#!/usr/bin/env python
""".. _howto-mdanalysis-workflow:

MDAnalysis Workflow
-------------------

Example using DielectricSpectrum with MDAnalysis.

This example shows that the refactored DielectricSpectrum class still works
exactly as before, maintaining backward compatibility.
"""

import MDAnalysis as mda
from spectrumkit import DielectricSpectrum

# %%
#
# Load your trajectory
u = mda.Universe("water.tpr", "water.trr")

# %%
#
# Select atoms (e.g., all atoms in the system)
atomgroup = u.select_atoms("all")

# %%
#
# Create DielectricSpectrum analysis
# This works exactly as before - the dipole calculation and spectrum
# calculation are still integrated in the class
analysis = DielectricSpectrum(
    atomgroup=atomgroup,
    temperature=300,
    output_prefix="water",
    segs=20,
    bins=200,
    binafter=20,
    nobin=False,
)

# %%
#
# Run the analysis
analysis.run()

# %%
#
# Access results
print(f"Average volume: {analysis.results.V:.2f} Ų")
print(f"Number of frames: {len(analysis.results.P)}")
print(f"Frequency points: {len(analysis.results.nu)}")
print(f"Frequency range: {analysis.results.nu[0]:.4f} - "
      f"{analysis.results.nu[-1]:.4f} THz")

# %%
#
# Save results
analysis.save()

print("\nAnalysis complete!")
print(f"Results saved with prefix: {analysis.output_prefix}")