Update app.py

app.py

@@ -55,11 +55,9 @@ 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(i) {{
     viewer.clear();
     viewer.addModel(frames[i], "xyz");
@@ -67,7 +65,6 @@ function initViewer_{viewer_id}() {{
     viewer.zoomTo();
     viewer.render();
   }}
-
   showFrame(0);
   if (frames.length > 1) {{
     setInterval(function() {{
@@ -94,20 +91,19 @@ def _load_orbmol_calc():
         _MODEL_CALC = ORBCalculator(orbff, device="cpu")
     return _MODEL_CALC
 
-def predict_molecule(xyz_content, charge=0, spin_multiplicity=1):
+def predict_molecule(structure_file, charge=0, spin_multiplicity=1):
     """
-    Single Point Energy + fuerzas (OrbMol). Toma XYZ en texto.
+    Single Point Energy + fuerzas (OrbMol). Ahora acepta archivos subidos.
     """
     try:
         calc = _load_orbmol_calc()
-        if not xyz_content or not xyz_content.strip():
-            return "Error: Please enter XYZ coordinates", "Error"
+        if not structure_file:
+            return "Error: Please upload a structure file", "Error"
 
-        with tempfile.NamedTemporaryFile(mode="w", suffix=".xyz", delete=False) as f:
-            f.write(xyz_content)
-            xyz_file = f.name
+        # structure_file es un objeto File de Gradio
+        file_path = structure_file.name if hasattr(structure_file, 'name') else structure_file
 
-        atoms = read(xyz_file)
+        atoms = read(file_path)
         atoms.info = {"charge": int(charge), "spin": int(spin_multiplicity)}
         atoms.calc = calc
 
@@ -120,11 +116,6 @@ def predict_molecule(xyz_content, charge=0, spin_multiplicity=1):
         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
-
         return "\n".join(lines), "Calculation completed with OrbMol"
     except Exception as e:
         return f"Error during calculation: {e}", "Error"
@@ -135,31 +126,17 @@ from simulation_scripts_orbmol import (
     run_relaxation_simulation,
 )
 
-def _string_looks_like_xyz(text: str) -> bool:
+# ==== Wrappers: ahora usan archivos subidos ====
+def md_wrapper(structure_file, charge, spin, steps, tempK, timestep_fs, ensemble):
     try:
-        first = (text or "").strip().splitlines()[0]
-        int(first.split()[0])
-        return True
-    except Exception:
-        return False
-
-def _to_file_if_xyz(input_or_path: str):
-    if isinstance(input_or_path, str) and _string_looks_like_xyz(input_or_path):
-        tf = tempfile.NamedTemporaryFile(mode="w", suffix=".xyz", delete=False)
-        tf.write(input_or_path)
-        tf.flush(); tf.close()
-        return tf.name, True
-    return input_or_path, False
-
-# ==== 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
-    try:
-        path_or_str, tmp_created = _to_file_if_xyz(xyz_content)
+        if not structure_file:
+            return ("Error: Please upload a structure file", None, "", "", "", None, "")
+
+        # structure_file es un objeto File de Gradio
+        file_path = structure_file.name if hasattr(structure_file, 'name') else structure_file
 
         traj_path, log_text, script_text, explanation = run_md_simulation(
-            path_or_str,
+            file_path,  # Pasar el path del archivo directamente
             int(steps),
             20,
             float(timestep_fs),
@@ -175,19 +152,17 @@ def md_wrapper(xyz_content, charge, spin, steps, tempK, timestep_fs, ensemble):
 
     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
-
-def relax_wrapper(xyz_content, steps, fmax, charge, spin, relax_cell):
-    tmp_created = False
-    path_or_str = xyz_content
+
+def relax_wrapper(structure_file, steps, fmax, charge, spin, relax_cell):
     try:
-        path_or_str, tmp_created = _to_file_if_xyz(xyz_content)
+        if not structure_file:
+            return ("Error: Please upload a structure file", None, "", "", "", None, "")
+
+        # structure_file es un objeto File de Gradio
+        file_path = structure_file.name if hasattr(structure_file, 'name') else structure_file
 
         traj_path, log_text, script_text, explanation = run_relaxation_simulation(
-            path_or_str,
+            file_path,  # Pasar el path del archivo directamente
             int(steps),
             float(fmax),
             int(charge),
@@ -201,30 +176,6 @@ def relax_wrapper(xyz_content, steps, fmax, charge, spin, relax_cell):
 
     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
-
-# ==== Ejemplos ====
-examples = [
-    ["""2
-Hydrogen molecule
-H 0.0 0.0 0.0
-H 0.0 0.0 0.74""", 0, 1],
-    ["""3
-Water molecule
-O 0.0000 0.0000 0.0000
-H 0.7571 0.0000 0.5864
-H -0.7571 0.0000 0.5864""", 0, 1],
-    ["""5
-Methane
-C 0.0000 0.0000 0.0000
-H 1.0890 0.0000 0.0000
-H -0.3630 1.0267 0.0000
-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:
@@ -234,24 +185,43 @@ with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo:
             with gr.Row():
                 with gr.Column(scale=2):
                     gr.Markdown("# OrbMol — Quantum-Accurate Molecular Predictions")
-                    gr.Markdown("Energías y fuerzas con **charge** y **spin multiplicity**.")
-                    xyz_input = gr.Textbox(label="XYZ Coordinates", lines=12, placeholder="Paste XYZ here…")
+                    gr.Markdown("Upload molecular structure files (.xyz, .pdb, .cif, .traj) for energy and force calculations.")
+                    
+                    # CAMBIADO: File upload en lugar de Textbox
+                    xyz_input = gr.File(
+                        label="Upload Structure File (.xyz/.pdb/.cif/.traj)",
+                        file_types=[".xyz", ".pdb", ".cif", ".traj", ".mol", ".sdf"],
+                        file_count="single"
+                    )
+                    
                     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")
                     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)
                     spe_status = gr.Textbox(label="Status", interactive=False, max_lines=1)
 
-            gr.Examples(examples=examples, inputs=[xyz_input, charge_input, spin_input])
+            # EJEMPLOS DE ARCHIVOS - puedes comentar esta línea si no quieres ejemplos
+            # gr.Examples(examples=[["examples/water.xyz", 0, 1]], inputs=[xyz_input, charge_input, spin_input])
+            
             run_spe.click(predict_molecule, [xyz_input, charge_input, spin_input], [spe_out, spe_status])
 
         # -------- MD --------
         with gr.Tab("Molecular Dynamics"):
             with gr.Row():
                 with gr.Column(scale=2):
-                    xyz_md = gr.Textbox(label="XYZ Coordinates or path (.xyz/.traj/.pdb/.cif)", lines=12, placeholder="Paste XYZ or path here…")
+                    gr.Markdown("## Molecular Dynamics Simulation")
+                    gr.Markdown("Upload your molecular structure and configure MD parameters.")
+                    
+                    # CAMBIADO: File upload en lugar de Textbox
+                    xyz_md = gr.File(
+                        label="Upload Structure File (.xyz/.pdb/.cif/.traj)",
+                        file_types=[".xyz", ".pdb", ".cif", ".traj", ".mol", ".sdf"],
+                        file_count="single"
+                    )
+                    
                     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")
@@ -282,7 +252,16 @@ 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 or path (.xyz/.traj/.pdb/.cif)", lines=12, placeholder="Paste XYZ or path here…")
+                    gr.Markdown("## Structure Relaxation/Optimization")
+                    gr.Markdown("Upload your molecular structure for geometry optimization.")
+                    
+                    # CAMBIADO: File upload en lugar de Textbox
+                    xyz_rlx = gr.File(
+                        label="Upload Structure File (.xyz/.pdb/.cif/.traj)",
+                        file_types=[".xyz", ".pdb", ".cif", ".traj", ".mol", ".sdf"],
+                        file_count="single"
+                    )
+                    
                     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():
@@ -310,4 +289,4 @@ 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)