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| import os | |
| import tempfile | |
| import numpy as np | |
| import gradio as gr | |
| 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}") | |
| # ==== Función para convertir trayectoria a archivo temporal PDB ==== | |
| def traj_to_molecule3d_file(traj_path): | |
| """ | |
| Convierte una trayectoria ASE (.traj) a un archivo PDB temporal para Molecule3D. | |
| Retorna el path del archivo temporal (.pdb). | |
| """ | |
| if not traj_path or not os.path.exists(traj_path): | |
| return None | |
| try: | |
| traj = Trajectory(traj_path) | |
| if len(traj) == 0: | |
| return None | |
| # Usar último frame para visualización estática | |
| atoms = traj[-1] | |
| # Crear archivo PDB temporal (formato aceptado por Molecule3D) | |
| with tempfile.NamedTemporaryFile(suffix=".pdb", delete=False) as f: | |
| pdb_path = f.name | |
| write(pdb_path, atoms) # extensión .pdb selecciona el formato automáticamente | |
| return pdb_path | |
| except Exception as e: | |
| print(f"Error converting trajectory: {e}") | |
| return None | |
| # ==== Fallback HTML con 3Dmol.js (por si acaso) ==== | |
| def traj_to_html(traj_path, width=520, height=520, interval_ms=200): | |
| """ | |
| Fallback HTML viewer (solo si Molecule3D no está disponible). | |
| """ | |
| 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}" | |
| try: | |
| traj = Trajectory(traj_path) | |
| 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>" | |
| xyz_frames = [] | |
| for atoms in traj: | |
| 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}") | |
| xyz_frames.append("\n".join(parts)) | |
| frames_json = str(xyz_frames).replace("'", '"') | |
| html = f""" | |
| <div style="margin-bottom:10px; padding:10px; background:#f5f5f5; border-radius:5px;"> | |
| <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); | |
| }} else {{ | |
| 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}); | |
| }} | |
| }} | |
| </script> | |
| """ | |
| return html | |
| # ==== OrbMol SPE directo (sin cambios) ==== | |
| from orb_models.forcefield import pretrained | |
| from orb_models.forcefield.calculator import ORBCalculator | |
| _MODEL_CALC = None | |
| def _load_orbmol_calc(): | |
| global _MODEL_CALC | |
| if _MODEL_CALC is None: | |
| orbff = pretrained.orb_v3_conservative_inf_omat( | |
| device="cpu", precision="float32-high" | |
| ) | |
| _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(): | |
| return "Error: Please enter XYZ coordinates", "Error" | |
| with tempfile.NamedTemporaryFile(mode="w", suffix=".xyz", delete=False) as f: | |
| f.write(xyz_content) | |
| xyz_file = f.name | |
| atoms = read(xyz_file) | |
| atoms.info = {"charge": int(charge), "spin": int(spin_multiplicity)} | |
| atoms.calc = calc | |
| energy = atoms.get_potential_energy() # eV | |
| forces = atoms.get_forces() # eV/Å | |
| lines = [f"Total Energy: {energy:.6f} eV", "", "Atomic Forces:"] | |
| 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 | |
| return "\n".join(lines), "Calculation completed with OrbMol" | |
| except Exception as e: | |
| return f"Error during calculation: {e}", "Error" | |
| # ==== Simulaciones (sin cambios) ==== | |
| from simulation_scripts_orbmol import ( | |
| run_md_simulation, | |
| run_relaxation_simulation, | |
| ) | |
| def _string_looks_like_xyz(text: str) -> bool: | |
| 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 actualizados para devolver archivos para Molecule3D | |
| 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) | |
| traj_path, log_text, script_text, explanation = run_md_simulation( | |
| path_or_str, | |
| int(steps), | |
| 20, # pre-relax fija | |
| float(timestep_fs), | |
| float(tempK), | |
| "NVT" if ensemble == "NVT" else "NVE", | |
| int(charge), | |
| int(spin), | |
| ) | |
| status = f"MD completed: {int(steps)} steps at {int(tempK)} K ({ensemble})" | |
| # Usar Molecule3D si está disponible, sino HTML | |
| if HAVE_MOL3D: | |
| pdb_file = traj_to_molecule3d_file(traj_path) | |
| return (status, traj_path, log_text, script_text, explanation, pdb_file, "") | |
| else: | |
| 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 | |
| def relax_wrapper(xyz_content, steps, fmax, charge, spin, relax_cell): | |
| tmp_created = False | |
| path_or_str = xyz_content | |
| try: | |
| path_or_str, tmp_created = _to_file_if_xyz(xyz_content) | |
| traj_path, log_text, script_text, explanation = run_relaxation_simulation( | |
| path_or_str, | |
| int(steps), | |
| float(fmax), | |
| int(charge), | |
| int(spin), | |
| bool(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_file = traj_to_molecule3d_file(traj_path) | |
| return (status, traj_path, log_text, script_text, explanation, pdb_file, "") | |
| else: | |
| 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 | |
| # ==== Ejemplos (sin cambios) ==== | |
| 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 actualizada ==== | |
| with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo: | |
| with gr.Tabs(): | |
| # -------- SPE (sin cambios) -------- | |
| with gr.Tab("Single Point Energy"): | |
| 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…") | |
| 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]) | |
| run_spe.click(predict_molecule, [xyz_input, charge_input, spin_input], [spe_out, spe_status]) | |
| # -------- MD (actualizada con Molecule3D) -------- | |
| 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…") | |
| 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") | |
| 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)") | |
| 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") | |
| 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) | |
| # 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_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, md_html], | |
| ) | |
| # -------- Relax (actualizada con Molecule3D) -------- | |
| 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…") | |
| 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) | |
| # 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_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, 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) | |