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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 | |
from rdkit import Chem | |
from rdkit.Chem import AllChem | |
from rdkit.Chem import rdFMCS |
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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 |
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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.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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# 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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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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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 | |
import timeit | |
| |
| |
def setup(): | |
| |
| |
energy = model((species, coordinates)).energies | |
|
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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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from openmm.app import ( | |
StateDataReporter, | |
DCDReporter, | |
CharmmPsfFile, | |
CharmmParameterSet, | |
Simulation, | |
PDBFile, | |
) | |
from openmm import ( | |
unit, |
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