Update app.py

app.py

@@ -6,58 +6,19 @@ 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
-    print("✅ gradio_molecule3d loaded successfully")
-except Exception as e:
-    HAVE_MOL3D = False
-    print(f"❌ gradio_molecule3d not available: {e}")
-
-# ==== Convierte .traj -> contenido PDB (string) para Molecule3D ====
-def traj_to_molecule3d_file(traj_path):
-    """
-    Lee el último frame de una .traj y devuelve el CONTENIDO PDB (string)
-    para pasarlo directamente a Molecule3D. No devuelve una ruta.
-    """
-    if not traj_path or not os.path.exists(traj_path):
-        return None
-    try:
-        traj = Trajectory(traj_path)
-        if len(traj) == 0:
-            return None
-
-        atoms = traj[-1]
+# ==== Forzar visor HTML con 3Dmol.js ====
+# (desactiva Molecule3D porque requiere formatos con conectividad)
+HAVE_MOL3D = False
 
-        # Escribir a PDB temporal y devolver su contenido como string
-        with tempfile.NamedTemporaryFile(suffix=".pdb", delete=False) as f:
-            pdb_path = f.name
-        write(pdb_path, atoms)
-
-        try:
-            with open(pdb_path, "r", encoding="utf-8", errors="ignore") as fh:
-                pdb_text = fh.read()
-        finally:
-            try:
-                os.remove(pdb_path)
-            except Exception:
-                pass
-
-        return pdb_text
-    except Exception as e:
-        print(f"Error converting trajectory: {e}")
-        return None
-
-# ==== Fallback HTML con 3Dmol.js (por si acaso) ====
+# ==== Fallback HTML con 3Dmol.js ====
 def traj_to_html(traj_path, width=520, height=520, interval_ms=200):
     """
-    Fallback HTML viewer (solo si Molecule3D no está disponible).
+    Lee una .traj de ASE y genera un visor HTML (3Dmol.js) con animación.
     """
     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}"
+    viewer_id = f"viewer_{abs(hash(traj_path)) % 100000}"
 
     try:
         traj = Trajectory(traj_path)
@@ -79,50 +40,47 @@ def traj_to_html(traj_path, width=520, height=520, interval_ms=200):
 
     html = f"""
 <div style="margin-bottom:10px; padding:10px; background:#f5f5f5; border-radius:5px;">
-    <strong>🧬 3D Molecular Viewer</strong> - {len(xyz_frames)} frames
+  <strong>🧬 3D Molecular Viewer</strong> — {len(xyz_frames)} frames
 </div>
 <div id="{viewer_id}" style="width:{width}px; height:{height}px; position:relative; border:2px solid #ddd; border-radius:8px; background:#fafafa;"></div>
 <script>
 if (typeof window.$3Dmol === 'undefined') {{
-    var script = document.createElement('script');
-    script.src = 'https://3dmol.org/build/3Dmol-min.js';
-    script.onload = function() {{
-        setTimeout(function() {{ initViewer_{viewer_id}(); }}, 100);
-    }};
-    document.head.appendChild(script);
+  var script = document.createElement('script');
+  script.src = 'https://3dmol.org/build/3Dmol-min.js';
+  script.onload = function() {{ setTimeout(function() {{ initViewer_{viewer_id}(); }}, 100); }};
+  document.head.appendChild(script);
 }} else {{
-    initViewer_{viewer_id}();
+  initViewer_{viewer_id}();
 }}
 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");
-        viewer.setStyle({{}}, {{stick: {{radius: 0.1}}, sphere: {{radius: 0.3}}}});
-        viewer.zoomTo();
-        viewer.render();
-    }}
-
-    showFrame(0);
-
-    if (frames.length > 1) {{
-        setInterval(function() {{
-            currentFrame = (currentFrame + 1) % frames.length;
-            showFrame(currentFrame);
-        }}, {interval_ms});
-    }}
+  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(i) {{
+    viewer.clear();
+    viewer.addModel(frames[i], "xyz");
+    viewer.setStyle({{}}, {{stick: {{}}, sphere: {{}}}});
+    viewer.zoomTo();
+    viewer.render();
+  }}
+
+  showFrame(0);
+  if (frames.length > 1) {{
+    setInterval(function() {{
+      currentFrame = (currentFrame + 1) % frames.length;
+      showFrame(currentFrame);
+    }}, {interval_ms});
+  }}
 }}
 </script>
 """
     return html
 
-# ==== OrbMol SPE directo (sin cambios) ====
+# ==== OrbMol SPE ====
 from orb_models.forcefield import pretrained
 from orb_models.forcefield.calculator import ORBCalculator
 
@@ -138,7 +96,7 @@ def _load_orbmol_calc():
 
 def predict_molecule(xyz_content, charge=0, spin_multiplicity=1):
     """
-    Single Point Energy + fuerzas. No escribe nada salvo un .xyz temporal.
+    Single Point Energy + fuerzas (OrbMol). Toma XYZ en texto.
     """
     try:
         calc = _load_orbmol_calc()
@@ -171,7 +129,7 @@ def predict_molecule(xyz_content, charge=0, spin_multiplicity=1):
     except Exception as e:
         return f"Error during calculation: {e}", "Error"
 
-# ==== Simulaciones (sin cambios) ====
+# ==== Simulaciones (helpers) ====
 from simulation_scripts_orbmol import (
     run_md_simulation,
     run_relaxation_simulation,
@@ -193,7 +151,7 @@ def _to_file_if_xyz(input_or_path: str):
         return tf.name, True
     return input_or_path, False
 
-# Wrappers actualizados para devolver PDB (string) a Molecule3D
+# ==== Wrappers: devuelven HTML (3Dmol.js) ====
 def md_wrapper(xyz_content, charge, spin, steps, tempK, timestep_fs, ensemble):
     tmp_created = False
     path_or_str = xyz_content
@@ -203,7 +161,7 @@ def md_wrapper(xyz_content, charge, spin, steps, tempK, timestep_fs, ensemble):
         traj_path, log_text, script_text, explanation = run_md_simulation(
             path_or_str,
             int(steps),
-            20,                          # pre-relax fija
+            20,
             float(timestep_fs),
             float(tempK),
             "NVT" if ensemble == "NVT" else "NVE",
@@ -212,13 +170,8 @@ def md_wrapper(xyz_content, charge, spin, steps, tempK, timestep_fs, ensemble):
         )
         status = f"MD completed: {int(steps)} steps at {int(tempK)} K ({ensemble})"
 
-        # Usar Molecule3D si está disponible, sino HTML
-        if HAVE_MOL3D:
-            pdb_text = traj_to_molecule3d_file(traj_path)
-            return (status, traj_path, log_text, script_text, explanation, pdb_text, "")
-        else:
-            html_value = traj_to_html(traj_path)
-            return (status, traj_path, log_text, script_text, explanation, None, html_value)
+        html_value = traj_to_html(traj_path)
+        return (status, traj_path, log_text, script_text, explanation, None, html_value)
 
     except Exception as e:
         return (f"Error: {e}", None, "", "", "", None, "")
@@ -243,24 +196,17 @@ def relax_wrapper(xyz_content, steps, fmax, charge, spin, relax_cell):
         )
         status = f"Relaxation finished (≤ {int(steps)} steps, fmax={float(fmax)} eV/Å)"
 
-        # Usar Molecule3D si está disponible, sino HTML
-        if HAVE_MOL3D:
-            pdb_text = traj_to_molecule3d_file(traj_path)
-            return (status, traj_path, log_text, script_text, explanation, pdb_text, "")
-        else:
-            html_value = traj_to_html(traj_path)
-            return (status, traj_path, log_text, script_text, explanation, None, html_value)
+        html_value = traj_to_html(traj_path)
+        return (status, traj_path, log_text, script_text, explanation, None, html_value)
 
     except Exception as e:
         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) ====
+# ==== Ejemplos ====
 examples = [
     ["""2
 Hydrogen molecule
@@ -280,10 +226,10 @@ H -0.3630 -0.5133 0.8887
 H -0.3630 -0.5133 -0.8887""", 0, 1],
 ]
 
-# ==== UI actualizada ====
+# ==== UI ====
 with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo:
     with gr.Tabs():
-        # -------- SPE (sin cambios) --------
+        # -------- SPE --------
         with gr.Tab("Single Point Energy"):
             with gr.Row():
                 with gr.Column(scale=2):
@@ -301,7 +247,7 @@ with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo:
             gr.Examples(examples=examples, inputs=[xyz_input, charge_input, spin_input])
             run_spe.click(predict_molecule, [xyz_input, charge_input, spin_input], [spe_out, spe_status])
 
-        # -------- MD (actualizada con Molecule3D) --------
+        # -------- MD --------
         with gr.Tab("Molecular Dynamics"):
             with gr.Row():
                 with gr.Column(scale=2):
@@ -320,15 +266,8 @@ 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")
-                        md_html = gr.HTML(visible=False)  # Oculto cuando usamos Molecule3D
-                    else:
-                        md_viewer = gr.HTML(visible=False)  # Placeholder
-                        md_html = gr.HTML(label="Trajectory Viewer")
-
+                    md_viewer_placeholder = gr.HTML(visible=False)  # no usamos Molecule3D
+                    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()
@@ -336,10 +275,10 @@ with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo:
             run_md_btn.click(
                 md_wrapper,
                 inputs=[xyz_md, charge_md, spin_md, steps_md, temp_md, timestep_md, ensemble_md],
-                outputs=[md_status, md_traj, md_log, md_script, md_explain, md_viewer, md_html],
+                outputs=[md_status, md_traj, md_log, md_script, md_explain, md_viewer_placeholder, md_html],
             )
 
-        # -------- Relax (actualizada con Molecule3D) --------
+        # -------- Relax --------
         with gr.Tab("Relaxation / Optimization"):
             with gr.Row():
                 with gr.Column(scale=2):
@@ -355,15 +294,8 @@ 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")
-                        rlx_html = gr.HTML(visible=False)  # Oculto cuando usamos Molecule3D
-                    else:
-                        rlx_viewer = gr.HTML(visible=False)  # Placeholder
-                        rlx_html = gr.HTML(label="Final Structure")
-
+                    rlx_viewer_placeholder = gr.HTML(visible=False)
+                    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()
@@ -371,7 +303,7 @@ with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo:
             run_rlx_btn.click(
                 relax_wrapper,
                 inputs=[xyz_rlx, steps_rlx, fmax_rlx, charge_rlx, spin_rlx, relax_cell],
-                outputs=[rlx_status, rlx_traj, rlx_log, rlx_script, rlx_explain, rlx_viewer, rlx_html],
+                outputs=[rlx_status, rlx_traj, rlx_log, rlx_script, rlx_explain, rlx_viewer_placeholder, rlx_html],
             )
 
 print("Starting OrbMol model loading…")