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 testAltIni(self):
test_input = ["-c", ALT_INI]
try:
main(test_input)
self.assertFalse(diff_lines(ALT_OUT, GOOD_ALT_OUT))
finally:
silent_remove(ALT_OUT, disable=DISABLE_REMOVE)
pass
def testFirstOnly(self):
test_input = ["-c", MULTI_FIRST_ONLY_INI]
try:
main(test_input)
self.assertFalse(diff_lines(REMOVE_H_OUT1, GOOD_KEEP_H_OUT1))
self.assertFalse(diff_lines(GAU_OUT1, GOOD_GAU_OUT1))
finally:
silent_remove(REMOVE_H_OUT1, disable=DISABLE_REMOVE)
silent_remove(GAU_OUT1, disable=DISABLE_REMOVE)
def testAltIniCommandLine(self):
# As ALT_INI, but command-line only
test_input = ["-t", 'tests/test_data/pdbs2gausscoms/gau_2.tpl',
'-f', 'tests/test_data/pdbs2gausscoms/pe_linear.pdb']
try:
main(test_input)
self.assertFalse(diff_lines(ALT_OUT, GOOD_ALT_OUT))
finally:
silent_remove(ALT_OUT, disable=DISABLE_REMOVE)
pass
def testDefIni(self):
test_input = ["-c", DEF_INI]
try:
main(test_input)
self.assertFalse(diff_lines(GAU_OUT1, GOOD_GAU_OUT1))
self.assertFalse(diff_lines(GAU_OUT2, GOOD_GAU_OUT2))
self.assertFalse(diff_lines(GAU_OUT3, GOOD_GAU_OUT3))
finally:
silent_remove(GAU_OUT1, disable=DISABLE_REMOVE)
silent_remove(GAU_OUT2, disable=DISABLE_REMOVE)
silent_remove(GAU_OUT3, disable=DISABLE_REMOVE)
def testRemoveH(self):
test_input = ["-c", REMOVE_H_INI]
try:
main(test_input)
self.assertFalse(diff_lines(REMOVE_H_OUT1, GOOD_REMOVE_H_OUT1))
self.assertFalse(diff_lines(REMOVE_H_OUT2, GOOD_REMOVE_H_OUT2))
self.assertFalse(diff_lines(REMOVE_H_OUT3, GOOD_REMOVE_H_OUT3))
finally:
silent_remove(REMOVE_H_OUT1, disable=DISABLE_REMOVE)
silent_remove(REMOVE_H_OUT2, disable=DISABLE_REMOVE)
silent_remove(REMOVE_H_OUT3, disable=DISABLE_REMOVE)
def testCommandLineOptions(self):
test_input = ["-t", "tests/test_data/pdbs2gausscoms/gau.tpl",
"-l", "tests/test_data/pdbs2gausscoms/pdb_list.txt"]
try:
main(test_input)
self.assertFalse(diff_lines(GAU_OUT1, GOOD_GAU_OUT1))
self.assertFalse(diff_lines(GAU_OUT2, GOOD_GAU_OUT2))
self.assertFalse(diff_lines(GAU_OUT3, GOOD_GAU_OUT3))
finally:
silent_remove(GAU_OUT1, disable=DISABLE_REMOVE)
silent_remove(GAU_OUT2, disable=DISABLE_REMOVE)
silent_remove(GAU_OUT3, disable=DISABLE_REMOVE)
def testRemoveHCommandLine(self):
# As ALT_INI, but command-line only
# make sure old files are cleaned up before starting
for fname in [REMOVE_H_OUT1, REMOVE_H_OUT2, REMOVE_H_OUT3]:
silent_remove(fname)
test_input = ["-t", 'tests/test_data/pdbs2gausscoms/gau.tpl',
'-f', 'tests/test_data/pdbs2gausscoms/pet_mono_f1hs.pdb', "-r", "-n", "1"]
try:
main(test_input)
self.assertFalse(diff_lines(REMOVE_H_OUT1, GOOD_REMOVE_H_OUT1))
self.assertFalse(os.path.isfile(REMOVE_H_OUT2))
self.assertFalse(os.path.isfile(REMOVE_H_OUT3))
finally:
silent_remove(REMOVE_H_OUT1, disable=DISABLE_REMOVE)
pass
def testRotateDihedral(self):
ini_file = os.path.join(SUB_DATA_DIR, "pchl_eq_mono_rs_ends.ini")
test_input = ["-c", ini_file]
expected_output = []
for num in range(1, 37):
expected_output.append(os.path.join(SUB_DATA_DIR, f"pchl_eq_mono_rs_ends_{num}.com"))
try:
for fname in expected_output:
silent_remove(fname)
main(test_input)
for fname in expected_output:
self.assertTrue(os.path.isfile(fname))
for ext in [1, 5, 36]:
self.assertFalse(diff_lines(os.path.join(SUB_DATA_DIR, f"pchl_eq_mono_rs_ends_{ext}.com"),
os.path.join(SUB_DATA_DIR, f"pchl_eq_mono_rs_ends_{ext}_good.com")))
finally:
for fname in expected_output:
silent_remove(fname)
pass
def testRotateDihedralMaxConfs(self):
expected_output = []
for num in range(1, 16):
expected_output.append(os.path.join(SUB_DATA_DIR, f"pchl_eq_mono_rs_ends_{num}.com"))
unexpected_file = os.path.join(SUB_DATA_DIR, "pchl_eq_mono_rs_ends_16.com")
ini_file = os.path.join(SUB_DATA_DIR, "pchl_eq_mono_rs_ends_max_conf.ini")
test_input = ["-c", ini_file]
try:
for fname in expected_output:
silent_remove(fname)
silent_remove(unexpected_file)
main(test_input)
for fname in expected_output:
self.assertTrue(os.path.isfile(fname))
self.assertFalse(os.path.isfile(unexpected_file))
# nums are diff because above, kept original, and here do not
self.assertFalse(diff_lines(os.path.join(SUB_DATA_DIR, "pchl_eq_mono_rs_ends_2.com"),
os.path.join(SUB_DATA_DIR, "pchl_eq_mono_rs_ends_1_good.com")))
self.assertFalse(diff_lines(os.path.join(SUB_DATA_DIR, "pchl_eq_mono_rs_ends_6.com"),
os.path.join(SUB_DATA_DIR, "pchl_eq_mono_rs_ends_5_good.com")))
finally:
for fname in expected_output:
silent_remove(fname)
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" in output)