def testPrintQMMMNoExclude(self):
try:
main(["-c", QM_OUT_INI])
self.assertFalse(diff_lines(MM_KIND_OUT, GOOD_MM_KIND_OUT))
self.assertFalse(diff_lines(QMMM_OUT, GOOD_QM_OUT))
self.assertFalse(diff_lines(VMD_ATOMS_OUT, GOOD_VMD_QM_ATOMS_OUT))
finally:
silent_remove(MM_KIND_OUT, disable=DISABLE_REMOVE)
silent_remove(QMMM_OUT, disable=DISABLE_REMOVE)
silent_remove(VMD_ATOMS_OUT, disable=DISABLE_REMOVE)
def testPrintQMMMNoExclude(self):
try:
main(["-c", QM_OUT_INI])
self.assertFalse(diff_lines(MM_KIND_OUT, GOOD_MM_KIND_OUT))
self.assertFalse(diff_lines(QMMM_OUT, GOOD_QM_OUT))
self.assertFalse(diff_lines(VMD_ATOMS_OUT, GOOD_VMD_QM_ATOMS_OUT))
finally:
silent_remove(MM_KIND_OUT)
silent_remove(QMMM_OUT)
silent_remove(VMD_ATOMS_OUT)
pass
def testPrintQMMM(self):
try:
test_input = ["-c", QMMM_OUT_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stdout(main, test_input) as output:
self.assertTrue("Total charge from QM atoms: -1.0" in output)
self.assertFalse(diff_lines(QMMM_OUT, GOOD_QMMM_OUT))
self.assertFalse(diff_lines(MM_KIND_OUT, GOOD_MM_KIND_OUT))
self.assertFalse(diff_lines(VMD_ATOMS_OUT, GOOD_VMD_ATOMS_OUT))
finally:
silent_remove(QMMM_OUT, disable=DISABLE_REMOVE)
silent_remove(MM_KIND_OUT, disable=DISABLE_REMOVE)
silent_remove(VMD_ATOMS_OUT, disable=DISABLE_REMOVE)
def testMissingRadius(self):
# Tests both providing a dictionary and not having an available radius (still prints everything, just missing
# one radius)
try:
test_input = ["-c", MISSING_RADIUS_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue(
"Did not find atom type 'XYZ' in the atom_type to radius dictionary"
in output)
self.assertFalse(diff_lines(QMMM_OUT, GOOD_QMMM_OUT))
self.assertFalse(diff_lines(MM_KIND_OUT, GOOD_MM_KIND_OUT))
self.assertFalse(diff_lines(VMD_ATOMS_OUT, GOOD_VMD_ATOMS_OUT))
finally:
silent_remove(QMMM_OUT, disable=DISABLE_REMOVE)
silent_remove(MM_KIND_OUT, disable=DISABLE_REMOVE)
silent_remove(VMD_ATOMS_OUT, disable=DISABLE_REMOVE)
def testRenumDictMol(self):
try:
main(["-c", MOL_DICT_INI])
self.assertFalse(diff_lines(DEF_OUT, GOOD_OUT))
finally:
silent_remove(DEF_OUT)
def testRenumDictMol(self):
try:
main(["-c", MOL_DICT_INI])
self.assertFalse(diff_lines(DEF_OUT, GOOD_OUT))
finally:
silent_remove(DEF_OUT, disable=DISABLE_REMOVE)
def testRenumMol(self):
try:
main(["-c", DEF_INI])
self.assertFalse(diff_lines(DEF_OUT, GOOD_OUT))
finally:
silent_remove(DEF_OUT)
def testStringResid(self):
test_input = ["-c", STRING_RESID_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("expected only integers" in output)
def testRenumReorderMol(self):
test_input = ["-c", MOL_RENUM_REORDER_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("does not currently support both" in output)