Update app.py

app.py

@@ -2,48 +2,41 @@ import os
 import tempfile
 import numpy as np
 import gradio as gr
-from ase.io import read
+from ase.io import read, write
 from ase.io.trajectory import Trajectory
 import hashlib
 
 # ==== Usar componente nativo Molecule3D ====
 try:
     from gradio_molecule3d import Molecule3D
-    HAVE_MOL3D = True  
+    HAVE_MOL3D = True
     print("✅ gradio_molecule3d loaded successfully")
 except Exception as e:
     HAVE_MOL3D = False
     print(f"❌ gradio_molecule3d not available: {e}")
 
-# ==== Función para convertir trayectoria a archivo temporal XYZ ====
+# ==== Función para convertir trayectoria a archivo temporal PDB ====
 def traj_to_molecule3d_file(traj_path):
     """
-    Convierte una trayectoria ASE (.traj) a un archivo XYZ temporal para Molecule3D.
-    Retorna el path del archivo temporal.
+    Convierte una trayectoria ASE (.traj) a un archivo PDB temporal para Molecule3D.
+    Retorna el path del archivo temporal (.pdb).
     """
     if not traj_path or not os.path.exists(traj_path):
         return None
-    
     try:
         traj = Trajectory(traj_path)
         if len(traj) == 0:
             return None
-            
+
         # Usar último frame para visualización estática
         atoms = traj[-1]
-        
-        # Crear archivo XYZ temporal
-        with tempfile.NamedTemporaryFile(mode='w', suffix='.xyz', delete=False) as f:
-            symbols = atoms.get_chemical_symbols()
-            coords = atoms.get_positions()
-            
-            f.write(f"{len(symbols)}\n")
-            f.write("Generated by OrbMol\n")
-            for s, (x, y, z) in zip(symbols, coords):
-                f.write(f"{s} {x:.6f} {y:.6f} {z:.6f}\n")
-            
-            return f.name
-        
+
+        # Crear archivo PDB temporal (formato aceptado por Molecule3D)
+        with tempfile.NamedTemporaryFile(suffix=".pdb", delete=False) as f:
+            pdb_path = f.name
+        write(pdb_path, atoms)  # extensión .pdb selecciona el formato automáticamente
+        return pdb_path
+
     except Exception as e:
         print(f"Error converting trajectory: {e}")
         return None
@@ -55,9 +48,9 @@ def traj_to_html(traj_path, width=520, height=520, interval_ms=200):
     """
     if not traj_path or not os.path.exists(traj_path):
         return "<div style='color:#b00; padding:20px;'>No trajectory file found</div>"
-    
+
     viewer_id = f"viewer_{abs(hash(traj_path)) % 10000}"
-    
+
     try:
         traj = Trajectory(traj_path)
         if len(traj) == 0:
@@ -95,11 +88,11 @@ if (typeof window.$3Dmol === 'undefined') {{
 function initViewer_{viewer_id}() {{
     var el = document.getElementById("{viewer_id}");
     if (!el || typeof $3Dmol === "undefined") return;
-    
+
     var viewer = $3Dmol.createViewer(el, {{backgroundColor: 'white'}});
     var frames = {frames_json};
     var currentFrame = 0;
-    
+
     function showFrame(frameIndex) {{
         viewer.clear();
         viewer.addModel(frames[frameIndex], "xyz");
@@ -107,9 +100,9 @@ function initViewer_{viewer_id}() {{
         viewer.zoomTo();
         viewer.render();
     }}
-    
+
     showFrame(0);
-    
+
     if (frames.length > 1) {{
         setInterval(function() {{
             currentFrame = (currentFrame + 1) % frames.length;
@@ -213,8 +206,8 @@ def md_wrapper(xyz_content, charge, spin, steps, tempK, timestep_fs, ensemble):
 
         # Usar Molecule3D si está disponible, sino HTML
         if HAVE_MOL3D:
-            xyz_file = traj_to_molecule3d_file(traj_path)
-            return (status, traj_path, log_text, script_text, explanation, xyz_file, "")
+            pdb_file = traj_to_molecule3d_file(traj_path)
+            return (status, traj_path, log_text, script_text, explanation, pdb_file, "")
         else:
             html_value = traj_to_html(traj_path)
             return (status, traj_path, log_text, script_text, explanation, None, html_value)
@@ -244,8 +237,8 @@ def relax_wrapper(xyz_content, steps, fmax, charge, spin, relax_cell):
 
         # Usar Molecule3D si está disponible, sino HTML
         if HAVE_MOL3D:
-            xyz_file = traj_to_molecule3d_file(traj_path)
-            return (status, traj_path, log_text, script_text, explanation, xyz_file, "")
+            pdb_file = traj_to_molecule3d_file(traj_path)
+            return (status, traj_path, log_text, script_text, explanation, pdb_file, "")
         else:
             html_value = traj_to_html(traj_path)
             return (status, traj_path, log_text, script_text, explanation, None, html_value)
@@ -254,8 +247,10 @@ def relax_wrapper(xyz_content, steps, fmax, charge, spin, relax_cell):
         return (f"Error: {e}", None, "", "", "", None, "")
     finally:
         if tmp_created and isinstance(path_or_str, str) and os.path.exists(path_or_str):
-            try: os.remove(path_or_str)
-            except Exception: pass
+            try:
+                os.remove(path_or_str)
+            except Exception:
+                pass
 
 # ==== Ejemplos (sin cambios) ====
 examples = [
@@ -317,7 +312,7 @@ with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo:
                 with gr.Column(variant="panel", min_width=520):
                     md_status = gr.Textbox(label="MD Status", interactive=False)
                     md_traj = gr.File(label="Trajectory (.traj)", interactive=False)
-                    
+
                     # Usar Molecule3D si está disponible
                     if HAVE_MOL3D:
                         md_viewer = Molecule3D(label="3D Molecular Viewer")
@@ -325,7 +320,7 @@ with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo:
                     else:
                         md_viewer = gr.HTML(visible=False)  # Placeholder
                         md_html = gr.HTML(label="Trajectory Viewer")
-                    
+
                     md_log = gr.Textbox(label="Log", interactive=False, lines=15, max_lines=25)
                     md_script = gr.Code(label="Reproduction Script", language="python", interactive=False, lines=20, max_lines=30)
                     md_explain = gr.Markdown()
@@ -352,7 +347,7 @@ with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo:
                 with gr.Column(variant="panel", min_width=520):
                     rlx_status = gr.Textbox(label="Status", interactive=False)
                     rlx_traj = gr.File(label="Trajectory (.traj)", interactive=False)
-                    
+
                     # Usar Molecule3D si está disponible
                     if HAVE_MOL3D:
                         rlx_viewer = Molecule3D(label="Final Structure")
@@ -360,7 +355,7 @@ with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo:
                     else:
                         rlx_viewer = gr.HTML(visible=False)  # Placeholder
                         rlx_html = gr.HTML(label="Final Structure")
-                    
+
                     rlx_log = gr.Textbox(label="Log", interactive=False, lines=15, max_lines=25)
                     rlx_script = gr.Code(label="Reproduction Script", language="python", interactive=False, lines=20, max_lines=30)
                     rlx_explain = gr.Markdown()
@@ -375,4 +370,4 @@ print("Starting OrbMol model loading…")
 _ = _load_orbmol_calc()
 
 if __name__ == "__main__":
-    demo.launch(server_name="0.0.0.0", server_port=7860, show_error=True)
+    demo.launch(server_name="0.0.0.0", server_port=7860, show_error=True)