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 read_mtz_sf(self, pathin):
"""Reads MTZ structure factor file
Return True on success, otherwise False
"""
logger.debug("Starting mtz read %s" % pathin)
suffix = '-dir'
prefix = 'rcsb-'
if self.__tmppath is not None and os.path.isdir(self.__tmppath):
workpath = tempfile.mkdtemp(suffix, prefix, self.__tmppath)
else:
workpath = tempfile.mkdtemp(suffix, prefix)
diagfn = os.path.join(workpath, "sf-convert-diags.cif")
ciffn = os.path.join(workpath, "sf-convert-datafile.cif")
dmpfn = os.path.join(workpath, "sf-convert-mtzdmp.log")
logfn = os.path.join(workpath, "sf-convert.log")
dp = RcsbDpUtility(siteId=self.__siteid, tmpPath=self.__tmppath)
dp.imp(pathin)
dp.op('annot-sf-convert')
dp.expLog(logfn)
dp.expList(dstPathList=[ciffn, diagfn, dmpfn])
if os.path.exists(ciffn):
ret = self.read_mmcif_sf(ciffn)
else:
ret = False
if self.__cleanup:
dp.cleanup()
shutil.rmtree(workpath, ignore_errors=True)
return ret
def testAnnotValidateListXrayTest(self):
"""Test create validation report for the test list of example PDB ids (NMR examples)"""
logger.info("\nStarting")
try:
for pdbId in self.__testValidateXrayIdList:
ofpdf = pdbId + "-valrpt.pdf"
ofxml = pdbId + "-valdata.xml"
offullpdf = pdbId + "-valrpt_full.pdf"
ofpng = pdbId + "-val-slider.png"
ofsvg = pdbId + "-val-slider.svg"
#
testFileValidateXyz = pdbId + ".cif"
testFileValidateSf = pdbId + "-sf.cif"
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
# dp.setDebugMode(True)
xyzPath = os.path.abspath(
os.path.join(self.__testFilePath, testFileValidateXyz))
sfPath = os.path.abspath(
os.path.join(self.__testFilePath, testFileValidateSf))
# dp.addInput(name="request_annotation_context", value="yes")
dp.addInput(name="request_validation_mode", value="annotate")
# dp.addInput(name="request_validation_mode", value="server")
dp.imp(xyzPath)
dp.addInput(name="sf_file_path", value=sfPath)
dp.op("annot-wwpdb-validate-all")
dp.expLog(pdbId + "-annot-validate-test.log")
dp.expList(dstPathList=[ofpdf, ofxml, offullpdf, ofpng, ofsvg])
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testAnnotMapCalc(self):
"""Test create density maps --"""
logger.info("\nStarting")
try:
for pdbId in ["1cbs", "3of4", "3oqp"]:
of2fofc = pdbId + "_2fofc.map"
offofc = pdbId + "_fofc.map"
testFileXyz = pdbId + ".cif"
testFileSf = pdbId + "-sf.cif"
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
xyzPath = os.path.join(self.__testFilePath, testFileXyz)
sfPath = os.path.join(self.__testFilePath, testFileSf)
dp.imp(xyzPath)
dp.addInput(name="sf_file_path", value=sfPath)
dp.op("annot-make-maps")
dp.expLog(pdbId + "-annot-make-maps.log")
dp.expList(dstPathList=[of2fofc, offofc])
# 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 testAnnotOmitMapCalc(self):
""" Test create density maps --
"""
logger.info("\nStarting %s %s\n" %
(self.__class__.__name__, sys._getframe().f_code.co_name))
try:
for pdbId in self.__testValidateIdList:
of2fofc = pdbId + "_map-omit-2fofc_P1.map"
offofc = pdbId + "_map-omit-fofc_P1.map"
testFileXyz = pdbId + ".cif"
testFileSf = pdbId + "-sf.cif"
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
dp.setDebugMode()
xyzPath = os.path.join(self.__testFilePath, testFileXyz)
sfPath = os.path.join(self.__testFilePath, testFileSf)
dp.imp(xyzPath)
dp.addInput(name="sf_file_path", value=sfPath)
dp.op("annot-make-maps")
dp.expLog(pdbId + "-annot-make-maps.log")
dp.expList(dstPathList=[of2fofc, offofc])
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def testAnnotValidateListNmrTest(self):
""" Test create validation report for the test list of example PDB ids (NMR examples)
"""
logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
count = 0
for pdbId in self.__testValidateNmrIdList:
ofpdf = pdbId + "-valrpt.pdf"
ofxml = pdbId + "-valdata.xml"
offullpdf = pdbId + "-valrpt_full.pdf"
ofpng = pdbId + "-val-slider.png"
ofsvg = pdbId + "-val-slider.svg"
#
testFileValidateXyz = pdbId + ".cif"
testFileValidateCs = pdbId + "-cs.cif"
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
xyzPath = os.path.abspath(os.path.join(self.__testFilePath, testFileValidateXyz))
csPath = os.path.abspath(os.path.join(self.__testFilePath, testFileValidateCs))
dp.addInput(name="request_annotation_context", value="yes")
# adding explicit selection of steps --
# Alternate
if count % 2 == 0:
dp.addInput(name="step_list", value=" coreclust,chemicalshifts,writexml,writepdf ")
count += 1
dp.imp(xyzPath)
dp.addInput(name="cs_file_path", value=csPath)
dp.op("annot-wwpdb-validate-all")
dp.expLog(pdbId + "-annot-validate-test.log")
dp.expList(dstPathList=[ofpdf, ofxml, offullpdf, ofpng, ofsvg])
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 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 testAnnotValidateListNmrTestRemote(self):
""" Test create validation report for the test list of example PDB ids (NMR examples)
"""
self.__lfh.write(
"\nStarting %s %s\n" %
(self.__class__.__name__, sys._getframe().f_code.co_name))
for pdbId in self.__testValidateNmrIdList:
self.__tmpPath = tempfile.mkdtemp(
dir=self.__siteWebAppsSessionsPath)
self.__lfh.write("\nStarting {} in {}\n".format(
pdbId, self.__tmpPath))
ofpdf = os.path.join(self.__tmpPath, pdbId + "-valrpt.pdf")
ofxml = os.path.join(self.__tmpPath, pdbId + "-valdata.xml")
offullpdf = os.path.join(self.__tmpPath,
pdbId + "-valrpt_full.pdf")
ofpng = os.path.join(self.__tmpPath, pdbId + "-val-slider.png")
ofsvg = os.path.join(self.__tmpPath, pdbId + "-val-slider.svg")
#
testFileValidateXyz = pdbId + ".cif"
testFileValidateCs = pdbId + "-cs.cif"
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
xyzPath = os.path.abspath(
os.path.join(self.__testFilePath, testFileValidateXyz))
csPath = os.path.abspath(
os.path.join(self.__testFilePath, testFileValidateCs))
dp.addInput(name="request_annotation_context", value="yes")
dp.addInput(name='run_dir',
value=os.path.join(
self.__siteWebAppsSessionsPath,
"validation_%s" % random.randrange(9999999)))
# adding explicit selection of steps --
# Alternate
#dp.addInput(name="step_list", value=" coreclust,chemicalshifts,writexml,writepdf ")
dp.addInput(name='kind', value='nmr')
dp.imp(xyzPath)
dp.addInput(name="cs_file_path", value=csPath)
# dp.setRunRemote()
ret = dp.op("annot-wwpdb-validate-all")
dp.expLog(
os.path.join(self.__tmpPath,
pdbId + "-annot-validate-test.log"))
dp.expList(dstPathList=[ofpdf, ofxml, offullpdf, ofpng, ofsvg])
# dp.cleanup()
self.assertTrue(ret == 0)
self.assertTrue(os.path.exists(ofpdf))
self.assertTrue(os.path.exists(ofxml))
self.assertTrue(os.path.exists(offullpdf))
self.assertTrue(os.path.exists(ofpng))
self.assertTrue(os.path.exists(ofsvg))
def testAnnotValidateListXrayTestRemote(self):
""" Test create validation report for the test list of example PDB ids (x-ray examples)
"""
self.__lfh.write(
"\nStarting %s %s\n" %
(self.__class__.__name__, sys._getframe().f_code.co_name))
for pdbId in self.__testValidateXrayIdList:
self.__tmpPath = tempfile.mkdtemp(
dir=self.__siteWebAppsSessionsPath)
self.__lfh.write("\nStarting {} in {}\n".format(
pdbId, self.__tmpPath))
ofpdf = os.path.join(self.__tmpPath, pdbId + "-valrpt.pdf")
ofxml = os.path.join(self.__tmpPath, pdbId + "-valdata.xml")
offullpdf = os.path.join(self.__tmpPath,
pdbId + "-valrpt_full.pdf")
ofpng = os.path.join(self.__tmpPath, pdbId + "-val-slider.png")
ofsvg = os.path.join(self.__tmpPath, pdbId + "-val-slider.svg")
#
testFileValidateXyz = pdbId + ".cif"
testFileValidateSf = pdbId + "-sf.cif"
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
# dp.setDebugMode(True)
xyzPath = os.path.abspath(
os.path.join(self.__testFilePath, testFileValidateXyz))
sfPath = os.path.abspath(
os.path.join(self.__testFilePath, testFileValidateSf))
# dp.addInput(name="request_annotation_context", value="yes")
dp.addInput(name="request_validation_mode", value="annotate")
dp.addInput(name='run_dir',
value=os.path.join(
self.__siteWebAppsSessionsPath,
"validation_%s" % random.randrange(9999999)))
# dp.addInput(name="request_validation_mode", value="server")
dp.imp(xyzPath)
dp.addInput(name="sf_file_path", value=sfPath)
# dp.setRunRemote()
ret = dp.op("annot-wwpdb-validate-all")
dp.expLog(
os.path.join(self.__tmpPath,
pdbId + "-annot-validate-test.log"))
dp.expList(dstPathList=[ofpdf, ofxml, offullpdf, ofpng, ofsvg])
# dp.cleanup()
self.assertTrue(ret == 0)
self.assertTrue(os.path.exists(ofpdf))
self.assertTrue(os.path.exists(ofxml))
self.assertTrue(os.path.exists(offullpdf))
self.assertTrue(os.path.exists(ofpng))
self.assertTrue(os.path.exists(ofsvg))
def testAnnotValidateXrayNeutronRemote(self):
"""Test create validation report for the test list of example PDB ids (x-ray examples)"""
logger.debug("\nStarting")
self.__tmpPath = tempfile.mkdtemp(dir=self.__siteWebAppsSessionsPath)
logger.debug("\nStarting x-ray neutron in %s\n", self.__tmpPath)
ofpdf = os.path.join(self.__tmpPath, "test-valrpt.pdf")
ofxml = os.path.join(self.__tmpPath, "test-valdata.xml")
offullpdf = os.path.join(self.__tmpPath, "test-valrpt_full.pdf")
ofpng = os.path.join(self.__tmpPath, "test-val-slider.png")
ofsvg = os.path.join(self.__tmpPath, "test-val-slider.svg")
#
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
# dp.setDebugMode(True)
xyzPath = os.path.abspath(
os.path.join(self.__testFilePath,
self.__testValidateXrayNeutronModel))
sfPath = os.path.abspath(
os.path.join(self.__testFilePath,
self.__testValidateXrayNeutronSF))
# dp.addInput(name="request_annotation_context", value="yes")
dp.addInput(name="request_validation_mode", value="annotate")
dp.addInput(name="run_dir",
value=os.path.join(
self.__siteWebAppsSessionsPath,
"validation_%s" % random.randrange(9999999)))
# dp.addInput(name="request_validation_mode", value="server")
dp.imp(xyzPath)
dp.addInput(name="sf_file_path", value=sfPath)
# dp.setRunRemote()
ret = dp.op("annot-wwpdb-validate-all")
dp.expLog(os.path.join(self.__tmpPath, "test-annot-validate-test.log"))
dp.expList(dstPathList=[ofpdf, ofxml, offullpdf, ofpng, ofsvg])
# dp.cleanup()
self.assertTrue(ret == 0)
self.assertTrue(os.path.exists(ofpdf))
self.assertTrue(os.path.exists(ofxml))
self.assertTrue(os.path.exists(offullpdf))
self.assertTrue(os.path.exists(ofpng))
self.assertTrue(os.path.exists(ofsvg))
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()
