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import numpy as np
import os
import pytest
import tempfile
from dynasor.trajectory.atomic_indices import parse_gromacs_index_file
@pytest.fixture
def index_fname():
this_dir = os.path.dirname(__file__)
index_fname = os.path.join(this_dir, 'trajectory_reader/trajectory_files/index_file_dump_long')
return index_fname
def test_parse_gromacs_index_file(index_fname):
atomic_indices = parse_gromacs_index_file(index_fname)
Br_inds = np.array(sorted(list(range(2, 320, 5)) + list(range(3, 320, 5)) + list(range(4, 320, 5)))) # noqa
assert sorted(atomic_indices) == ['Br', 'Cs', 'Pb']
assert np.allclose(atomic_indices['Cs'], np.arange(0, 320, 5))
assert np.allclose(atomic_indices['Pb'], np.arange(1, 320, 5))
assert np.allclose(atomic_indices['Br'], Br_inds)
def test_raise_file_does_not_exists():
fname = 'asd'
with pytest.raises(ValueError):
parse_gromacs_index_file(fname)
def test_duplicate_groups_in_indexfile():
# write dummy file with duplicate Cs group
s = b"""[ Cs ]
1 6 11 16
[ Pb ]
2 7 12 17
[ Br ]
3 4 5
[ Cs ]
101 106 111 116
"""
f = tempfile.NamedTemporaryFile(delete=False)
f.write(s)
f.seek(0)
atomic_indices = parse_gromacs_index_file(f.name)
assert atomic_indices['Cs'].tolist() == [100, 105, 110, 115]
assert atomic_indices['Pb'].tolist() == [1, 6, 11, 16]
assert atomic_indices['Br'].tolist() == [2, 3, 4]
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