def testAddElements(self):
try:
silent_remove(ADD_ELEMENT_OUT)
main(["-c", ADD_ELEMENT_INI])
self.assertFalse(diff_lines(ADD_ELEMENT_OUT, GOOD_ADD_ELEMENT_OUT))
finally:
silent_remove(ADD_ELEMENT_OUT, disable=DISABLE_REMOVE)
def testEmreAddElements(self):
# As above, but a larger/different PDB
try:
main(["-c", EMRE_ADD_ELEMENT_INI])
self.assertFalse(diff_lines(EMRE_ADD_ELEMENT_OUT, GOOD_EMRE_ADD_ELEMENT_OUT))
finally:
silent_remove(EMRE_ADD_ELEMENT_OUT, disable=DISABLE_REMOVE)
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 testPrintQMMM(self):
try:
main(["-c", QMMM_OUT_INI])
self.assertFalse(diff_lines(QMMM_PDB_OUT, QMMM_PDB_IN))
self.assertFalse(diff_lines(QMMM_OUT, GOOD_QMMM_OUT))
self.assertFalse(diff_lines(VMD_ATOMS_OUT, GOOD_VMD_ATOMS_OUT))
finally:
silent_remove(QMMM_PDB_OUT, disable=DISABLE_REMOVE)
silent_remove(QMMM_OUT, disable=DISABLE_REMOVE)
silent_remove(VMD_ATOMS_OUT, disable=DISABLE_REMOVE)
def testCheckWaterOrder(self):
test_input = ["-c", CHECK_WATER_ORDER_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
try:
with capture_stderr(main, test_input) as output:
for message in WATER_OUT_OF_ORDER_MESSAGES:
self.assertTrue(message in output)
self.assertLess(len(output), 650)
finally:
silent_remove(DEF_OUT, disable=DISABLE_REMOVE)
def testAddElemReadDict(self):
# There will be a missing element because of a missing key in the specified dictionary
test_input = ["-c", READ_ELEM_DICT_INI]
try:
silent_remove(ADD_ELEMENT_OUT)
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
silent_remove(ADD_ELEMENT_OUT)
with capture_stderr(main, test_input) as output:
self.assertTrue("Please add atom type" in output)
self.assertFalse(diff_lines(ADD_ELEMENT_OUT, GOOD_READ_ELEM_OUT))
finally:
silent_remove(ADD_ELEMENT_OUT, disable=DISABLE_REMOVE)
def testAddElemReadDictNoOverwrite(self):
# Make sure preserves the element from the original pdb even though not in the read dict
test_input = ["-c", READ_ELEM_DICT_KEEP_ELEM_INI]
try:
silent_remove(DEF_OUT)
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
else:
with capture_stderr(main, ["-c", READ_ELEM_DICT_KEEP_ELEM_INI]) as output:
self.assertTrue("Please add atom type" in output)
self.assertFalse(diff_lines(DEF_OUT, GOOD_ADD_ELEMENT_OUT))
finally:
silent_remove(DEF_OUT, disable=DISABLE_REMOVE)
def testAddElementsMissingType(self):
test_input = ["-c", ADD_ELEMENT_MISSING_TYPE_INI]
try:
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
else:
with capture_stderr(main, test_input) as output:
# testing that only get the warning once, so check output length. May change wording a bit,
# so checked than less than length + a buffer (which is less than if multiple warnings are printed)
self.assertLess(len(output), 200)
self.assertTrue("Please add atom type" in output)
self.assertFalse(diff_lines(ADD_ELEMENT_MISSING_OUT, ADD_ELEMENT_MISSING_ORIG))
finally:
silent_remove(ADD_ELEMENT_MISSING_OUT, disable=DISABLE_REMOVE)
def testChangeRenumMol(self):
try:
main(["-c", MOL_CHANGE_RENUM_INI])
self.assertFalse(diff_lines(DEF_OUT, GOOD_MOL_CHANGE_RENUM_OUT))
finally:
silent_remove(DEF_OUT, disable=DISABLE_REMOVE)
