Update app.py

app.py

@@ -1,3 +1,4 @@
+# app.py
 import os
 import tempfile
 import numpy as np
@@ -5,17 +6,26 @@ import gradio as gr
 from ase.io import read
 from ase.io.trajectory import Trajectory
 
-# ==== Intentar visor nativo como en UMA ====
+# ----- Kill-switch para desactivar el visor si molesta (export VIS_DISABLED=1) -----
+VIS_DISABLED = os.environ.get("VIS_DISABLED", "0") == "1"
+
+# ==== Intentar visor nativo como en UMA (opcional) ====
 try:
     from gradio_molecule3d import Molecule3D
-    HAVE_MOL3D = True
+    HAVE_MOL3D = True and not VIS_DISABLED
 except Exception:
     HAVE_MOL3D = False
 
-
 # ==== Fallback HTML con 3Dmol.js ====
 def traj_to_html(traj_path, width=520, height=520, interval_ms=200):
-    traj = Trajectory(traj_path)
+    """
+    Render de una trayectoria ASE (.traj) con 3Dmol.js (sin depender de Jupyter).
+    """
+    try:
+        traj = Trajectory(traj_path)
+    except Exception as e:
+        return f"<div style='color:#b00'>Error leyendo trayectoria: {e}</div>"
+
     xyz_frames = []
     for atoms in traj:
         symbols = atoms.get_chemical_symbols()
@@ -25,32 +35,48 @@ def traj_to_html(traj_path, width=520, height=520, interval_ms=200):
             parts.append(f"{s} {x:.6f} {y:.6f} {z:.6f}")
         xyz_frames.append("\n".join(parts))
 
+    if not xyz_frames:
+        return "<div style='color:#555'>Empty trajectory</div>"
+
     html = f"""
-<div id="viewer_md" style="width:{width}px; height:{height}px;"></div>
+<div id="viewer_md" style="width:{width}px; height:{height}px; position:relative;"></div>
 <script src="https://3dmol.org/build/3Dmol-min.js"></script>
 <script>
 (function() {{
-  var viewer = $3Dmol.createViewer("viewer_md", {{backgroundColor: 'white'}});
-  var frames = {xyz_frames!r};
-  var i = 0;
-  function show(i) {{
-    viewer.clear();
-    viewer.addModel(frames[i], "xyz");
-    viewer.setStyle({{}}, {{stick: {{}}}});
-    viewer.zoomTo();
-    viewer.render();
+  function ready(fn) {{
+    if (document.readyState !== 'loading') fn();
+    else document.addEventListener('DOMContentLoaded', fn);
   }}
-  if(frames.length>0) show(0);
-  if(frames.length>1) setInterval(function(){{
-    i=(i+1)%frames.length; show(i);
-  }}, {int(interval_ms)});
+  ready(function() {{
+    var el = document.getElementById("viewer_md");
+    if (!el || typeof $3Dmol === "undefined") {{
+      el.innerHTML = '<div style="padding:8px;color:#b00">3Dmol.js no cargó. Reintenta o habilita CORS.</div>';
+      return;
+    }}
+    var viewer = $3Dmol.createViewer(el, {{backgroundColor: 'white'}});
+    var frames = {xyz_frames!r};
+    var i = 0;
+    function show(k) {{
+      viewer.clear();
+      viewer.addModel(frames[k], "xyz");
+      viewer.setStyle({{}}, {{stick: {{}}}});
+      viewer.zoomTo();
+      viewer.render();
+    }}
+    show(0);
+    if (frames.length > 1) {{
+      setInterval(function() {{
+        i = (i + 1) % frames.length;
+        show(i);
+      }}, {int(interval_ms)});
+    }}
+  }});
 }})();
 </script>
 """
     return html
 
-
-# ==== OrbMol SPE directo ====
+# ==== OrbMol SPE directo (tu calculadora NO se toca) ====
 from orb_models.forcefield import pretrained
 from orb_models.forcefield.calculator import ORBCalculator
 
@@ -64,8 +90,10 @@ def _load_orbmol_calc():
         _MODEL_CALC = ORBCalculator(orbff, device="cpu")
     return _MODEL_CALC
 
-
 def predict_molecule(xyz_content, charge=0, spin_multiplicity=1):
+    """
+    Single Point Energy + fuerzas. No escribe nada salvo un .xyz temporal.
+    """
     try:
         calc = _load_orbmol_calc()
         if not xyz_content or not xyz_content.strip():
@@ -79,30 +107,31 @@ def predict_molecule(xyz_content, charge=0, spin_multiplicity=1):
         atoms.info = {"charge": int(charge), "spin": int(spin_multiplicity)}
         atoms.calc = calc
 
-        energy = atoms.get_potential_energy()
-        forces = atoms.get_forces()
+        energy = atoms.get_potential_energy()  # eV
+        forces = atoms.get_forces()            # eV/Å
 
         lines = [f"Total Energy: {energy:.6f} eV", "", "Atomic Forces:"]
-        for i, f in enumerate(forces):
-            lines.append(f"Atom {i+1}: [{f[0]:.4f}, {f[1]:.4f}, {f[2]:.4f}] eV/Å")
+        for i, fc in enumerate(forces):
+            lines.append(f"Atom {i+1}: [{fc[0]:.4f}, {fc[1]:.4f}, {fc[2]:.4f}] eV/Å")
         max_force = float(np.max(np.linalg.norm(forces, axis=1)))
         lines += ["", f"Max Force: {max_force:.4f} eV/Å"]
 
-        try: os.unlink(xyz_file)
-        except Exception: pass
+        try:
+            os.unlink(xyz_file)
+        except Exception:
+            pass
 
         return "\n".join(lines), "Calculation completed with OrbMol"
     except Exception as e:
         return f"Error during calculation: {e}", "Error"
 
-
-# ==== Simulaciones (helpers locales) ====
+# ==== Simulaciones (helpers locales, ya los tienes en simulation_scripts_orbmol.py) ====
 from simulation_scripts_orbmol import (
     run_md_simulation,
     run_relaxation_simulation,
 )
 
-# Convierte textbox XYZ a fichero temporal si es necesario (para ASE)
+# --- Utilidad: si el usuario pega XYZ en el textbox, guardamos a .xyz temporal ---
 def _string_looks_like_xyz(text: str) -> bool:
     try:
         first = (text or "").strip().splitlines()[0]
@@ -119,7 +148,6 @@ def _to_file_if_xyz(input_or_path: str):
         return tf.name, True
     return input_or_path, False
 
-
 # Wrappers: devuelven SIEMPRE (status, traj_path, log, script, explain, html_fallback)
 def md_wrapper(xyz_content, charge, spin, steps, tempK, timestep_fs, ensemble):
     tmp_created = False
@@ -130,7 +158,7 @@ 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
+            20,                          # pre-relax fija
             float(timestep_fs),
             float(tempK),
             "NVT" if ensemble == "NVT" else "NVE",
@@ -139,7 +167,7 @@ def md_wrapper(xyz_content, charge, spin, steps, tempK, timestep_fs, ensemble):
         )
         status = f"MD completed: {int(steps)} steps at {int(tempK)} K ({ensemble})"
 
-        html_value = "" if HAVE_MOL3D else traj_to_html(traj_path)
+        html_value = "" if (VIS_DISABLED or HAVE_MOL3D) else traj_to_html(traj_path)
         return (status, traj_path, log_text, script_text, explanation, html_value)
 
     except Exception as e:
@@ -149,7 +177,6 @@ def md_wrapper(xyz_content, charge, spin, steps, tempK, timestep_fs, ensemble):
             try: os.remove(path_or_str)
             except Exception: pass
 
-
 def relax_wrapper(xyz_content, steps, fmax, charge, spin, relax_cell):
     tmp_created = False
     path_or_str = xyz_content
@@ -166,7 +193,7 @@ def relax_wrapper(xyz_content, steps, fmax, charge, spin, relax_cell):
         )
         status = f"Relaxation finished (≤ {int(steps)} steps, fmax={float(fmax)} eV/Å)"
 
-        html_value = "" if HAVE_MOL3D else traj_to_html(traj_path)
+        html_value = "" if (VIS_DISABLED or HAVE_MOL3D) else traj_to_html(traj_path)
         return (status, traj_path, log_text, script_text, explanation, html_value)
 
     except Exception as e:
@@ -176,7 +203,6 @@ def relax_wrapper(xyz_content, steps, fmax, charge, spin, relax_cell):
             try: os.remove(path_or_str)
             except Exception: pass
 
-
 # ==== Ejemplos ====
 examples = [
     ["""2
@@ -197,7 +223,6 @@ H -0.3630 -0.5133 0.8887
 H -0.3630 -0.5133 -0.8887""", 0, 1],
 ]
 
-
 # ==== UI ====
 with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo:
     with gr.Tabs():
@@ -209,8 +234,8 @@ with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo:
                     gr.Markdown("Energías y fuerzas con **charge** y **spin multiplicity**.")
                     xyz_input = gr.Textbox(label="XYZ Coordinates", lines=12, placeholder="Paste XYZ here…")
                     with gr.Row():
-                        charge_input = gr.Slider(0, -10, 10, 1, label="Charge")
-                        spin_input = gr.Slider(1, 1, 11, 1, label="Spin Multiplicity")
+                        charge_input = gr.Slider(minimum=-10, maximum=10, value=0, step=1, label="Charge")
+                        spin_input = gr.Slider(minimum=1, maximum=11, value=1, step=1, label="Spin Multiplicity")
                     run_spe = gr.Button("Run OrbMol Prediction", variant="primary")
                 with gr.Column(variant="panel", min_width=500):
                     spe_out = gr.Textbox(label="Energy & Forces", lines=15, interactive=False)
@@ -223,15 +248,15 @@ with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo:
         with gr.Tab("Molecular Dynamics"):
             with gr.Row():
                 with gr.Column(scale=2):
-                    xyz_md = gr.Textbox(label="XYZ Coordinates", lines=12, placeholder="Paste XYZ here…")
+                    xyz_md = gr.Textbox(label="XYZ Coordinates or path (.xyz/.traj/.pdb/.cif)", lines=12, placeholder="Paste XYZ or path here…")
                     with gr.Row():
-                        charge_md = gr.Slider(0, -10, 10, 1, label="Charge")
-                        spin_md = gr.Slider(1, 1, 11, 1, label="Spin Multiplicity")
+                        charge_md = gr.Slider(minimum=-10, maximum=10, value=0, step=1, label="Charge")
+                        spin_md = gr.Slider(minimum=1, maximum=11, value=1, step=1, label="Spin Multiplicity")
                     with gr.Row():
-                        steps_md = gr.Slider(100, 10, 2000, 10, label="Steps")
-                        temp_md = gr.Slider(300, 10, 1500, 10, label="Temperature (K)")
+                        steps_md = gr.Slider(minimum=10, maximum=2000, value=100, step=10, label="Steps")
+                        temp_md = gr.Slider(minimum=10, maximum=1500, value=300, step=10, label="Temperature (K)")
                     with gr.Row():
-                        timestep_md = gr.Slider(1.0, 0.1, 5.0, 0.1, label="Timestep (fs)")
+                        timestep_md = gr.Slider(minimum=0.1, maximum=5.0, value=1.0, step=0.1, label="Timestep (fs)")
                         ensemble_md = gr.Radio(["NVE", "NVT"], value="NVE", label="Ensemble")
                     run_md_btn = gr.Button("Run MD Simulation", variant="primary")
 
@@ -258,7 +283,7 @@ with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo:
                     md_script = gr.Code(label="Reproduction Script", language="python", interactive=False, lines=20, max_lines=30)
                     md_explain = gr.Markdown()
 
-            # NOTA: no actualizamos md_viewer directamente; se refresca al cambiar md_traj
+            # NOTA: el visor Molecule3D se refresca cuando cambia md_traj (no hay que conectarlo)
             run_md_btn.click(
                 md_wrapper,
                 inputs=[xyz_md, charge_md, spin_md, steps_md, temp_md, timestep_md, ensemble_md],
@@ -269,12 +294,12 @@ with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo:
         with gr.Tab("Relaxation / Optimization"):
             with gr.Row():
                 with gr.Column(scale=2):
-                    xyz_rlx = gr.Textbox(label="XYZ Coordinates", lines=12, placeholder="Paste XYZ here…")
-                    steps_rlx = gr.Slider(300, 1, 2000, 1, label="Max Steps")
-                    fmax_rlx = gr.Slider(0.05, 0.001, 0.5, 0.001, label="Fmax (eV/Å)")
+                    xyz_rlx = gr.Textbox(label="XYZ Coordinates or path (.xyz/.traj/.pdb/.cif)", lines=12, placeholder="Paste XYZ or path here…")
+                    steps_rlx = gr.Slider(minimum=1, maximum=2000, value=300, step=1, label="Max Steps")
+                    fmax_rlx = gr.Slider(minimum=0.001, maximum=0.5, value=0.05, step=0.001, label="Fmax (eV/Å)")
                     with gr.Row():
-                        charge_rlx = gr.Slider(0, -10, 10, 1, label="Charge")
-                        spin_rlx = gr.Slider(1, 1, 11, 1, label="Spin")
+                        charge_rlx = gr.Slider(minimum=-10, maximum=10, value=0, step=1, label="Charge")
+                        spin_rlx = gr.Slider(minimum=1, maximum=11, value=1, step=1, label="Spin")
                     relax_cell = gr.Checkbox(False, label="Relax Unit Cell")
                     run_rlx_btn = gr.Button("Run Optimization", variant="primary")