Spaces:
Sleeping
Sleeping
| 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 | |
| from simulation_scripts_orbmol import load_orbmol_model, run_md_simulation, run_relaxation_simulation | |
| import hashlib | |
| DEFAULT_MOLECULAR_REPRESENTATIONS = [ | |
| { | |
| "model": 0, | |
| "chain": "", | |
| "resname": "", | |
| "style": "sphere", | |
| "color": "Jmol", | |
| "around": 0, | |
| "byres": False, | |
| "scale": 0.3, | |
| }, | |
| { | |
| "model": 0, | |
| "chain": "", | |
| "resname": "", | |
| "style": "stick", | |
| "color": "Jmol", | |
| "around": 0, | |
| "byres": False, | |
| "scale": 0.2, | |
| }, | |
| ] | |
| DEFAULT_MOLECULAR_SETTINGS = { | |
| "backgroundColor": "white", | |
| "orthographic": False, | |
| "disableFog": False, | |
| } | |
| def convert_to_pdb_for_viewer(file_path): | |
| if not file_path or not os.path.exists(file_path): | |
| return None | |
| try: | |
| atoms = read(file_path) | |
| cache_dir = os.path.join(tempfile.gettempdir(), "gradio") | |
| os.makedirs(cache_dir, exist_ok=True) | |
| pdb_path = os.path.join(cache_dir, f"mol_{hashlib.md5(file_path.encode()).hexdigest()[:12]}.pdb") | |
| write(pdb_path, atoms, format="proteindatabank") | |
| return pdb_path | |
| except Exception as e: | |
| print(f"Error converting to PDB: {e}") | |
| return None | |
| def predict_molecule(structure_file, task_name, charge=0, spin_multiplicity=1): | |
| try: | |
| calc = load_orbmol_model(task_name) | |
| 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) | |
| if task_name in ["OMol", "OMol-Direct"]: | |
| atoms.info = {"charge": int(charge), "spin": int(spin_multiplicity)} | |
| atoms.calc = calc | |
| energy = atoms.get_potential_energy() | |
| forces = atoms.get_forces() | |
| lines = [ | |
| f"Model: {task_name}", | |
| 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"] | |
| pdb_file = convert_to_pdb_for_viewer(file_path) | |
| return "\n".join(lines), f"Calculation completed with {task_name}", pdb_file | |
| except Exception as e: | |
| import traceback | |
| traceback.print_exc() | |
| return f"Error during calculation: {e}", "Error", None | |
| def md_wrapper(structure_file, task_name, charge, spin, steps, tempK, timestep_fs, ensemble): | |
| try: | |
| if not structure_file: | |
| return ("Error: Please upload a structure file", None, "", "", "", None) | |
| traj_path, log_text, script_text, explanation = run_md_simulation( | |
| structure_file, | |
| int(steps), | |
| 20, | |
| float(timestep_fs), | |
| float(tempK), | |
| "NVT" if ensemble == "NVT" else "NVE", | |
| str(task_name), | |
| int(charge), | |
| int(spin), | |
| ) | |
| status = f"MD completed: {int(steps)} steps at {int(tempK)} K ({ensemble})" | |
| pdb_file = convert_to_pdb_for_viewer(traj_path) | |
| return (status, traj_path, log_text, script_text, explanation, pdb_file) | |
| except Exception as e: | |
| import traceback | |
| traceback.print_exc() | |
| return (f"Error: {e}", None, "", "", "", None) | |
| def relax_wrapper(structure_file, task_name, steps, fmax, charge, spin, relax_cell): | |
| try: | |
| if not structure_file: | |
| return ("Error: Please upload a structure file", None, "", "", "", None) | |
| traj_path, log_text, script_text, explanation = run_relaxation_simulation( | |
| structure_file, | |
| int(steps), | |
| float(fmax), | |
| str(task_name), | |
| int(charge), | |
| int(spin), | |
| bool(relax_cell), | |
| ) | |
| status = f"Relaxation finished (<={int(steps)} steps, fmax={float(fmax)} eV/Å)" | |
| pdb_file = convert_to_pdb_for_viewer(traj_path) | |
| return (status, traj_path, log_text, script_text, explanation, pdb_file) | |
| except Exception as e: | |
| import traceback | |
| traceback.print_exc() | |
| return (f"Error: {e}", None, "", "", "", None) | |
| with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo: | |
| with gr.Tabs(): | |
| with gr.Tab("Home"): | |
| gr.Image("logo_color_text.png", show_share_button=False, show_download_button=False, show_label=False, show_fullscreen_button=False) | |
| gr.Markdown("# OrbMol — Quantum-Accurate Molecular Predictions") | |
| gr.Markdown("Welcome to the OrbMol demo! Use the tabs above to access different functionalities:") | |
| gr.Markdown("1. **Single Point Energy**: Calculate energies and forces for a given molecular structure.") | |
| gr.Markdown("2. **Molecular Dynamics**: Run MD simulations using OrbMol-trained potentials.") | |
| gr.Markdown("3. **Relaxation / Optimization**: Optimize molecular structures to their minimum-energy configurations.") | |
| gr.Markdown("Supported file formats: `.xyz`, `.pdb`, `.cif`, `.traj`, `.mol`, `.sdf`.") | |
| gr.Markdown("## Pretrained Models") | |
| gr.Markdown("**OMol** and **OMol-Direct**") | |
| gr.Markdown("- **Training dataset**: OMol25 (>100M calculations on small molecules, biomolecules, metal complexes, and electrolytes).") | |
| gr.Markdown("- **Level of theory**: wB97M-V/def2-TZVPD with non-local dispersion; solvation treated explicitly.") | |
| gr.Markdown("- **Inputs**: total charge & spin multiplicity.") | |
| gr.Markdown("- **Applications**: biology, organic chemistry, protein folding, small-molecule drugs, organic liquids, homogeneous catalysis.") | |
| gr.Markdown("- **Caveats**: trained only on aperiodic systems → periodic/inorganic cases may not work well.") | |
| gr.Markdown("- **Difference**: OMol enforces energy–force consistency; OMol-Direct relaxes this for efficiency.") | |
| gr.Markdown("**OMat**") | |
| gr.Markdown("- **Training dataset**: OMat24 (>100M inorganic calculations, from Materials Project, Alexandria, and far-from-equilibrium samples).") | |
| gr.Markdown("- **Level of theory**: PBE/PBE+U with Materials Project settings; VASP 54 pseudopotentials; no dispersion.") | |
| gr.Markdown("- **Inputs**: No support for spin and charge. Spin polarization included but magnetic state cannot be selected.") | |
| gr.Markdown("- **Applications**: inorganic discovery, photovoltaics, alloys, superconductors, electronic/optical materials.") | |
| gr.Markdown("- **Caveats**: magnetic effects may be incompletely captured.") | |
| gr.Markdown("## Technical Foundation") | |
| gr.Markdown("All models are based on the **Orb-v3 architecture**, the latest generation of Orb universal interatomic potentials, combining transferability with quantum-level accuracy.") | |
| gr.Markdown("## Resources & Support") | |
| gr.Markdown("- [Orb-v3 paper](https://arxiv.org/abs/2504.06231)") | |
| gr.Markdown("- [Orb-Models GitHub repository](https://github.com/orbital-materials/orb-models)") | |
| gr.Markdown("- For issues/questions, please open a GitHub issue or contact the developers.") | |
| with gr.Tab("Single Point Energy"): | |
| with gr.Row(): | |
| with gr.Column(scale=2): | |
| gr.Markdown("# OrbMol — Quantum-Accurate Molecular Predictions") | |
| gr.Markdown("**Supported formats:** .xyz, .pdb, .cif, .traj, .mol, .sdf") | |
| xyz_input = gr.File(label="Upload Structure File", file_types=[".xyz", ".pdb", ".cif", ".traj", ".mol", ".sdf"], file_count="single") | |
| task_name_spe = gr.Radio(["OMol", "OMat", "OMol-Direct"], value="OMol", label="Model Type") | |
| with gr.Row(): | |
| charge_input = gr.Slider(-10, 10, 0, step=1, label="Charge") | |
| spin_input = gr.Slider(1, 11, 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) | |
| spe_viewer = Molecule3D(label="Input Structure Viewer", reps=DEFAULT_MOLECULAR_REPRESENTATIONS, config=DEFAULT_MOLECULAR_SETTINGS) | |
| task_name_spe.change( | |
| lambda x: ( | |
| gr.update(visible=x in ["OMol", "OMol-Direct"]), | |
| gr.update(visible=x in ["OMol", "OMol-Direct"]) | |
| ), | |
| [task_name_spe], | |
| [charge_input, spin_input] | |
| ) | |
| run_spe.click(predict_molecule, [xyz_input, task_name_spe, charge_input, spin_input], [spe_out, spe_status, spe_viewer]) | |
| with gr.Tab("Molecular Dynamics"): | |
| with gr.Row(): | |
| with gr.Column(scale=2): | |
| gr.Markdown("## Molecular Dynamics Simulation") | |
| xyz_md = gr.File(label="Upload Structure File", file_types=[".xyz", ".pdb", ".cif", ".traj", ".mol", ".sdf"], file_count="single") | |
| task_name_md = gr.Radio(["OMol", "OMat", "OMol-Direct"], value="OMol", label="Model Type") | |
| with gr.Row(): | |
| charge_md = gr.Slider(-10, 10, 0, step=1, label="Charge") | |
| spin_md = gr.Slider(1, 11, 1, step=1, label="Spin Multiplicity") | |
| with gr.Row(): | |
| steps_md = gr.Slider(10, 2000, 100, step=10, label="Steps") | |
| temp_md = gr.Slider(10, 1500, 300, step=10, label="Temperature (K)") | |
| with gr.Row(): | |
| timestep_md = gr.Slider(0.1, 5.0, 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="MD Result Viewer", reps=DEFAULT_MOLECULAR_REPRESENTATIONS, config=DEFAULT_MOLECULAR_SETTINGS) | |
| md_log = gr.Textbox(label="Log", interactive=False, lines=15) | |
| md_script = gr.Code(label="Reproduction Script", language="python", interactive=False, lines=20) | |
| md_explain = gr.Markdown() | |
| task_name_md.change( | |
| lambda x: ( | |
| gr.update(visible=x in ["OMol", "OMol-Direct"]), | |
| gr.update(visible=x in ["OMol", "OMol-Direct"]) | |
| ), | |
| [task_name_md], | |
| [charge_md, spin_md] | |
| ) | |
| run_md_btn.click(md_wrapper, [xyz_md, task_name_md, charge_md, spin_md, steps_md, temp_md, timestep_md, ensemble_md], [md_status, md_traj, md_log, md_script, md_explain, md_viewer]) | |
| with gr.Tab("Relaxation / Optimization"): | |
| with gr.Row(): | |
| with gr.Column(scale=2): | |
| gr.Markdown("## Structure Relaxation/Optimization") | |
| xyz_rlx = gr.File(label="Upload Structure File", file_types=[".xyz", ".pdb", ".cif", ".traj", ".mol", ".sdf"], file_count="single") | |
| task_name_rlx = gr.Radio(["OMol", "OMat", "OMol-Direct"], value="OMol", label="Model Type") | |
| with gr.Row(): | |
| steps_rlx = gr.Slider(1, 2000, 300, step=1, label="Max Steps") | |
| fmax_rlx = gr.Slider(0.001, 0.5, 0.05, step=0.001, label="Fmax (eV/Å)") | |
| with gr.Row(): | |
| charge_rlx = gr.Slider(-10, 10, 0, step=1, label="Charge") | |
| spin_rlx = gr.Slider(1, 11, 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=DEFAULT_MOLECULAR_REPRESENTATIONS, config=DEFAULT_MOLECULAR_SETTINGS) | |
| rlx_log = gr.Textbox(label="Log", interactive=False, lines=15) | |
| rlx_script = gr.Code(label="Reproduction Script", language="python", interactive=False, lines=20) | |
| rlx_explain = gr.Markdown() | |
| task_name_rlx.change( | |
| lambda x: ( | |
| gr.update(visible=x in ["OMol", "OMol-Direct"]), | |
| gr.update(visible=x in ["OMol", "OMol-Direct"]) | |
| ), | |
| [task_name_rlx], | |
| [charge_rlx, spin_rlx] | |
| ) | |
| run_rlx_btn.click(relax_wrapper, [xyz_rlx, task_name_rlx, steps_rlx, fmax_rlx, charge_rlx, spin_rlx, relax_cell], [rlx_status, rlx_traj, rlx_log, rlx_script, rlx_explain, rlx_viewer]) | |
| if __name__ == "__main__": | |
| demo.launch(server_name="0.0.0.0", server_port=7860, show_error=True) | |