8 +470,8 @@ Covalent Bond Detection Factor (Default: 0.85)
 
 **Typical values**:
 
-- **0.70**: Very strict covalent bond detection
-- **0.85** (default): Standard bond detection based on typical covalent/VdW ratio
+- **0.55**: Strict covalent bond detection
+- **0.60** (default): Standard bond detection based on typical covalent/VdW ratio
 - **1.00**: Maximum permissive (uses full Van der Waals radii sum)
 
 Analysis Mode

hbat-2.2.14/docs/source/pdbfixing.rst

@@ -0,0 +1,172 @@
+PDB Structure Fixing
+====================
+
+This document provides details about HBAT's PDB fixing capabilities, which can automatically enhance protein structures by adding missing atoms, converting residues, and cleaning up structural issues.
+
+.. contents:: Table of Contents
+   :local:
+   :depth: 1
+
+Overview
+--------
+
+HBAT includes integrated PDB structure fixing capabilities that can significantly improve the quality of structural analysis by:
+
+- Adding missing hydrogen atoms using OpenBabel or PDBFixer
+- Adding missing heavy atoms using PDBFixer  
+- Converting non-standard residues to standard equivalents
+- Removing unwanted heterogens while optionally keeping water molecules
+- Improving structure quality for more accurate interaction analysis
+
+These capabilities are particularly valuable when working with:
+
+- Crystal structures missing hydrogen atoms
+- Low-resolution structures with incomplete side chains
+- NMR structures requiring standardization
+- Structures containing non-standard amino acid residues
+- Structures with unwanted ligands or contaminants
+
+Why PDB Fixing is Important
+---------------------------
+
+Most PDB structures from X-ray crystallography lack hydrogen atoms because they are too small to be reliably determined at typical resolutions. Since hydrogen bonds are critical for:
+
+- Protein stability: Secondary and tertiary structure maintenance
+- Enzyme catalysis: Active site interactions and mechanism
+- Protein-protein interactions: Interface stabilization
+- Ligand binding: Drug-target interactions
+
+Accurate hydrogen placement is essential for meaningful interaction analysis.
+
+Supported Methods
+-----------------
+
+HBAT supports two powerful methods for structure enhancement: PDBFixer and OpenBabel.
+
+.. list-table::
+   :header-rows: 1
+   :widths: 25 35 40
+
+   * - Capability
+     - OpenBabel
+     - PDBFixer
+   * - Add hydrogens
+     - ✓ Fast and reliable
+     - ✓ pH-dependent protonation
+   * - Add heavy atoms
+     - ✗ Not supported
+     - ✓ Complete missing atoms
+   * - Convert residues
+     - ✗ Limited
+     - ✓ Comprehensive database
+   * - Remove heterogens
+     - ✗ Not supported
+     - ✓ Selective removal
+   * - Speed
+     - Very fast
+     - Moderate
+   * - Dependencies
+     - Lightweight
+     - Requires OpenMM
+   * - Documentation
+     - `OpenBabel documentation <https://open-babel.readthedocs.io/en/latest/Command-line_tools/babel.html>`_
+     - `PDBFixer Documentation <https://htmlpreview.github.io/?https://github.com/abhishektiwari/pdbfixer-wheel/blob/master/Manual.html>`_
+
+PDB Fixing Parameters
+---------------------
+
+HBAT provides comprehensive control over structure fixing through various parameters:
+
+Core Parameters
+~~~~~~~~~~~~~~~
+
+.. list-table::
+   :header-rows: 1
+   :widths: 25 15 10 50
+
+   * - Parameter
+     - Default
+     - Type
+     - Description
+   * - ``fix_pdb_enabled``
+     - True
+     - Boolean
+     - Enable/disable PDB structure fixing
+   * - ``fix_pdb_method``
+     - "pdbfixer"
+     - String
+     - Method to use: "openbabel" or "pdbfixer"
+   * - ``fix_pdb_add_hydrogens``
+     - True
+     - Boolean
+     - Add missing hydrogen atoms
+   * - ``fix_pdb_add_heavy_atoms``
+     - False
+     - Boolean
+     - Add missing heavy atoms (PDBFixer only)
+   * - ``fix_pdb_replace_nonstandard``
+     - False
+     - Boolean
+     - Convert non-standard residues (PDBFixer only)
+   * - ``fix_pdb_remove_heterogens``
+     - False
+     - Boolean
+     - Remove unwanted heterogens (PDBFixer only)
+   * - ``fix_pdb_keep_water``
+     - True
+     - Boolean
+     - Keep water molecules when removing heterogens
+
+
+.. image:: https://static.abhishek-tiwari.com/hbat/pdb-fixing-ui-v1.png
+   :width: 600px
+   :align: center
+   :alt: PDB Fixing Parameters in HBAT GUI
+
+Advanced Parameters
+~~~~~~~~~~~~~~~~~~~
+
+For PDBFixer, additional options are available but there are not supported by HBAT yet.
+
+.. list-table::
+   :header-rows: 1
+   :widths: 25 15 60
+
+   * - Parameter
+     - Default
+     - Description
+   * - ``pH``
+     - 7.0
+     - pH value for protonation state determination
+   * - ``model_residues``
+     - False
+     - Add missing residues to complete chains
+   * - ``keep_ids``
+     - True
+     - Preserve original atom numbering
+
+
+References and Further Reading
+------------------------------
+
+OpenBabel
+~~~~~~~~~
+
+- O'Boyle, N.M. et al. "Open Babel: An open chemical toolbox" J. Cheminform. 3, 33 (2011)
+- OpenBabel Documentation: http://openbabel.org/docs/
+
+PDBFixer
+~~~~~~~~
+
+- Eastman, P. et al. "OpenMM 4: A Reusable, Extensible, Hardware Independent Library" J. Chem. Theory Comput. 9, 461-469 (2013)
+- PDBFixer Documentation: https://github.com/openmm/pdbfixer
+
+Structure Preparation
+~~~~~~~~~~~~~~~~~~~~~
+
+- Madhavi Sastry, G. et al. "Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments" J. Comput. Aided Mol. Des. 27, 221-234 (2013)
+- Shelley, J.C. et al. "A versatile approach for assigning partial charges and valence electron densities in proteins" J. Comput. Chem. 28, 1145-1152 (2007)
+
+----
+
+For questions about PDB fixing functionality or specific use cases, please refer to the HBAT documentation or open an issue on the GitHub repository.

{hbat-2.2.13.dev31 → hbat-2.2.14}/hbat/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '2.2.13.dev31'
-__version_tuple__ = version_tuple = (2, 2, 13, 'dev31')
+__version__ = version = '2.2.14'
+__version_tuple__ = version_tuple = (2, 2, 14)

{hbat-2.2.13.dev31 → hbat-2.2.14}/hbat/gui/parameter_panel.py

@@ -846,7 +846,7 @@ class ParameterPanel:
         if "pdb_fixing" in params:
             pdb_fix = params["pdb_fixing"]
             self.fix_pdb_enabled.set(pdb_fix.get("enabled", False))
-            self.fix_pdb_method.set(pdb_fix.get("method", "openbabel"))
+            self.fix_pdb_method.set(pdb_fix.get("method", "pdbfixer"))
             self.fix_pdb_add_hydrogens.set(pdb_fix.get("add_hydrogens", True))
             self.fix_pdb_add_heavy_atoms.set(pdb_fix.get("add_heavy_atoms", False))
             self.fix_pdb_replace_nonstandard.set(

{hbat-2.2.13.dev31 → hbat-2.2.14}/tests/integration/test_molecular_validation.py

@@ -176,7 +176,12 @@ class TestMolecularValidation:
     
     def test_reference_structure_consistency(self, sample_pdb_file):
         """Test consistency of results for reference structure (6RSA)."""
-        analyzer = MolecularInteractionAnalyzer()
+        from hbat.core.analysis import AnalysisParameters
+        
+        # Create parameters with PDB fixing disabled for consistent results
+        params = AnalysisParameters(fix_pdb_enabled=False)
+        
+        analyzer = MolecularInteractionAnalyzer(parameters=params)
         
         # Run analysis twice to test consistency
         success1 = analyzer.analyze_file(sample_pdb_file)
@@ -184,7 +189,7 @@ class TestMolecularValidation:
         stats1 = analyzer.get_summary()
         
         # Create new analyzer for second run
-        analyzer2 = MolecularInteractionAnalyzer()
+        analyzer2 = MolecularInteractionAnalyzer(parameters=params)
         success2 = analyzer2.analyze_file(sample_pdb_file)
         assert success2, "Second analysis should succeed"
         stats2 = analyzer2.get_summary()