app.py

import os
import re
import numpy as np
import gradio as gr
from ase.io import read, write
from ase.io.trajectory import Trajectory

# =========================
# 3Dmol.js helpers (preview y trayectorias)
# =========================

def _atoms_to_xyz_block(atoms):
    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}")
    return "\n".join(parts)

def structure_to_html(file_path, width=520, height=520):
    """Renderiza estructura única en 3Dmol.js sin correr cálculos."""
    if not file_path or not os.path.exists(file_path):
        return "<div style='color:#b00; padding:20px;'>No structure file found</div>"
    try:
        atoms = read(file_path)
    except Exception as e:
        return f"<div style='color:#b00; padding:20px;'>Error reading structure: {e}</div>"

    xyz_block = _atoms_to_xyz_block(atoms).replace("`", "\\`")
    viewer_id = f"viewer_{abs(hash(('single', file_path))) % 100000}"
    return f"""
<div style="margin-bottom:10px; padding:10px; background:#f5f5f5; border-radius:5px;">
  <strong>🧬 3D Molecular Viewer</strong> — preview (no compute)
</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>
const _load3Dmol = (ok) => {{
  if (typeof window.$3Dmol !== 'undefined') return ok();
  const s=document.createElement('script');
  s.src='https://3dmol.org/build/3Dmol-min.js';
  s.onload=ok; document.head.appendChild(s);
}};
_load3Dmol(() => {{
  const el=document.getElementById("{viewer_id}");
  if(!el||typeof $3Dmol==='undefined') return;
  const v=$3Dmol.createViewer(el, {{backgroundColor:'white'}});
  v.addModel(`{xyz_block}`, "xyz");
  v.setStyle({{}}, {{stick:{{}}, sphere:{{}}}});
  v.zoomTo(); v.render();
}});
</script>
"""

def traj_to_html(traj_path, width=520, height=520, interval_ms=200):
    """Animación 3Dmol.js desde .traj de ASE."""
    if not traj_path or not os.path.exists(traj_path):
        return "<div style='color:#b00; padding:20px;'>No trajectory file found</div>"
    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>"

    frames = [_atoms_to_xyz_block(at) for at in traj]
    frames_json = str(frames).replace("'", '"')
    viewer_id = f"viewer_{abs(hash(traj_path)) % 100000}"
    return f"""
<div style="margin-bottom:10px; padding:10px; background:#f5f5f5; border-radius:5px;">
  <strong>🧬 3D Molecular Viewer</strong> — {len(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>
const _load3Dmol = (ok) => {{
  if (typeof window.$3Dmol !== 'undefined') return ok();
  const s=document.createElement('script');
  s.src='https://3dmol.org/build/3Dmol-min.js';
  s.onload=ok; document.head.appendChild(s);
}};
_load3Dmol(() => {{
  const el=document.getElementById("{viewer_id}");
  if(!el||typeof $3Dmol==='undefined') return;
  const v=$3Dmol.createViewer(el, {{backgroundColor:'white'}});
  const frames={frames_json};
  let idx=0;
  function draw(i){{
    v.clear(); v.addModel(frames[i], "xyz");
    v.setStyle({{}}, {{stick:{{}}, sphere:{{}}}});
    v.zoomTo(); v.render();
  }}
  draw(0);
  if(frames.length>1){{
    setInterval(()=>{{ idx=(idx+1)%frames.length; draw(idx); }}, {interval_ms});
  }}
}});
</script>
"""

# =========================
# 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)."""
    try:
        calc = _load_orbmol_calc()
        if not structure_file:
            return "Error: Please upload a structure file", "Error"
        file_path = structure_file  # gr.File(type='filepath') -> str

        if not os.path.exists(file_path):
            return f"Error: File not found: {file_path}", "Error"
        if os.path.getsize(file_path) == 0:
            return f"Error: Empty file: {file_path}", "Error"

        atoms = read(file_path)
        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:"]
        norms = np.linalg.norm(forces, axis=1)
        for i, fc in enumerate(forces):
            lines.append(f"Atom {i+1}: [{fc[0]:.4f}, {fc[1]:.4f}, {fc[2]:.4f}] eV/Å")
        lines += ["", f"Max Force: {float(np.max(norms)):.4f} eV/Å"]

        return "\n".join(lines), "Calculation completed with OrbMol"
    except Exception as e:
        return f"Error during calculation: {e}", "Error"

# =========================
# Simulaciones (helpers) y parsing de log
# =========================
from simulation_scripts_orbmol import (
    run_md_simulation,
    run_relaxation_simulation,
)

ENERGY_PATTERNS = [
    re.compile(r"(?:^|\\s)(?:step|iter|i)\\s*[:=]?\\s*(\\d+).*?(?:E|energy)\\s*[:=]?\\s*(-?\\d+(?:\\.\\d+)?(?:[eE][+-]?\\d+)?)"),
    re.compile(r"(?:^|\\s)E(?:nergy)?\\s*[:=]?\\s*(-?\\d+(?:\\.\\d+)?(?:[eE][+-]?\\d+)?)"),
]

def extract_energy_series(log_text):
    steps, energies = [], []
    if not log_text:
        return steps, energies
    for line in log_text.splitlines():
        m = ENERGY_PATTERNS[0].search(line)
        if m:
            steps.append(int(m.group(1)))
            energies.append(float(m.group(2)))
            continue
        m2 = ENERGY_PATTERNS[1].search(line)
        if m2:
            steps.append(len(steps))
            energies.append(float(m2.group(1)))
    return steps, energies

def plot_energy(steps, energies, title):
    import matplotlib.pyplot as plt
    fig = plt.figure(figsize=(5,3.2))
    if steps:
        plt.plot(steps, energies, linewidth=1.6)
        plt.xlabel("Step")
    else:
        plt.plot(range(len(energies)), energies, linewidth=1.6)
        plt.xlabel("Index")
    plt.ylabel("Energy (eV)")
    plt.title(title)
    plt.tight_layout()
    return fig

# =========================
# Wrappers MD / Relax (devuelven: status, traj, log, script, explain, html, plot)
# =========================
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
        if not os.path.exists(file_path):
            return ("Error: File not found: " + str(file_path), None, "", "", "", "", None)
        if os.path.getsize(file_path) == 0:
            return ("Error: Empty file: " + str(file_path), None, "", "", "", "", None)

        traj_path, log_text, script_text, explanation = run_md_simulation(
            file_path,
            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)
        s, e = extract_energy_series(log_text)
        fig = plot_energy(s, e, "MD: Energy vs Step")
        return (status, traj_path, log_text, script_text, explanation, html_value, fig)
    except Exception as e:
        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
        if not os.path.exists(file_path):
            return ("Error: File not found: " + str(file_path), None, "", "", "", "", None)
        if os.path.getsize(file_path) == 0:
            return ("Error: Empty file: " + str(file_path), None, "", "", "", "", None)

        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)"
        html_value = traj_to_html(traj_path)
        s, e = extract_energy_series(log_text)
        fig = plot_energy(s, e, "Relaxation: Energy vs Step")
        return (status, traj_path, log_text, script_text, explanation, html_value, fig)
    except Exception as e:
        return (f"Error: {e}", None, "", "", "", "", None)

def preview_structure(structure_file):
    """Preview inmediato al subir archivo en SPE."""
    if not structure_file:
        return "<div style='color:#b00; padding:20px;'>Upload a file to preview</div>"
    if not os.path.exists(structure_file):
        return "<div style='color:#b00; padding:20px;'>File not found</div>"
    if os.path.getsize(structure_file) == 0:
        return "<div style='color:#b00; padding:20px;'>Empty file</div>"
    return structure_to_html(structure_file)

# =========================
# 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, .mol, .sdf) for preview and calculation.")
                    xyz_input = gr.File(
                        label="Upload Structure File",
                        file_types=[".xyz", ".pdb", ".cif", ".traj", ".mol", ".sdf"],
                        file_count="single",
                        type="filepath",
                    )
                    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=520):
                    spe_preview = gr.HTML(label="Structure Preview")
                    spe_out = gr.Textbox(label="Energy & Forces", lines=15, interactive=False)
                    spe_status = gr.Textbox(label="Status", interactive=False, max_lines=1)

            # Preview inmediato (sin cálculo)
            xyz_input.change(preview_structure, inputs=[xyz_input], outputs=[spe_preview])
            # Cálculo SPE
            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):
                    gr.Markdown("## Molecular Dynamics Simulation")
                    xyz_md = gr.File(
                        label="Upload Structure File",
                        file_types=[".xyz", ".pdb", ".cif", ".traj", ".mol", ".sdf"],
                        file_count="single",
                        type="filepath",
                    )
                    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_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()
                    md_plot = gr.Plot(label="Energy vs Step")

            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_html, md_plot],
            )

        # -------- 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",
                        type="filepath",
                    )
                    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_html = gr.HTML(label="Final Structure / Trajectory")
                    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()
                    rlx_plot = gr.Plot(label="Energy vs Step")

            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_html, rlx_plot],
            )

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)