Add BioEmu Nextflow pipeline implementation

calculate_gibbs.py

@@ -0,0 +1,121 @@
+#!/usr/bin/env python3
+
+import argparse
+import numpy as np
+import mdtraj as md
+from sklearn.cluster import KMeans
+import pandas as pd
+import matplotlib.pyplot as plt
+import os
+
+def parse_args():
+    parser = argparse.ArgumentParser(description='Calculate Gibbs free energy from protein structure ensembles')
+    parser.add_argument('--samples', required=True, help='Path to XTC trajectory file with structure samples')
+    parser.add_argument('--topology', required=True, help='Path to PDB topology file')
+    parser.add_argument('--temperature', type=float, default=300.0, help='Temperature in Kelvin')
+    parser.add_argument('--output', required=True, help='Output CSV file for free energy data')
+    parser.add_argument('--n_clusters', type=int, default=5, help='Number of conformational clusters')
+    parser.add_argument('--plot', help='Path to save energy plot (optional)')
+    return parser.parse_args()
+
+def main():
+    args = parse_args()
+    
+    # Load trajectory
+    print(f"Loading trajectory {args.samples} with topology {args.topology}")
+    traj = md.load(args.samples, top=args.topology)
+    
+    # Calculate RMSD to first frame
+    print("Calculating RMSD to reference structure")
+    # Align to the first frame
+    traj.superpose(traj, 0)
+    # Calculate RMSD for CA atoms only
+    atom_indices = traj.topology.select('name CA')
+    distances = np.zeros(traj.n_frames)
+    for i in range(traj.n_frames):
+        # Fixed line - using slicing instead of frame parameter
+        distances[i] = md.rmsd(traj[i:i+1], traj[0:1], atom_indices=atom_indices)[0]
+    
+    # Feature extraction for clustering
+    # Use the RMSD and radius of gyration as features
+    rg = md.compute_rg(traj)
+    features = np.column_stack((distances, rg))
+    
+    # Cluster structures
+    print(f"Clustering structures into {args.n_clusters} states")
+    kmeans = KMeans(n_clusters=args.n_clusters, random_state=42)
+    labels = kmeans.fit_predict(features)
+    
+    # Calculate state populations
+    unique_labels, counts = np.unique(labels, return_counts=True)
+    populations = counts / len(labels)
+    
+    # Calculate free energies
+    R = 0.0019872041 # kcal/(mol·K)
+    T = args.temperature
+    RT = R * T
+    
+    # Reference state is the most populated one
+    reference_idx = np.argmax(populations)
+    reference_pop = populations[reference_idx]
+    
+    # Calculate ΔG values 
+    free_energies = -RT * np.log(populations / reference_pop)
+    
+    # Get representative structures from each cluster
+    representatives = []
+    for i in range(args.n_clusters):
+        cluster_frames = np.where(labels == i)[0]
+        if len(cluster_frames) > 0:
+            # Find frame closest to cluster center
+            cluster_features = features[cluster_frames]
+            center_dists = np.linalg.norm(cluster_features - kmeans.cluster_centers_[i], axis=1)
+            center_idx = cluster_frames[np.argmin(center_dists)]
+            representatives.append(int(center_idx))
+        else:
+            representatives.append(-1)  # No members in this cluster
+    
+    # Create results dataframe
+    results = pd.DataFrame({
+        'Cluster': unique_labels,
+        'Population': populations,
+        'DeltaG_kcal_mol': free_energies,
+        'Representative_Frame': representatives
+    })
+    
+    # Sort by free energy
+    results = results.sort_values('DeltaG_kcal_mol')
+    
+    # Save results
+    results.to_csv(args.output, index=False)
+    print(f"Results saved to {args.output}")
+    
+    # Print summary
+    print("\nFree Energy Summary:")
+    print(results)
+    
+    # Calculate overall free energy range
+    print(f"\nFree energy range: {np.max(free_energies) - np.min(free_energies):.2f} kcal/mol")
+    
+    # Create plot if requested
+    if args.plot:
+        plt.figure(figsize=(10, 6))
+        
+        # Plot free energy for each cluster
+        plt.bar(range(len(unique_labels)), free_energies, alpha=0.7)
+        plt.xlabel('Cluster')
+        plt.ylabel('ΔG (kcal/mol)')
+        plt.title('Free Energy Landscape')
+        plt.xticks(range(len(unique_labels)))
+        plt.grid(axis='y', linestyle='--', alpha=0.7)
+        
+        # Add population as text on bars
+        for i, (energy, pop) in enumerate(zip(free_energies, populations)):
+            plt.text(i, energy + 0.1, f"{pop*100:.1f}%", ha='center')
+        
+        plt.tight_layout()
+        plt.savefig(args.plot, dpi=300)
+        print(f"Plot saved to {args.plot}")
+
+if __name__ == "__main__":
+    main()