from chemlab.notebook import download_molecule, display_molecule

arg = download_molecule("arginine")
display_molecule(arg)

# let's make an arginine box
from chemlab.core import System
from chemlab.notebook import display_system

import numpy as np

copies = []
for i in range(100):
    tmp = arg.copy()
    tmp.r_array += np.random.random(3) * 3.0
    copies.append(tmp)

system = System(copies)

display_system(system)

from chemlab.notebook import display_trajectory

# Let's scramble those coordinates
frames = system.r_array + np.random.random((100, system.n_atoms, 3))

display_trajectory(system, frames)

from chemlab.notebook import load_remote_system, load_remote_trajectory, load_trajectory, display_trajectory

system = load_remote_system("https://github.com/chemlab/chemlab-testdata/raw/master/water.gro")
system.guess_bonds()
t, frames = load_remote_trajectory("https://github.com/chemlab/chemlab-testdata/raw/master/trajout.xtc")

tc, mv = display_trajectory(system, frames)

# Change the speed
tc.fps = 10