Update app.py

app.py

@@ -1,4 +1,7 @@
-# app.py
+# التثبيت (لو مش مثبت)
+!pip install rdkit-pypi py3Dmol transformers selfies biopython gradio -q
+
+# الاستيراد
 from Bio import PDB
 from transformers import AutoTokenizer, AutoModelForCausalLM
 from rdkit import Chem
@@ -20,11 +23,13 @@ model_name = "ncfrey/ChemGPT-1.2B"
 tokenizer = AutoTokenizer.from_pretrained(model_name)
 model = AutoModelForCausalLM.from_pretrained(model_name)
 
+# تحميل ملف PDB
 def load_pdb(file_obj):
     parser = PDB.PDBParser(QUIET=True)
     structure = parser.get_structure('protein', file_obj)
     return structure
 
+# عرض البروتين ثلاثي الأبعاد
 def get_protein_3d_html(pdb_str):
     view = py3Dmol.view(width=600, height=400)
     view.addModel(pdb_str, "pdb")
@@ -32,6 +37,7 @@ def get_protein_3d_html(pdb_str):
     view.zoomTo()
     return view._make_html()
 
+# تنظيف وتحويل SELFIES إلى SMILES
 def clean_and_decode_selfies(raw_output):
     tokens = re.findall(r'\[[^\[\]]+\]', raw_output)
     valid_tokens = [t for t in tokens if all(x not in t for x in ['Branch', 'Ring', 'expl'])]
@@ -44,6 +50,7 @@ def clean_and_decode_selfies(raw_output):
     except:
         return None
 
+# توليد SMILES
 def generate_multiple_valid_smiles(prompt, n=10, max_length=100):
     valid_smiles = set()
     tries = 0
@@ -64,6 +71,7 @@ def generate_multiple_valid_smiles(prompt, n=10, max_length=100):
         tries += 1
     return list(valid_smiles)
 
+# الوظيفة الرئيسية
 def generate_from_pdb(pdb_file):
     try:
         if isinstance(pdb_file, (str, bytes)):
@@ -73,13 +81,13 @@ def generate_from_pdb(pdb_file):
             pdb_str = pdb_bytes.decode('utf-8', errors='ignore')
 
         if len(pdb_str.strip()) == 0:
-            return "❌ The file is empty or invalid.", None, None
+            return "❌ الملف فارغ أو غير صالح", None, None
 
         pdb_file_io = io.StringIO(pdb_str)
         try:
             load_pdb(pdb_file_io)
         except Exception as e:
-            return f"❌ Error parsing the PDB file:\n{str(e)}", None, None
+            return f"❌ خطأ أثناء تحليل ملف PDB:\n{str(e)}", None, None
 
         html_3d = get_protein_3d_html(pdb_str)
 
@@ -87,61 +95,38 @@ def generate_from_pdb(pdb_file):
         smiles_list = generate_multiple_valid_smiles(prompt, n=10)
 
         if not smiles_list:
-            return "❌ No valid SMILES generated.", html_3d, None
+            return "❌ لم يتم توليد أي SMILES صالحة", html_3d, None
 
         smiles_txt = "\n".join(smiles_list)
         smiles_file_path = "/tmp/generated_smiles.txt"
         with open(smiles_file_path, "w") as f:
             f.write(smiles_txt)
 
-        return "✅ Molecules generated successfully.", html_3d, smiles_file_path
+        return "✅ تم توليد المركبات بنجاح", html_3d, smiles_file_path
 
     except Exception as e:
-        return f"❌ An unexpected error occurred:\n{str(e)}", None, None
+        return f"❌ حدث خطأ:\n{str(e)}", None, None
 
-# CSS to beautify the interface
+# CSS لتجميل الواجهة
 css = """
-body {
-    background-color: #f0f9ff;
-    font-family: 'Segoe UI', sans-serif;
-}
-h1 {
-    color: #003d66;
-    text-align: center;
-    font-size: 32px;
-}
-.gr-box {
-    border: 1px solid #cce7ff;
-    background-color: #ffffff;
-    border-radius: 15px;
-    padding: 20px;
-    box-shadow: 0 2px 8px rgba(0, 128, 255, 0.1);
-}
-button {
-    background-color: #007acc !important;
-    color: white !important;
-    font-weight: bold;
-    border-radius: 10px !important;
-}
+body {background-color: #f0f9ff;}
+h1 {color: #004d66; text-align: center;}
 """
 
+# واجهة Gradio
 with gr.Blocks(css=css) as demo:
-    gr.Markdown("""
-    <h1>🔬 Drug-like Molecule Generation from PDB using ChemGPT</h1>
-    <p>🧪 Upload a PDB file containing mutations in the KRAS protein. The system will generate suitable SMILES drug candidates.</p>
-    """)
+    gr.Markdown("<h1>🔬 Drug-like Molecule Generation from PDB using ChemGPT</h1>")
+    gr.Markdown("🧪 Upload a PDB file containing mutations in the KRAS protein. The system will generate suitable SMILES drug candidates.")
     with gr.Row():
         pdb_input = gr.File(label="📁 Upload PDB File")
-        run_btn = gr.Button("🚀 Generate Molecules")
-
+        run_btn = gr.Button("🚀 Generate Compounds")
     status = gr.Textbox(label="📢 Status")
-    view3d = gr.HTML(label="🧬 3D Structure View")
+    view3d = gr.HTML(label="🧬 3D Structure Viewer")
     file_output = gr.File(label="📄 Download SMILES File")
-
     run_btn.click(
         fn=generate_from_pdb,
         inputs=pdb_input,
         outputs=[status, view3d, file_output]
     )
 
-demo.launch(share=True)
+demo.launch(share=True)  # خليها True لو عايز لينك عام