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# fmt: off
import io
import pytest
from ase import Atoms
from ase.io.sdf import get_num_atoms_sdf_v2000, read_sdf
DIFFICULT_BUT_VALID_FIRST_LINE = '184192 0 0 0 0 0 0 0 0999 V2000'
VALID_SDF_V2000_COFFEE = '''
RDKit 3D
24 0 0 0 0 0 0 0 0 0999 V2000
0.4700 2.5688 0.0006 O 0 0 0 0 0 0 0 0 0 0 0 0
-3.1271 -0.4436 -0.0003 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.9686 -1.3125 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
2.2182 0.1412 -0.0003 N 0 0 0 0 0 0 0 0 0 0 0 0
-1.3477 1.0797 -0.0001 N 0 0 0 0 0 0 0 0 0 0 0 0
1.4119 -1.9372 0.0002 N 0 0 0 0 0 0 0 0 0 0 0 0
0.8579 0.2592 -0.0008 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3897 -1.0264 -0.0004 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0307 1.4220 -0.0006 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.9061 -0.2495 -0.0004 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5032 -1.1998 0.0003 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4276 -2.6960 0.0008 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1926 1.2061 0.0003 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.2969 2.1881 0.0007 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5163 -1.5787 0.0008 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.0451 -3.1973 -0.8937 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.5186 -2.7596 0.0011 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.0447 -3.1963 0.8957 H 0 0 0 0 0 0 0 0 0 0 0 0
4.1992 0.7801 0.0002 H 0 0 0 0 0 0 0 0 0 0 0 0
3.0468 1.8092 -0.8992 H 0 0 0 0 0 0 0 0 0 0 0 0
3.0466 1.8083 0.9004 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.8087 3.1651 -0.0003 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.9322 2.1027 0.8881 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.9346 2.1021 -0.8849 H 0 0 0 0 0 0 0 0 0 0 0 0
M END
$$$$
'''
def test_read_sdf() -> None:
"""Test SDF V2000 reader."""
with io.StringIO(VALID_SDF_V2000_COFFEE) as file_obj:
atoms: Atoms = read_sdf(file_obj)
assert len(atoms) == 24
assert atoms.get_chemical_symbols() == ['O', 'O', 'N', 'N', 'N', 'N', 'C',
'C', 'C', 'C', 'C',
'C', 'C', 'C', 'H', 'H', 'H', 'H',
'H', 'H', 'H', 'H',
'H', 'H']
assert atoms.get_positions()[0] == pytest.approx((0.4700, 2.5688, 0.0006))
assert atoms.get_positions()[-1] == pytest.approx(
(-2.9346, 2.1021, -0.8849))
def test_get_num_atoms_sdf_v2000() -> None:
"""Test the reading of the first line."""
assert get_num_atoms_sdf_v2000(DIFFICULT_BUT_VALID_FIRST_LINE) == 184
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