hbat 2.2.9.dev27__tar.gz → 2.2.10.dev28__tar.gz

{hbat-2.2.9.dev27 → hbat-2.2.10.dev28}/.github/workflows/test.yml

@@ -21,10 +21,10 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     
-    - name: Install GraphViz
+    - name: Install system dependencies
       run: |
         sudo apt-get update
-        sudo apt-get install -y graphviz
+        sudo apt-get install -y graphviz xvfb
     
     - name: Install dependencies
       run: |
@@ -39,11 +39,15 @@ jobs:
       run: make type-check
     
     - name: Run tests
-      run: make test
+      run: xvfb-run -a make test
+      env:
+        DISPLAY: :99
     
     - name: Run coverage
-      run: make test-coverage
+      run: xvfb-run -a make test-coverage
       if: matrix.python-version == '3.10'
+      env:
+        DISPLAY: :99
     
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v5

{hbat-2.2.9.dev27 → hbat-2.2.10.dev28}/CODE_OF_CONDUCT.md

@@ -60,8 +60,7 @@ representative at an online or offline event.
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported to the community leaders responsible for enforcement at
-``pwessel at hawaii dot edu``, ``leouieda at gmail dot com``, or
-``meghanj at hawaii dot edu``. All complaints will be reviewed and investigated
+``hbat at abhishek-tiwari dot com``. All complaints will be reviewed and investigated
 promptly and fairly.
 
 All community leaders are obligated to respect the privacy and security of the

{hbat-2.2.9.dev27 → hbat-2.2.10.dev28}/Makefile

@@ -76,7 +76,7 @@ test-coverage:
 
 test-gui:
 	@echo "Running GUI tests..."
-	pytest tests/gui/ -v -m "gui"
+	pytest tests/ -v -m "gui"
 
 test-unit:
 	@echo "Running unit tests..."

{hbat-2.2.9.dev27 → hbat-2.2.10.dev28}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: hbat
-Version: 2.2.9.dev27
+Version: 2.2.10.dev28
 Summary: Hydrogen Bond Analysis Tool for PDB structures
 Author-email: Abhishek Tiwari <hbat@abhishek-tiwari.com>
 License-Expression: MIT
@@ -93,6 +93,7 @@ A Python package to automate the analysis of potential hydrogen bonds and simila
 
 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.
 
+![HBAT GUI](https://static.abhishek-tiwari.com/hbat/hbat-window-v1.png)
 
 ## Features
 
@@ -109,6 +110,8 @@ HBAT v2  is a modern Python re-implementation of the original Perl-based tool de
 
 Please review [HBAT documentation](https://hbat.abhishek-tiwari.com/) for more details.
 
+![Cooperativity chain visualization](https://static.abhishek-tiwari.com/hbat/6rsa-pdb-chain-6.png)
+
 ### Supported Interactions
 
 1. **Hydrogen Bonds**: O-H...O, N-H...O, N-H...N, and other X-H...Y interactions

{hbat-2.2.9.dev27 → hbat-2.2.10.dev28}/README.md

@@ -25,6 +25,7 @@ A Python package to automate the analysis of potential hydrogen bonds and simila
 
 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.
 
+![HBAT GUI](https://static.abhishek-tiwari.com/hbat/hbat-window-v1.png)
 
 ## Features
 
@@ -41,6 +42,8 @@ HBAT v2  is a modern Python re-implementation of the original Perl-based tool de
 
 Please review [HBAT documentation](https://hbat.abhishek-tiwari.com/) for more details.
 
+![Cooperativity chain visualization](https://static.abhishek-tiwari.com/hbat/6rsa-pdb-chain-6.png)
+
 ### Supported Interactions
 
 1. **Hydrogen Bonds**: O-H...O, N-H...O, N-H...N, and other X-H...Y interactions

{hbat-2.2.9.dev27 → hbat-2.2.10.dev28}/docs/source/api/constants/pdb_constants.rst

@@ -63,6 +63,15 @@ Water molecule recognition patterns.
 
 .. autodata:: hbat.constants.pdb_constants.WATER_MOLECULES
 
+Classification Codes
+~~~~~~~~~~~~~~~~~~~~
+
+Single letter codes for molecular classification systems.
+
+.. autodata:: hbat.constants.pdb_constants.RESIDUE_TYPE_CODES
+.. autodata:: hbat.constants.pdb_constants.BACKBONE_SIDECHAIN_CODES
+.. autodata:: hbat.constants.pdb_constants.AROMATIC_CODES
+
 Atom Name Mapping
 ~~~~~~~~~~~~~~~~~
 

{hbat-2.2.9.dev27 → hbat-2.2.10.dev28}/docs/source/cli.rst

@@ -166,11 +166,11 @@ Basic analysis with default parameters:
 
    hbat protein.pdb
 
-Save results to a text file:
+Save results to a CSV file (default format):
 
 .. code-block:: bash
 
-   hbat protein.pdb -o results.txt
+   hbat protein.pdb -o results.csv
 
 Use custom hydrogen bond criteria:
 
@@ -182,7 +182,7 @@ Export results in multiple formats:
 
 .. code-block:: bash
 
-   hbat protein.pdb -o results.txt --json results.json --csv results.csv
+   hbat protein.pdb -o results.csv --json results.json
 
 Use a high-resolution preset:
 
@@ -236,23 +236,36 @@ The default text output includes:
 JSON Output
 ~~~~~~~~~~~
 
-The JSON format provides structured data with:
+The JSON format automatically generates separate files for each interaction type with structured data:
 
 - Metadata section with version and file information
-- Complete statistics
+- Complete statistics for each interaction type
 - Arrays of interactions with all geometric parameters
-- Atom coordinates for further processing
+- Atom coordinates and structural properties for further processing
+
+When using ``--json results.json``, HBAT creates:
+- ``results_h_bonds.json``
+- ``results_halogen_bonds.json``
+- ``results_pi_interactions.json``
+- ``results_cooperativity_chains.json``
 
 CSV Output
 ~~~~~~~~~~
 
-The CSV format includes separate sections for:
+The CSV format automatically generates separate files for each interaction type:
 
-- Hydrogen bonds with all parameters
-- Halogen bonds with geometric data
+- Hydrogen bonds with donor-acceptor properties and backbone/sidechain classification
+- Halogen bonds with geometric data and structural properties  
 - π interactions with distance and angle information
+- Cooperativity chains showing interaction networks
+
+When using ``--csv results.csv``, HBAT creates:
+- ``results_h_bonds.csv``
+- ``results_halogen_bonds.csv``
+- ``results_pi_interactions.csv``
+- ``results_cooperativity_chains.csv``
 
-Each section has appropriate column headers for easy import into spreadsheet applications.
+Each file includes comprehensive data with appropriate column headers for easy import into spreadsheet applications.
 
 Exit Codes
 ----------

{hbat-2.2.9.dev27 → hbat-2.2.10.dev28}/docs/source/index.rst

@@ -73,6 +73,10 @@ Welcome to HBAT (Hydrogen Bond Analysis Tool) documentation!
 
 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.
 
+.. image:: https://static.abhishek-tiwari.com/hbat/hbat-window-v1.png
+   :alt: HBAT GUI
+   :align: center
+
 .. toctree::
    :maxdepth: 1
    :caption: User Guide
@@ -126,7 +130,7 @@ Basic usage
 .. code-block:: bash
 
    hbat input.pdb                          # Basic analysis
-   hbat input.pdb -o results.txt           # Save results to file
+   hbat input.pdb -o results.csv           # Save results to CSV file (default)
 
 See full CLI options :doc:`cli`.
 
@@ -137,10 +141,13 @@ Features
 - **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
+- **Multiple Output Formats**: Support for CSV (default), JSON, and formatted text output with automated file generation for each interaction type
 - **GUI Interface**: User-friendly graphical interface for interactive analysis
 - **Command Line Tool**: Scriptable CLI for batch processing and automation
 
+.. image:: https://static.abhishek-tiwari.com/hbat/6rsa-pdb-chain-6.png
+   :alt: Cooperativity chain visualization
+   :align: center
 
 Cite HBAT
 ---------

{hbat-2.2.9.dev27 → hbat-2.2.10.dev28}/docs/source/quickstart.rst

@@ -14,7 +14,7 @@ See full CLI options :doc:`cli`.
 .. code-block:: bash
 
    hbat input.pdb                          # Basic analysis
-   hbat input.pdb -o results.txt           # Save results to file
+   hbat input.pdb -o results.csv           # Save results to CSV file (default)
    hbat input.pdb --hb-distance 3.0        # Custom H-bond distance cutoff
    hbat input.pdb --mode local             # Local interactions only
    hbat input.pdb --json results.json      # Export to JSON format

{hbat-2.2.9.dev27 → hbat-2.2.10.dev28}/hbat/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '2.2.9.dev27'
-__version_tuple__ = version_tuple = (2, 2, 9, 'dev27')
+__version__ = version = '2.2.10.dev28'
+__version_tuple__ = version_tuple = (2, 2, 10, 'dev28')

{hbat-2.2.9.dev27 → hbat-2.2.10.dev28}/hbat/constants/misc.py

@@ -9,11 +9,11 @@ from .app import APP_VERSION
 class GUIDefaults:
     """Default values for GUI interface."""
 
-    # Window settings
-    WINDOW_WIDTH = 1800
-    WINDOW_HEIGHT = 900
-    MIN_WINDOW_WIDTH = 1200
-    MIN_WINDOW_HEIGHT = 800
+    # Window settings - optimized for standard displays (1366x768, 1920x1080)
+    WINDOW_WIDTH = 1280
+    WINDOW_HEIGHT = 720
+    MIN_WINDOW_WIDTH = 1024
+    MIN_WINDOW_HEIGHT = 680
 
     # Layout settings
     LEFT_PANEL_WIDTH = 400  # Initial pane position

{hbat-2.2.9.dev27 → hbat-2.2.10.dev28}/hbat/constants/pdb_constants.py

@@ -792,7 +792,7 @@ Used for:
     - Ion binding site analysis
 """
 
-RESIDUE_TYPES: List[str] = ["DNA", "RNA", "PROTEIN", "LIGAND"]
+RESIDUE_TYPES: List[str] = ["DNA", "RNA", "PROTEIN", "LIGAND", "WATER"]
 """List[str]: Standard residue type classifications for molecular analysis.
 
 Classification categories for different types of molecular residues:
@@ -800,6 +800,8 @@ Classification categories for different types of molecular residues:
     - RNA: Ribonucleotide residues (A, G, C, U, I)
     - PROTEIN: Amino acid residues (20 standard amino acids and variants)
     - LIGAND: Ligands, cofactors, metals, and other heteroatom residues
+    - WATER: Water molecules and solvent
+
 
 Used for:
     - Residue type identification and classification
@@ -813,6 +815,7 @@ RESIDUE_TYPE_CODES: Dict[str, str] = {
     "DNA": "D",
     "RNA": "R",
     "PROTEIN": "P",
+    "WATER": "W",
     "LIGAND": "L",
 }
 """Dict[str, str]: Single letter codes for residue types.
@@ -821,6 +824,7 @@ Mapping of full residue type names to compact single letter codes:
     - "DNA" → "D": Deoxyribonucleotide residues
     - "RNA" → "R": Ribonucleotide residues  
     - "PROTEIN" → "P": Amino acid residues
+    - "WATER" → "W": Water molecules and solvent
     - "LIGAND" → "L": Ligands, cofactors, metals, and other heteroatom residues
 
 Used for compact representation in hydrogen bond descriptions and atom records.

{hbat-2.2.9.dev27 → hbat-2.2.10.dev28}/hbat/core/atom_classifier.py

@@ -19,6 +19,7 @@ from ..constants.pdb_constants import (
     RESIDUES_WITH_AROMATIC_RINGS,
     RING_ATOMS_FOR_RESIDUES_WITH_AROMATIC_RINGS,
     RNA_RESIDUES,
+    WATER_MOLECULES,
 )
 
 
@@ -27,7 +28,7 @@ def classify_residue_type(res_name: str) -> str:
 
     :param res_name: Three-letter residue name (e.g., 'ALA', 'DA', 'HOH')
     :type res_name: str
-    :returns: Single letter code for residue type ('P', 'D', 'R', 'L')
+    :returns: Single letter code for residue type ('P', 'D', 'R', 'W', 'L')
     :rtype: str
     """
     res_name = res_name.strip().upper()
@@ -38,6 +39,8 @@ def classify_residue_type(res_name: str) -> str:
         return RESIDUE_TYPE_CODES["DNA"]  # "D"
     elif res_name in RNA_RESIDUES:
         return RESIDUE_TYPE_CODES["RNA"]  # "R"
+    elif res_name in WATER_MOLECULES:
+        return RESIDUE_TYPE_CODES["WATER"]  # "W"
     else:
         return RESIDUE_TYPE_CODES["LIGAND"]  # "L"
 

{hbat-2.2.9.dev27 → hbat-2.2.10.dev28}/hbat/core/interactions.py

@@ -220,24 +220,24 @@ class HydrogenBond(MolecularInteraction):
     including the participating atoms, geometric parameters, and
     classification information.
 
-    :param donor: The hydrogen bond donor atom
-    :type donor: Atom
+    :param _donor: The hydrogen bond donor atom
+    :type _donor: Atom
     :param hydrogen: The hydrogen atom in the bond
     :type hydrogen: Atom
-    :param acceptor: The hydrogen bond acceptor atom
-    :type acceptor: Atom
+    :param _acceptor: The hydrogen bond acceptor atom
+    :type _acceptor: Atom
     :param distance: H...A distance in Angstroms
     :type distance: float
     :param angle: D-H...A angle in radians
     :type angle: float
-    :param donor_acceptor_distance: D...A distance in Angstroms
-    :type donor_acceptor_distance: float
+    :param _donor_acceptor_distance: D...A distance in Angstroms
+    :type _donor_acceptor_distance: float
     :param bond_type: Classification of the hydrogen bond type
     :type bond_type: str
-    :param donor_residue: Identifier for donor residue
-    :type donor_residue: str
-    :param acceptor_residue: Identifier for acceptor residue
-    :type acceptor_residue: str
+    :param _donor_residue: Identifier for donor residue
+    :type _donor_residue: str
+    :param _acceptor_residue: Identifier for acceptor residue
+    :type _acceptor_residue: str
     """
 
     def __init__(
@@ -252,6 +252,27 @@ class HydrogenBond(MolecularInteraction):
         _donor_residue: str,
         _acceptor_residue: str,
     ):
+        """Initialize a HydrogenBond object.
+
+        :param _donor: The hydrogen bond donor atom
+        :type _donor: Atom
+        :param hydrogen: The hydrogen atom in the bond
+        :type hydrogen: Atom
+        :param _acceptor: The hydrogen bond acceptor atom
+        :type _acceptor: Atom
+        :param distance: H...A distance in Angstroms
+        :type distance: float
+        :param angle: D-H...A angle in radians
+        :type angle: float
+        :param _donor_acceptor_distance: D...A distance in Angstroms
+        :type _donor_acceptor_distance: float
+        :param bond_type: Classification of the hydrogen bond type
+        :type bond_type: str
+        :param _donor_residue: Identifier for donor residue
+        :type _donor_residue: str
+        :param _acceptor_residue: Identifier for acceptor residue
+        :type _acceptor_residue: str
+        """
         self._donor = _donor
         self.hydrogen = hydrogen
         self._acceptor = _acceptor
@@ -301,7 +322,7 @@ class HydrogenBond(MolecularInteraction):
         return self._acceptor_residue
 
     def get_interaction_type(self) -> str:
-        return "hydrogen_bond"
+        return "H-Bond"
 
     def get_donor_interaction_distance(self) -> float:
         """Distance from donor to hydrogen."""
@@ -394,18 +415,18 @@ class HalogenBond(MolecularInteraction):
 
     :param halogen: The halogen atom (F, Cl, Br, I)
     :type halogen: Atom
-    :param acceptor: The electron donor/acceptor atom
-    :type acceptor: Atom
+    :param _acceptor: The electron donor/acceptor atom
+    :type _acceptor: Atom
     :param distance: X...A distance in Angstroms
     :type distance: float
     :param angle: C-X...A angle in radians
     :type angle: float
     :param bond_type: Classification of the halogen bond type
     :type bond_type: str
-    :param halogen_residue: Identifier for halogen-containing residue
-    :type halogen_residue: str
-    :param acceptor_residue: Identifier for acceptor residue
-    :type acceptor_residue: str
+    :param _halogen_residue: Identifier for halogen-containing residue
+    :type _halogen_residue: str
+    :param _acceptor_residue: Identifier for acceptor residue
+    :type _acceptor_residue: str
     """
 
     def __init__(
@@ -418,6 +439,23 @@ class HalogenBond(MolecularInteraction):
         _halogen_residue: str,
         _acceptor_residue: str,
     ):
+        """Initialize a HalogenBond object.
+
+        :param halogen: The halogen atom (F, Cl, Br, I)
+        :type halogen: Atom
+        :param _acceptor: The electron donor/acceptor atom
+        :type _acceptor: Atom
+        :param distance: X...A distance in Angstroms
+        :type distance: float
+        :param angle: C-X...A angle in radians
+        :type angle: float
+        :param bond_type: Classification of the halogen bond type
+        :type bond_type: str
+        :param _halogen_residue: Identifier for halogen-containing residue
+        :type _halogen_residue: str
+        :param _acceptor_residue: Identifier for acceptor residue
+        :type _acceptor_residue: str
+        """
         self.halogen = halogen
         self._acceptor = _acceptor
         self._distance = distance
@@ -426,6 +464,9 @@ class HalogenBond(MolecularInteraction):
         self._halogen_residue = _halogen_residue
         self._acceptor_residue = _acceptor_residue
 
+        # Generate donor-acceptor property description
+        self._donor_acceptor_properties = self._generate_donor_acceptor_description()
+
     # Backward compatibility properties
     @property
     def distance(self) -> float:
@@ -467,7 +508,7 @@ class HalogenBond(MolecularInteraction):
         return self._acceptor_residue
 
     def get_interaction_type(self) -> str:
-        return "halogen_bond"
+        return "X-Bond"
 
     def get_donor_interaction_distance(self) -> float:
         """Distance from donor to interaction point (0 for halogen bonds)."""
@@ -494,11 +535,61 @@ class HalogenBond(MolecularInteraction):
         # by ensuring the halogen is bonded to carbon
         return True  # Assuming validation was done during creation
 
+    def _generate_donor_acceptor_description(self) -> str:
+        """Generate donor-acceptor property description string.
+
+        Describes the halogen bond in terms of:
+        - Donor properties: residue type, backbone/sidechain, aromatic (halogen donor)
+        - Acceptor properties: residue type, backbone/sidechain, aromatic
+
+        Format: "donor_props-acceptor_props" (e.g., "PSN-LBN", "LSN-PSA")
+
+        :returns: Property description string
+        :rtype: str
+        """
+        # Get halogen (donor) properties
+        donor_residue_type = getattr(self.halogen, "residue_type", "L")
+        donor_backbone_sidechain = getattr(self.halogen, "backbone_sidechain", "S")
+        donor_aromatic = getattr(self.halogen, "aromatic", "N")
+
+        # Get acceptor properties
+        acceptor_residue_type = getattr(self._acceptor, "residue_type", "L")
+        acceptor_backbone_sidechain = getattr(self._acceptor, "backbone_sidechain", "S")
+        acceptor_aromatic = getattr(self._acceptor, "aromatic", "N")
+
+        # Build property strings
+        donor_props = f"{donor_residue_type}{donor_backbone_sidechain}{donor_aromatic}"
+        acceptor_props = (
+            f"{acceptor_residue_type}{acceptor_backbone_sidechain}{acceptor_aromatic}"
+        )
+
+        return f"{donor_props}-{acceptor_props}"
+
+    @property
+    def donor_acceptor_properties(self) -> str:
+        """Get the donor-acceptor property description.
+
+        :returns: Property description string
+        :rtype: str
+        """
+        return self._donor_acceptor_properties
+
+    def get_backbone_sidechain_interaction(self) -> str:
+        """Get simplified backbone/sidechain interaction description.
+
+        :returns: Interaction type (B-B, B-S, S-B, S-S)
+        :rtype: str
+        """
+        donor_bs = getattr(self.halogen, "backbone_sidechain", "S")
+        acceptor_bs = getattr(self._acceptor, "backbone_sidechain", "S")
+        return f"{donor_bs}-{acceptor_bs}"
+
     def __str__(self) -> str:
         return (
             f"X-Bond: {self._halogen_residue}({self.halogen.name}) - "
             f"{self._acceptor_residue}({self._acceptor.name}) "
-            f"[{self.distance:.2f}Å, {math.degrees(self.angle):.1f}°]"
+            f"[{self.distance:.2f}Å, {math.degrees(self.angle):.1f}°] "
+            f"[{self.get_backbone_sidechain_interaction()}] [{self.donor_acceptor_properties}]"
         )
 
 
@@ -508,8 +599,8 @@ class PiInteraction(MolecularInteraction):
     This class stores information about a detected X-H...π interaction,
     where a hydrogen bond donor interacts with an aromatic π system.
 
-    :param donor: The hydrogen bond donor atom
-    :type donor: Atom
+    :param _donor: The hydrogen bond donor atom
+    :type _donor: Atom
     :param hydrogen: The hydrogen atom
     :type hydrogen: Atom
     :param pi_center: Center of the aromatic π system
@@ -518,10 +609,10 @@ class PiInteraction(MolecularInteraction):
     :type distance: float
     :param angle: D-H...π angle in radians
     :type angle: float
-    :param donor_residue: Identifier for donor residue
-    :type donor_residue: str
-    :param pi_residue: Identifier for π-containing residue
-    :type pi_residue: str
+    :param _donor_residue: Identifier for donor residue
+    :type _donor_residue: str
+    :param _pi_residue: Identifier for π-containing residue
+    :type _pi_residue: str
     """
 
     def __init__(
@@ -534,6 +625,23 @@ class PiInteraction(MolecularInteraction):
         _donor_residue: str,
         _pi_residue: str,
     ):
+        """Initialize a PiInteraction object.
+
+        :param _donor: The hydrogen bond donor atom
+        :type _donor: Atom
+        :param hydrogen: The hydrogen atom
+        :type hydrogen: Atom
+        :param pi_center: Center of the aromatic π system
+        :type pi_center: NPVec3D
+        :param distance: H...π distance in Angstroms
+        :type distance: float
+        :param angle: D-H...π angle in radians
+        :type angle: float
+        :param _donor_residue: Identifier for donor residue
+        :type _donor_residue: str
+        :param _pi_residue: Identifier for π-containing residue
+        :type _pi_residue: str
+        """
         self._donor = _donor
         self.hydrogen = hydrogen
         self.pi_center = pi_center
@@ -581,7 +689,7 @@ class PiInteraction(MolecularInteraction):
         return self._pi_residue
 
     def get_interaction_type(self) -> str:
-        return "pi_interaction"
+        return "π–Inter"
 
     def get_donor_interaction_distance(self) -> float:
         """Distance from donor to hydrogen."""
@@ -716,6 +824,15 @@ class CooperativityChain(MolecularInteraction):
         chain_length: int,
         chain_type: str,
     ):
+        """Initialize a CooperativityChain object.
+
+        :param interactions: List of interactions in the chain
+        :type interactions: List[Union[HydrogenBond, HalogenBond, PiInteraction]]
+        :param chain_length: Number of interactions in the chain
+        :type chain_length: int
+        :param chain_type: Description of the interaction types in the chain
+        :type chain_type: str
+        """
         self.interactions = interactions
         self.chain_length = chain_length
         self.chain_type = chain_type  # e.g., "H-Bond -> X-Bond -> π-Int"
@@ -887,8 +1004,8 @@ class CooperativityChain(MolecularInteraction):
     def _get_interaction_symbol(self, interaction_type: str) -> str:
         """Get display symbol for interaction type."""
         symbols = {
-            "hydrogen_bond": "->",
-            "halogen_bond": "=X=>",
-            "pi_interaction": "~π~>",
+            "H-Bond": "->",
+            "X-Bond": "=X=>",
+            "π–Inter": "~π~>",
         }
         return symbols.get(interaction_type, "->")

{hbat-2.2.9.dev27 → hbat-2.2.10.dev28}/hbat/core/np_analyzer.py

@@ -77,7 +77,18 @@ class NPMolecularInteractionAnalyzer:
         self.progress_callback: Optional[Callable[[str], None]] = None
 
     def analyze_file(self, pdb_file: str) -> bool:
-        """Analyze a PDB file for molecular interactions."""
+        """Analyze a PDB file for molecular interactions.
+
+        Performs comprehensive analysis of hydrogen bonds, halogen bonds, π interactions,
+        and cooperativity chains in the provided PDB structure. Optionally applies PDB
+        fixing to add missing atoms if enabled in parameters.
+
+        :param pdb_file: Path to PDB file to analyze
+        :type pdb_file: str
+        :returns: True if analysis completed successfully, False if parsing failed
+        :rtype: bool
+        :raises Exception: If PDB fixing fails when enabled
+        """
         self._analysis_start_time = time.time()
         self._pdb_fixing_info = {}
 

{hbat-2.2.9.dev27 → hbat-2.2.10.dev28}/hbat/core/structure.py

@@ -176,6 +176,12 @@ class Atom:
     :type charge: str
     :param record_type: PDB record type (ATOM or HETATM)
     :type record_type: str
+    :param residue_type: Residue type classification (P=Protein, D=DNA, R=RNA, L=Ligand)
+    :type residue_type: str
+    :param backbone_sidechain: Backbone/sidechain classification (B=Backbone, S=Sidechain)
+    :type backbone_sidechain: str
+    :param aromatic: Aromatic classification (A=Aromatic, N=Non-aromatic)
+    :type aromatic: str
     """
 
     def __init__(
@@ -225,6 +231,12 @@ class Atom:
         :type charge: str
         :param record_type: PDB record type (ATOM or HETATM)
         :type record_type: str
+        :param residue_type: Residue type classification (P=Protein, D=DNA, R=RNA, L=Ligand)
+        :type residue_type: str
+        :param backbone_sidechain: Backbone/sidechain classification (B=Backbone, S=Sidechain)
+        :type backbone_sidechain: str
+        :param aromatic: Aromatic classification (A=Aromatic, N=Non-aromatic)
+        :type aromatic: str
         """
         self.serial = serial
         self.name = name

{hbat-2.2.9.dev27 → hbat-2.2.10.dev28}/hbat/gui/chain_visualization.py

@@ -77,7 +77,7 @@ class ChainVisualizationWindow:
         """Create the visualization window."""
         self.viz_window = tk.Toplevel(self.parent)
         self.viz_window.title(f"Cooperativity Chain Visualization - {self.chain_id}")
-        self.viz_window.geometry("1000x1000")
+        self.viz_window.geometry("900x700")
 
         # Create main container frames
         main_frame = ttk.Frame(self.viz_window)

{hbat-2.2.9.dev27 → hbat-2.2.10.dev28}/hbat/gui/export_manager.py

@@ -45,6 +45,12 @@ EXPORT_FORMATS = {
         "description": "Encapsulated PostScript",
         "filetypes": [("EPS files", "*.eps")],
     },
+    "dot": {
+        "name": "DOT Source",
+        "extension": ".dot",
+        "description": "GraphViz DOT language source file",
+        "filetypes": [("DOT files", "*.dot")],
+    },
 }