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Fix rdkit tests #4640

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Merged
merged 4 commits into from
Jul 24, 2024
Merged

Fix rdkit tests #4640

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10fc8df
Fix rdkit tests
IAlibay Jul 22, 2024
810de26
Add back importorskip
IAlibay Jul 22, 2024
b36f8ae
a different sanity check
IAlibay Jul 22, 2024
1378d5c
Update test_universe.py
IAlibay Jul 23, 2024
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3 changes: 0 additions & 3 deletions testsuite/MDAnalysisTests/converters/test_rdkit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,6 @@

import MDAnalysis as mda
import numpy as np
from numpy.lib import NumpyVersion
import pytest
from MDAnalysis.topology.guessers import guess_atom_element
from MDAnalysisTests.datafiles import GRO, PDB_full, PDB_helix, mol2_molecule
Expand Down Expand Up @@ -56,8 +55,6 @@
reason="only for min dependencies build")
class TestRequiresRDKit(object):
def test_converter_requires_rdkit(self):
if NumpyVersion(np.__version__) >= "2.0.0":
pytest.skip("RDKit not compatible with NumPy 2")
u = mda.Universe(PDB_full)
with pytest.raises(ImportError,
match="RDKit is required for the RDKitConverter"):
Expand Down
10 changes: 3 additions & 7 deletions testsuite/MDAnalysisTests/converters/test_rdkit_parser.py
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Expand Up @@ -24,7 +24,6 @@
import warnings
import pytest
import numpy as np
from numpy.lib import NumpyVersion
from numpy.testing import assert_equal

import MDAnalysis as mda
Expand All @@ -33,12 +32,9 @@

# TODO: remove these shims when RDKit
# has a release supporting NumPy 2
if NumpyVersion(np.__version__) < "2.0.0":
Chem = pytest.importorskip('rdkit.Chem')
AllChem = pytest.importorskip('rdkit.Chem.AllChem')
else:
Chem = pytest.importorskip("RDKit_does_not_support_NumPy_2")
AllChem = pytest.importorskip("RDKit_does_not_support_NumPy_2")
Chem = pytest.importorskip('rdkit.Chem')
AllChem = pytest.importorskip('rdkit.Chem.AllChem')


class RDKitParserBase(ParserBase):
parser = mda.converters.RDKitParser.RDKitParser
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31 changes: 14 additions & 17 deletions testsuite/MDAnalysisTests/core/test_universe.py
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Expand Up @@ -30,7 +30,6 @@
import warnings

import numpy as np
from numpy.lib import NumpyVersion
from numpy.testing import (
assert_allclose,
assert_almost_equal,
Expand Down Expand Up @@ -225,10 +224,7 @@ def test_universe_empty_ROMol(self):

class TestUniverseFromSmiles(object):
def setup_class(self):
if NumpyVersion(np.__version__) < "2.0.0":
pytest.importorskip("rdkit.Chem")
else:
pytest.importorskip("RDKit_does_not_support_NumPy_2")
pytest.importorskip("rdkit.Chem")

def test_default(self):
smi = "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
Expand Down Expand Up @@ -284,21 +280,22 @@ def test_rdkit_kwargs(self):


def test_coordinates(self):
# We manually create the molecule to compare coordinates
# coordinate generation is pseudo random across different machines
# even with the same seed, so we create a molecule to compare
# coordinates against. See PR #4640
from rdkit import Chem
from rdkit.Chem import AllChem
mol = Chem.MolFromSmiles('C', sanitize=True)
mol = Chem.AddHs(mol)
AllChem.EmbedMultipleConfs(mol, numConfs=2, randomSeed=42)
expected = [c.GetPositions() for c in mol.GetConformers()]

# now the mda way
u = mda.Universe.from_smiles("C", numConfs=2,
rdkit_kwargs=dict(randomSeed=42))
assert u.trajectory.n_frames == 2
expected = np.array([
[[-0.02209686, 0.00321505, 0.01651974],
[-0.6690088 , 0.8893599 , -0.1009085 ],
[-0.37778795, -0.8577519 , -0.58829606],
[ 0.09642092, -0.3151253 , 1.0637809 ],
[ 0.97247267, 0.28030226, -0.3910961 ]],
[[-0.0077073 , 0.00435363, 0.01834692],
[-0.61228824, -0.83705765, -0.38619974],
[-0.41925883, 0.9689095 , -0.3415968 ],
[ 0.03148226, -0.03256683, 1.1267245 ],
[ 1.0077721 , -0.10363862, -0.41727486]]], dtype=np.float32)
assert_almost_equal(u.trajectory.coordinate_array, expected)
assert_allclose(u.trajectory.coordinate_array, expected, rtol=1e-7)


class TestUniverse(object):
Expand Down
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