1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
|
# fmt: off
"""Tests for PubChem."""
import json
from io import BytesIO
import pytest
from ase.data import pubchem
from ase.data.pubchem import (
analyze_input,
pubchem_atoms_conformer_search,
pubchem_atoms_search,
pubchem_conformer_search,
pubchem_search,
)
@pytest.fixture
def mock_pubchem(monkeypatch) -> None:
"""Mock `pubchem`."""
def mock_search_pubchem_raw_222(*args, **kwargs):
"""Mock `search_pubchem_raw` for ammonia (CID=222)."""
data222 = b'222\n -OEChem-10071914343D\n\n 4 3 0 0 0 0 0 0 0999 V2000\n 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n -0.4417 0.2906 0.8711 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.7256 0.6896 -0.1907 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.4875 -0.8701 0.2089 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 1 3 1 0 0 0 0\n 1 4 1 0 0 0 0\nM END\n> <PUBCHEM_COMPOUND_CID>\n222\n\n> <PUBCHEM_CONFORMER_RMSD>\n0.4\n\n> <PUBCHEM_CONFORMER_DIVERSEORDER>\n1\n\n> <PUBCHEM_MMFF94_PARTIAL_CHARGES>\n4\n1 -1.08\n2 0.36\n3 0.36\n4 0.36\n\n> <PUBCHEM_EFFECTIVE_ROTOR_COUNT>\n0\n\n> <PUBCHEM_PHARMACOPHORE_FEATURES>\n1\n1 1 cation\n\n> <PUBCHEM_HEAVY_ATOM_COUNT>\n1\n\n> <PUBCHEM_ATOM_DEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_BOND_DEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_BOND_UDEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_ISOTOPIC_ATOM_COUNT>\n0\n\n> <PUBCHEM_COMPONENT_COUNT>\n1\n\n> <PUBCHEM_CACTVS_TAUTO_COUNT>\n1\n\n> <PUBCHEM_CONFORMER_ID>\n000000DE00000001\n\n> <PUBCHEM_MMFF94_ENERGY>\n0\n\n> <PUBCHEM_FEATURE_SELFOVERLAP>\n5.074\n\n> <PUBCHEM_SHAPE_FINGERPRINT>\n260 1 18410856563934756871\n\n> <PUBCHEM_SHAPE_MULTIPOLES>\n15.6\n0.51\n0.51\n0.51\n0\n0\n0\n0\n0\n0\n0\n0\n0\n0\n\n> <PUBCHEM_SHAPE_SELFOVERLAP>\n14.89\n\n> <PUBCHEM_SHAPE_VOLUME>\n15.6\n\n> <PUBCHEM_COORDINATE_TYPE>\n2\n5\n10\n\n$$$$\n' # noqa
r = BytesIO(data222)
return r.read().decode('utf-8')
def mock_available_conformer_search_222(*args, **kwargs):
"""Mock `available_conformer_search` for ammonia (CID=222)."""
conformer222 = b'{\n "InformationList": {\n "Information": [\n {\n "CID": 222,\n "ConformerID": [\n "000000DE00000001"\n ]\n }\n ]\n }\n}\n' # noqa
r = BytesIO(conformer222)
record = r.read().decode('utf-8')
record = json.loads(record)
return record['InformationList']['Information'][0]['ConformerID']
f = mock_search_pubchem_raw_222
monkeypatch.setattr(pubchem, 'search_pubchem_raw', f)
f = mock_available_conformer_search_222
monkeypatch.setattr(pubchem, 'available_conformer_search', f)
def test_pubchem_search(mock_pubchem) -> None:
"""Test if `pubchem_search` handles given arguments correctly."""
data = pubchem_search('ammonia')
atoms = data.get_atoms()
assert atoms.get_chemical_symbols() == ['N', 'H', 'H', 'H']
data.get_pubchem_data()
def test_pubchem(mock_pubchem) -> None:
# check the various entry styles and the functions that return atoms
pubchem_search(cid=241).get_atoms()
pubchem_atoms_search(smiles='CCOH')
pubchem_atoms_conformer_search('octane')
def test_pubchem_conformer_search(mock_pubchem) -> None:
"""Test if `pubchem_conformer_search` runs as expected."""
confs = pubchem_conformer_search('octane')
for _ in confs:
pass
def test_multiple_search(mock_pubchem) -> None:
"""Check that you can't pass in two args."""
with pytest.raises(ValueError):
pubchem_search(name='octane', cid=222)
def test_empty_search(mock_pubchem) -> None:
"""Check that you must pass at least one arg."""
with pytest.raises(ValueError):
pubchem_search()
def test_triple_bond() -> None:
"""Check if hash (`#`) is converted to hex (`%23`)."""
assert analyze_input(smiles='CC#N')[0] == 'CC%23N'
|
