gRNAde MCP Server

#!/usr/bin/env python3 """ Use Case 3: RNA Secondary Structure Analysis - Minimal Version This script provides basic RNA secondary structure analysis including: - Secondary structure prediction using EternaFold - Dot-bracket notation parsing and validation - Basic structure statistics Usage: python examples/use_case_3_structure_analysis_minimal.py --sequence "GGGGAAAACCCC" --predict --output analysis_results.json Dependencies: - All gRNAde dependencies """ import argparse import json import os import numpy as np from datetime import datetime from typing import Optional, Dict, List, Tuple, Union # gRNAde imports import sys sys.path.append('repo/geometric-rna-design') try: from src.data.sec_struct_utils import ( predict_sec_struct, pdb_to_sec_struct, dotbracket_to_adjacency, dotbracket_to_paired ) except ImportError as e: print(f"Error importing gRNAde modules: {e}") print("Please make sure you're running this from the MCP root directory") exit(1) def validate_dotbracket(structure: str) -> Tuple[bool, str]: """ Simple dot-bracket validation function. """ try: stack = [] for char in structure: if char == '(': stack.append(char) elif char == ')': if not stack: return False, "Unmatched closing parenthesis" stack.pop() elif char not in '.()[]{}': return False, f"Invalid character: {char}" if stack: return False, "Unmatched opening parenthesis" return True, "Valid" except Exception as e: return False, f"Validation error: {e}" def get_paired_positions(structure: str) -> List[Tuple[int, int]]: """ Get paired positions from dot-bracket notation. """ paired_positions = [] stack = [] for i, char in enumerate(structure): if char == '(': stack.append(i) elif char == ')': if stack: j = stack.pop() paired_positions.append((j, i)) return paired_positions def get_pseudoknot_order(structure: str) -> int: """ Determine pseudoknot order (simplified version). """ # This is a simplified implementation # Real pseudoknot analysis would be more complex if '[' in structure and ']' in structure: return 1 return 0 def analyze_structure_properties(structure: str) -> Dict: """ Analyze basic properties of a secondary structure. """ paired_positions = get_paired_positions(structure) unpaired_count = structure.count('.') paired_count = len(structure) - unpaired_count return { "length": len(structure), "paired_positions": len(paired_positions), "unpaired_positions": unpaired_count, "pairing_percentage": paired_count / len(structure) if len(structure) > 0 else 0, "total_base_pairs": len(paired_positions), "has_pseudoknots": '[' in structure or ']' in structure, "pseudoknot_order": get_pseudoknot_order(structure) } def analyze_rna_structure( sequence: Optional[str] = None, pdb_file: Optional[str] = None, secondary_structure: Optional[str] = None, predict_structure: bool = True, include_pseudoknots: bool = True, visualize: bool = False, output_file: Optional[str] = None ) -> Dict: """ Main analysis function for RNA structure. """ results = { "timestamp": datetime.now().isoformat(), "input": {}, "structure_analysis": {}, "predictions": {}, "summary": {} } # Record input parameters results["input"] = { "sequence": sequence, "pdb_file": pdb_file, "secondary_structure": secondary_structure, "predict_structure": predict_structure, "include_pseudoknots": include_pseudoknots } try: # Get sequence and structure if sequence is None and pdb_file is None and secondary_structure is None: raise ValueError("Must provide sequence, PDB file, or secondary structure") # Handle different input types if pdb_file and sequence: print(f"📄 Analyzing PDB structure: {pdb_file}") try: predicted_structure = pdb_to_sec_struct(pdb_file, sequence) results["predictions"]["from_pdb"] = predicted_structure secondary_structure = predicted_structure except Exception as e: print(f"⚠️ Warning: Could not extract structure from PDB: {e}") print("Proceeding with sequence-only analysis") # Predict structure if requested if predict_structure and sequence: print(f"🔬 Predicting secondary structure for sequence: {sequence[:50]}...") try: predicted_structure = predict_sec_struct(sequence) results["predictions"]["eternafold"] = predicted_structure if secondary_structure is None: secondary_structure = predicted_structure except Exception as e: print(f"⚠️ Warning: Structure prediction failed: {e}") # Analyze structure if we have one if secondary_structure: print(f"📊 Analyzing structure: {secondary_structure[:50]}...") # Validate structure is_valid, error_msg = validate_dotbracket(secondary_structure) if is_valid: structure_props = analyze_structure_properties(secondary_structure) results["structure_analysis"] = { "valid_dotbracket": True, **structure_props } print(f"✅ Structure analysis complete") print(f" Length: {structure_props['length']}") print(f" Base pairs: {structure_props['total_base_pairs']}") print(f" Pairing: {structure_props['pairing_percentage']:.1%}") else: results["structure_analysis"] = { "valid_dotbracket": False, "error": error_msg } print(f"❌ Invalid structure: {error_msg}") # Summary results["summary"] = { "analysis_successful": bool(results["structure_analysis"]), "has_structure": secondary_structure is not None, "has_prediction": bool(results["predictions"]), "total_runtime_info": "Analysis completed" } # Save results if requested if output_file: os.makedirs(os.path.dirname(output_file), exist_ok=True) with open(output_file, 'w') as f: json.dump(results, f, indent=2) print(f"💾 Results saved to: {output_file}") return results except Exception as e: error_results = { "timestamp": datetime.now().isoformat(), "error": str(e), "input": results["input"] } if output_file: with open(output_file, 'w') as f: json.dump(error_results, f, indent=2) print(f"❌ Analysis failed: {e}") return error_results def main(): """Main function with CLI interface.""" parser = argparse.ArgumentParser( description="RNA Secondary Structure Analysis", formatter_class=argparse.RawDescriptionHelpFormatter, epilog=""" Examples: python use_case_3_structure_analysis_minimal.py --sequence "GGGGAAAACCCC" --predict python use_case_3_structure_analysis_minimal.py --pdb examples/data/structures/RNASolo.pdb --sequence "GGGGAAAACCCC" python use_case_3_structure_analysis_minimal.py --secondary_structure "((((....))))" """ ) # Input options parser.add_argument('--sequence', type=str, help='RNA sequence to analyze') parser.add_argument('--pdb', type=str, help='PDB file containing RNA structure') parser.add_argument('--secondary_structure', type=str, help='Secondary structure in dot-bracket notation') # Analysis options parser.add_argument('--predict', action='store_true', help='Predict secondary structure using EternaFold') parser.add_argument('--include_pseudoknots', action='store_true', default=True, help='Include pseudoknot analysis') parser.add_argument('--visualize', action='store_true', help='Generate structure visualization (if available)') # Output options parser.add_argument('--output', type=str, help='Output file for analysis results (JSON format)') args = parser.parse_args() # Validate inputs if not any([args.sequence, args.pdb, args.secondary_structure]): parser.error("Must provide at least one of: --sequence, --pdb, or --secondary_structure") print("🧬 Starting RNA Structure Analysis") print("=" * 50) # Run analysis results = analyze_rna_structure( sequence=args.sequence, pdb_file=args.pdb, secondary_structure=args.secondary_structure, predict_structure=args.predict, include_pseudoknots=args.include_pseudoknots, visualize=args.visualize, output_file=args.output ) # Print summary print("\n📋 Analysis Summary:") print("=" * 50) if results.get("structure_analysis"): analysis = results["structure_analysis"] if analysis.get("valid_dotbracket"): print(f"✅ Valid structure analyzed") print(f" Length: {analysis.get('length', 'N/A')}") print(f" Base pairs: {analysis.get('total_base_pairs', 'N/A')}") print(f" Pairing: {analysis.get('pairing_percentage', 0):.1%}") print(f" Has pseudoknots: {analysis.get('has_pseudoknots', False)}") else: print(f"❌ Structure validation failed: {analysis.get('error', 'Unknown error')}") if results.get("predictions"): print(f"🔬 Predictions generated: {list(results['predictions'].keys())}") if results.get("error"): print(f"❌ Error occurred: {results['error']}") return 1 print("\n🎉 Analysis complete!") return 0 if __name__ == '__main__': exit(main())