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##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2017 Stanford University and the Authors
#
# Authors: Matthew Harrigan
# Contributors:
#
# MDTraj is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 2.1
# of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with MDTraj. If not, see <http://www.gnu.org/licenses/>.
##############################################################################
import itertools
import os
import numpy as np
import pytest
import mdtraj as md
from mdtraj import element
from mdtraj.utils.unitcell import check_valid_unitcell_angles
flaky_pdb_dl = pytest.mark.flaky(rerun=3, reason="github-node flaky pdb dl")
@pytest.fixture(scope="session")
def get_fn():
test_dir = os.path.dirname(os.path.abspath(__file__))
def _get_fn(fn):
return f"{test_dir}/data/{fn}"
return _get_fn
@pytest.fixture(scope="function")
def gen_random_ptraj(request):
"""Fixture for preparing a test trajectories with random coordinates
and unitcell
"""
request.cls.N_FRAMES = N_FRAMES = 20
request.cls.N_ATOMS = N_ATOMS = 20
request.cls.rng = rng = np.random.default_rng()
request.cls.xyz = xyz = np.asarray(rng.standard_normal((N_FRAMES, N_ATOMS, 3), dtype=np.float32))
request.cls.pairs = np.array(list(itertools.combinations(range(N_ATOMS), 2)), dtype=np.int32)
request.cls.times = np.array([[i, 0] for i in range(N_FRAMES)[::2]], dtype=np.int32)
request.cls.ptraj = md.Trajectory(xyz=xyz, topology=None)
request.cls.ptraj.unitcell_vectors = np.ascontiguousarray(
rng.standard_normal((N_FRAMES, 3, 3)) + 2 * np.eye(3, 3),
dtype=np.float32,
)
while True:
# RNG can give us unitcells with zero or imaginary volume.
# This `while` loop guarantees that we don't get that.
request.cls.ptraj.unitcell_vectors = np.ascontiguousarray(
rng.standard_normal((N_FRAMES, 3, 3)) + 2 * np.eye(3, 3),
dtype=np.float32,
)
if np.all([check_valid_unitcell_angles(*row) for row in request.cls.ptraj.unitcell_angles]):
break
@pytest.fixture(scope="function")
def h5traj(tmp_path):
xyz = np.around(np.random.randn(10, 5, 3).astype(np.float32), 2)
topology = md.Topology()
chain = topology.add_chain()
residue = topology.add_residue("ALA", chain)
topology.add_atom("CA", element.carbon, residue)
topology.add_atom("HG1", element.hydrogen, residue)
topology.add_atom("SG", element.sulfur, residue)
topology.add_atom("OD1", element.oxygen, residue)
topology.add_atom("NE", element.nitrogen, residue)
time = np.arange(10) ** 2
unitcell_lengths = np.array([[1.1, 1.2, 1.3]] * 10)
unitcell_angles = np.array([[90, 90, 95]] * 10)
traj = md.Trajectory(
xyz,
topology=topology,
time=time,
unitcell_lengths=unitcell_lengths,
unitcell_angles=unitcell_angles,
)
fn = f"{tmp_path}/ref.h5"
traj.save(fn)
return traj, fn, str(tmp_path)
@pytest.fixture(scope="function")
def h5traj_full_metadata(tmp_path):
# h5 trajectory with full bond metadata and formal charge
# for use testing roundtrip of topologies
# added because fixture above (h5traj) is used
# in many tests where full data is not roundtripped.
# PR2101
from mdtraj.core.topology import Double, Single
xyz = np.around(np.random.randn(10, 5, 3).astype(np.float32), 2)
topology = md.Topology()
chain = topology.add_chain()
residue = topology.add_residue("ALA", chain)
ca = topology.add_atom("CA", element.carbon, residue, formal_charge=0)
hg1 = topology.add_atom("HG1", element.hydrogen, residue, formal_charge=1)
sg = topology.add_atom("SG", element.sulfur, residue, formal_charge=-1)
od1 = topology.add_atom("OD1", element.oxygen, residue, formal_charge=-1)
ne = topology.add_atom("NE", element.nitrogen, residue, formal_charge=1)
topology.add_bond(ca, hg1, order=1, type=Single)
topology.add_bond(ca, sg, order=2, type=Double)
topology.add_bond(od1, ne, order=1, type=Single)
time = np.arange(10) ** 2
unitcell_lengths = np.array([[1.1, 1.2, 1.3]] * 10)
unitcell_angles = np.array([[90, 90, 95]] * 10)
traj = md.Trajectory(
xyz,
topology=topology,
time=time,
unitcell_lengths=unitcell_lengths,
unitcell_angles=unitcell_angles,
)
fn = f"{tmp_path}/ref.h5"
traj.save(fn)
return traj, fn, str(tmp_path)
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