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app.py

@@ -7,9 +7,8 @@ from datetime import datetime
 import gradio as gr
 import pandas as pd
 from huggingface_hub import snapshot_download
-
 from rdkit import Chem
-from rdkit.Chem import Descriptors, Crippen, Lipinski, rdMolDescriptors, QED
+from rdkit.Chem import Descriptors, Crippen, Lipinski, rdMolDescriptors, QED, AllChem
 
 
 BUNDLE_REPO = os.getenv("BUNDLE_REPO", "abdullahsamra/egfr-ai-bundle")
@@ -155,8 +154,8 @@ def score_smiles(smiles_text):
             "Outputs are computational predictions only.",
         ],
     }
-
-    return df, response
+    csv_path = write_results_csv(df)
+    return df, response, csv_path
 
 
 def get_example_table():
@@ -423,7 +422,80 @@ def generate_job_demo(num_molecules, return_top_k, docking_mode, generation_back
     return job_summary, df, response, str(csv_path)
 
 
+def write_results_csv(df: pd.DataFrame, filename: str = "score_smiles_results.csv"):
+    out_dir = Path("outputs")
+    out_dir.mkdir(parents=True, exist_ok=True)
+    out_path = out_dir / filename
+    df.to_csv(out_path, index=False)
+    return str(out_path)
+
+
+def smiles_to_3d_file(smiles: str, file_format: str = "sdf"):
+    smiles = str(smiles).strip()
+    file_format = str(file_format).lower().strip()
+
+    if file_format not in ["sdf", "mol", "pdb"]:
+        return None, {
+            "status": "error",
+            "message": "Unsupported format. Choose sdf, mol, or pdb.",
+        }
+
+    mol = Chem.MolFromSmiles(smiles)
+    if mol is None:
+        return None, {
+            "status": "error",
+            "input_smiles": smiles,
+            "message": "Invalid SMILES.",
+        }
+
+    canonical_smiles = Chem.MolToSmiles(mol, isomericSmiles=True)
+
+    mol = Chem.AddHs(mol)
+
+    params = AllChem.ETKDGv3()
+    params.randomSeed = 42
+
+    embed_status = AllChem.EmbedMolecule(mol, params)
+    if embed_status != 0:
+        return None, {
+            "status": "error",
+            "input_smiles": smiles,
+            "canonical_smiles": canonical_smiles,
+            "message": "3D embedding failed.",
+        }
+
+    try:
+        AllChem.UFFOptimizeMolecule(mol, maxIters=500)
+        optimization_status = "UFF optimized"
+    except Exception as e:
+        optimization_status = f"UFF optimization failed, using embedded geometry only: {e}"
+
+    out_dir = Path("outputs/ligands")
+    out_dir.mkdir(parents=True, exist_ok=True)
+
+    safe_name = "ligand_3d"
+    out_path = out_dir / f"{safe_name}.{file_format}"
+
+    if file_format == "sdf":
+        writer = Chem.SDWriter(str(out_path))
+        writer.write(mol)
+        writer.close()
+    elif file_format == "mol":
+        Chem.MolToMolFile(mol, str(out_path))
+    elif file_format == "pdb":
+        Chem.MolToPDBFile(mol, str(out_path))
+
+    meta = {
+        "status": "completed",
+        "input_smiles": smiles,
+        "canonical_smiles": canonical_smiles,
+        "file_format": file_format,
+        "file_path": str(out_path),
+        "optimization_status": optimization_status,
+        "note": "This is a generated 3D conformer from SMILES, not a docked protein-ligand pose.",
+    }
 
+    return str(out_path), meta
 
 loaded_ok, loaded_msg = download_bundle_light()
 
@@ -466,6 +538,8 @@ Important:
         score_btn = gr.Button("Score SMILES")
         score_table = gr.Dataframe(label="Results table")
         score_json = gr.JSON(label="Backend-style JSON response")
+        score_csv = gr.File(label="Download CSV")
+
 
         score_btn.click(
             score_smiles,
@@ -553,6 +627,43 @@ Generate -> Enrich -> Optional Docking
             outputs=[example_table, example_json],
         )
 
+        with gr.Tab("SMILES to 3D File"):
+            gr.Markdown(
+            """
+Convert a SMILES string into a downloadable 3D ligand file.
+
+Supported formats:
+
+- SDF
+- MOL
+- PDB
+
+Important: this creates a 3D conformer from SMILES. It is not a docked pose inside the EGFR binding pocket.
+"""
+        )
+
+        smiles_3d_input = gr.Textbox(
+            label="SMILES",
+            value="CCO",
+            lines=2,
+        )
+
+        format_input = gr.Radio(
+            choices=["sdf", "mol", "pdb"],
+            value="sdf",
+            label="Output file format",
+        )
+
+        make_3d_btn = gr.Button("Generate 3D ligand file")
+        ligand_file = gr.File(label="Download 3D ligand file")
+        ligand_meta = gr.JSON(label="3D file metadata")
+
+        make_3d_btn.click(
+            smiles_to_3d_file,
+            inputs=[smiles_3d_input, format_input],
+            outputs=[ligand_file, ligand_meta],
+        )
+        
     with gr.Tab("Docking Contract"):
         gr.Markdown(
             """