Update

.ipynb_checkpoints/app-checkpoint.py

@@ -27,7 +27,7 @@ from gradio_molecule3d import Molecule3D
 # Biopython imports
 from Bio.PDB import PDBParser, Select, PDBIO
 from Bio.PDB.DSSP import DSSP
-from Bio.PDB import PDBList  # Corrected import
+from Bio.PDB import PDBList
 
 from matplotlib import cm  # For color mapping
 from matplotlib.colors import Normalize
@@ -225,7 +225,7 @@ def score_to_color(score):
 
 def process_pdb(pdb_id):
     # Fetch PDB file
-    pdbl = PDBList()  # Corrected instantiation
+    pdbl = PDBList()
     pdb_path = pdbl.retrieve_pdb_file(pdb_id, pdir='pdb_files', file_format='pdb')
 
     if not pdb_path or not os.path.exists(pdb_path):
@@ -243,20 +243,37 @@ def process_pdb(pdb_id):
     # Prepare result string
     result_str = "\n".join([f"{aa}: {score:.2f}" for aa, score in zip(sequence, normalized_scores)])
 
-    # Prepare residue-based coloring for Molecule3D
-    reps = []
-    for i, score in enumerate(normalized_scores):
-        reps.append({
+    # Prepare representations for Molecule3D
+    reps = [
+        {
             "model": 0,
-            "chain": chain.get_id(),
-            "residue_range": f"{i}-{i}",
-            "style": "stick",
-            "color": score_to_color(score),
-            "byres": True,
+            "style": "cartoon",
+            "color": "whiteCarbon",
+            "residue_range": "",
+            "around": 0,
+            "byres": False,
             "visible": True
-        })
+        }
+    ]
 
-    molecule_viewer = Molecule3D(reps=reps)
+    # 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
+            })
+
+    # Create Molecule3D with the PDB file and representations
+    molecule_viewer = Molecule3D(
+        file=filtered_pdb_path, 
+        reps=reps
+    )
 
     return result_str, molecule_viewer
 

app.py

@@ -27,7 +27,7 @@ from gradio_molecule3d import Molecule3D
 # Biopython imports
 from Bio.PDB import PDBParser, Select, PDBIO
 from Bio.PDB.DSSP import DSSP
-from Bio.PDB import PDBList  # Corrected import
+from Bio.PDB import PDBList
 
 from matplotlib import cm  # For color mapping
 from matplotlib.colors import Normalize
@@ -225,7 +225,7 @@ def score_to_color(score):
 
 def process_pdb(pdb_id):
     # Fetch PDB file
-    pdbl = PDBList()  # Corrected instantiation
+    pdbl = PDBList()
     pdb_path = pdbl.retrieve_pdb_file(pdb_id, pdir='pdb_files', file_format='pdb')
 
     if not pdb_path or not os.path.exists(pdb_path):
@@ -243,20 +243,37 @@ def process_pdb(pdb_id):
     # Prepare result string
     result_str = "\n".join([f"{aa}: {score:.2f}" for aa, score in zip(sequence, normalized_scores)])
 
-    # Prepare residue-based coloring for Molecule3D
-    reps = []
-    for i, score in enumerate(normalized_scores):
-        reps.append({
+    # Prepare representations for Molecule3D
+    reps = [
+        {
             "model": 0,
-            "chain": chain.get_id(),
-            "residue_range": f"{i}-{i}",
-            "style": "stick",
-            "color": score_to_color(score),
-            "byres": True,
+            "style": "cartoon",
+            "color": "whiteCarbon",
+            "residue_range": "",
+            "around": 0,
+            "byres": False,
             "visible": True
-        })
+        }
+    ]
 
-    molecule_viewer = Molecule3D(reps=reps)
+    # 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
+            })
+
+    # Create Molecule3D with the PDB file and representations
+    molecule_viewer = Molecule3D(
+        file=filtered_pdb_path, 
+        reps=reps
+    )
 
     return result_str, molecule_viewer