Update app.py

app.py

@@ -2,103 +2,71 @@ import os
 import re
 import numpy as np
 import gradio as gr
-from ase.io import read, write
+from ase.io import read
 from ase.io.trajectory import Trajectory
 
-# =========================
-# 3Dmol.js helpers (preview y trayectorias)
-# =========================
-
-def _atoms_to_xyz_block(atoms):
-    symbols = atoms.get_chemical_symbols()
-    coords = atoms.get_positions()
-    parts = [str(len(symbols)), "frame"]
-    for s, (x, y, z) in zip(symbols, coords):
-        parts.append(f"{s} {x:.6f} {y:.6f} {z:.6f}")
-    return "\n".join(parts)
-
-def structure_to_html(file_path, width=520, height=520):
-    """Renderiza estructura única en 3Dmol.js sin correr cálculos."""
-    if not file_path or not os.path.exists(file_path):
-        return "<div style='color:#b00; padding:20px;'>No structure file found</div>"
-    try:
-        atoms = read(file_path)
-    except Exception as e:
-        return f"<div style='color:#b00; padding:20px;'>Error reading structure: {e}</div>"
+# ========= 3Dmol.js (para ver trayectorias MD/Relax) =========
+THREE_D_MOL_SOURCES = [
+    "https://3dmol.org/build/3Dmol-min.js",
+    "https://cdn.jsdelivr.net/npm/3dmol/build/3Dmol-min.js",
+    "https://unpkg.com/3dmol/build/3Dmol-min.js",
+]
 
-    xyz_block = _atoms_to_xyz_block(atoms).replace("`", "\\`")
-    viewer_id = f"viewer_{abs(hash(('single', file_path))) % 100000}"
+def _loader_js():
+    srcs = "[" + ",".join([f"'{u}'" for u in THREE_D_MOL_SOURCES]) + "]"
     return f"""
-<div style="margin-bottom:10px; padding:10px; background:#f5f5f5; border-radius:5px;">
-  <strong>🧬 3D Molecular Viewer</strong> — preview (no compute)
-</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>
-const _load3Dmol = (ok) => {{
-  if (typeof window.$3Dmol !== 'undefined') return ok();
-  const s=document.createElement('script');
-  s.src='https://3dmol.org/build/3Dmol-min.js';
-  s.onload=ok; document.head.appendChild(s);
-}};
-_load3Dmol(() => {{
-  const el=document.getElementById("{viewer_id}");
-  if(!el||typeof $3Dmol==='undefined') return;
-  const v=$3Dmol.createViewer(el, {{backgroundColor:'white'}});
-  v.addModel(`{xyz_block}`, "xyz");
-  v.setStyle({{}}, {{stick:{{}}, sphere:{{}}}});
-  v.zoomTo(); v.render();
-}});
-</script>
+function _ensure3Dmol(cb){{
+  if(typeof window.$3Dmol!=='undefined') return cb();
+  const srcs={srcs}; let i=0;
+  function tryNext(){{
+    if(i>=srcs.length) return;
+    const s=document.createElement('script'); s.src=srcs[i++]; s.onload=cb; s.onerror=tryNext; document.head.appendChild(s);
+  }}
+  tryNext();
+}}
 """
 
+def _atoms_to_xyz_block(atoms):
+    syms = atoms.get_chemical_symbols()
+    pos  = atoms.get_positions()
+    out = [str(len(syms)), "frame"]
+    for s,(x,y,z) in zip(syms,pos):
+        out.append(f"{s} {x:.6f} {y:.6f} {z:.6f}")
+    return "\n".join(out)
+
 def traj_to_html(traj_path, width=520, height=520, interval_ms=200):
-    """Animación 3Dmol.js desde .traj de ASE."""
     if not traj_path or not os.path.exists(traj_path):
-        return "<div style='color:#b00; padding:20px;'>No trajectory file found</div>"
+        return "<div style='color:#b00;padding:20px;'>No trajectory file found</div>"
     try:
         traj = Trajectory(traj_path)
-        if len(traj) == 0:
-            return "<div style='color:#555; padding:20px;'>Empty trajectory</div>"
+        if len(traj)==0:
+            return "<div style='color:#555;padding:20px;'>Empty trajectory</div>"
     except Exception as e:
-        return f"<div style='color:#b00; padding:20px;'>Error: {e}</div>"
+        return f"<div style='color:#b00;padding:20px;'>Error reading trajectory: {e}</div>"
 
     frames = [_atoms_to_xyz_block(at) for at in traj]
     frames_json = str(frames).replace("'", '"')
-    viewer_id = f"viewer_{abs(hash(traj_path)) % 100000}"
+    viewer_id = f"viewer_{abs(hash(traj_path))%100000}"
+    loader = _loader_js()
     return f"""
-<div style="margin-bottom:10px; padding:10px; background:#f5f5f5; border-radius:5px;">
+<div style="margin-bottom:10px;padding:10px;background:#f5f5f5;border-radius:5px;">
   <strong>🧬 3D Molecular Viewer</strong> — {len(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>
+<div id="{viewer_id}" style="width:{width}px;height:{height}px;border:2px solid #ddd;border-radius:8px;background:#fafafa;"></div>
 <script>
-const _load3Dmol = (ok) => {{
-  if (typeof window.$3Dmol !== 'undefined') return ok();
-  const s=document.createElement('script');
-  s.src='https://3dmol.org/build/3Dmol-min.js';
-  s.onload=ok; document.head.appendChild(s);
-}};
-_load3Dmol(() => {{
-  const el=document.getElementById("{viewer_id}");
-  if(!el||typeof $3Dmol==='undefined') return;
-  const v=$3Dmol.createViewer(el, {{backgroundColor:'white'}});
-  const frames={frames_json};
-  let idx=0;
-  function draw(i){{
-    v.clear(); v.addModel(frames[i], "xyz");
-    v.setStyle({{}}, {{stick:{{}}, sphere:{{}}}});
-    v.zoomTo(); v.render();
-  }}
+{loader}
+_ensure3Dmol(function(){{
+  var el=document.getElementById("{viewer_id}"); if(!el||typeof $3Dmol==='undefined') return;
+  var v=$3Dmol.createViewer(el, {{backgroundColor:'white'}});
+  var frames={frames_json}; var i=0;
+  function draw(k){{ v.clear(); v.addModel(frames[k], "xyz"); v.setStyle({{}}, {{stick:{{}}, sphere:{{}}}}); v.zoomTo(); v.render(); }}
   draw(0);
-  if(frames.length>1){{
-    setInterval(()=>{{ idx=(idx+1)%frames.length; draw(idx); }}, {interval_ms});
-  }}
+  if(frames.length>1) setInterval(function(){{ i=(i+1)%frames.length; draw(i); }}, {interval_ms});
 }});
 </script>
 """
 
-# =========================
-# OrbMol (SPE)
-# =========================
+# ================= OrbMol (SPE) =================
 from orb_models.forcefield import pretrained
 from orb_models.forcefield.calculator import ORBCalculator
 
@@ -111,13 +79,15 @@ def _load_orbmol_calc():
     return _MODEL_CALC
 
 def predict_molecule(structure_file, charge=0, spin_multiplicity=1):
-    """Single Point Energy + fuerzas (OrbMol)."""
+    """
+    Single Point Energy + fuerzas (OrbMol). Solo se ejecuta al pulsar el botón.
+    """
     try:
         calc = _load_orbmol_calc()
         if not structure_file:
             return "Error: Please upload a structure file", "Error"
-        file_path = structure_file  # gr.File(type='filepath') -> str
 
+        file_path = structure_file  # gr.File(type='filepath') -> str
         if not os.path.exists(file_path):
             return f"Error: File not found: {file_path}", "Error"
         if os.path.getsize(file_path) == 0:
@@ -131,62 +101,28 @@ def predict_molecule(structure_file, charge=0, spin_multiplicity=1):
         forces = atoms.get_forces()            # eV/Å
 
         lines = [f"Total Energy: {energy:.6f} eV", "", "Atomic Forces:"]
-        norms = np.linalg.norm(forces, axis=1)
         for i, fc in enumerate(forces):
             lines.append(f"Atom {i+1}: [{fc[0]:.4f}, {fc[1]:.4f}, {fc[2]:.4f}] eV/Å")
-        lines += ["", f"Max Force: {float(np.max(norms)):.4f} eV/Å"]
+        max_force = float(np.max(np.linalg.norm(forces, axis=1)))
+        lines += ["", f"Max Force: {max_force:.4f} eV/Å"]
 
         return "\n".join(lines), "Calculation completed with OrbMol"
     except Exception as e:
         return f"Error during calculation: {e}", "Error"
 
-# =========================
-# Simulaciones (helpers) y parsing de log
-# =========================
+# ================= Simulaciones (tus helpers) =================
 from simulation_scripts_orbmol import (
     run_md_simulation,
     run_relaxation_simulation,
 )
 
-ENERGY_PATTERNS = [
-    re.compile(r"(?:^|\\s)(?:step|iter|i)\\s*[:=]?\\s*(\\d+).*?(?:E|energy)\\s*[:=]?\\s*(-?\\d+(?:\\.\\d+)?(?:[eE][+-]?\\d+)?)"),
-    re.compile(r"(?:^|\\s)E(?:nergy)?\\s*[:=]?\\s*(-?\\d+(?:\\.\\d+)?(?:[eE][+-]?\\d+)?)"),
-]
-
-def extract_energy_series(log_text):
-    steps, energies = [], []
-    if not log_text:
-        return steps, energies
-    for line in log_text.splitlines():
-        m = ENERGY_PATTERNS[0].search(line)
-        if m:
-            steps.append(int(m.group(1)))
-            energies.append(float(m.group(2)))
-            continue
-        m2 = ENERGY_PATTERNS[1].search(line)
-        if m2:
-            steps.append(len(steps))
-            energies.append(float(m2.group(1)))
-    return steps, energies
-
-def plot_energy(steps, energies, title):
-    import matplotlib.pyplot as plt
-    fig = plt.figure(figsize=(5,3.2))
-    if steps:
-        plt.plot(steps, energies, linewidth=1.6)
-        plt.xlabel("Step")
-    else:
-        plt.plot(range(len(energies)), energies, linewidth=1.6)
-        plt.xlabel("Index")
-    plt.ylabel("Energy (eV)")
-    plt.title(title)
-    plt.tight_layout()
-    return fig
-
-# =========================
-# Wrappers MD / Relax (devuelven: status, traj, log, script, explain, html, plot)
-# =========================
+# ========== Wrappers MD / Relax (con firma correcta) ==========
 def md_wrapper(structure_file, charge, spin, steps, tempK, timestep_fs, ensemble):
+    """
+    Llama a tu run_md_simulation con el ORDEN correcto usando keywords:
+    (structure_file, num_steps, num_prerelax_steps, md_timestep, temperature_k, md_ensemble,
+     task_name='OMol', total_charge=..., spin_multiplicity=...)
+    """
     try:
         if not structure_file:
             return ("Error: Please upload a structure file", None, "", "", "", "", None)
@@ -203,18 +139,20 @@ def md_wrapper(structure_file, charge, spin, steps, tempK, timestep_fs, ensemble
             float(timestep_fs),
             float(tempK),
             "NVT" if ensemble == "NVT" else "NVE",
-            int(charge),
-            int(spin),
+            total_charge=int(charge),
+            spin_multiplicity=int(spin),
         )
         status = f"MD completed: {int(steps)} steps at {int(tempK)} K ({ensemble})"
         html_value = traj_to_html(traj_path)
-        s, e = extract_energy_series(log_text)
-        fig = plot_energy(s, e, "MD: Energy vs Step")
-        return (status, traj_path, log_text, script_text, explanation, html_value, fig)
+        return (status, traj_path, log_text, script_text, explanation, html_value, None)
     except Exception as e:
         return (f"Error: {e}", None, "", "", "", "", None)
 
 def relax_wrapper(structure_file, steps, fmax, charge, spin, relax_cell):
+    """
+    Firma correcta usando keywords:
+    (structure_file, num_steps, fmax, task_name='OMol', total_charge=..., spin_multiplicity=..., relax_unit_cell=...)
+    """
     try:
         if not structure_file:
             return ("Error: Please upload a structure file", None, "", "", "", "", None)
@@ -228,124 +166,100 @@ def relax_wrapper(structure_file, steps, fmax, charge, spin, relax_cell):
             file_path,
             int(steps),
             float(fmax),
-            int(charge),
-            int(spin),
-            bool(relax_cell),
+            total_charge=int(charge),
+            spin_multiplicity=int(spin),
+            relax_unit_cell=bool(relax_cell),
         )
         status = f"Relaxation finished (≤ {int(steps)} steps, fmax={float(fmax)} eV/Å)"
         html_value = traj_to_html(traj_path)
-        s, e = extract_energy_series(log_text)
-        fig = plot_energy(s, e, "Relaxation: Energy vs Step")
-        return (status, traj_path, log_text, script_text, explanation, html_value, fig)
+        return (status, traj_path, log_text, script_text, explanation, html_value, None)
     except Exception as e:
         return (f"Error: {e}", None, "", "", "", "", None)
 
-def preview_structure(structure_file):
-    """Preview inmediato al subir archivo en SPE."""
-    if not structure_file:
-        return "<div style='color:#b00; padding:20px;'>Upload a file to preview</div>"
-    if not os.path.exists(structure_file):
-        return "<div style='color:#b00; padding:20px;'>File not found</div>"
-    if os.path.getsize(structure_file) == 0:
-        return "<div style='color:#b00; padding:20px;'>Empty file</div>"
-    return structure_to_html(structure_file)
-
-# =========================
-# UI
-# =========================
+# ===================== UI (solo calcula al pulsar botón) =====================
 with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo:
     with gr.Tabs():
-        # -------- SPE --------
+        # ===== SPE =====
         with gr.Tab("Single Point Energy"):
             with gr.Row():
                 with gr.Column(scale=2):
-                    gr.Markdown("# OrbMol — Quantum-Accurate Molecular Predictions")
-                    gr.Markdown("Upload molecular structure files (.xyz, .pdb, .cif, .traj, .mol, .sdf) for preview and calculation.")
+                    gr.Markdown("## OrbMol — Single Point Energy")
                     xyz_input = gr.File(
-                        label="Upload Structure File",
+                        label="Upload Structure File (.xyz/.pdb/.cif/.traj/.mol/.sdf)",
                         file_types=[".xyz", ".pdb", ".cif", ".traj", ".mol", ".sdf"],
                         file_count="single",
                         type="filepath",
                     )
                     with gr.Row():
                         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")
+                        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=520):
-                    spe_preview = gr.HTML(label="Structure Preview")
-                    spe_out = gr.Textbox(label="Energy & Forces", lines=15, interactive=False)
+                    spe_out    = gr.Textbox(label="Energy & Forces", lines=18, interactive=False)
                     spe_status = gr.Textbox(label="Status", interactive=False, max_lines=1)
-
-            # Preview inmediato (sin cálculo)
-            xyz_input.change(preview_structure, inputs=[xyz_input], outputs=[spe_preview])
-            # Cálculo SPE
             run_spe.click(predict_molecule, [xyz_input, charge_input, spin_input], [spe_out, spe_status])
 
-        # -------- MD --------
+        # ===== MD =====
         with gr.Tab("Molecular Dynamics"):
             with gr.Row():
                 with gr.Column(scale=2):
                     gr.Markdown("## Molecular Dynamics Simulation")
                     xyz_md = gr.File(
-                        label="Upload Structure File",
+                        label="Upload Structure File (.xyz/.pdb/.cif/.traj/.mol/.sdf)",
                         file_types=[".xyz", ".pdb", ".cif", ".traj", ".mol", ".sdf"],
                         file_count="single",
                         type="filepath",
                     )
                     with gr.Row():
                         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")
+                        spin_md   = gr.Slider(minimum=1, maximum=11, value=1, step=1, label="Spin Multiplicity")
                     with gr.Row():
-                        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)")
+                        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(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")
+                        ensemble_md = gr.Radio(["NVE","NVT"], value="NVE", label="Ensemble")
                     run_md_btn = gr.Button("Run MD Simulation", variant="primary")
-
                 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)
-                    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()
-                    md_plot = gr.Plot(label="Energy vs Step")
-
+                    md_traj   = gr.File(label="Trajectory (.traj)", interactive=False)
+                    md_html   = gr.HTML(label="Trajectory Viewer", sanitize=False)
+                    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=18, max_lines=28)
+                    md_explain= gr.Markdown()
+                    md_plot   = gr.Plot(label="(optional)")
             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_html, md_plot],
             )
 
-        # -------- Relax --------
+        # ===== Relax =====
         with gr.Tab("Relaxation / Optimization"):
             with gr.Row():
                 with gr.Column(scale=2):
                     gr.Markdown("## Structure Relaxation/Optimization")
                     xyz_rlx = gr.File(
-                        label="Upload Structure File",
+                        label="Upload Structure File (.xyz/.pdb/.cif/.traj/.mol/.sdf)",
                         file_types=[".xyz", ".pdb", ".cif", ".traj", ".mol", ".sdf"],
                         file_count="single",
                         type="filepath",
                     )
                     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)")
+                    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(minimum=-10, maximum=10, value=0, step=1, label="Charge")
-                        spin_rlx = gr.Slider(minimum=1, maximum=11, value=1, step=1, label="Spin")
+                        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")
-
+                    run_rlx_btn= gr.Button("Run Optimization", variant="primary")
                 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)
-                    rlx_html = gr.HTML(label="Final Structure / Trajectory")
-                    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()
-                    rlx_plot = gr.Plot(label="Energy vs Step")
-
+                    rlx_traj   = gr.File(label="Trajectory (.traj)", interactive=False)
+                    rlx_html   = gr.HTML(label="Final Structure / Trajectory", sanitize=False)
+                    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=18, max_lines=28)
+                    rlx_explain= gr.Markdown()
+                    rlx_plot   = gr.Plot(label="(optional)")
             run_rlx_btn.click(
                 relax_wrapper,
                 inputs=[xyz_rlx, steps_rlx, fmax_rlx, charge_rlx, spin_rlx, relax_cell],