Spaces:
Running
Running
| import os | |
| os.environ["TORCH_DYNAMO_DISABLE"] = "1" | |
| import tempfile | |
| import numpy as np | |
| import gradio as gr | |
| from ase.io import read, write | |
| from ase.io.trajectory import Trajectory | |
| from gradio_molecule3d import Molecule3D | |
| import hashlib | |
| import shutil | |
| # ==== util: PDB writer robusto para Molecule3D ==== | |
| def _pdb_cache_path(prefix: str, key: str) -> str: | |
| gradio_cache_dir = os.path.join(tempfile.gettempdir(), "gradio") | |
| os.makedirs(gradio_cache_dir, exist_ok=True) | |
| return os.path.join(gradio_cache_dir, f"{prefix}_{key}.pdb") | |
| def _write_pdb_with_fallback(atoms, pdb_path: str) -> str | None: | |
| """ | |
| Intenta escribir PDB con ASE usando el id correcto ('proteindatabank'). | |
| Si falla, crea un PDB minimal válido (líneas ATOM + END) suficiente para gradio_molecule3d. | |
| Devuelve la ruta si existe y tiene tamaño > 0, en caso contrario None. | |
| """ | |
| try: | |
| # writer id correcto en ASE para PDB | |
| write(pdb_path, atoms, format="proteindatabank") | |
| except Exception as e: | |
| print(f"ASE PDB writer failed: {e} — trying manual minimal PDB") | |
| try: | |
| xyz = atoms.get_positions() | |
| syms = atoms.get_chemical_symbols() | |
| with open(pdb_path, "w") as f: | |
| serial = 1 | |
| for (sym, (x, y, z)) in zip(syms, xyz): | |
| # Campos esenciales: 'ATOM', serial, nombre (símbolo), resname, chain, res seq, coords y elemento | |
| f.write( | |
| f"ATOM {serial:5d} {sym:<3s} MOL A 1 " | |
| f"{x:8.3f}{y:8.3f}{z:8.3f} 1.00 0.00 {sym:>2s}\n" | |
| ) | |
| serial += 1 | |
| f.write("END\n") | |
| except Exception as e2: | |
| print(f"Manual PDB fallback failed: {e2}") | |
| return None | |
| # Validación | |
| if os.path.exists(pdb_path) and os.path.getsize(pdb_path) > 0: | |
| print(f"✅ PDB created: {pdb_path} ({os.path.getsize(pdb_path)} bytes)") | |
| try: | |
| with open(pdb_path, "r") as f: | |
| preview = f.read(160) | |
| print(f"PDB preview: {preview[:120]}...") | |
| except Exception: | |
| pass | |
| return pdb_path | |
| print("❌ PDB file not created or empty") | |
| return None | |
| # ==== Molecule3D viewer preparation CORREGIDO ==== | |
| def prepare_molecule_for_viewer(traj_path): | |
| """Convert trajectory to format compatible with Molecule3D viewer""" | |
| if not traj_path or not os.path.exists(traj_path): | |
| print("No trajectory path provided or file doesn't exist") | |
| return None | |
| try: | |
| traj = Trajectory(traj_path) | |
| if len(traj) == 0: | |
| print("Empty trajectory") | |
| return None | |
| print(f"Preparing viewer: {len(traj)} frames, {len(traj[-1])} atoms") | |
| atoms = traj[-1] | |
| # clave única por posiciones del último frame | |
| pos_hash = hashlib.md5(atoms.get_positions().tobytes()).hexdigest()[:12] | |
| pdb_path = _pdb_cache_path("molecule", pos_hash) | |
| if os.path.exists(pdb_path) and os.path.getsize(pdb_path) > 0: | |
| print(f"PDB already exists: {pdb_path}") | |
| return pdb_path | |
| return _write_pdb_with_fallback(atoms, pdb_path) | |
| except Exception as e: | |
| print(f"Error preparing molecule for viewer: {e}") | |
| import traceback; traceback.print_exc() | |
| return None | |
| # ==== Función para convertir archivo inicial a PDB para SPE ==== | |
| def prepare_input_for_viewer(structure_file): | |
| """Convert input structure file to PDB for Molecule3D viewer""" | |
| if not structure_file or not os.path.exists(structure_file): | |
| return None | |
| try: | |
| atoms = read(structure_file) | |
| key = hashlib.md5(str(structure_file).encode()).hexdigest()[:12] | |
| pdb_path = _pdb_cache_path("input", key) | |
| if os.path.exists(pdb_path) and os.path.getsize(pdb_path) > 0: | |
| print(f"Input PDB already exists: {pdb_path}") | |
| return pdb_path | |
| return _write_pdb_with_fallback(atoms, pdb_path) | |
| except Exception as e: | |
| print(f"Error preparing input for viewer: {e}") | |
| return None | |
| # ==== 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(structure_file, charge=0, spin_multiplicity=1): | |
| """ | |
| Single Point Energy + fuerzas (OrbMol). Acepta archivos subidos. | |
| """ | |
| try: | |
| calc = _load_orbmol_calc() | |
| if not structure_file: | |
| return "Error: Please upload a structure file", "Error", None | |
| file_path = structure_file | |
| if not os.path.exists(file_path): | |
| return f"Error: File not found: {file_path}", "Error", None | |
| if os.path.getsize(file_path) == 0: | |
| return f"Error: Empty file: {file_path}", "Error", None | |
| atoms = read(file_path) | |
| atoms.info = {"charge": int(charge), "spin": int(spin_multiplicity)} | |
| atoms.calc = calc | |
| energy = atoms.get_potential_energy() | |
| forces = atoms.get_forces() | |
| 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"] | |
| # Preparar PDB para visualización | |
| pdb_file = prepare_input_for_viewer(file_path) | |
| return "\n".join(lines), "Calculation completed with OrbMol", pdb_file | |
| except Exception as e: | |
| import traceback; traceback.print_exc() | |
| return f"Error during calculation: {e}", "Error", None | |
| # ==== Simulaciones (helpers) ==== | |
| from simulation_scripts_orbmol import ( | |
| run_md_simulation, | |
| run_relaxation_simulation, | |
| ) | |
| # ==== Wrappers con debug y Molecule3D ==== | |
| 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) | |
| file_path = structure_file | |
| print(f"MD Wrapper: Processing {file_path}") | |
| traj_path, log_text, script_text, explanation = run_md_simulation( | |
| file_path, | |
| int(steps), | |
| 20, # pre-relax steps | |
| 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})" | |
| print(f"MD completed, trajectory: {traj_path}") | |
| pdb_file = prepare_molecule_for_viewer(traj_path) | |
| print(f"PDB file for Molecule3D: {pdb_file}") | |
| return (status, traj_path, log_text, script_text, explanation, pdb_file) | |
| except Exception as e: | |
| print(f"MD Wrapper Error: {e}") | |
| import traceback; traceback.print_exc() | |
| return (f"Error: {e}", None, "", "", "", None) | |
| def relax_wrapper(structure_file, steps, fmax, charge, spin, relax_cell): | |
| try: | |
| if not structure_file: | |
| return ("Error: Please upload a structure file", None, "", "", "", None) | |
| file_path = structure_file | |
| print(f"Relax Wrapper: Processing {file_path}") | |
| traj_path, log_text, script_text, explanation = run_relaxation_simulation( | |
| file_path, | |
| int(steps), | |
| float(fmax), | |
| int(charge), | |
| int(spin), | |
| bool(relax_cell), | |
| ) | |
| status = f"Relaxation finished (≤ {int(steps)} steps, fmax={float(fmax)} eV/Å)" | |
| print(f"Relaxation completed, trajectory: {traj_path}") | |
| pdb_file = prepare_molecule_for_viewer(traj_path) | |
| print(f"PDB file for Molecule3D: {pdb_file}") | |
| return (status, traj_path, log_text, script_text, explanation, pdb_file) | |
| except Exception as e: | |
| print(f"Relax Wrapper Error: {e}") | |
| import traceback; traceback.print_exc() | |
| return (f"Error: {e}", None, "", "", "", None) | |
| # ==== 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("Upload molecular structure files (.xyz, .pdb, .cif, .traj) for energy and force calculations.") | |
| 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) | |
| spe_viewer = Molecule3D( | |
| label="Input Structure Viewer", | |
| reps=[ | |
| { | |
| "model": 0, "chain": "", "resname": "", | |
| "style": "stick", "color": "whiteCarbon", | |
| "residue_range": "", "around": 0, "byres": False, "visible": True, "opacity": 1.0 | |
| } | |
| ] | |
| ) | |
| run_spe.click(predict_molecule, [xyz_input, charge_input, spin_input], [spe_out, spe_status, spe_viewer]) | |
| # -------- MD -------- | |
| with gr.Tab("Molecular Dynamics"): | |
| with gr.Row(): | |
| with gr.Column(scale=2): | |
| gr.Markdown("## Molecular Dynamics Simulation") | |
| gr.Markdown("Upload your molecular structure and configure MD parameters.") | |
| 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") | |
| 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 = Molecule3D( | |
| label="Final Structure Viewer (Last MD Frame)", | |
| reps=[ | |
| { | |
| "model": 0, "chain": "", "resname": "", | |
| "style": "stick", "color": "whiteCarbon", | |
| "residue_range": "", "around": 0, "byres": False, "visible": True, "opacity": 1.0 | |
| }, | |
| { | |
| "model": 0, "chain": "", "resname": "", | |
| "style": "sphere", "color": "whiteCarbon", | |
| "residue_range": "", "around": 0, "byres": False, "visible": True, "opacity": 0.7 | |
| } | |
| ] | |
| ) | |
| 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], | |
| ) | |
| # -------- 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.") | |
| 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 = Molecule3D( | |
| label="Optimized Structure Viewer", | |
| reps=[ | |
| { | |
| "model": 0, "chain": "", "resname": "", | |
| "style": "stick", "color": "whiteCarbon", | |
| "residue_range": "", "around": 0, "byres": False, "visible": True, "opacity": 1.0 | |
| }, | |
| { | |
| "model": 0, "chain": "", "resname": "", | |
| "style": "sphere", "color": "whiteCarbon", | |
| "residue_range": "", "around": 0, "byres": False, "visible": True, "opacity": 0.7 | |
| } | |
| ] | |
| ) | |
| 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], | |
| ) | |
| 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) | |