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 # ==== Forzar visor HTML con 3Dmol.js ==== # (desactiva Molecule3D porque requiere formatos con conectividad) HAVE_MOL3D = False # ==== Fallback HTML con 3Dmol.js ==== def traj_to_html(traj_path, width=520, height=520, interval_ms=200): """ Lee una .traj de ASE y genera un visor HTML (3Dmol.js) con animación. """ if not traj_path or not os.path.exists(traj_path): return "
No trajectory file found
" viewer_id = f"viewer_{abs(hash(traj_path)) % 100000}" try: traj = Trajectory(traj_path) if len(traj) == 0: return "
Empty trajectory
" except Exception as e: return f"
Error: {e}
" 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"""
🧬 3D Molecular Viewer — {len(xyz_frames)} frames
""" return html # ==== OrbMol SPE ==== 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 (OrbMol). Toma XYZ en texto. """ 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 (helpers) ==== 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: 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) traj_path, log_text, script_text, explanation = run_md_simulation( path_or_str, int(steps), 20, 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})" 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)" 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 ==== 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: with gr.Tabs(): # -------- SPE -------- 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 -------- 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) 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): 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) 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)