def testAnnotMtz2PdbxGood(self):
""" Test mtz to pdbx conversion (good mtz)
"""
self.__lfh.write(
"\nStarting %s %s\n" %
(self.__class__.__name__, sys._getframe().f_code.co_name))
diagfn = os.path.join(self.__tmpPath, "sf-convert-diags.cif")
ciffn = os.path.join(self.__tmpPath, "sf-convert-datafile.cif")
dmpfn = os.path.join(self.__tmpPath, "sf-convert-mtzdmp.log")
#
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
mtzPath = os.path.join(self.__testFilePath, self.__testFileMtzGood)
dp.imp(mtzPath)
dp.setTimeout(15)
ret = dp.op("annot-sf-convert")
dp.expLog(os.path.join(self.__tmpPath, "sf-convert.log"))
dp.expList(dstPathList=[ciffn, diagfn, dmpfn])
# dp.cleanup()
self.assertTrue(ret == 0)
self.assertTrue(ciffn)
self.assertTrue(diagfn)
self.assertTrue(dmpfn)
def testAnnotMtz2PdbxBad(self):
"""Test mtz to pdbx conversion"""
logger.info("\nStarting")
try:
diagfn = "sf-convert-diags-bad.cif"
ciffn = "sf-convert-datafile-bad.cif"
dmpfn = "sf-convert-mtzdmp-bad.log"
#
# self.__testFileMtzRunaway = "bad-runaway.mtz"
# self.__testFileXyzRunaway = "bad-runaway.cif"
#
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
mtzPath = os.path.join(self.__testFilePath, self.__testFileMtzBad)
dp.imp(mtzPath)
# xyzPath=os.path.join(self.__testFilePath,self.__testFileXyzBad)
dp.setTimeout(15)
# dp.addInput(name="xyz_file_path",value=xyzPath)
dp.op("annot-sf-convert")
dp.expLog("sf-convert-bad.log")
dp.expList(dstPathList=[ciffn, diagfn, dmpfn])
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testAnnotMtz2PdbxBadTimeout(self):
""" Test mtz to pdbx conversion
"""
logger.info("\nStarting %s %s\n" %
(self.__class__.__name__, sys._getframe().f_code.co_name))
try:
diagfn = "sf-convert-diags-bad-runaway.cif"
ciffn = "sf-convert-datafile-bad-runaway.cif"
dmpfn = "sf-convert-mtzdmp-bad-runaway.log"
#
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
dp.setDebugMode()
mtzPath = os.path.join(self.__testFilePath,
self.__testFileMtzRunaway)
dp.imp(mtzPath)
dp.setTimeout(15)
dp.op("annot-sf-convert")
dp.expLog("sf-convert-runaway.log")
dp.expList(dstPathList=[ciffn, diagfn, dmpfn])
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def mtz2Pdbx(self,
mtzFilePath,
outSfFilePath,
pdbxFilePath=None,
logFilePath=None,
diagsFilePath=None,
dumpFilePath=None,
timeout=120):
""" Convert input MTZ format to PDBx sf file.
"""
try:
diagfn = logFilePath if logFilePath is not None else "sf-convert-diags.cif"
dmpfn = dumpFilePath if dumpFilePath is not None else "sf-convert-mtzdmp.log"
#
dp = RcsbDpUtility(tmpPath=self.__sessionPath,
siteId=self.__siteId,
verbose=self.__verbose,
log=self.__lfh)
dp.imp(mtzFilePath)
dp.setTimeout(timeout)
if pdbxFilePath is not None:
dp.addInput(name="xyz_file_path", value=pdbxFilePath)
dp.op("annot-sf-convert")
dp.expLog(logFilePath)
dp.expList(dstPathList=[outSfFilePath, diagfn, dmpfn])
if (not self.__debug):
dp.cleanup()
return True
except:
self.__lfh.write(
"+DataFileAdapter.mtz2Pdbx() - failing for mtz file path %s output path %s\n"
% (mtzFilePath, outSfFilePath))
traceback.print_exc(file=self.__lfh)
return False
def testAnnotMtz2PdbxGood(self):
"""Test mtz to pdbx conversion (good mtz)"""
logger.info("\nStarting")
try:
diagfn = "sf-convert-diags.cif"
ciffn = "sf-convert-datafile.cif"
dmpfn = "sf-convert-mtzdmp.log"
#
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
dp.setDebugMode()
mtzPath = os.path.join(self.__testFilePath, self.__testFileMtzGood)
dp.imp(mtzPath)
dp.setTimeout(15)
dp.op("annot-sf-convert")
dp.expLog("sf-convert.log")
dp.expList(dstPathList=[ciffn, diagfn, dmpfn])
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
