masster 0.4.3__py3-none-any.whl → 0.4.5__py3-none-any.whl

masster/sample/adducts.py

@@ -14,24 +14,24 @@ Functions:
 
 import numpy as np
 import polars as pl
-from typing import List, Dict, Any
+from typing import List, Dict
 from itertools import combinations
 
 # Import defaults class for external use
-from masster.sample.defaults.find_adducts_def import find_adducts_defaults
+from master.sample.defaults.find_adducts_def import find_adducts_defaults
 
 
 def _get_adducts(self, adducts_list: list = None, **kwargs):
     """
     Generate comprehensive adduct specifications including multiply charged species and combinations.
-    
+
     This method consolidates all adduct generation logic into a single optimized helper
     that produces a polars DataFrame with all possible adduct combinations, properly
     formatted names like [M+H]1+ or [M-H2O+2H]2+, and respecting charge constraints.
-    
+
     Uses parameters from find_adducts_defaults() by default, which can be overridden
     by providing keyword arguments.
-    
+
     Parameters
     ----------
     adducts_list : List[str], optional
@@ -42,7 +42,7 @@ def _get_adducts(self, adducts_list: list = None, **kwargs):
         - charge_min: Minimum charge to consider (default from find_adducts_defaults)
         - charge_max: Maximum charge to consider (default from find_adducts_defaults)
         - max_combinations: Maximum number of adduct components to combine (default 4)
-        
+
     Returns
     -------
     pl.DataFrame
@@ -56,177 +56,201 @@ def _get_adducts(self, adducts_list: list = None, **kwargs):
     """
     # Get default parameters from find_adducts_defaults
     defaults = self.find_adducts_defaults()
-    
+
     # Use provided parameters or defaults
     if adducts_list is None:
         adducts_list = defaults.get_openms_adducts()
-        
-    charge_min = kwargs.get('charge_min', defaults.charge_min)
-    charge_max = kwargs.get('charge_max', defaults.charge_max)
-    max_combinations = kwargs.get('max_combinations', 4)
-    
+
+    charge_min = kwargs.get("charge_min", defaults.charge_min)
+    charge_max = kwargs.get("charge_max", defaults.charge_max)
+    max_combinations = kwargs.get("max_combinations", 4)
+
     # Parse base adduct specifications
     base_specs = []
-    
+
     for adduct_str in adducts_list:
-        if not isinstance(adduct_str, str) or ':' not in adduct_str:
+        if not isinstance(adduct_str, str) or ":" not in adduct_str:
             continue
-            
+
         try:
-            parts = adduct_str.split(':')
+            parts = adduct_str.split(":")
             if len(parts) != 3:
                 continue
-                
+
             formula_part = parts[0]
-            charge = int(parts[1]) 
+            charge = int(parts[1])
             probability = float(parts[2])
-            
+
             # Calculate mass shift from formula
             mass_shift = _calculate_formula_mass_shift(formula_part)
-            
-            base_specs.append({
-                'formula': formula_part,
-                'charge': charge,
-                'mass_shift': mass_shift,
-                'probability': probability,
-                'raw_string': adduct_str
-            })
-            
+
+            base_specs.append(
+                {
+                    "formula": formula_part,
+                    "charge": charge,
+                    "mass_shift": mass_shift,
+                    "probability": probability,
+                    "raw_string": adduct_str,
+                },
+            )
+
         except (ValueError, IndexError):
             continue
-    
+
     # Generate all valid combinations
     combinations_list = []
-    
+
     # Separate specs by charge type
-    positive_specs = [spec for spec in base_specs if spec['charge'] > 0]
-    negative_specs = [spec for spec in base_specs if spec['charge'] < 0]
-    neutral_specs = [spec for spec in base_specs if spec['charge'] == 0]
-    
+    positive_specs = [spec for spec in base_specs if spec["charge"] > 0]
+    negative_specs = [spec for spec in base_specs if spec["charge"] < 0]
+    neutral_specs = [spec for spec in base_specs if spec["charge"] == 0]
+
     # 1. Single adducts
     for spec in base_specs:
-        if charge_min <= spec['charge'] <= charge_max:
+        if charge_min <= spec["charge"] <= charge_max:
             formatted_name = _format_adduct_name([spec])
-            combinations_list.append({
-                'components': [spec],
-                'formatted_name': formatted_name,
-                'total_mass_shift': spec['mass_shift'],
-                'total_charge': spec['charge'],
-                'combined_probability': spec['probability'],
-                'complexity': 1
-            })
-    
+            combinations_list.append(
+                {
+                    "components": [spec],
+                    "formatted_name": formatted_name,
+                    "total_mass_shift": spec["mass_shift"],
+                    "total_charge": spec["charge"],
+                    "combined_probability": spec["probability"],
+                    "complexity": 1,
+                },
+            )
+
     # 2. Generate multiply charged versions (2H+, 3H+, etc.)
     for spec in positive_specs + negative_specs:
-        base_charge = spec['charge']
+        base_charge = spec["charge"]
         for multiplier in range(2, min(max_combinations + 1, 5)):
             total_charge = base_charge * multiplier
             if charge_min <= total_charge <= charge_max:
                 components = [spec] * multiplier
                 formatted_name = _format_adduct_name(components)
-                
-                combinations_list.append({
-                    'components': components,
-                    'formatted_name': formatted_name,
-                    'total_mass_shift': spec['mass_shift'] * multiplier,
-                    'total_charge': total_charge,
-                    'combined_probability': spec['probability'] ** multiplier,
-                    'complexity': multiplier
-                })
-    
+
+                combinations_list.append(
+                    {
+                        "components": components,
+                        "formatted_name": formatted_name,
+                        "total_mass_shift": spec["mass_shift"] * multiplier,
+                        "total_charge": total_charge,
+                        "combined_probability": spec["probability"] ** multiplier,
+                        "complexity": multiplier,
+                    },
+                )
+
     # 3. Mixed combinations (2-component)
     if max_combinations >= 2:
         # Positive + Neutral
         for pos_spec in positive_specs:
             for neut_spec in neutral_specs:
-                total_charge = pos_spec['charge'] + neut_spec['charge']
+                total_charge = pos_spec["charge"] + neut_spec["charge"]
                 if charge_min <= total_charge <= charge_max:
                     components = [pos_spec, neut_spec]
                     formatted_name = _format_adduct_name(components)
-                    combinations_list.append({
-                        'components': components,
-                        'formatted_name': formatted_name,
-                        'total_mass_shift': pos_spec['mass_shift'] + neut_spec['mass_shift'],
-                        'total_charge': total_charge,
-                        'combined_probability': pos_spec['probability'] * neut_spec['probability'],
-                        'complexity': 2
-                    })
-        
+                    combinations_list.append(
+                        {
+                            "components": components,
+                            "formatted_name": formatted_name,
+                            "total_mass_shift": pos_spec["mass_shift"]
+                            + neut_spec["mass_shift"],
+                            "total_charge": total_charge,
+                            "combined_probability": pos_spec["probability"]
+                            * neut_spec["probability"],
+                            "complexity": 2,
+                        },
+                    )
+
         # Different charged species
         for combo in combinations(positive_specs, 2):
-            if combo[0]['formula'] != combo[1]['formula']:
-                total_charge = combo[0]['charge'] + combo[1]['charge']
+            if combo[0]["formula"] != combo[1]["formula"]:
+                total_charge = combo[0]["charge"] + combo[1]["charge"]
                 if charge_min <= total_charge <= charge_max:
                     components = list(combo)
                     formatted_name = _format_adduct_name(components)
-                    combinations_list.append({
-                        'components': components,
-                        'formatted_name': formatted_name,
-                        'total_mass_shift': combo[0]['mass_shift'] + combo[1]['mass_shift'],
-                        'total_charge': total_charge,
-                        'combined_probability': combo[0]['probability'] * combo[1]['probability'],
-                        'complexity': 2
-                    })
-    
+                    combinations_list.append(
+                        {
+                            "components": components,
+                            "formatted_name": formatted_name,
+                            "total_mass_shift": combo[0]["mass_shift"]
+                            + combo[1]["mass_shift"],
+                            "total_charge": total_charge,
+                            "combined_probability": combo[0]["probability"]
+                            * combo[1]["probability"],
+                            "complexity": 2,
+                        },
+                    )
+
     # 4. 3-component combinations (limited for performance)
     if max_combinations >= 3:
         for pos_spec in positive_specs[:2]:
             for neut_combo in combinations(neutral_specs[:2], 2):
                 components = [pos_spec] + list(neut_combo)
-                total_charge = sum(spec['charge'] for spec in components)
-                
+                total_charge = sum(spec["charge"] for spec in components)
+
                 if charge_min <= total_charge <= charge_max:
                     formatted_name = _format_adduct_name(components)
-                    total_mass_shift = sum(spec['mass_shift'] for spec in components)
-                    combined_prob = np.prod([spec['probability'] for spec in components])
-                    
-                    combinations_list.append({
-                        'components': components,
-                        'formatted_name': formatted_name,
-                        'total_mass_shift': total_mass_shift,
-                        'total_charge': total_charge,
-                        'combined_probability': combined_prob,
-                        'complexity': 3
-                    })
-    
+                    total_mass_shift = sum(spec["mass_shift"] for spec in components)
+                    combined_prob = np.prod(
+                        [spec["probability"] for spec in components],
+                    )
+
+                    combinations_list.append(
+                        {
+                            "components": components,
+                            "formatted_name": formatted_name,
+                            "total_mass_shift": total_mass_shift,
+                            "total_charge": total_charge,
+                            "combined_probability": combined_prob,
+                            "complexity": 3,
+                        },
+                    )
+
     # Convert to polars DataFrame
     if combinations_list:
-        combinations_list.sort(key=lambda x: (-x['combined_probability'], x['complexity']))
-        
-        adducts_df = pl.DataFrame([
-            {
-                'name': combo['formatted_name'],
-                'charge': combo['total_charge'], 
-                'mass_shift': combo['total_mass_shift'],
-                'probability': combo['combined_probability'],
-                'complexity': combo['complexity'],
-                'components': combo['components']
-            }
-            for combo in combinations_list
-        ])
+        combinations_list.sort(
+            key=lambda x: (-x["combined_probability"], x["complexity"]),
+        )
+
+        adducts_df = pl.DataFrame(
+            [
+                {
+                    "name": combo["formatted_name"],
+                    "charge": combo["total_charge"],
+                    "mass_shift": combo["total_mass_shift"],
+                    "probability": combo["combined_probability"],
+                    "complexity": combo["complexity"],
+                    "components": combo["components"],
+                }
+                for combo in combinations_list
+            ],
+        )
     else:
         # Return empty DataFrame with correct schema
-        adducts_df = pl.DataFrame({
-            'name': [],
-            'charge': [],
-            'mass_shift': [],
-            'probability': [],
-            'complexity': [],
-            'components': []
-        })
-    
+        adducts_df = pl.DataFrame(
+            {
+                "name": [],
+                "charge": [],
+                "mass_shift": [],
+                "probability": [],
+                "complexity": [],
+                "components": [],
+            },
+        )
+
     return adducts_df
 
 
 def _calculate_formula_mass_shift(formula: str) -> float:
     """
     Calculate mass shift from formula string like "+H", "-H2O", "+Na-H", etc.
-    
+
     Parameters
     ----------
     formula : str
         Formula string (e.g., "+H", "-H2O", "+Na-H")
-        
+
     Returns
     -------
     float
@@ -234,59 +258,59 @@ def _calculate_formula_mass_shift(formula: str) -> float:
     """
     # Standard atomic masses
     atomic_masses = {
-        'H': 1.007825,
-        'C': 12.0,
-        'N': 14.003074,
-        'O': 15.994915,
-        'Na': 22.989769,
-        'K': 38.963707,
-        'Li': 7.016003,
-        'Ca': 39.962591,
-        'Mg': 23.985042,
-        'Fe': 55.934938,
-        'Cl': 34.968853,
-        'Br': 78.918336,
-        'I': 126.904473,
-        'P': 30.973762,
-        'S': 31.972071
+        "H": 1.007825,
+        "C": 12.0,
+        "N": 14.003074,
+        "O": 15.994915,
+        "Na": 22.989769,
+        "K": 38.963707,
+        "Li": 7.016003,
+        "Ca": 39.962591,
+        "Mg": 23.985042,
+        "Fe": 55.934938,
+        "Cl": 34.968853,
+        "Br": 78.918336,
+        "I": 126.904473,
+        "P": 30.973762,
+        "S": 31.972071,
     }
-    
+
     total_mass = 0.0
-    
+
     # Parse formula by splitting on + and - while preserving the operators
     parts = []
     current_part = ""
     current_sign = 1
-    
+
     for char in formula:
-        if char == '+':
+        if char == "+":
             if current_part:
                 parts.append((current_sign, current_part))
             current_part = ""
             current_sign = 1
-        elif char == '-':
+        elif char == "-":
             if current_part:
                 parts.append((current_sign, current_part))
             current_part = ""
             current_sign = -1
         else:
             current_part += char
-    
+
     if current_part:
         parts.append((current_sign, current_part))
-    
+
     # Process each part
     for sign, part in parts:
         if not part:
             continue
-            
+
         # Parse element and count (e.g., "H2O" -> H:2, O:1)
         elements = _parse_element_counts(part)
-        
+
         for element, count in elements.items():
             if element in atomic_masses:
                 total_mass += sign * atomic_masses[element] * count
-    
+
     return total_mass
 
 
@@ -294,25 +318,25 @@ def _parse_element_counts(formula_part: str) -> Dict[str, int]:
     """Parse element counts from a formula part like 'H2O' -> {'H': 2, 'O': 1}"""
     elements = {}
     i = 0
-    
+
     while i < len(formula_part):
         # Get element (uppercase letter, possibly followed by lowercase)
         element = formula_part[i]
         i += 1
-        
+
         while i < len(formula_part) and formula_part[i].islower():
             element += formula_part[i]
             i += 1
-        
+
         # Get count (digits following element)
         count_str = ""
         while i < len(formula_part) and formula_part[i].isdigit():
             count_str += formula_part[i]
             i += 1
-        
+
         count = int(count_str) if count_str else 1
         elements[element] = elements.get(element, 0) + count
-    
+
     return elements
 
 
@@ -320,51 +344,56 @@ def _format_adduct_name(components: List[Dict]) -> str:
     """Format adduct name from components like [M+H]1+ or [M+2H]2+ or [M+2(H+Na)]3+"""
     if not components:
         return "[M]"
-    
+
     # Count occurrences of each formula
     from collections import Counter
-    formula_counts = Counter(comp['formula'] for comp in components)
-    total_charge = sum(comp['charge'] for comp in components)
-    
+
+    formula_counts = Counter(comp["formula"] for comp in components)
+    total_charge = sum(comp["charge"] for comp in components)
+
     # Build formula part with proper multipliers
     formula_parts = []
-    for formula, count in sorted(formula_counts.items()):  # Sort for consistent ordering
+    for formula, count in sorted(
+        formula_counts.items(),
+    ):  # Sort for consistent ordering
         if count == 1:
             formula_parts.append(formula)
         else:
             # For multiple occurrences, use count prefix (e.g., 2H, 3Na)
             # Handle special case where formula might already start with + or -
-            if formula.startswith(('+', '-')):
+            if formula.startswith(("+", "-")):
                 sign = formula[0]
                 base_formula = formula[1:]
                 formula_parts.append(f"{sign}{count}{base_formula}")
             else:
                 formula_parts.append(f"{count}{formula}")
-    
+
     # Combine formula parts
     formula = "".join(formula_parts)
-    
+
     # Format charge
     if total_charge == 0:
         charge_str = ""
     elif abs(total_charge) == 1:
         charge_str = "1+" if total_charge > 0 else "1-"
     else:
-        charge_str = f"{abs(total_charge)}+" if total_charge > 0 else f"{abs(total_charge)}-"
-    
+        charge_str = (
+            f"{abs(total_charge)}+" if total_charge > 0 else f"{abs(total_charge)}-"
+        )
+
     return f"[M{formula}]{charge_str}"
 
 
 def find_adducts(self, **kwargs):
     """Detect adduct relationships among detected features using improved OpenMS-like algorithm.
 
-    This method implements a corrected version of the OpenMS MetaboliteFeatureDeconvolution 
+    This method implements a corrected version of the OpenMS MetaboliteFeatureDeconvolution
     algorithm that properly enforces RT constraints and avoids the mass tolerance dominance
     issues present in the original C++ implementation.
 
     Key improvements over OpenMS:
     - Early RT filtering prevents expensive mass calculations for temporally incompatible features
-    - Strict mass tolerance (0.01 Da default) prevents inappropriate mass relationships  
+    - Strict mass tolerance (0.01 Da default) prevents inappropriate mass relationships
     - RT constraints are properly enforced throughout the algorithm
     - Connected components analysis respects both mass AND RT constraints
     - Probability-based scoring for adduct assignment
@@ -381,9 +410,9 @@ def find_adducts(self, **kwargs):
     Side effects:
         Updates ``self.features_df`` with adduct information columns.
     """
-    # Initialize parameters  
+    # Initialize parameters
     params = find_adducts_defaults()
-    
+
     for key, value in kwargs.items():
         if isinstance(value, find_adducts_defaults):
             params = value
@@ -393,24 +422,28 @@ def find_adducts(self, **kwargs):
                 if params.set(key, value, validate=True):
                     self.logger.debug(f"Updated parameter {key} = {value}")
                 else:
-                    self.logger.warning(f"Failed to set parameter {key} = {value} (validation failed)")
+                    self.logger.warning(
+                        f"Failed to set parameter {key} = {value} (validation failed)",
+                    )
             else:
                 self.logger.warning(f"Unknown parameter {key} ignored")
 
     # Check if features_df exists and has data
-    if not hasattr(self, 'features_df') or len(self.features_df) == 0:
-        self.logger.warning("No features available for adduct detection. Run find_features() first.")
+    if not hasattr(self, "features_df") or len(self.features_df) == 0:
+        self.logger.warning(
+            "No features available for adduct detection. Run find_features() first.",
+        )
         return
 
     self.logger.info("Adduct detection...")
 
     # Validate required columns
-    required_cols = ['mz', 'rt']
+    required_cols = ["mz", "rt"]
     missing_cols = [col for col in required_cols if col not in self.features_df.columns]
     if missing_cols:
         self.logger.error(f"Required columns missing from features_df: {missing_cols}")
         return
-    
+
     # Check if we have any features to process
     if len(self.features_df) == 0:
         self.logger.warning("No features available for adduct detection")
@@ -424,130 +457,151 @@ def find_adducts(self, **kwargs):
 
     # Get parameters
     adducts_list = params.get_openms_adducts()
-    charge_min = params.get("charge_min")  
+    charge_min = params.get("charge_min")
     charge_max = params.get("charge_max")
     retention_max_diff = params.get("retention_max_diff")
     mass_max_diff = params.get("mass_max_diff")
     unit = params.get("unit")
     min_probability = params.get("min_probability")
 
-    self.logger.debug(f"Processing {len(self.features_df)} features with {len(adducts_list)} base adducts")
-    self.logger.debug(f"RT tolerance: {retention_max_diff}s, Mass tolerance: {mass_max_diff} {unit}")
+    self.logger.debug(
+        f"Processing {len(self.features_df)} features with {len(adducts_list)} base adducts",
+    )
+    self.logger.debug(
+        f"RT tolerance: {retention_max_diff}s, Mass tolerance: {mass_max_diff} {unit}",
+    )
     self.logger.debug(f"Min probability threshold: {min_probability}")
 
     # Generate comprehensive adduct specifications using the Sample method
     adducts_df = self._get_adducts(
         adducts_list=adducts_list,
-        charge_min=charge_min, 
+        charge_min=charge_min,
         charge_max=charge_max,
-        max_combinations=4
+        max_combinations=4,
     )
-    
+
     self.logger.debug(f"Generated {len(adducts_df)} total adduct combinations")
-    
+
     # Filter adducts by minimum probability threshold
     if min_probability > 0.0:
         adducts_before_filter = len(adducts_df)
         adducts_df = adducts_df.filter(pl.col("probability") >= min_probability)
         adducts_after_filter = len(adducts_df)
         filtered_count = adducts_before_filter - adducts_after_filter
-        
-        self.logger.debug(f"Filtered {filtered_count} low-probability adducts (< {min_probability})")
+
+        self.logger.debug(
+            f"Filtered {filtered_count} low-probability adducts (< {min_probability})",
+        )
         self.logger.debug(f"Remaining adducts for analysis: {adducts_after_filter}")
-        
+
         if len(adducts_df) == 0:
-            self.logger.warning(f"No adducts remaining after probability filtering (min_probability={min_probability})")
+            self.logger.warning(
+                f"No adducts remaining after probability filtering (min_probability={min_probability})",
+            )
             return
-    
+
     # Implement the adduct detection algorithm directly here
     import numpy as np
-    
+
     # Get parameters
     charge_max = params.get("charge_max")
     retention_max_diff = params.get("retention_max_diff")
     mass_max_diff = params.get("mass_max_diff")
     unit = params.get("unit")
-    
+
     # Sort features by RT for efficient RT-sweep processing (OpenMS approach)
     # Store original row positions before sorting for correct index mapping
     features_with_positions = self.features_df.with_row_index("original_position")
     features_sorted = features_with_positions.sort("rt")
     n_features = len(features_sorted)
-    
+
     # Extract arrays for fast processing
     feature_mzs = features_sorted.select("mz").to_numpy().flatten()
     feature_rts = features_sorted.select("rt").to_numpy().flatten()
-    
+
     # Convert adducts to arrays for vectorized operations
     adduct_mass_shifts = adducts_df.select("mass_shift").to_numpy().flatten()
     adduct_charges = adducts_df.select("charge").to_numpy().flatten()
     adduct_names = adducts_df.select("name").to_series().to_list()
     adduct_probs = adducts_df.select("probability").to_numpy().flatten()
 
-    self.logger.debug(f"RT-sweep processing: {n_features} features × {len(adducts_df)} adduct combinations")
-    
+    self.logger.debug(
+        f"RT-sweep processing: {n_features} features × {len(adducts_df)} adduct combinations",
+    )
+
     # Phase 1: RT-sweep line algorithm with early RT filtering (fixes OpenMS flaw #1)
     candidate_edges = []
-    
+
     for i_rt in range(n_features):
         mz1 = feature_mzs[i_rt]
         rt1 = feature_rts[i_rt]
-        
+
         # RT-window sweep: only check features within RT tolerance (early filtering)
         for j_rt in range(i_rt + 1, n_features):
             rt2 = feature_rts[j_rt]
             rt_diff = rt2 - rt1
-            
+
             # Early RT constraint check (fixes OpenMS issue where RT was checked too late)
             if rt_diff > retention_max_diff:
                 break  # Features are RT-sorted, so no more valid pairs
-            
+
             mz2 = feature_mzs[j_rt]
-            
+
             # Phase 2: Check for valid mass relationships with strict tolerance (fixes OpenMS flaw #2)
             for adduct_idx, mass_shift in enumerate(adduct_mass_shifts):
                 charge = adduct_charges[adduct_idx]
-                
+
                 # Calculate mass tolerance (per feature, as in OpenMS)
-                if unit == 'ppm':
+                if unit == "ppm":
                     tol1 = mass_max_diff * mz1 * 1e-6
                     tol2 = mass_max_diff * mz2 * 1e-6
                     combined_tolerance = tol1 + tol2
                 else:  # Da
-                    combined_tolerance = 2 * mass_max_diff  # Combined tolerance for both features
-                
+                    combined_tolerance = (
+                        2 * mass_max_diff
+                    )  # Combined tolerance for both features
+
                 # Check both directions of mass relationship
                 if charge != 0:
                     # For charged adducts: m/z relationship
-                    mass_diff_12 = (mz2 * abs(charge)) - (mz1 * abs(charge)) 
+                    mass_diff_12 = (mz2 * abs(charge)) - (mz1 * abs(charge))
                     expected_mass_diff = mass_shift
-                    
+
                     if abs(mass_diff_12 - expected_mass_diff) <= combined_tolerance:
                         # Valid mass relationship found
-                        candidate_edges.append({
-                            'i': i_rt, 'j': j_rt,
-                            'rt_diff': rt_diff,
-                            'mass_error': abs(mass_diff_12 - expected_mass_diff),
-                            'adduct_idx': adduct_idx,
-                            'charge1': charge if mass_diff_12 > 0 else -charge,
-                            'charge2': -charge if mass_diff_12 > 0 else charge,
-                            'probability': adduct_probs[adduct_idx]
-                        })
+                        candidate_edges.append(
+                            {
+                                "i": i_rt,
+                                "j": j_rt,
+                                "rt_diff": rt_diff,
+                                "mass_error": abs(mass_diff_12 - expected_mass_diff),
+                                "adduct_idx": adduct_idx,
+                                "charge1": charge if mass_diff_12 > 0 else -charge,
+                                "charge2": -charge if mass_diff_12 > 0 else charge,
+                                "probability": adduct_probs[adduct_idx],
+                            },
+                        )
                 else:
                     # For neutral adducts: direct mass shift
                     mass_diff_12 = mz2 - mz1
                     if abs(mass_diff_12 - mass_shift) <= combined_tolerance:
-                        candidate_edges.append({
-                            'i': i_rt, 'j': j_rt,
-                            'rt_diff': rt_diff,
-                            'mass_error': abs(mass_diff_12 - mass_shift),
-                            'adduct_idx': adduct_idx,
-                            'charge1': 0, 'charge2': 0,
-                            'probability': adduct_probs[adduct_idx]
-                        })
-
-    self.logger.debug(f"Found {len(candidate_edges)} candidate edges after RT+mass filtering")
-    
+                        candidate_edges.append(
+                            {
+                                "i": i_rt,
+                                "j": j_rt,
+                                "rt_diff": rt_diff,
+                                "mass_error": abs(mass_diff_12 - mass_shift),
+                                "adduct_idx": adduct_idx,
+                                "charge1": 0,
+                                "charge2": 0,
+                                "probability": adduct_probs[adduct_idx],
+                            },
+                        )
+
+    self.logger.debug(
+        f"Found {len(candidate_edges)} candidate edges after RT+mass filtering",
+    )
+
     if len(candidate_edges) == 0:
         self.logger.info("No adduct relationships found")
         return
@@ -557,23 +611,23 @@ def find_adducts(self, **kwargs):
     adjacency = {}
     for i in range(n_features):
         adjacency[i] = []
-    
+
     for edge in candidate_edges:
-        i, j = edge['i'], edge['j']
+        i, j = edge["i"], edge["j"]
         adjacency[i].append(j)
         adjacency[j].append(i)
-    
+
     # Find connected components using DFS
     visited = [False] * n_features
     components = []
-    
+
     def dfs(node, component):
         visited[node] = True
         component.append(node)
         for neighbor in adjacency[node]:
             if not visited[neighbor]:
                 dfs(neighbor, component)
-    
+
     for i in range(n_features):
         if not visited[i] and len(adjacency[i]) > 0:
             component = []
@@ -589,53 +643,60 @@ def find_adducts(self, **kwargs):
     group_assignments = [0] * n_features
     mass_shift_assignments = [0.0] * n_features
     neutral_mass_assignments = [0.0] * n_features
-    
+
     for group_id, component in enumerate(components, 1):
         # Find the most likely base ion (highest intensity or lowest m/z as proxy)
         component_mzs = [feature_mzs[idx] for idx in component]
         base_idx_in_component = np.argmin(component_mzs)  # Lowest m/z as base
         base_feature_idx = component[base_idx_in_component]
         base_mz = feature_mzs[base_feature_idx]
-        
+
         # Assign base ion
         base_adduct = "[M+H]1+" if charge_max > 0 else "[M-H]1-"
         base_charge = 1 if charge_max > 0 else -1
         base_mass_shift = 1.007825 if charge_max > 0 else -1.007825  # H mass
-        
+
         adduct_assignments[base_feature_idx] = base_adduct
         adduct_charges_assigned[base_feature_idx] = base_charge
         group_assignments[base_feature_idx] = group_id
         mass_shift_assignments[base_feature_idx] = base_mass_shift
-        
+
         # Calculate neutral mass for base ion
         base_mz_measured = feature_mzs[base_feature_idx]
-        neutral_mass_assignments[base_feature_idx] = base_mz_measured * abs(base_charge) - base_mass_shift
-        
+        neutral_mass_assignments[base_feature_idx] = (
+            base_mz_measured * abs(base_charge) - base_mass_shift
+        )
+
         # Assign other features based on their relationships to base
         for feature_idx in component:
             if feature_idx == base_feature_idx:
                 continue
-                
+
             group_assignments[feature_idx] = group_id
-            
+
             # Find best adduct assignment based on mass difference and probability
             feature_mz = feature_mzs[feature_idx]
             best_score = -np.inf
             best_assignment = "[M+?]1+"
             best_charge = 1
             best_mass_shift = 1.007825  # Default to H mass shift for [M+?]1+
-            
+
             # Check all possible adducts
-            for adduct_idx, (mass_shift, charge, name, prob) in enumerate(zip(
-                adduct_mass_shifts, adduct_charges, adduct_names, adduct_probs)):
-                
+            for adduct_idx, (mass_shift, charge, name, prob) in enumerate(
+                zip(
+                    adduct_mass_shifts,
+                    adduct_charges,
+                    adduct_names,
+                    adduct_probs,
+                ),
+            ):
                 if charge != 0:
                     expected_mz = base_mz + mass_shift / abs(charge)
                 else:
                     expected_mz = base_mz + mass_shift
-                
+
                 mass_error = abs(expected_mz - feature_mz)
-                
+
                 # Combined score: probability + mass accuracy
                 if mass_error < mass_max_diff * 2:  # Within tolerance
                     score = prob - mass_error * 0.1  # Weight mass accuracy
@@ -648,48 +709,52 @@ def find_adducts(self, **kwargs):
             adduct_assignments[feature_idx] = best_assignment
             adduct_charges_assigned[feature_idx] = best_charge
             mass_shift_assignments[feature_idx] = best_mass_shift
-            
+
             # Calculate neutral mass
-            neutral_mass_assignments[feature_idx] = feature_mz * abs(best_charge) - best_mass_shift
+            neutral_mass_assignments[feature_idx] = (
+                feature_mz * abs(best_charge) - best_mass_shift
+            )
 
     # Assign fallback adduct for features not processed in connected components (isolated features)
     for i in range(n_features):
         if adduct_assignments[i] is None:
             fallback_charge = 1 if charge_max > 0 else -1
             fallback_mass_shift = 1.007825 if charge_max > 0 else -1.007825  # Assume H
-            
+
             adduct_assignments[i] = "[M+?]1+"
             adduct_charges_assigned[i] = fallback_charge
             group_assignments[i] = 0  # No group assignment for isolated features
             mass_shift_assignments[i] = fallback_mass_shift
-            
+
             # Calculate neutral mass for isolated features
             feature_mz = feature_mzs[i]
-            neutral_mass_assignments[i] = feature_mz * abs(fallback_charge) - fallback_mass_shift
+            neutral_mass_assignments[i] = (
+                feature_mz * abs(fallback_charge) - fallback_mass_shift
+            )
 
     # Map back to original feature order using stored positions
     original_indices = features_sorted.select("original_position").to_numpy().flatten()
-    
+
     # Create final assignments in original order (same size as original DataFrame)
     final_adducts = [None] * len(self.features_df)
     final_charges = [0] * len(self.features_df)
     final_groups = [0] * len(self.features_df)
     final_mass_shifts = [0.0] * len(self.features_df)
     final_neutral_masses = [0.0] * len(self.features_df)
-    
+
     for sorted_idx, orig_idx in enumerate(original_indices):
         final_adducts[orig_idx] = adduct_assignments[sorted_idx]
         final_charges[orig_idx] = adduct_charges_assigned[sorted_idx]
         final_groups[orig_idx] = group_assignments[sorted_idx]
         final_mass_shifts[orig_idx] = mass_shift_assignments[sorted_idx]
         final_neutral_masses[orig_idx] = neutral_mass_assignments[sorted_idx]
-    
+
     # Update features DataFrame with correct column ordering
     # Insert adduct columns in the specified order after iso_of column
-    
+
     # Get current columns
     current_columns = self.features_df.columns
-    
+
     # Find the position of iso_of column
     try:
         iso_of_index = current_columns.index("iso_of")
@@ -698,42 +763,51 @@ def find_adducts(self, **kwargs):
         # If iso_of doesn't exist, append at the end
         insert_position = len(current_columns)
         self.logger.warning("iso_of column not found, adding adduct columns at the end")
-    
+
     # Remove any existing adduct columns first
-    adduct_column_names = ["adduct", "adduct_charge", "adduct_mass_shift", "adduct_mass_neutral", "adduct_group"]
-    df_without_adducts = self.features_df.select([col for col in current_columns if col not in adduct_column_names])
-    
+    adduct_column_names = [
+        "adduct",
+        "adduct_charge",
+        "adduct_mass_shift",
+        "adduct_mass_neutral",
+        "adduct_group",
+    ]
+    df_without_adducts = self.features_df.select(
+        [col for col in current_columns if col not in adduct_column_names],
+    )
+
     # Split columns at insertion point
     columns_before = df_without_adducts.columns[:insert_position]
     columns_after = df_without_adducts.columns[insert_position:]
-    
+
     # Create the new column order with adduct columns in the correct position
-    new_column_order = (
-        list(columns_before) + 
-        adduct_column_names + 
-        list(columns_after)
-    )
-    
+    new_column_order = list(columns_before) + adduct_column_names + list(columns_after)
+
     # Add adduct columns to the dataframe
-    self.features_df = df_without_adducts.with_columns([
-        pl.Series("adduct", final_adducts),
-        pl.Series("adduct_charge", final_charges),
-        pl.Series("adduct_mass_shift", final_mass_shifts),
-        pl.Series("adduct_mass_neutral", final_neutral_masses),
-        pl.Series("adduct_group", final_groups)
-    ]).select(new_column_order)
+    self.features_df = df_without_adducts.with_columns(
+        [
+            pl.Series("adduct", final_adducts),
+            pl.Series("adduct_charge", final_charges),
+            pl.Series("adduct_mass_shift", final_mass_shifts),
+            pl.Series("adduct_mass_neutral", final_neutral_masses),
+            pl.Series("adduct_group", final_groups),
+        ],
+    ).select(new_column_order)
 
     # Summary statistics
     total_with_adducts = sum(1 for x in final_adducts if x is not None)
     total_groups = max(final_groups) if final_groups else 0
-    
-    self.logger.info(f"Adduct detection completed: {total_with_adducts} features with adducts in {total_groups} groups")
+
+    self.logger.info(
+        f"Adduct detection completed: {total_with_adducts} features with adducts in {total_groups} groups",
+    )
 
     # Store parameters including the actual processed adducts list
     history_params = params.to_dict()
     # Convert the filtered adducts dataframe to a list of adduct specifications for history
-    history_params['adducts'] = adducts_df.select(['name', 'charge', 'mass_shift', 'probability']).to_dicts()
-    
+    history_params["adducts"] = adducts_df.select(
+        ["name", "charge", "mass_shift", "probability"],
+    ).to_dicts()
+
     self.store_history(["find_adducts"], history_params)
     self.logger.debug("Parameters stored successfully")
-