def testHelp(self):
test_input = ['-h']
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertFalse(output)
with capture_stdout(main, test_input) as output:
self.assertTrue("optional arguments" in output)
def testNTripleBond(self):
test_input = ["-c", N_TRIPLE_BOND_INI]
try:
main(test_input)
self.assertFalse(diff_lines(CP_N_OUT, GOOD_CP_N_OUT))
self.assertFalse(diff_lines(F2_N_OUT, GOOD_F2_N_OUT))
finally:
silent_remove(CP_N_OUT, disable=DISABLE_REMOVE)
silent_remove(F2_N_OUT, disable=DISABLE_REMOVE)
pass
def testSepMolecules(self):
# to help when there is a reactant or product complex that is two different molecules; ignores the
# larger distance between the atoms belonging to two different molecules
test_input = ["-c", IGNORE_MAX_INI]
try:
main(test_input)
self.assertFalse(diff_lines(CP_TPA_OUT, GOOD_CP_TPA_OUT))
self.assertFalse(diff_lines(F2_TPA_OUT, GOOD_F2_TPA_OUT))
finally:
silent_remove(CP_TPA_OUT, disable=DISABLE_REMOVE)
silent_remove(F2_TPA_OUT, disable=DISABLE_REMOVE)
pass
def testMetalBond(self):
# Uses a longer bond cut-off when one of the atoms is a metal
test_input = ["-c", METAL_BOND_INI]
try:
main(test_input)
self.assertFalse(diff_lines(CP_METAL_OUT, GOOD_CP_METAL_OUT))
self.assertFalse(diff_lines(F1_METAL_OUT, GOOD_F1_METAL_OUT))
self.assertFalse(diff_lines(F2_METAL_OUT, GOOD_F2_METAL_OUT))
finally:
silent_remove(CP_METAL_OUT, disable=DISABLE_REMOVE)
silent_remove(F1_METAL_OUT, disable=DISABLE_REMOVE)
silent_remove(F2_METAL_OUT, disable=DISABLE_REMOVE)
pass
def testNTripleBondSubDir(self):
# Test that output files were created in subdir
test_input = ["-c", N_TRIPLE_BOND_SUB_DIR_INI]
try:
silent_remove(TEMP_DIR, dir_with_files=True)
main(test_input)
self.assertFalse(diff_lines(CP_N_OUT_SUB_DIR, GOOD_CP_N_OUT))
self.assertFalse(diff_lines(F2_N_OUT_SUB_DIR, GOOD_F2_N_OUT))
finally:
silent_remove(TEMP_DIR,
disable=DISABLE_REMOVE,
dir_with_files=True)
pass
def testDubO(self):
test_input = ["-c", DIMER_INI]
try:
main(test_input)
self.assertFalse(diff_lines(CP_DI_18_24_OUT, GOOD_CP_DI_18_24_OUT))
self.assertFalse(diff_lines(F2_DI_18_24_OUT, GOOD_F2_DI_18_24_OUT))
self.assertFalse(diff_lines(CP_DI_18_16_OUT, GOOD_CP_DI_18_16_OUT))
self.assertFalse(diff_lines(F1_DI_18_16_OUT, GOOD_F1_DI_18_16_OUT))
self.assertFalse(diff_lines(F2_DI_18_16_OUT, GOOD_F2_DI_18_16_OUT))
finally:
silent_remove(CP_DI_18_24_OUT, disable=DISABLE_REMOVE)
silent_remove(F2_DI_18_24_OUT, disable=DISABLE_REMOVE)
silent_remove(CP_DI_18_16_OUT, disable=DISABLE_REMOVE)
silent_remove(F1_DI_18_16_OUT, disable=DISABLE_REMOVE)
silent_remove(F2_DI_18_16_OUT, disable=DISABLE_REMOVE)
pass
def testCPFooter(self):
# Checks adding a multiline footer
# Also checks making the output directory the current directory using 'output_directory =' in the ini
test_input = ["-c", ADD_CP_FOOTER_INI]
try:
main(test_input)
self.assertFalse(
diff_lines(CP_FOOTER_CP_OUT, GOOD_CP_FOOTER_CP_OUT))
self.assertFalse(
diff_lines(CP_FOOTER_F1_OUT, GOOD_CP_FOOTER_F1_OUT))
self.assertFalse(
diff_lines(CP_FOOTER_F2_OUT, GOOD_CP_FOOTER_F2_OUT))
finally:
silent_remove(CP_FOOTER_CP_OUT, disable=DISABLE_REMOVE)
silent_remove(CP_FOOTER_F1_OUT, disable=DISABLE_REMOVE)
silent_remove(CP_FOOTER_F2_OUT, disable=DISABLE_REMOVE)
pass
def testLonelyFragments(self):
test_input = ["-c", LONELY_INI]
try:
main(test_input)
self.assertFalse(diff_lines(CP_20_21_OUT, GOOD_CP_20_21_OUT))
self.assertFalse(diff_lines(CP_22_23_OUT, GOOD_CP_22_23_OUT))
self.assertFalse(diff_lines(CP_24_18_OUT, GOOD_CP_24_18_OUT))
self.assertFalse(diff_lines(F2_20_21_OUT, GOOD_F2_20_21_OUT))
self.assertFalse(diff_lines(F2_22_23_OUT, GOOD_F2_22_23_OUT))
self.assertFalse(diff_lines(F2_24_18_OUT, GOOD_F2_24_18_OUT))
finally:
silent_remove(CP_20_21_OUT, disable=DISABLE_REMOVE)
silent_remove(CP_22_23_OUT, disable=DISABLE_REMOVE)
silent_remove(CP_24_18_OUT, disable=DISABLE_REMOVE)
silent_remove(F2_20_21_OUT, disable=DISABLE_REMOVE)
silent_remove(F2_22_23_OUT, disable=DISABLE_REMOVE)
silent_remove(F2_24_18_OUT, disable=DISABLE_REMOVE)
pass
def testDefIni(self):
test_input = ["-c", DEF_INI]
try:
main(test_input)
self.assertFalse(diff_lines(CP_15_14_OUT, GOOD_CP_15_14_OUT))
self.assertFalse(diff_lines(CP_14_15_OUT, GOOD_CP_14_15_OUT))
self.assertFalse(diff_lines(F1_14_15_OUT, GOOD_F1_14_15_OUT))
self.assertFalse(diff_lines(F2_14_15_OUT, GOOD_F2_14_15_OUT))
self.assertEqual(len(diff_lines(F1_15_14_OUT, GOOD_F1_14_15_OUT)),
2)
self.assertEqual(len(diff_lines(F2_15_14_OUT, GOOD_F2_14_15_OUT)),
2)
finally:
silent_remove(CP_15_14_OUT, disable=DISABLE_REMOVE)
silent_remove(CP_14_15_OUT, disable=DISABLE_REMOVE)
silent_remove(F1_14_15_OUT, disable=DISABLE_REMOVE)
silent_remove(F2_14_15_OUT, disable=DISABLE_REMOVE)
silent_remove(F1_15_14_OUT, disable=DISABLE_REMOVE)
silent_remove(F2_15_14_OUT, disable=DISABLE_REMOVE)
pass
def testDubCC(self):
test_input = ["-c", CC_INI]
try:
main(test_input)
self.assertFalse(diff_lines(CP_CC_12_11_OUT, GOOD_CP_CC_12_11_OUT))
self.assertFalse(diff_lines(F1_CC_12_11_OUT, GOOD_F1_CC_12_11_OUT))
self.assertFalse(diff_lines(F2_CC_12_11_OUT, GOOD_F2_CC_12_11_OUT))
self.assertFalse(diff_lines(CP_CC_12_38_OUT, GOOD_CP_CC_12_38_OUT))
self.assertFalse(diff_lines(F2_CC_12_38_OUT, GOOD_F2_CC_12_38_OUT))
self.assertFalse(diff_lines(CP_CC_13_12_OUT, GOOD_CP_CC_13_12_OUT))
self.assertFalse(diff_lines(F1_CC_13_12_OUT, GOOD_F1_CC_13_12_OUT))
self.assertFalse(diff_lines(F2_CC_13_12_OUT, GOOD_F2_CC_13_12_OUT))
finally:
silent_remove(CP_CC_12_11_OUT, disable=DISABLE_REMOVE)
silent_remove(F1_CC_12_11_OUT, disable=DISABLE_REMOVE)
silent_remove(F2_CC_12_11_OUT, disable=DISABLE_REMOVE)
silent_remove(CP_CC_12_38_OUT, disable=DISABLE_REMOVE)
silent_remove(F2_CC_12_38_OUT, disable=DISABLE_REMOVE)
silent_remove(CP_CC_13_12_OUT, disable=DISABLE_REMOVE)
silent_remove(F1_CC_13_12_OUT, disable=DISABLE_REMOVE)
silent_remove(F2_CC_13_12_OUT, disable=DISABLE_REMOVE)
pass
def testMissingFile(self):
test_input = ['-c', MISSING_FILE_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("No such file or directory" in output)