app.py

import os
os.environ["TORCH_DYNAMO_DISABLE"] = "1"
import subprocess
import sys
from pathlib import Path
import tempfile
import numpy as np
import gradio as gr
from ase.io import read, write
from ase.io.trajectory import Trajectory
from simulation_scripts_orbmol import load_orbmol_model, run_md_simulation, run_relaxation_simulation
import hashlib

# ==== Configuración Molecule3D ====
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,
}

# ==== Conversión a PDB para Molecule3D ====
def convert_to_pdb_for_viewer(file_path):
    """Convierte cualquier archivo a PDB para Molecule3D"""
    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

# ==== OrbMol SPE ====
def predict_molecule(structure_file, task_name, charge=0, spin_multiplicity=1):
    """Single Point Energy + fuerzas (OrbMol)"""
    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

# ==== Wrappers MD y Relax ====
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)

# ==== MAIN FUNCTION ====
def main():
    with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo:
        with gr.Tabs():
            # -------- HOME --------
            with gr.Tab("Home"):
                with gr.Row():
                    with gr.Column(scale=1):
                        gr.Markdown("## Learn more about OrbMol")
                        
                        with gr.Accordion("What is OrbMol?", open=False):
                            gr.Markdown("""
OrbMol is a suite of quantum-accurate machine learning models for molecular predictions. Built on the **Orb-v3 architecture**, OrbMol provides fast and accurate calculations of energies, forces, and molecular properties.
                            """)
                        
                        with gr.Accordion("Available Models", open=False):
                            gr.Markdown("""
**OMol** and **OMol-Direct**
- Training dataset: OMol25 (>100M calculations)
- Level of theory: ωB97M-V/def2-TZVPD
- Applications: biology, organic chemistry, drug discovery

**OMat**
- Training dataset: OMat24 (>100M inorganic calculations)
- Level of theory: PBE/PBE+U
- Applications: materials discovery, photovoltaics, alloys
                            """)
                        
                        with gr.Accordion("Supported File Formats", open=False):
                            gr.Markdown("""
Supported formats: `.xyz`, `.pdb`, `.cif`, `.traj`, `.mol`, `.sdf`
                            """)
                        
                        with gr.Accordion("Resources & Support", open=False):
                            gr.Markdown("""
- [Orb-v3 paper](https://arxiv.org/abs/2504.06231)
- [Orb-Models GitHub](https://github.com/orbital-materials/orb-models)
                            """)
                    
                    with gr.Column(scale=2):
                        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 OrbMol! Use the tabs above to access:

1. **Single Point Energy**: Calculate energies and forces
2. **Molecular Dynamics**: Run MD simulations  
3. **Relaxation / Optimization**: Optimize structures

Supported formats: `.xyz`, `.pdb`, `.cif`, `.traj`, `.mol`, `.sdf`
                        """)
            
            # -------- SPE --------
            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]
                )

            # -------- MD --------
            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]
                )

            # -------- Relax --------
            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]
                )

        demo.queue(default_concurrency_limit=None)
        demo.launch(ssr_mode=False)


if __name__ == "__main__":
    os.makedirs("/data/custom_inputs/errors", exist_ok=True)

    # On load, build and install the gradio_molecule3d fork
    subprocess.call(
        ["gradio", "cc", "install"], cwd=Path(__file__).parent / "gradio_molecule3d/"
    )
    subprocess.call(
        ["gradio", "cc", "build"], cwd=Path(__file__).parent / "gradio_molecule3d/"
    )
    subprocess.call(
        [
            sys.executable,
            "-m",
            "pip",
            "install",
            Path(__file__).parent
            / "gradio_molecule3d/"
            / "dist/gradio_molecule3d-0.0.7-py3-none-any.whl",
        ],
        cwd=Path(__file__).parent.parent,
    )

    # Load gradio_molecule3d only once it's built and installed
    from gradio_molecule3d import Molecule3D

    main()