Calculate Grid Box based on reference ligand

python scripts/main.py --receptor protein.pdb --reference-ligand ligand.pdb --software vina

Manually specify Box parameters

python scripts/main.py --receptor protein.pdb --center-x 10.5 --center-y -5.2 --center-z 20.1 --size-x 20 --size-y 20 --size-z 20 --software vina


### As Python Module

```python
from scripts.main import DockingConfigurator

config = DockingConfigurator()

# Calculate box from receptor and active site
config.from_active_site("protein.pdb", ["A:120", "A:145", "A:189"])
config.write_vina_config("config.txt", exhaustiveness=32)

# Calculate box from receptor and reference ligand
config.from_reference_ligand("protein.pdb", "ligand.pdb", padding=5.0)
config.write_autodock4_gpf("protein.gpf", spacing=0.375)

Parameter Description

Command Line Parameters

Parameter	Description	Required
`--receptor`	Receptor protein PDB file path	Yes
`--software`	Docking software type (vina/autodock4)	Yes
`--active-site-residues`	Active site residue list, format: "chain:residue_number"	No
`--reference-ligand`	Reference ligand PDB/MOL file	No
`--center-x/y/z`	Grid Box center coordinates	No
`--size-x/y/z`	Grid Box dimensions (Å)	No
`--spacing`	Grid spacing (AutoDock4 only)	No (default 0.375)
`--exhaustiveness`	Search exhaustiveness (Vina only)	No (default 32)
`--output`	Output file path	No

Output

AutoDock Vina: Generates config.txt configuration file
AutoDock4: Generates .gpf (Grid Parameter File) and corresponding macromolecule files

Dependencies

Python 3.8+
numpy

Examples

# Example 1: Using active site residues
python scripts/main.py --receptor 1abc_receptor.pdb --active-site-residues "A:45,A:92,A:156" --software vina --output vina_config.txt

# Example 2: Using reference ligand with custom Box size
python scripts/main.py --receptor kinase.pdb --reference-ligand ATP.pdb --software vina --size-x 25 --size-y 25 --size-z 25

# Example 3: AutoDock4 configuration
python scripts/main.py --receptor protein.pdb --active-site-residues "A:100" --software autodock4 --spacing 0.375 --output protein.gpf

Notes

Input PDB files should have water molecules and heteroatoms removed (unless needed)
It is recommended to protonate and calculate charges for the receptor (using AutoDock Tools, etc.)
Grid Box size should be sufficient to cover ligand conformational space, typically 20-30Å
Active site residues should include catalytic residues and key binding residues

Risk Assessment

Risk Indicator	Assessment	Level
Code Execution	Python/R scripts executed locally	Medium
Network Access	No external API calls	Low
File System Access	Read input files, write output files	Medium
Instruction Tampering	Standard prompt guidelines	Low
Data Exposure	Output files saved to workspace	Low

Security Checklist

No hardcoded credentials or API keys
No unauthorized file system access (../)
Output does not expose sensitive information
Prompt injection protections in place
Input file paths validated (no ../ traversal)
Output directory restricted to workspace
Script execution in sandboxed environment
Error messages sanitized (no stack traces exposed)
Dependencies audited

Prerequisites

No additional Python packages required.

Evaluation Criteria

Success Metrics

Successfully executes main functionality
Output meets quality standards
Handles edge cases gracefully
Performance is acceptable

Test Cases

Basic Functionality: Standard input → Expected output
Edge Case: Invalid input → Graceful error handling
Performance: Large dataset → Acceptable processing time

Lifecycle Status

Current Stage: Draft
Next Review Date: 2026-03-06
Known Issues: None
Planned Improvements:
- Performance optimization
- Additional feature support

protein-docking-configurator

Protein Docking Configurator

Features

Usage

As Command Line Tool