Update app.py

app.py

@@ -6,8 +6,7 @@ from ase.io import read, write
 from ase.io.trajectory import Trajectory
 import hashlib
 
-# ==== Forzar visor HTML con 3Dmol.js ====
-# (desactiva Molecule3D porque requiere formatos con conectividad)
+# ==== Forzar visor HTML con 3Dmol.js (sin gradio_molecule3d) ====
 HAVE_MOL3D = False
 
 # ==== Fallback HTML con 3Dmol.js ====
@@ -93,15 +92,21 @@ def _load_orbmol_calc():
 
 def predict_molecule(structure_file, charge=0, spin_multiplicity=1):
     """
-    Single Point Energy + fuerzas (OrbMol). Ahora acepta archivos subidos.
+    Single Point Energy + fuerzas (OrbMol). Maneja archivos de Gradio correctamente.
     """
     try:
         calc = _load_orbmol_calc()
         if not structure_file:
             return "Error: Please upload a structure file", "Error"
 
-        # structure_file es un objeto File de Gradio
-        file_path = structure_file.name if hasattr(structure_file, 'name') else structure_file
+        # En Gradio (con type='filepath'), structure_file es directamente un path (str)
+        file_path = structure_file
+
+        # Verificar que el archivo existe y no está vacío
+        if not os.path.exists(file_path):
+            return f"Error: File not found: {file_path}", "Error"
+        if os.path.getsize(file_path) == 0:
+            return f"Error: Empty file: {file_path}", "Error"
 
         atoms = read(file_path)
         atoms.info = {"charge": int(charge), "spin": int(spin_multiplicity)}
@@ -126,17 +131,22 @@ from simulation_scripts_orbmol import (
     run_relaxation_simulation,
 )
 
-# ==== Wrappers: ahora usan archivos subidos ====
+# ==== Wrappers (MD / Relax): usan directamente el path ====
 def md_wrapper(structure_file, charge, spin, steps, tempK, timestep_fs, ensemble):
     try:
         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
+        file_path = structure_file  # ya es un path (str)
+
+        # Validaciones rápidas
+        if not os.path.exists(file_path):
+            return ("Error: File not found: " + str(file_path), None, "", "", "", None, "")
+        if os.path.getsize(file_path) == 0:
+            return ("Error: Empty file: " + str(file_path), None, "", "", "", None, "")
 
         traj_path, log_text, script_text, explanation = run_md_simulation(
-            file_path,  # Pasar el path del archivo directamente
+            file_path,
             int(steps),
             20,
             float(timestep_fs),
@@ -158,11 +168,16 @@ def relax_wrapper(structure_file, steps, fmax, charge, spin, relax_cell):
         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
+        file_path = structure_file  # ya es un path (str)
+
+        # Validaciones rápidas
+        if not os.path.exists(file_path):
+            return ("Error: File not found: " + str(file_path), None, "", "", "", None, "")
+        if os.path.getsize(file_path) == 0:
+            return ("Error: Empty file: " + str(file_path), None, "", "", "", None, "")
 
         traj_path, log_text, script_text, explanation = run_relaxation_simulation(
-            file_path,  # Pasar el path del archivo directamente
+            file_path,
             int(steps),
             float(fmax),
             int(charge),
@@ -187,11 +202,12 @@ with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo:
                     gr.Markdown("# OrbMol — Quantum-Accurate Molecular Predictions")
                     gr.Markdown("Upload molecular structure files (.xyz, .pdb, .cif, .traj) for energy and force calculations.")
                     
-                    # CAMBIADO: File upload en lugar de Textbox
+                    # IMPORTANTE: type='filepath'
                     xyz_input = gr.File(
-                        label="Upload Structure File (.xyz/.pdb/.cif/.traj)",
+                        label="Upload Structure File (.xyz/.pdb/.cif/.traj/.mol/.sdf)",
                         file_types=[".xyz", ".pdb", ".cif", ".traj", ".mol", ".sdf"],
-                        file_count="single"
+                        file_count="single",
+                        type="filepath"
                     )
                     
                     with gr.Row():
@@ -203,9 +219,6 @@ with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo:
                     spe_out = gr.Textbox(label="Energy & Forces", lines=15, interactive=False)
                     spe_status = gr.Textbox(label="Status", interactive=False, max_lines=1)
 
-            # 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 --------
@@ -215,11 +228,11 @@ with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo:
                     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)",
+                        label="Upload Structure File (.xyz/.pdb/.cif/.traj/.mol/.sdf)",
                         file_types=[".xyz", ".pdb", ".cif", ".traj", ".mol", ".sdf"],
-                        file_count="single"
+                        file_count="single",
+                        type="filepath"
                     )
                     
                     with gr.Row():
@@ -234,59 +247,4 @@ with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo:
                     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_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()
-
-            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_placeholder, md_html],
-            )
-
-        # -------- Relax --------
-        with gr.Tab("Relaxation / Optimization"):
-            with gr.Row():
-                with gr.Column(scale=2):
-                    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():
-                        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")
-
-                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_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()
-
-            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_placeholder, rlx_html],
-            )
-
-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)
+                    md_status = gr.Text_