added aliphatic index, boman index and hydrophobicity to the features

features.py

@@ -12,6 +12,11 @@ def extract_features(sequence: Seq) -> Dict[str, float]:
     charge = calculate_charge(sequence)
     hydrophobic_ratio = sum(amino_acid_count[aa] for aa in 'AILMFPWV') / len(sequence)
 
+    # Additional features
+    aliphatic_index = calculate_aliphatic_index(amino_acid_percent)
+    boman_index = calculate_boman_index(sequence)
+    hydrophobicity = calculate_hydrophobicity(sequence)
+
     return {
         'length': len(sequence),
         'weight': analyser.molecular_weight(),
@@ -22,9 +27,12 @@ def extract_features(sequence: Seq) -> Dict[str, float]:
         'turn_fraction': analyser.secondary_structure_fraction()[1],
         'sheet_fraction': analyser.secondary_structure_fraction()[2],
         'gravy': analyser.gravy(),
-        'charge': charge,  # New feature
-        'hydrophobic_ratio': hydrophobic_ratio,  # New feature
-        'flexibility': analyser.flexibility(),  # New feature
+        'charge': charge,
+        'hydrophobic_ratio': hydrophobic_ratio,
+        'flexibility': analyser.flexibility(),
+        'aliphatic_index': aliphatic_index,  # New feature
+        'boman_index': boman_index,  # New feature
+        'hydrophobicity': hydrophobicity,  # New feature
         **{f'{aa}_percent': percent for aa, percent in amino_acid_percent.items()}
     }
 
@@ -48,4 +56,26 @@ def compute_conjoint_triad(sequence: str) -> List[int]:
         triad = (groups[sequence[i]], groups[sequence[i+1]], groups[sequence[i+2]])
         features[triad[0]*49 + triad[1]*7 + triad[2]] += 1
 
-    return features
+    return features
+
+def calculate_aliphatic_index(amino_acid_percent: Dict[str, float]) -> float:
+    """Calculate the aliphatic index of a protein sequence."""
+    return (100 * amino_acid_percent.get('A', 0) +
+            2.9 * amino_acid_percent.get('V', 0) +
+            3.9 * (amino_acid_percent.get('I', 0) + amino_acid_percent.get('L', 0)))
+
+def calculate_boman_index(sequence: Seq) -> float:
+    """Calculate the Boman (Potential Protein Interaction) index."""
+    aa_values = {'L': -4.92, 'I': -4.92, 'V': -4.04, 'F': -2.98, 'M': -2.35,
+                 'W': -2.33, 'A': -1.89, 'C': -1.85, 'G': -1.05, 'Y': -0.14,
+                 'T': 0.69, 'S': 0.84, 'H': 2.06, 'Q': 2.36, 'K': 2.71,
+                 'N': 2.95, 'E': 3.81, 'D': 3.98, 'R': 4.38, 'P': 0}
+    return sum(aa_values.get(aa, 0) for aa in str(sequence)) / len(sequence)
+
+def calculate_hydrophobicity(sequence: Seq) -> float:
+    """Calculate the overall hydrophobicity of a protein sequence using the Kyte-Doolittle scale."""
+    kd_scale = {'A': 1.8, 'R': -4.5, 'N': -3.5, 'D': -3.5, 'C': 2.5,
+                'Q': -3.5, 'E': -3.5, 'G': -0.4, 'H': -3.2, 'I': 4.5,
+                'L': 3.8, 'K': -3.9, 'M': 1.9, 'F': 2.8, 'P': -1.6,
+                'S': -0.8, 'T': -0.7, 'W': -0.9, 'Y': -1.3, 'V': 4.2}
+    return sum(kd_scale.get(aa, 0) for aa in str(sequence)) / len(sequence)