def testSetDistMult(self):
try:
main(["-c", GLU_MULT_DIST_INI])
self.assertFalse(diff_lines(GLU_MULT_DIST_OUT1, GOOD_GLU_MULT_DIST_OUT1))
self.assertFalse(diff_lines(GLU_MULT_DIST_OUT2, GOOD_GLU_MULT_DIST_OUT2))
finally:
silent_remove(GLU_MULT_DIST_OUT1)
silent_remove(GLU_MULT_DIST_OUT2)
def testReordGluDeprot(self):
"""
Tests that can handle an emtpy line in the data file and make a data number dictionary
"""
try:
main(["-c", REORD_GLU_INI])
self.assertFalse(diff_lines(GLU_DEPROT_ATOM_NUM_DICT, GLU_DEPROT_ATOM_NUM_DICT_GOOD))
finally:
silent_remove(GLU_DEPROT_OUT)
silent_remove(GLU_DEPROT_ATOM_NUM_DICT)
def testAtomNumTypeDict(self):
try:
main(["-c", GLUE_GLUP_INI])
self.assertFalse(diff_lines(GLUP_GLUE_ATOM_NUM_DICT, GLUP_GLUE_ATOM_NUM_DICT_GOOD))
self.assertFalse(diff_lines(GLUP_GLUE_ATOM_TYPE_DICT, GLUP_GLUE_ATOM_TYPE_DICT_GOOD))
self.assertFalse(diff_lines(GLUP_AS_GLUE, GLUP_AS_GLUE_GOOD, delimiter=" "))
finally:
silent_remove(GLUP_GLUE_ATOM_NUM_DICT, disable=DISABLE_REMOVE)
silent_remove(GLUP_GLUE_ATOM_TYPE_DICT, disable=DISABLE_REMOVE)
silent_remove(GLUP_AS_GLUE, disable=DISABLE_REMOVE)
def testAtomNumTypeDict(self):
try:
main(["-c", GLUE_GLUP_INI])
self.assertFalse(diff_lines(GLUP_GLUE_ATOM_NUM_DICT, GLUP_GLUE_ATOM_NUM_DICT_GOOD))
self.assertFalse(diff_lines(GLUP_GLUE_ATOM_TYPE_DICT, GLUP_GLUE_ATOM_TYPE_DICT_GOOD))
self.assertFalse(diff_lines(GLUP_AS_GLUE, GLUP_AS_GLUE_GOOD))
finally:
silent_remove(GLUP_GLUE_ATOM_NUM_DICT)
silent_remove(GLUP_GLUE_ATOM_TYPE_DICT)
silent_remove(GLUP_AS_GLUE)
def testAdjustAtom(self):
try:
main(["-c", GLU_ADJUST_ATOM_INI])
self.assertFalse(diff_lines(GLU_ADJUST_OUT_0, GLU_ADJUST_TPL))
self.assertFalse(diff_lines(GLU_ADJUST_OUT_NEG1, GOOD_GLU_ADJUST_OUT_NEG1))
self.assertFalse(diff_lines(GLU_ADJUST_OUT_1, GOOD_GLU_ADJUST_OUT_1))
self.assertFalse(diff_lines(GLU_ADJUST_OUT_2, GOOD_GLU_ADJUST_OUT_2))
finally:
silent_remove(GLU_ADJUST_OUT_NEG1, disable=DISABLE_REMOVE)
silent_remove(GLU_ADJUST_OUT_0, disable=DISABLE_REMOVE)
silent_remove(GLU_ADJUST_OUT_1, disable=DISABLE_REMOVE)
silent_remove(GLU_ADJUST_OUT_2, disable=DISABLE_REMOVE)
def testReordGluDeprot(self):
"""
Tests that can handle an emtpy line in the data file and make a data number dictionary
"""
try:
main(["-c", REORD_GLU_INI])
self.assertFalse(diff_lines(GLU_DEPROT_ATOM_NUM_DICT, GLU_DEPROT_ATOM_NUM_DICT_GOOD))
# for debugging:
# with open(GLU_DEPROT_OUT) as f:
# with open(GLU_DEPROT_DATA) as g:
# for d_line, g_line in zip(f, g):
# if d_line.strip() != g_line.strip():
# print(d_line.strip())
# print(g_line.strip())
finally:
silent_remove(GLU_DEPROT_OUT)
silent_remove(GLU_DEPROT_ATOM_NUM_DICT)
def testSetDist(self):
try:
main(["-c", GLU_DIST_INI])
self.assertFalse(diff_lines(GLU_DIST_OUT, GOOD_GLU_DIST_OUT))
finally:
silent_remove(GLU_DIST_OUT)
def testSerca(self):
try:
main(["-c", SERCA_INI])
self.assertFalse(diff_lines(SERCA_OUT, SERCA_GOOD_OUT))
finally:
silent_remove(SERCA_OUT, disable=DISABLE_REMOVE)
def testSetDistOneAtom(self):
test_input = ["-c", GLU_DIST_ONE_ATOM_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("WARNING: Use the 'atoms_dist' keyword" in output)
def testAdjustAtomTooLargeInt(self):
test_input = ["-c", GLU_ADJUST_ATOM_TOO_LARGE_INT_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("found only" in output)
def testAdjustAtomTooFewXYZ(self):
test_input = ["-c", GLU_ADJUST_ATOM_TOO_FEW_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("comma-separated list" in output)
def testAdjustAtomZeroSteps(self):
test_input = ["-c", GLU_ADJUST_ATOM_NO_STEPS_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("positive number of steps" in output)
def testAdjustAtomNonInt(self):
test_input = ["-c", GLU_ADJUST_ATOM_NON_INT_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("keyword must be a positive integer" in output)
def testSerca(self):
try:
main(["-c", SERCA_INI])
self.assertFalse(diff_lines(SERCA_OUT, SERCA_GOOD_OUT))
finally:
silent_remove(SERCA_OUT)
