Presets Management#

HBAT provides parameter presets for common analysis scenarios. These presets optimize interaction detection parameters for different structure types and analysis goals.

Overview #

Parameter presets allow you to quickly apply optimized settings for specific use cases without manually adjusting individual parameters. HBAT includes built-in example presets and supports creating custom presets for your specific analysis needs.

Available Example Presets #

HBAT includes several predefined presets in the example_presets/ directory:

Preset File	Description	Use Case
high_resolution.hbat	Strict criteria for high-quality structures	X-ray structures with excellent resolution (< 1.5Å)
standard_resolution.hbat	Default HBAT parameters	Most protein crystal structures (1.5-2.5Å)
low_resolution.hbat	More permissive criteria	Lower resolution structures (> 2.5Å)
nmr_structures.hbat	Accounts for structural flexibility	Solution NMR structures
strong_interactions_only.hbat	Very strict criteria	Focus on the strongest interactions
drug_design_strict.hbat	Optimized for protein-ligand analysis	Drug discovery applications
membrane_proteins.hbat	Adapted for membrane environments	Transmembrane proteins
weak_interactions_permissive.hbat	Captures weak but significant interactions	Comprehensive interaction analysis

Preset Management in GUI #

HBAT’s GUI provides preset management through the Settings → Manage Presets menu option.

Accessing Preset Manager#

Open HBAT GUI
Navigate to Settings menu
Select Manage Presets
Preset Manager dialog will open

Loading Presets#

To load an example preset:

Open Preset Manager (Settings → Manage Presets → Load Preset)
In the preset list, select your desired preset
Click Load Preset button
The parameters will be applied to your current analysis settings

Saving Custom Presets#

To save your current parameters as a preset:

Configure your desired parameters in the Geometry Cutoffs dialog
Open Preset Manager (Settings → Manage Presets → Save Preset)
Enter name and description for your preset
Click Save Preset button

Note: Built-in example presets cannot be deleted, only custom presets can be removed.

Command Line Usage #

Using Presets from CLI#

# List all available presets
hbat --list-presets

# Use a built-in preset
hbat protein.pdb --preset standard_resolution
hbat protein.pdb --preset drug_design_strict
hbat protein.pdb --preset high_resolution

# Use preset with parameter overrides
hbat protein.pdb --preset standard_resolution --hb-distance 3.2
hbat protein.pdb --preset nmr_structures --whb-angle 140

# Use custom preset file (full path)
hbat protein.pdb --preset /path/to/my_custom.hbat

# Use preset from current directory
hbat protein.pdb --preset my_custom.hbat

Preset Resolution Order#

When using --preset, HBAT searches for presets in this order:

Absolute path: If the preset name is an absolute path and exists, use it directly
Relative path: If the preset name is a relative path and exists, use it from current directory
Example presets: Look for the preset in the example_presets/ directory (with or without .hbat extension)
Custom presets: Search in user’s custom preset directory
Error: If not found, display an error and list available presets

Parameter Override Behavior#

When using --preset, the preset parameters are loaded first
Any additional CLI parameters will override the corresponding preset values
Only explicitly provided CLI parameters override preset values (not defaults)

# Example: Use standard preset but with stricter hydrogen bond criteria
hbat protein.pdb --preset standard_resolution --hb-distance 2.8 --hb-angle 130

Preset File Format #

HBAT presets are saved as JSON files with the following structure:

{
  "format_version": "1.0",
  "application": "HBAT",
  "created": "2024-01-15T10:30:00.000000",
  "description": "Custom preset description",
  "parameters": {
    "hydrogen_bonds": {
      "h_a_distance_cutoff": 2.5,
      "dha_angle_cutoff": 120.0,
      "d_a_distance_cutoff": 3.5
    },
    "weak_hydrogen_bonds": {
      "h_a_distance_cutoff": 3.6,
      "dha_angle_cutoff": 150.0,
      "d_a_distance_cutoff": 3.5
    },
    "halogen_bonds": {
      "x_a_distance_cutoff": 3.9,
      "dxa_angle_cutoff": 150.0
    },
    "pi_interactions": {
      "h_pi_distance_cutoff": 3.5,
      "dh_pi_angle_cutoff": 110.0,
      "ccl_pi_distance_cutoff": 3.5,
      "ccl_pi_angle_cutoff": 145.0,
      "cbr_pi_distance_cutoff": 3.5,
      "cbr_pi_angle_cutoff": 155.0,
      "ci_pi_distance_cutoff": 3.6,
      "ci_pi_angle_cutoff": 165.0,
      "ch_pi_distance_cutoff": 3.5,
      "ch_pi_angle_cutoff": 110.0,
      "nh_pi_distance_cutoff": 3.2,
      "nh_pi_angle_cutoff": 115.0,
      "oh_pi_distance_cutoff": 3.0,
      "oh_pi_angle_cutoff": 115.0,
      "sh_pi_distance_cutoff": 3.8,
      "sh_pi_angle_cutoff": 105.0
    },
    "general": {
      "covalent_cutoff_factor": 0.85,
      "analysis_mode": "complete"
    },
    "pdb_fixing": {
      "enabled": true,
      "method": "pdbfixer",
      "add_hydrogens": true,
      "add_heavy_atoms": false,
      "replace_nonstandard": false,
      "remove_heterogens": false,
      "keep_water": true
    }
  }
}

Preset Storage Locations #

Example Presets (built-in):

Located in example_presets/ folder within the HBAT installation
Read-only preset files optimized for common scenarios
Cannot be modified or deleted

Custom Presets (user-created):

Windows: %USERPROFILE%\.hbat\presets\
macOS/Linux: ~/.hbat/presets/
Created when you save custom parameter configurations
Can be modified, renamed, or deleted

Creating Effective Custom Presets #

Tips for Custom Preset Creation#

Name your presets descriptively:

Use clear, specific names (e.g., “my_drug_screening”, “tight_hbonds_only”)
Avoid generic names like “preset1” or “test”

Document your parameters:

Include meaningful descriptions in the preset file
Note the intended use case and rationale for parameter choices

Test your presets:

Validate preset performance on known test cases
Compare results with standard presets to ensure expected behavior

Consider parameter interactions:

Ensure distance and angle cutoffs are compatible
Test edge cases where parameters might conflict

Common Use Cases for Custom Presets#

Specialized Analysis:

{
  "description": "Ultra-strict preset for high-confidence interactions only",
  "parameters": {
    "hydrogen_bonds": {
      "h_a_distance_cutoff": 2.2,
      "dha_angle_cutoff": 140.0,
      "d_a_distance_cutoff": 3.2
    }
  }
}

Permissive Screening:

{
  "description": "Permissive preset for comprehensive interaction screening",
  "parameters": {
    "hydrogen_bonds": {
      "h_a_distance_cutoff": 3.0,
      "dha_angle_cutoff": 110.0,
      "d_a_distance_cutoff": 4.0
    },
    "weak_hydrogen_bonds": {
      "h_a_distance_cutoff": 4.0,
      "dha_angle_cutoff": 140.0
    }
  }
}

Method-Specific Presets:

Create presets tailored to your specific research methodology, instrument capabilities, or analysis pipeline requirements.

Troubleshooting #

Common Issues#

Preset not found:

Check preset name spelling
Verify preset file exists in expected location
Use --list-presets to see available options

Invalid preset format:

Ensure JSON syntax is correct
Verify all required fields are present
Check parameter value ranges

Permission errors:

Ensure write permissions to custom preset directory
Check file system permissions for preset files

Parameter conflicts:

Verify parameter combinations are logical
Test preset with known structures before production use

For questions about preset creation or troubleshooting preset issues, please refer to the HBAT documentation or open an issue on the GitHub repository.

Presets Management

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