Update

.ipynb_checkpoints/app-checkpoint.py

@@ -215,10 +215,10 @@ def fetch_pdb(pdb_id):
         print(f"Error fetching PDB: {e}")
         return None
 
-# Function to map scores to colors (blue for low scores, red for high scores)
+
 def score_to_color(score):
-    norm = Normalize(vmin=0, vmax=1)  # Assuming scores are normalized between 0 and 1
-    color_map = cm.get_cmap('coolwarm')  # Use a blue-to-red colormap
+    norm = Normalize(vmin=0, vmax=1)  # Normalize scores between 0 and 1
+    color_map = cm.coolwarm  # Directly use the colormap (e.g., 'cividis', 'coolwarm', etc.)
     rgba = color_map(norm(score))  # Get RGBA values
     hex_color = '#{:02x}{:02x}{:02x}'.format(int(rgba[0] * 255), int(rgba[1] * 255), int(rgba[2] * 255))
     return hex_color
@@ -247,8 +247,10 @@ def process_pdb(pdb_id):
     reps = [
         {
             "model": 0,
+            "chain": "",
+            "resname": "",
             "style": "cartoon",
-            "color": "whiteCarbon",
+            "color": "spectrum",
             "residue_range": "",
             "around": 0,
             "byres": False,
@@ -257,21 +259,20 @@ def process_pdb(pdb_id):
     ]
 
     # Add color-coded residues based on binding site scores
-    for i, score in enumerate(normalized_scores):
-        if score > 0.7:  # You can adjust this threshold
-            reps.append({
-                "model": 0,
-                "chain": chain.get_id(),
-                "style": "stick",
-                "color": score_to_color(score),
-                "residue_range": f"{i+1}-{i+1}",
-                "byres": True,
-                "visible": True
-            })
+    #for i, score in enumerate(normalized_scores):
+    #    if score > 0.7:  # You can adjust this threshold
+    #        reps.append({
+    #            "model": 0,
+    #            "chain": chain.get_id(),
+    #            "style": "stick",
+    #            "color": score_to_color(score),
+    #            "residue_range": f"{i+1}-{i+1}",
+    #            "byres": True,
+    #            "visible": True
+    #        })
 
     # Create Molecule3D with the PDB file and representations
     molecule_viewer = Molecule3D(
-        file=filtered_pdb_path, 
         reps=reps
     )
 

app.py

@@ -215,10 +215,10 @@ def fetch_pdb(pdb_id):
         print(f"Error fetching PDB: {e}")
         return None
 
-# Function to map scores to colors (blue for low scores, red for high scores)
+
 def score_to_color(score):
-    norm = Normalize(vmin=0, vmax=1)  # Assuming scores are normalized between 0 and 1
-    color_map = cm.get_cmap('coolwarm')  # Use a blue-to-red colormap
+    norm = Normalize(vmin=0, vmax=1)  # Normalize scores between 0 and 1
+    color_map = cm.coolwarm  # Directly use the colormap (e.g., 'cividis', 'coolwarm', etc.)
     rgba = color_map(norm(score))  # Get RGBA values
     hex_color = '#{:02x}{:02x}{:02x}'.format(int(rgba[0] * 255), int(rgba[1] * 255), int(rgba[2] * 255))
     return hex_color
@@ -247,8 +247,10 @@ def process_pdb(pdb_id):
     reps = [
         {
             "model": 0,
+            "chain": "",
+            "resname": "",
             "style": "cartoon",
-            "color": "whiteCarbon",
+            "color": "spectrum",
             "residue_range": "",
             "around": 0,
             "byres": False,
@@ -257,21 +259,20 @@ def process_pdb(pdb_id):
     ]
 
     # Add color-coded residues based on binding site scores
-    for i, score in enumerate(normalized_scores):
-        if score > 0.7:  # You can adjust this threshold
-            reps.append({
-                "model": 0,
-                "chain": chain.get_id(),
-                "style": "stick",
-                "color": score_to_color(score),
-                "residue_range": f"{i+1}-{i+1}",
-                "byres": True,
-                "visible": True
-            })
+    #for i, score in enumerate(normalized_scores):
+    #    if score > 0.7:  # You can adjust this threshold
+    #        reps.append({
+    #            "model": 0,
+    #            "chain": chain.get_id(),
+    #            "style": "stick",
+    #            "color": score_to_color(score),
+    #            "residue_range": f"{i+1}-{i+1}",
+    #            "byres": True,
+    #            "visible": True
+    #        })
 
     # Create Molecule3D with the PDB file and representations
     molecule_viewer = Molecule3D(
-        file=filtered_pdb_path, 
         reps=reps
     )