Separate functions from regularize_homologous_chains

[sikaoguo22]

This is what we used in the book chapter tutorial, we need to modify the codes to match this

# 1. Initialize the Model: 
pdb_id = '8y7s'
save_dir = '~/Documents/8y7s_dir'
pdb_model = ion.PDBModel(pdb_id, save_dir)

# 2. Coarse-Grain the Structure:
pdb_model.coarse_grain()

# 3. Define Reaction Rates:
pdb_model.define_reaction_rates()

# 4. Generate Executable Input Files:
simulation = ion.Simulation(pdb_model, save_dir)
simulation.generate_nerdss_input()

# 5. Customize Simulation Parameters:
simulation.modify_inp_file(
    {'nItr': 20000000, 'timeStep': 0.5,
    'timeWrite': 20000, 'pdbWrite': 2000000, 
    'A': 130, 'WaterBox': [600.0, 600.0, 600.0]}
    )

# 6. Run Simulation:
nerdss_install_path="~/NERDSS/"
sim_dir=f"{save_dir}/nerdss_output"
simulation.run_new_simulations(
    sim_dir=sim_dir,
    nerdss_dir=nerdss_install_path,
    )

# 7. Analyze Simulation Output
analysis = ion.Analysis(sim_dir)
analysis.plot_figure(
    figure_type='line',
    x='time',
    y='count',
    legend=["A: 1.", "A: 4.",]
    )