From da7b61932c95346068c03c841e03f4b6cbe706b0 Mon Sep 17 00:00:00 2001
From: Michael Strobel <lidstromfan29@gmail.com>
Date: Fri, 20 Feb 2026 15:00:01 -0800
Subject: [PATCH] Fix charge=0 breaking things.

---
 modifinder/classes/ModiFinder.py                   | 14 ++++++++++----
 .../engines/alignment/CosineAlignmentEngine.py     |  8 +++++---
 2 files changed, 15 insertions(+), 7 deletions(-)

diff --git a/modifinder/classes/ModiFinder.py b/modifinder/classes/ModiFinder.py
index 38b5080..7d912ea 100644
--- a/modifinder/classes/ModiFinder.py
+++ b/modifinder/classes/ModiFinder.py
@@ -136,18 +136,20 @@ def __init__(
         --------
 
         """
-
         self.network = None
         self.unknowns = None
         self.ppm_tolerance = ppm_tolerance
+
+        # Add ppm_tolerance to kwargs
+        kwargs["ppm_tolerance"] = ppm_tolerance
         
         if alignmentEngine is None:
-            self.alignmentEngine = CosineAlignmentEngine(ppm_tolerance = self.ppm_tolerance, **kwargs)
+            self.alignmentEngine = CosineAlignmentEngine(**kwargs)
         else:
             self.alignmentEngine = alignmentEngine
         
         if annotationEngine is None:
-            self.annotationEngine = MAGMaAnnotationEngine(ppm_tolerance = self.ppm_tolerance, **kwargs)
+            self.annotationEngine = MAGMaAnnotationEngine(**kwargs)
         else:
             self.annotationEngine = annotationEngine
 
@@ -230,7 +232,11 @@ def add_adjusted_edge(self, u, v, edgeDetail: EdgeDetail = None, **kwargs):
         smaller = u if self.network.nodes[u]["compound"].spectrum.precursor_mz <= self.network.nodes[v]["compound"].spectrum.precursor_mz else v
         larger = u if self.network.nodes[u]["compound"].spectrum.precursor_mz > self.network.nodes[v]["compound"].spectrum.precursor_mz else v
         if edgeDetail is None:
-            edgeDetail = self.alignmentEngine.align_single(self.network.nodes[smaller]["compound"].spectrum, self.network.nodes[larger]["compound"].spectrum, **kwargs)
+
+            edgeDetail = self.alignmentEngine.align_single(
+                self.network.nodes[smaller]["compound"].spectrum,
+                self.network.nodes[larger]["compound"].spectrum, 
+                **kwargs)
         
         self.update_edge(smaller, larger, edgeDetail, **kwargs)
     
diff --git a/modifinder/engines/alignment/CosineAlignmentEngine.py b/modifinder/engines/alignment/CosineAlignmentEngine.py
index d49524d..c02e839 100644
--- a/modifinder/engines/alignment/CosineAlignmentEngine.py
+++ b/modifinder/engines/alignment/CosineAlignmentEngine.py
@@ -26,16 +26,17 @@ def _cosine_fast(
         spec_other (Spectrum): Second spectrum
         mz_tolerance (float): Tolerance in Da for fragment m/z values, if None, it is not used.
         ppm_tolerance (float): Tolerance in ppm for fragment m/z values, if None, it is not used.
-        allow_shift (bool): _description_
+        allow_shift (bool): Shift for m/z values. If not 0, hybrid search is performed. shift = prec_mz(qry) - prec_mz(ref)
 
     Returns:
         Tuple[float, List[Tuple[int, int]]]: _description_
     """
-    
+
     if mz_tolerance is None and ppm_tolerance is None:
         raise ModiFinderError("At least one of mz_tolerance or ppm_tolerance must be provided.")
-    
     precursor_charge = spec.precursor_charge if spec.precursor_charge is not None else 1
+    if precursor_charge == 0:
+        precursor_charge = 1
     precursor_mass_diff = (
         spec.precursor_mz - spec_other.precursor_mz
     ) * precursor_charge
@@ -169,6 +170,7 @@ def align_single(
         Returns:
             EdgeDetail: the edge detail object
         """
+
         cosine, matched_peaks = _cosine_fast(
             SpectrumTuple1,
             SpectrumTuple2,