Ejemplo n.º 1
0
 def testOwnAtoms(self):
     try:
         main(["-c", GLUE_GLUP_OWN_ATOMS_INI])
         self.assertFalse(diff_lines(GLUE_SELECT_OUT, GLUE_SELECT_OWN_OUT_GOOD))
         self.assertFalse(diff_lines(GLUP_SELECT_OUT, GLUP_SELECT_OWN_OUT_GOOD))
     finally:
         [silent_remove(o_file, disable=DISABLE_REMOVE) for o_file in [GLUE_SELECT_OUT, GLUP_SELECT_OUT]]
Ejemplo n.º 2
0
 def testMultFileToPDBXYZ(self):
     # When checking output, ignore differences in version and time
     try:
         test_input = ["-c", MULT_2PDB_INI]
         if logger.isEnabledFor(logging.DEBUG):
             main(test_input)
         with capture_stdout(main, test_input) as output:
             self.assertTrue(
                 '"tests/test_data/cp2k_proc/glu_2.5_1.0.out",-283.341542,"False","False"'
                 in output)
             self.assertTrue(
                 '"tests/test_data/cp2k_proc/glu_2.5_1.05-1.out",-283.526959,"True","True"'
                 in output)
         diffs = diff_lines(GLU_PDB_OUT, GOOD_GLU_PDB_OUT)
         diffs1 = diff_lines(GLU_PDB_OUT2, GOOD_GLU_PDB_OUT2)
         for diff_list in [diffs, diffs1]:
             self.assertEqual(len(diff_list), 2)
             self.assertTrue("Created on " in diff_list[0])
         self.assertFalse(diff_lines(GLU_XYZ_OUT, GOOD_GLU_XYZ_OUT))
     finally:
         silent_remove(GLU_PDB_OUT, disable=DISABLE_REMOVE)
         silent_remove(GLU_PDB_OUT1, disable=DISABLE_REMOVE)
         silent_remove(GLU_PDB_OUT2, disable=DISABLE_REMOVE)
         silent_remove(GLU_XYZ_OUT, disable=DISABLE_REMOVE)
         silent_remove(GLU_XYZ_OUT1, disable=DISABLE_REMOVE)
         silent_remove(GLU_XYZ_OUT2, disable=DISABLE_REMOVE)
Ejemplo n.º 3
0
 def testWaterMol(self):
     try:
         main(["-c", WATER_MOL_INI, "-p"])
         self.assertFalse(diff_lines(DEF_CI_OUT1, GOOD_WATER_MOL_OUT1))
         self.assertFalse(diff_lines(DEF_CI_OUT2, GOOD_WATER_MOL_OUT2))
     finally:
         silent_remove(DEF_CI_OUT1, disable=DISABLE_REMOVE)
         silent_remove(DEF_CI_OUT2, disable=DISABLE_REMOVE)
Ejemplo n.º 4
0
 def testSortFromLammps(self):
     try:
         main(["-c", SORT_FROM_LAMMPS_INI])
         self.assertFalse(diff_lines(SORT_FROM_LAMMPS, SORT_FROM_LAMMPS_GOOD))
         self.assertFalse(diff_lines(SELECT_FROM_LAMMPS, SELECT_FROM_LAMMPS_GOOD))
     finally:
         silent_remove(SORT_FROM_LAMMPS, disable=DISABLE_REMOVE)
         silent_remove(SELECT_FROM_LAMMPS, disable=DISABLE_REMOVE)
Ejemplo n.º 5
0
 def testSpecOverwrite(self):
     try:
         main([str(EXP_TEMP), "-o"])
         self.assertFalse(diff_lines(ORIG_WHAM_OUT, GOOD_ORIG_WHAM_OUT))
         self.assertFalse(diff_lines(SHORT_WHAM_OUT, GOOD_SHORT_WHAM_OUT))
     finally:
         silent_remove(ORIG_WHAM_OUT, disable=DISABLE_REMOVE)
         silent_remove(SHORT_WHAM_OUT, disable=DISABLE_REMOVE)
Ejemplo n.º 6
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 def testGood(self):
     try:
         main([PB_GOOD])
         self.assertEqual(2, len(diff_lines(PB_GOOD_XYZ, PB_REF_XYZ, delimiter=" ")))
         self.assertEqual(0, len(diff_lines(PB_GOOD_LOG, PB_REF_LOG)))
     finally:
         silent_remove(PB_GOOD_LOG)
         silent_remove(PB_GOOD_XYZ)
Ejemplo n.º 7
0
 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)
Ejemplo n.º 8
0
 def testWaterMol(self):
     try:
         main(["-c", WATER_MOL_INI])
         self.assertFalse(diff_lines(WATER_MOL_OUT1, GOOD_WATER_MOL_OUT1))
         self.assertFalse(diff_lines(WATER_MOL_OUT2, GOOD_WATER_MOL_OUT2))
     finally:
         silent_remove(WATER_MOL_OUT1, disable=DISABLE_REMOVE)
         silent_remove(WATER_MOL_OUT2, disable=DISABLE_REMOVE)
Ejemplo n.º 9
0
 def testSpecOverwrite(self):
     try:
         main([str(EXP_TEMP), "-o"])
         self.assertFalse(diff_lines(ORIG_WHAM_OUT, GOOD_ORIG_WHAM_OUT))
         self.assertFalse(diff_lines(SHORT_WHAM_OUT, GOOD_SHORT_WHAM_OUT))
     finally:
         silent_remove(ORIG_WHAM_OUT, disable=DISABLE_REMOVE)
         silent_remove(SHORT_WHAM_OUT, disable=DISABLE_REMOVE)
Ejemplo n.º 10
0
 def testCiInfo(self):
     try:
         main(["-c", CI_INI])
         self.assertFalse(diff_lines(DEF_CI_OUT1, GOOD_CI_OUT1))
         self.assertEquals(1, len(diff_lines(DEF_CI_OUT2, BAD_CI_OUT2)))
         self.assertFalse(diff_lines(DEF_CI_OUT2, GOOD_CI_OUT2))
     finally:
         silent_remove(DEF_CI_OUT1)
         silent_remove(DEF_CI_OUT2)
Ejemplo n.º 11
0
 def testCiInfo(self):
     try:
         main(["-c", CI_INI])
         self.assertFalse(diff_lines(DEF_CI_OUT1, GOOD_CI_OUT1))
         self.assertEqual(1, len(diff_lines(DEF_CI_OUT2, BAD_CI_OUT2)))
         self.assertFalse(diff_lines(DEF_CI_OUT2, GOOD_CI_OUT2))
     finally:
         silent_remove(DEF_CI_OUT1, disable=DISABLE_REMOVE)
         silent_remove(DEF_CI_OUT2, disable=DISABLE_REMOVE)
Ejemplo n.º 12
0
 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)
Ejemplo n.º 13
0
 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)
Ejemplo n.º 14
0
 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)
Ejemplo n.º 15
0
 def testImptAtoms(self):
     try:
         main(["-c", GLUE_GLUP_IMP_ATOMS_INI])
         self.assertFalse(diff_lines(GLUE_SELECT_OUT, GLUE_SELECT_OUT_GOOD))
         self.assertFalse(diff_lines(GLUP_SELECT_OUT, GLUP_SELECT_OUT_GOOD))
     finally:
         [
             silent_remove(o_file, disable=DISABLE_REMOVE)
             for o_file in [GLUE_SELECT_OUT, GLUP_SELECT_OUT]
         ]
Ejemplo n.º 16
0
 def testSortFromLammps(self):
     try:
         main(["-c", SORT_FROM_LAMMPS_INI])
         self.assertFalse(
             diff_lines(SORT_FROM_LAMMPS, SORT_FROM_LAMMPS_GOOD))
         self.assertFalse(
             diff_lines(SELECT_FROM_LAMMPS, SELECT_FROM_LAMMPS_GOOD))
     finally:
         silent_remove(SORT_FROM_LAMMPS, disable=DISABLE_REMOVE)
         silent_remove(SELECT_FROM_LAMMPS, disable=DISABLE_REMOVE)
Ejemplo n.º 17
0
 def testGood(self):
     try:
         # main(["-c", DEF_INI])
         with capture_stdout(main, ["-c", DEF_INI]) as output:
             self.assertTrue("total charge" in output)
         self.assertFalse(diff_lines(VMD_OUT, GOOD_VMD_OUT))
         self.assertFalse(diff_lines(WATER_OUT, GOOD_WATER_OUT))
     finally:
         silent_remove(VMD_OUT)
         silent_remove(WATER_OUT)
Ejemplo n.º 18
0
 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)
         silent_remove(QMMM_OUT)
         silent_remove(VMD_ATOMS_OUT)
Ejemplo n.º 19
0
 def testOneFileToDataXYZ(self):
     # When checking output, ignore differences in version and time
     try:
         main(["-c", ONE_2DATA_INI])
         diffs = diff_lines(GLU_DATA_OUT, GOOD_GLU_DATA_OUT)
         self.assertEqual(len(diffs), 2)
         self.assertTrue("Created on " in diffs[0])
         self.assertFalse(diff_lines(GLU_XYZ_OUT, GOOD_GLU_XYZ_OUT))
     finally:
         silent_remove(GLU_DATA_OUT, disable=DISABLE_REMOVE)
         silent_remove(GLU_XYZ_OUT, disable=DISABLE_REMOVE)
Ejemplo n.º 20
0
 def testHist(self):
     try:
         main(["-f", HIST_INPUT, "-n", "-d", ",", "-s"])
         for p_file in [HIST_PNG1, HIST_PNG2, HIST_PNG3]:
             self.assertGreater(os.path.getsize(p_file), 10000)
         self.assertFalse(diff_lines(HIST_OUT, GOOD_HIST_OUT))
         self.assertFalse(diff_lines(HIST_COUNT, GOOD_HIST_COUNT))
     finally:
         [silent_remove(o_file,
                        disable=DISABLE_REMOVE) for o_file in [HIST_PNG1, HIST_PNG2, HIST_PNG3,
                                                               HIST_OUT, HIST_COUNT, ]]
Ejemplo n.º 21
0
 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
Ejemplo n.º 22
0
 def testHist(self):
     try:
         main(["-f", HIST_INPUT, "-n", "-d", ",", "-s"])
         for p_file in [HIST_PNG1, HIST_PNG2, HIST_PNG3]:
             self.assertGreater(os.path.getsize(p_file), 10000)
         self.assertFalse(diff_lines(HIST_OUT, GOOD_HIST_OUT))
         self.assertFalse(diff_lines(HIST_COUNT, GOOD_HIST_COUNT))
     finally:
         [silent_remove(o_file,
                        disable=DISABLE_REMOVE) for o_file in [HIST_PNG1, HIST_PNG2, HIST_PNG3,
                                                               HIST_OUT, HIST_COUNT, ]]
Ejemplo n.º 23
0
 def testMakeEqPar(self):
     try:
         for o_file in MULTI_OUT_FILES:
             silent_remove(o_file)
         main(["-c", PAR_EQ_INI])
         self.assertFalse(diff_lines(MULTI_PAR_OUT1, GOOD_MULTI_PAR_OUT1))
         self.assertFalse(diff_lines(MULTI_PAR_OUT2, GOOD_PAR_OUT))
         self.assertFalse(diff_lines(MULTI_PAR_OUT3, GOOD_MULTI_PAR_OUT3))
     finally:
         for o_file in MULTI_OUT_FILES:
             silent_remove(o_file, disable=DISABLE_REMOVE)
Ejemplo n.º 24
0
 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)
Ejemplo n.º 25
0
 def testMakeParStartLow(self):
     # For this test, there is exactly one value provided for each parameter, and x_0 is too low
     silent_remove(PAR_OUT)
     silent_remove(COPY_PAR)
     try:
         main(["-c", CONV_INI])
         self.assertFalse(diff_lines(PAR_OUT, GOOD_PAR_OUT2))
         self.assertFalse(diff_lines(COPY_PAR, GOOD_PAR_OUT2))
     finally:
         silent_remove(PAR_OUT, disable=DISABLE_REMOVE)
         silent_remove(COPY_PAR, disable=DISABLE_REMOVE)
         silent_remove(SCRIPT_OUT, disable=DISABLE_REMOVE)
Ejemplo n.º 26
0
 def testPrintQMMM(self):
     try:
         # main(["-c", QMMM_OUT_INI])
         with capture_stdout(main, ["-c", QMMM_OUT_INI]) 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)
         silent_remove(MM_KIND_OUT)
         silent_remove(VMD_ATOMS_OUT)
Ejemplo n.º 27
0
 def testGood(self):
     try:
         test_input = ["-c", DEF_INI]
         if logger.isEnabledFor(logging.DEBUG):
             main(test_input)
         with capture_stdout(main, test_input) as output:
             self.assertTrue("total charge" in output)
         self.assertFalse(diff_lines(VMD_OUT, GOOD_VMD_OUT))
         self.assertFalse(diff_lines(WATER_OUT, GOOD_WATER_OUT))
     finally:
         silent_remove(VMD_OUT)
         silent_remove(WATER_OUT)
Ejemplo n.º 28
0
 def testMakeOneMultiPar(self):
     # Now, one parameter has multiple values
     try:
         for o_file in MULTI_OUT_FILES:
             silent_remove(o_file)
         main(["-c", PAR_ONE_MULTI_INI])
         self.assertFalse(diff_lines(MULTI_PAR_OUT1, GOOD_MULTI_PAR_OUT1))
         self.assertFalse(diff_lines(MULTI_PAR_OUT2, GOOD_PAR_OUT))
         self.assertFalse(diff_lines(MULTI_PAR_OUT3, GOOD_MULTI_PAR_OUT3))
     finally:
         for o_file in MULTI_OUT_FILES:
             silent_remove(o_file, disable=DISABLE_REMOVE)
Ejemplo n.º 29
0
 def testCollectBestWResidNoInitialBest(self):
     try:
         # Ensure that this is not already a summary file
         silent_remove(ALL_BEST_STR, disable=DISABLE_REMOVE)
         main([
             "-c", DA_GAUSS_INI, "-f", FITEVB_OUT1, "-s", ALL_BEST_STR,
             "-r", FIT_HIJ, FIT_REP1
         ])
         self.assertFalse(diff_lines(DEF_OUT, GOOD_INP_OUT1))
         self.assertFalse(diff_lines(ALL_BEST_STR, GOOD_ALL_BEST_NEW))
     finally:
         silent_remove(DEF_OUT, disable=DISABLE_REMOVE)
         silent_remove(ALL_BEST_STR, disable=DISABLE_REMOVE)
Ejemplo n.º 30
0
 def testOneStateEachFileCiInfo(self):
     """
     Make sure can handle input that only has one state (such steps have a vector instead of a matrix)
     this time, printing a separate output for each file
     And, skip one-state-steps
     """
     try:
         main(["-c", CI_ONE_STATE_EACH_FILE_INI])
         self.assertFalse(diff_lines(DEF_ONE_STATE_OUT, GOOD_ONE_STATE_OUT))
         self.assertFalse(diff_lines(DEF_ONE_STATE_OUT2, GOOD_ONE_STATE_OUT2))
     finally:
         silent_remove(DEF_ONE_STATE_OUT)
         silent_remove(DEF_ONE_STATE_OUT2)
Ejemplo n.º 31
0
 def testMissingRadius(self):
     # Tests both providing a dictionary and not having an available radius (still prints everything, just missing
     # one radius)
     try:
         with capture_stderr(main, ["-c", MISSING_RADIUS_INI]) 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.assertEqual(3, len(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)
         silent_remove(MM_KIND_OUT)
         silent_remove(VMD_ATOMS_OUT)
Ejemplo n.º 32
0
 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)
Ejemplo n.º 33
0
 def testOneStateEachFileCiInfo(self):
     """
     Make sure can handle input that only has one state (such steps have a vector instead of a matrix)
     this time, printing a separate output for each file
     And, skip one-state-steps
     """
     try:
         main(["-c", CI_ONE_STATE_EACH_FILE_INI])
         self.assertFalse(diff_lines(DEF_ONE_STATE_OUT, GOOD_ONE_STATE_OUT))
         self.assertFalse(
             diff_lines(DEF_ONE_STATE_OUT2, GOOD_ONE_STATE_OUT2))
     finally:
         silent_remove(DEF_ONE_STATE_OUT, disable=DISABLE_REMOVE)
         silent_remove(DEF_ONE_STATE_OUT2, disable=DISABLE_REMOVE)
Ejemplo n.º 34
0
 def testMakeParStartHigh(self):
     # Testing that starting from an x_0 too high still ends at the same answer
     # Also check specifying par file name in command line; should overwrite what is in the config file
     try:
         silent_remove(ALT_PAR_FNAME)
         main(["-c", CONV_ALT_INI, "-f", ALT_PAR_FNAME])
         self.assertFalse(diff_lines(ALT_PAR_FNAME, GOOD_PAR_OUT2))
         self.assertFalse(diff_lines(RESID_PAR_OUT, GOOD_PAR_OUT2))
     finally:
         silent_remove(ALT_PAR_FNAME, disable=DISABLE_REMOVE)
         silent_remove(SCRIPT_OUT, disable=DISABLE_REMOVE)
         silent_remove(RESID_PAR_OUT, disable=DISABLE_REMOVE)
         for file_name in OTHER_RESID_NAMES:
             silent_remove(os.path.join(DATA_DIR, file_name), disable=DISABLE_REMOVE)
Ejemplo n.º 35
0
 def testFileListToData(self):
     try:
         silent_remove(GLU_DATA_OUT)
         test_input = ["-c", MULT_2DATA_INI]
         main(test_input)
         diffs = diff_lines(GLU_DATA_OUT, GOOD_GLU_DATA_OUT)
         diffs1 = diff_lines(GLU_DATA_OUT2, GOOD_GLU_DATA_OUT2)
         for diff_list in [diffs, diffs1]:
             self.assertEqual(len(diff_list), 2)
             self.assertTrue("Created on " in diff_list[0])
     finally:
         silent_remove(GLU_DATA_OUT, disable=DISABLE_REMOVE)
         silent_remove(GLU_DATA_OUT1, disable=DISABLE_REMOVE)
         silent_remove(GLU_DATA_OUT2, disable=DISABLE_REMOVE)
 def testGoodInput(self):
     test_input = ["-l", GLU_LIST]
     if logger.isEnabledFor(logging.DEBUG):
         main(test_input)
     try:
         with capture_stdout(main, test_input) as output:
             self.assertTrue("1429         47     -0.274     -0.728     -0.387      0.470" in output)
             self.assertTrue("1429         53     -0.215      0.156      0.269      0.822" in output)
         self.assertFalse(diff_lines(GLU_SUM, GOOD_GLU_SUM))
         self.assertFalse(diff_lines(GLU_OUT1, GOOD_GLU_OUT1, delimiter=" "))
         self.assertFalse(diff_lines(GLU_OUT2, GOOD_GLU_OUT2, delimiter=" "))
     finally:
         silent_remove(GLU_SUM, disable=DISABLE_REMOVE)
         silent_remove(GLU_OUT1, disable=DISABLE_REMOVE)
         silent_remove(GLU_OUT2, disable=DISABLE_REMOVE)
Ejemplo n.º 37
0
 def testMultiLineSepIni(self):
     # have different rows create different files
     # test that if the prefix is already used, number it
     # test if nothing common in the file base names, number it
     try:
         main(["-f", MULTI_LINE_CMP_LIST, "-s", "-l", SUB_DATA_DIR])
         self.assertFalse(diff_lines(LINE1_OUT, GOOD_LINE1_OUT))
         self.assertFalse(diff_lines(LINE2_OUT, GOOD_LINE2_OUT))
         self.assertFalse(diff_lines(LINE3_OUT, GOOD_LINE1_OUT))
         self.assertFalse(diff_lines(LINE4_OUT, GOOD_LINE1_OUT))
     finally:
         silent_remove(LINE1_OUT, disable=DISABLE_REMOVE)
         silent_remove(LINE2_OUT, disable=DISABLE_REMOVE)
         silent_remove(LINE3_OUT, disable=DISABLE_REMOVE)
         silent_remove(LINE4_OUT, disable=DISABLE_REMOVE)
Ejemplo n.º 38
0
 def testNoOpt(self):
     # Testing that will run without any params specified to be optimized
     silent_remove(PAR_OUT)
     test_input = ["-c", PAR_INI]
     if logger.isEnabledFor(logging.DEBUG):
         main(test_input)
     try:
         with capture_stderr(main, test_input) as output:
             self.assertTrue("No parameters will be optimized" in output)
         self.assertFalse(diff_lines(PAR_OUT, GOOD_PAR_OUT2))
         self.assertFalse(diff_lines(COPY_PAR, GOOD_PAR_OUT2))
     finally:
         silent_remove(PAR_OUT, disable=DISABLE_REMOVE)
         silent_remove(COPY_PAR, disable=DISABLE_REMOVE)
         silent_remove(SCRIPT_OUT, disable=DISABLE_REMOVE)
Ejemplo n.º 39
0
 def testMultiLineSepIni(self):
     # have different rows create different files
     # test that if the prefix is already used, number it
     # test if nothing common in the file base names, number it
     try:
         main(["-f", MULTI_LINE_CMP_LIST, "-s", "-l", SUB_DATA_DIR])
         self.assertFalse(diff_lines(LINE1_OUT, GOOD_LINE1_OUT))
         self.assertFalse(diff_lines(LINE2_OUT, GOOD_LINE2_OUT))
         self.assertFalse(diff_lines(LINE3_OUT, GOOD_LINE1_OUT))
         self.assertFalse(diff_lines(LINE4_OUT, GOOD_LINE1_OUT))
     finally:
         silent_remove(LINE1_OUT, disable=DISABLE_REMOVE)
         silent_remove(LINE2_OUT, disable=DISABLE_REMOVE)
         silent_remove(LINE3_OUT, disable=DISABLE_REMOVE)
         silent_remove(LINE4_OUT, disable=DISABLE_REMOVE)
Ejemplo n.º 40
0
 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)
Ejemplo n.º 41
0
 def testSubsetCiInfo(self):
     with capture_stderr(main, ["-c", CI_SUBSET_INI]) as output:
         self.assertTrue("found no data from" in output)
         self.assertFalse(diff_lines(DEF_CI_SUBSET_OUT, GOOD_CI_SUBSET_OUT))
         silent_remove(DEF_CI_SUBSET_OUT)
         silent_remove(DEF_CI_OUT1)
         silent_remove(DEF_CI_OUT2)
Ejemplo n.º 42
0
 def testWaterMolCombine(self):
     # Should skip the timestep with only 1 state
     try:
         main(["-c", WATER_MOL_COMB_INI])
         self.assertFalse(diff_lines(WATER_MOL_COMB_OUT, GOOD_WATER_MOL_COMB_OUT))
     finally:
         silent_remove(WATER_MOL_COMB_OUT)
Ejemplo n.º 43
0
 def testGlu(self):
     try:
         data2pdb.main(["-c", GLU_INI])
         self.assertFalse(diff_lines(GLU_OUT, GOOD_GLU_OUT))
     finally:
         silent_remove(PDB_TPL_OUT)
         silent_remove(GLU_OUT)
Ejemplo n.º 44
0
 def testDefInp(self):
     try:
         with capture_stdout(main, ["-f", DEF_INPUT, "-c", DEF_INI]) as output:
             self.assertTrue("Keeping 2 of 4 rows based on filtering criteria" in output)
         self.assertFalse(diff_lines(CSV_OUT, GOOD_CSV_OUT))
     finally:
         silent_remove(CSV_OUT)
Ejemplo n.º 45
0
 def testDefInp(self):
     test_input = ["-c", DEF_INI, "-f", DEF_INPUT]
     try:
         main(test_input)
         self.assertFalse(diff_lines(DEF_OUT, GOOD_OUT))
     finally:
         silent_remove(DEF_OUT, disable=DISABLE_REMOVE)
Ejemplo n.º 46
0
 def testGlu(self):
     try:
         data2pdb.main(["-c", GLU_INI])
         self.assertFalse(diff_lines(GLU_OUT, GOOD_GLU_OUT))
     finally:
         silent_remove(PDB_TPL_OUT)
         silent_remove(GLU_OUT)
Ejemplo n.º 47
0
 def testDefInp(self):
     try:
         with capture_stdout(main, ["-f", DEF_INPUT]) as output:
             self.assertTrue(GOOD_OUT in output)
             self.assertFalse(diff_lines(CSV_OUT, GOOD_CSV_OUT))
     finally:
         silent_remove(CSV_OUT, disable=DISABLE_REMOVE)
Ejemplo n.º 48
0
 def testDefInp(self):
     test_input = ["-c", DEF_INI, "-f", DEF_INPUT]
     try:
         main(test_input)
         self.assertFalse(diff_lines(DEF_OUT, GOOD_OUT))
     finally:
         silent_remove(DEF_OUT, disable=DISABLE_REMOVE)
Ejemplo n.º 49
0
 def testMaxTimestepsCalcHIJ(self):
     try:
         with capture_stdout(main, ["-c", HIJ_INI]) as output:
             self.assertTrue("Reached the maximum timesteps" in output)
         self.assertFalse(diff_lines(HIJ_OUT, GOOD_HIJ_OUT))
     finally:
         silent_remove(HIJ_OUT, disable=DISABLE_REMOVE)
Ejemplo n.º 50
0
 def testIncompDump(self):
     try:
         with capture_stderr(main, ["-c", INCOMP_DUMP_INI_PATH]) as output:
             self.assertTrue("WARNING" in output)
         self.assertFalse(diff_lines(DEF_GOFR_INCOMP_OUT, GOOD_HO_GOFR_OUT_PATH))
     finally:
         silent_remove(DEF_GOFR_INCOMP_OUT, disable=DISABLE_REMOVE)
Ejemplo n.º 51
0
 def testHO_OO_HH_OHGofR(self):
     try:
         main(["-c", HO_OO_HH_OH_GOFR_INI])
         self.assertFalse(
             diff_lines(DEF_GOFR_OUT, GOOD_HO_OO_HH_OH_GOFR_OUT))
     finally:
         silent_remove(DEF_GOFR_OUT, disable=DISABLE_REMOVE)
Ejemplo n.º 52
0
 def testCalcProps(self):
     try:
         test_input = ["-c", CALC_GLU_PROPS_INI, "-p"]
         main(test_input)
         self.assertFalse(diff_lines(HIJ_NEW_GLU2_OUT, GOOD_GLU_PROPS_OUT))
     finally:
         silent_remove(HIJ_NEW_GLU2_OUT, disable=DISABLE_REMOVE)
Ejemplo n.º 53
0
 def testAddNothing(self):
     # this first test does not really doing anything, and warns the user
     try:
         with capture_stderr(main, [INPUT_PATH]) as output:
             self.assertTrue("Return file will be the same as the input" in output)
         self.assertFalse(diff_lines(INPUT_PATH, DEF_OUT_PATH))
     finally:
         silent_remove(DEF_OUT_PATH)
Ejemplo n.º 54
0
 def testDupCol(self):
     test_input = ["-f", DUP_COL_CMP_LIST]
     if logger.isEnabledFor(logging.DEBUG):
         main(test_input)
     with capture_stderr(main, test_input) as output:
         self.assertFalse(diff_lines(DEF_OUT, GOOD_OUT))
         self.assertTrue("Non-unique column" in output)
     silent_remove(DEF_OUT, disable=DISABLE_REMOVE)
Ejemplo n.º 55
0
 def testNoMinNonFloat(self):
     # Tests both handling when no min section is specified and non-floats in the file to be analyzed
     test_input = ["-f", NON_FLOAT_INPUT, "-c", NO_MIN_INI]
     try:
         main(test_input)
         self.assertFalse(diff_lines(NON_FLOAT_OUT, GOOD_NON_FLOAT_OUT))
     finally:
         silent_remove(NON_FLOAT_OUT)
Ejemplo n.º 56
0
 def testBinMax2(self):
     # In this input, both bins have more than the max entries
     test_input = ["-f", BIN_INPUT, "-c", BIN_MAX2_INI]
     try:
         main(test_input)
         self.assertFalse(diff_lines(DEF_BIN_OUT, GOOD_BIN_MAX2_OUT))
     finally:
         silent_remove(DEF_BIN_OUT, disable=DISABLE_REMOVE)
Ejemplo n.º 57
0
 def testCompDihAlt(self):
     # Test it is okay with sections in the 1st but not 2nd file
     with capture_stderr(main, ["-c", COMP_DIH_ALT_INI]) as output:
         self.assertTrue("WARNING:  Skipping section" in output)
     try:
         self.assertFalse(diff_lines(COMP_DIH_ALT_OUT, COMP_DIH_ALT_OUT_GOOD))
     finally:
         silent_remove(COMP_DIH_ALT_OUT, disable=DISABLE_REMOVE)
Ejemplo n.º 58
0
 def testReorderAtoms(self):
     try:
         with capture_stdout(main, ["-c", DEF_INI]) as output:
             for message in WATER_OUT_OF_ORDER_MESSAGES:
                 self.assertFalse(message in output)
         self.assertFalse(diff_lines(DEF_OUT, GOOD_OUT))
     finally:
         silent_remove(DEF_OUT)