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"""Test OpenBabel executables from Python
Note: Python bindings not used
On Windows or Linux, you can run these tests at the commandline
in the build folder with:
"C:\Program Files\CMake 2.6\bin\ctest.exe" -C CTestTestfile.cmake
-R pytest -VV
You could also "chdir" into build/test and run the test file directly:
python ../../../test/testsmartssym.py
In both cases, the test file is run directly from the source folder,
and so you can quickly develop the tests and try them out.
"""
import os
import unittest
import pdb
from testbabel import run_exec, executable, log, BaseTest
def checkmatch(query, molecules):
result = []
for smi in molecules:
output, error = run_exec("obabel -:%s -s%s -osmi" % (smi, query))
result.append(output.strip() != "")
return result
def fastcheckmatch(query, molecules):
"""May fail where Open Babel does not output the input query, e.g.
[C@@]([H])(Br)(Cl)I is output as [C@@H](Br)(Cl)I"""
output, error = run_exec("\n".join(molecules), "obabel -ismi -s%s -osmi" % query)
converted = [x.rstrip() for x in output.split("\n")]
results = [smi in converted for smi in molecules]
return results
class TestSmartsSym(BaseTest):
"""Base class for a series of tests relating to symmetry"""
def testSelfMatch(self):
"""Verify that a molecule matches itself"""
data = [
'[C@@](F)(Br)(Cl)I',
'[C@](F)(Br)(Cl)I',
'F[C@](Br)(Cl)I',
'[C@H](Br)(Cl)I',
'Br[C@H](Cl)I',
'[C@]1(Br)(Cl)NC1',
'[C@@]1(Br)(Cl)NC1',
'Br[C@]1(Cl)NC1',
'C1N[C@]1(Cl)Br',
'F[C@]1(Br)N[C@]1(Br)Cl',
'[C@H]1(Cl)NC1'
]
for smi in data:
output, error = run_exec("obabel -:%s -s%s -osmi" % (smi, smi))
self.assertEqual(output.rstrip(), smi)
def testTetStereo(self):
data = ['[C@@](F)(Br)(Cl)I',
'[C@](F)(Br)(Cl)I',
'F[C@](Br)(Cl)I',
'F[C@@](Br)(Cl)I',
'C(F)(Br)(Cl)I',
'FC(Br)(Cl)I']
self.assertEqual(fastcheckmatch(data[0], data[0:6]),
[True, False, False, True, False, False])
self.assertEqual(fastcheckmatch(data[2], data[0:6]),
[False, True, True, False, False, False])
self.assertEqual(fastcheckmatch(data[4], data[0:6]), [True]*6)
def testTetStereoImplicitH(self):
data = ['[C@H](Br)(Cl)I',
'[C@@H](Br)(Cl)I',
'Br[C@H](Cl)I',
'Br[C@@H](Cl)I',
'BrC(Cl)I',
'BrC([H])(Cl)I',
'Br[C@@]([H])(Cl)I'
]
self.assertEqual(checkmatch(data[0], data[0:7]),
[True, False, False, True, False, False, True])
self.assertEqual(checkmatch(data[2], data[0:7]),
[False, True, True, False, False, False, False])
self.assertEqual(checkmatch(data[4], data[0:7]), [True]*7)
self.assertEqual(checkmatch(data[6], data[0:7]),
[True, False, False, True, False, False, True])
def testRingClosures(self):
data = ['[C@]1(Br)(Cl)NC1',
'[C@@]1(Br)(Cl)NC1',
'Br[C@]1(Cl)NC1',
'Br[C@@]1(Cl)NC1',
'C1N[C@]1(Cl)Br',
'C1NC1(Cl)Br']
self.assertEqual(fastcheckmatch(data[0], data[0:6]),
[True, False, False, True, True, False])
self.assertEqual(fastcheckmatch(data[2], data[0:6]),
[False, True, True, False, False, False])
self.assertEqual(fastcheckmatch(data[5], data[0:6]), [True]*6)
if __name__ == "__main__":
testsuite = []
allclasses = [TestSmartsSym]
for myclass in allclasses:
suite = unittest.TestLoader().loadTestsFromTestCase(myclass)
testsuite.append(suite)
unittest.TextTestRunner().run(unittest.TestSuite(testsuite))
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