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from openmm.app import (
    StateDataReporter,
    DCDReporter,
    CharmmPsfFile,
    Simulation,
    CharmmCrdFile,
)
from openmm import (
    unit,
    VerletIntegrator,

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from openmm.app import (
    StateDataReporter,
    DCDReporter,
    CharmmPsfFile,
    CharmmParameterSet,
    Simulation,
    PDBFile,
)
from openmm import (
    unit,

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# imports
import openmm as mm
from openmm.app import Simulation
from openff.evaluator.protocols import coordinates
from openff.evaluator.utils import packmol
from openff.toolkit.typing.engines.smirnoff import ForceField
from openff.units import unit
from openff.toolkit.topology import Molecule, Topology
from openmmml import MLPotential

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import torchani
import torch
import timeit
​
​
def setup():
​
​
    energy = model((species, coordinates)).energies
​

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import torchani
from memory_profiler import profile
import torch

@profile
def setup():
    nr_of_methans = 10
    nr_of_frames = 100
    device = 'cpu'
    model = torchani.models.ANI1ccx(periodic_table_index=True).to(device)

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import torchani
import torch
model = torchani.models.ANI1ccx()
import neutromeratio

import numpy as np
import mdtraj as md
import nglview
from tqdm import tqdm
import pickle

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# atom2svg.py by @biochem_fan  
# VERSION: 200213
# License: GPLv2 or later (ask me if this is inconvenient for you)
#
# LIMITATIONS:
# - This supports only a single chain. If you have more chains, shift residue IDs and merge chains.
#
# TODO:
# - Residue numbers (how to pack??)

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from openmmtools.testsystems import WaterBox
import matplotlib.pyplot as plt
from simtk import unit
import numpy as np
import torchani
import torch
import time

# openmm units
distance_unit = unit.nanometer

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from openmmtools.testsystems import DHFRExplicit
from openmmtools.testsystems import WaterBox
import matplotlib.pyplot as plt

from simtk import unit
import numpy as np
import torchani
import torch
import time
from simtk import unit

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from openmmtools.constants import kB
from simtk import unit
import numpy as np
from tqdm import tqdm
from IPython.core.display import display, HTML
from IPython.display import SVG
from rdkit.Chem.Draw import IPythonConsole
import mdtraj as md
#from utils import * 
import nglview