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)