def testFixSpecialPosition(self):
""" Test for fixing atoms on special position
"""
logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
#
inpPath = os.path.join(self.__testFilePath, self.__testFileValidateXyz)
dp.imp(inpPath)
dp.op("annot-dcc-fix-special-position")
dp.expLog("special-position-fix.log")
dp.exp("special-position-output-fix.log")
# No output - none on special
self.assertEqual(['missing'], dp.getResultPathList())
f = open('special-position-output-fix.log', 'r')
lines = f.read()
f.close()
self.assertIn('No atoms sit on special position', lines)
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
# This case has atoms on special position that needs correction
try:
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
#
# dp.setDebugMode(True)
#
inpPath = os.path.join(self.__testFilePath, self.__testSpecialPosition)
dp.imp(inpPath)
dp.op("annot-dcc-fix-special-position")
dp.expLog("special-position-fix2.log")
dp.exp("special-position-output-fix2.log")
print(dp.getResultPathList())
# We expect output
self.assertNotEqual(['missing'], dp.getResultPathList())
dp.expList(dstPathList=['special-position-out-fix2.cif'])
# Check output - for differences...
f = open('special-position-output-fix2.log', 'r')
lines = f.read()
f.close()
self.assertIn('Error: Wrong occupancy of 1.00 for atom (O : id=D_HOH_1)', lines)
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def pdbx2Assemblies(self, idCode, inpFilePath, outPath=".", indexFilePath=None):
"""Create model assemby files from input PDBx model file."""
try:
pdbxPath = inpFilePath
logPath = os.path.join(self.__sessionPath, "pdbx-assembly.log")
# indexFilePath=os.path.join(self.__sessionPath,"pdbx-assembly-index.txt")
#
dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
dp.imp(pdbxPath)
if idCode is not None:
dp.addInput(name="deposition_data_set_id", value=idCode, type="param")
if indexFilePath is not None:
dp.addInput(name="index_file_path", value=indexFilePath, type="param")
dp.op("annot-gen-assem-pdbx")
dp.expLog(logPath)
pthList = dp.getResultPathList()
# wrkPath = dp.getWorkingDir()
for pth in pthList:
if os.access(pth, os.R_OK):
(_t, fn) = os.path.split(pth)
shutil.copyfile(pth, os.path.join(outPath, fn))
# if (not self.__debug):
# dp.cleanup()
#
if self.__verbose:
self.__lfh.write("+DataFileAdapter.pdbx2Assemblies() - input model file path: %s\n" % inpFilePath)
self.__lfh.write("+DataFileAdapter.pdbx2Assemblies() - assembly output paths: %r\n" % pthList)
return True
except: # noqa: E722 pylint: disable=bare-except
self.__lfh.write("+DataFileAdapter.pdbx2Assemblies() - failing for input file path %s output path %s\n" % (inpFilePath, outPath))
traceback.print_exc(file=self.__lfh)
return False
