Update app.py

app.py

@@ -9,6 +9,7 @@ import matplotlib.pyplot as plt
 import seaborn as sns
 import requests
 import io
+import re
 from PIL import Image
 import base64
 
@@ -320,6 +321,8 @@ def predict_admet_properties(smiles_dict: dict):
     log += f"✅ Predicted ADMET properties for {len(df)} molecules.\n"
     return df, log
 
+# --- MODIFIED FUNCTION ---
+# This is the updated function from the old app to correctly render 2D molecules.
 def visualize_molecule_2d_3d(smiles: str, name: str):
     """Generates a side-by-side 2D SVG and 3D py3Dmol HTML view for a single molecule."""
     log = ""
@@ -328,16 +331,21 @@ def visualize_molecule_2d_3d(smiles: str, name: str):
         if not mol: return f"<p>Invalid SMILES for {name}</p>", f"❌ Invalid SMILES for {name}"
         
         drawer = Draw.rdMolDraw2D.MolDraw2DSVG(400, 300)
+        # Set dark theme colors for 2D drawing
         drawer.drawOptions().clearBackground = False
         drawer.drawOptions().addStereoAnnotation = True
         drawer.drawOptions().baseFontSize = 0.8
         drawer.drawOptions().circleAtoms = False
-        drawer.drawOptions().highlightColour = (1, 0.5, 0)
-        drawer.drawOptions().backgroundColour = (0.11, 0.11, 0.11)
-        drawer.drawOptions().symbolColour = (1, 1, 1)
-        drawer.drawOptions().defaultColour = (1, 1, 1)
+        drawer.drawOptions().highlightColour = (1, 0.5, 0)  # Orange for highlights
+        
+        # Set colors for dark background visibility
+        drawer.drawOptions().backgroundColour = (0.11, 0.11, 0.11)  # Dark background
+        drawer.drawOptions().symbolColour = (1, 1, 1)  # White symbols
+        drawer.drawOptions().defaultColour = (1, 1, 1)  # White default color
+        
+        # Try to set annotation color (this might help with (R)/(S) labels)
         try:
-            drawer.drawOptions().annotationColour = (1, 1, 1)
+            drawer.drawOptions().annotationColour = (1, 1, 1)  # White annotations
         except:
             pass
 
@@ -345,13 +353,51 @@ def visualize_molecule_2d_3d(smiles: str, name: str):
         drawer.FinishDrawing()
         svg_2d = drawer.GetDrawingText().replace('svg:', '')
 
-        import re
+        # More aggressive SVG text color fixes - target all possible black text variations
+        
+        # First, comprehensive string replacements
         svg_2d = svg_2d.replace('stroke="black"', 'stroke="white"')
         svg_2d = svg_2d.replace('fill="black"', 'fill="white"')
         svg_2d = svg_2d.replace('stroke="#000000"', 'stroke="#FFFFFF"')
         svg_2d = svg_2d.replace('fill="#000000"', 'fill="#FFFFFF"')
+        svg_2d = svg_2d.replace('stroke="#000"', 'stroke="#FFF"')
+        svg_2d = svg_2d.replace('fill="#000"', 'fill="#FFF"')
+        svg_2d = svg_2d.replace('stroke:black', 'stroke:white')
+        svg_2d = svg_2d.replace('fill:black', 'fill:white')
+        svg_2d = svg_2d.replace('stroke:#000000', 'stroke:#FFFFFF')
+        svg_2d = svg_2d.replace('fill:#000000', 'fill:#FFFFFF')
+        svg_2d = svg_2d.replace('stroke:#000', 'stroke:#FFF')
+        svg_2d = svg_2d.replace('fill:#000', 'fill:#FFF')
+        svg_2d = svg_2d.replace('stroke="rgb(0,0,0)"', 'stroke="rgb(255,255,255)"')
+        svg_2d = svg_2d.replace('fill="rgb(0,0,0)"', 'fill="rgb(255,255,255)"')
+        svg_2d = svg_2d.replace('stroke:rgb(0,0,0)', 'stroke:rgb(255,255,255)')
+        svg_2d = svg_2d.replace('fill:rgb(0,0,0)', 'fill:rgb(255,255,255)')
+        svg_2d = svg_2d.replace('color="black"', 'color="white"')
+        svg_2d = svg_2d.replace('color:#000000', 'color:#FFFFFF')
+        svg_2d = svg_2d.replace('color:#000', 'color:#FFF')
+        
+        # Aggressive regex-based fixes for all text elements
+        # Remove any existing fill attributes from text elements and add white fill
+        svg_2d = re.sub(r'<text([^>]*?)\s+fill="[^"]*"([^>]*?)>', r'<text\1\2 fill="white">', svg_2d)
+        svg_2d = re.sub(r'<text([^>]*?)(?<!fill="white")>', r'<text\1 fill="white">', svg_2d)
+        
+        # Fix style attributes in text elements
+        svg_2d = re.sub(r'<text([^>]*?)style="([^"]*?)fill:\s*(?:black|#000000|#000|rgb\(0,0,0\))([^"]*?)"([^>]*?)>', 
+                       r'<text\1style="\2fill:white\3"\4>', svg_2d)
+        
+        # If text elements don't have any fill specified, ensure they get white
         svg_2d = re.sub(r'<text(?![^>]*fill=)([^>]*?)>', r'<text fill="white"\1>', svg_2d)
         
+        # Clean up any duplicate fill attributes
+        svg_2d = re.sub(r'fill="white"\s+fill="white"', 'fill="white"', svg_2d)
+        
+        # Final catch-all: replace any remaining black in the entire SVG
+        svg_2d = re.sub(r'\bblack\b', 'white', svg_2d)
+        svg_2d = re.sub(r'#000000', '#FFFFFF', svg_2d)
+        svg_2d = re.sub(r'#000\b', '#FFF', svg_2d)
+        svg_2d = re.sub(r'rgb\(0,\s*0,\s*0\)', 'rgb(255,255,255)', svg_2d)
+        
+        # Embed the SVG within a div with a dark background for consistency
         svg_2d = f'<div style="background-color: #1C1C1C; padding: 10px; border-radius: 5px;">{svg_2d}</div>'
 
         mol_3d = Chem.AddHs(mol)
@@ -546,18 +592,14 @@ with tab1:
         props_df, log_props = calculate_molecular_properties(smiles_list)
         full_log += log_props
         
-        # --- MODIFIED LOGIC ---
-        # assess_drug_likeness now returns two dataframes: one for analysis/plotting, one for display
         analysis_df, display_df, log_lipinski = assess_drug_likeness(props_df)
         full_log += log_lipinski
         
-        # The plotting function uses the 'analysis_df' with the boolean 'Drug_Like' column
         props_plot, log_plot = plot_properties_dashboard(analysis_df)
         full_log += log_plot
         full_log += "\n--- Phase 1 Analysis Complete ---"
         st.session_state.log_p1 = full_log
         
-        # The display dataframe has the pretty emojis
         lipinski_cols = ['Molecule', 'MW', 'LogP', 'HBD', 'HBA', 'Lipinski_Violations', 'Drug_Like']
         lipinski_subset_df = display_df[lipinski_cols] if not display_df.empty else pd.DataFrame(columns=lipinski_cols)