Feng Change tot the processor for the SAXS L1 loss

src/metfish/analysis/processor.py

@@ -8,7 +8,7 @@
 from biopandas.pdb import PandasPdb
 from typing import List, Dict, Tuple, Optional
 
-from metfish.utils import get_lddt, save_aligned_pdb, get_Pr
+from metfish.utils import get_rmsd, get_lddt, save_aligned_pdb, get_Pr
 
 
 class ProteinStructureAnalyzer:
@@ -35,6 +35,9 @@ def calculate_metrics(self,
 
         # Calculate SAXS KL divergence
         saxs_kldiv = self._calculate_saxs_kldiv(p_of_r_a, p_of_r_b, r_a, r_b)
+
+        # Calculate SAXS L1 loss
+        saxs_l1 = self._calculate_saxs_l1(p_of_r_a, p_of_r_b, r_a, r_b)
 
         # calculate radius of gyration
         md_obj_a = md.load(fname_a)
@@ -55,6 +58,7 @@ def calculate_metrics(self,
             'rmsd': rmsd,
             'lddt': lddt,
             'saxs_kldiv': saxs_kldiv,
+            'saxs_l1': saxs_l1,
             'rg_a': rg_a,
             'rg_b': rg_b,
             'rg_diff': rg_diff,
@@ -86,6 +90,25 @@ def _calculate_saxs_kldiv(self,
         saxs_b_padded = (saxs_b_padded + eps) / np.sum(saxs_b_padded + eps)
 
         return np.sum(rel_entr(saxs_a_padded, saxs_b_padded))
+
+    def _calculate_saxs_l1(self, 
+                          p_of_r_a: np.ndarray, 
+                          p_of_r_b: np.ndarray,
+                          r_a: np.ndarray,
+                          r_b: np.ndarray) -> float:
+        """Calculate L1 loss (MAE) between SAXS profiles."""
+        max_len = max(len(r_a), len(r_b))
+
+        # Pad both arrays to same length
+        saxs_a_padded = np.pad(p_of_r_a, (0, max_len - len(r_a)), 
+                              mode='constant', constant_values=0)
+        saxs_b_padded = np.pad(p_of_r_b, (0, max_len - len(r_b)), 
+                              mode='constant', constant_values=0)
+
+        # Calculate L1 loss (sum of absolute differences)
+        return np.sum(np.abs(saxs_a_padded - saxs_b_padded))
+
+
 
 class ModelComparisonProcessor:
     """Process and create comparison dataframes for multiple models."""
@@ -118,15 +141,35 @@ def _get_apo_holo_pairs(self) -> List[Tuple[str, str]]:
         return None
 
     def _create_comparisons_list(self) -> List[Tuple[str, str]]:
-        comparisons=[('out', 'target'), ('out', 'out_alt'), ('target', 'target_alt')]
-        all_comparisons = [
-            tuple(c.replace('out', f'out_{t}') for c in comp)
-            for comp in comparisons
-            if any('out' == x or 'out_alt' == x for x in comp)
-            for t in self.tags
-        ]
-        all_comparisons.extend([tuple(f'out_{x}' for x in comb) for comb in itertools.combinations(self.tags, 2)])
-        return all_comparisons
+        """
+        Generate all comparison pairs for protein structure analysis.
+
+        Returns:
+            List of (structure_a, structure_b) tuples representing all comparisons:
+            - 3 model vs target comparisons (AF vs target, NMR vs target, NMA vs target)
+            - 3 model vs alternative structure comparisons (AF vs AF_alt, NMR vs NMR_alt, NMA vs NMA_alt)
+            - 1 target vs alternative target comparison (target vs target_alt)
+            - 3 cross-model comparisons (AF vs NMR, AF vs NMA, NMR vs NMA)
+            Total: 10 comparisons per protein
+        """
+        comparisons = []
+
+        # 1. Each model vs target (3 comparisons)
+        for model_tag in self.tags.keys():
+            comparisons.append((f'out_{model_tag}', 'target'))
+
+        # 2. Each model vs its alternative structure (3 comparisons)
+        for model_tag in self.tags.keys():
+            comparisons.append((f'out_{model_tag}', f'out_alt_{model_tag}'))
+
+        # 3. Target vs alternative target (1 comparison)
+        comparisons.append(('target', 'target_alt'))
+
+        # 4. Cross-model comparisons (3 comparisons: AF vs NMR, AF vs NMA, NMR vs NMA)
+        for model_a, model_b in itertools.combinations(self.tags.keys(), 2):
+            comparisons.append((f'out_{model_a}', f'out_{model_b}'))
+
+        return comparisons
 
     def get_comparison_df(self,
                           names: List[str] = None,

src/metfish/analysis/visualizer.py

@@ -263,4 +263,4 @@ def _plot_protein_saxs_summary(self, name: str, ax: plt.Axes):
         ax.set_ylabel('P(r)', fontsize=8)
         ax.set_title(name, fontsize=9, fontweight='bold')
         sns.despine(ax=ax)
-
+