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 testChemicalShiftCoordinateCheck2(self):
"""Test upload check of one CS file --- Using a processed chemical shift file"""
logger.info("\nStarting")
try:
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
dp.setDebugMode(flag=True)
inpPath = os.path.join(self.__testFilePath, self.__testConcatCS)
xyzPath = os.path.abspath(
os.path.join(self.__testFilePath, self.__testFileNmrModel))
outPath = "output-cs-file-concat.cif"
chkPath = "cs-diag-atom-name-check-concat.cif"
dp.imp(inpPath)
dp.addInput(name="coordinate_file_path", value=xyzPath)
dp.addInput(name="chemical_shifts_coord_check_file_path",
value=chkPath)
dp.op("annot-chem-shifts-atom-name-check")
dp.expLog("annot-chem-shifts-atom-name-check-concat.log")
dp.exp(outPath)
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testAnnotDccReport(self):
""" Test create DCC report -
"""
logger.info("\nStarting %s %s\n" %
(self.__class__.__name__, sys._getframe().f_code.co_name))
try:
ofn = "dcc-report.cif"
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
dp.setDebugMode()
xyzPath = os.path.join(self.__testFilePath,
self.__testFileValidateXyz)
sfPath = os.path.join(self.__testFilePath,
self.__testFileValidateSf)
dp.imp(xyzPath)
dp.addInput(name="sf_file_path", value=sfPath)
dp.op("annot-dcc-report")
dp.expLog("dcc-report.log")
dp.exp(ofn)
# dp.expList(dstPathList=[ofpdf,ofxml])
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def testUploadShiftListCheck(self):
"""Test upload check of one CS file --- Upload multiple files"""
logger.info("\nStarting")
try:
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
dp.setDebugMode(flag=True)
inpPath = os.path.join(self.__testFilePath, self.__testFileStarCs)
outPath = "output-cs-file-full-2.cif"
chkPath = "cs-diag-upload-check-2.cif"
dp.addInput(name="chemical_shifts_file_path_list",
value=[inpPath, inpPath])
dp.addInput(name="chemical_shifts_auth_file_name_list",
value=["cs_file_1", "cs_file_2"])
dp.addInput(name="chemical_shifts_upload_check_file_path",
value=chkPath)
dp.op("annot-chem-shifts-upload-check")
dp.expLog("annot-chem-shifts-upload-check-2.log")
dp.exp(outPath)
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testChemicalShiftCoordinateCheck2Alt(self):
""" Test upload check of one CS file --- Using the wrong model to generate errors
"""
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)
dp.setDebugMode(flag=True)
inpPath = os.path.join(self.__testFilePath, self.__testConcatCS)
xyzPath = os.path.abspath(os.path.join(self.__testFilePath, self.__testFileNmrModelAlt))
outPath = "output-cs-file-concat-alt.cif"
chkPath = "cs-diag-atom-name-check-concat-alt.cif"
dp.imp(inpPath)
dp.addInput(name="coordinate_file_path", value=xyzPath)
dp.addInput(name="chemical_shifts_coord_check_file_path", value=chkPath)
dp.op("annot-chem-shifts-atom-name-check")
dp.expLog("annot-chem-shifts-atom-name-check-concat-alt.log")
dp.exp(outPath)
#
if os.access(chkPath, os.R_OK):
csr = PdbxChemShiftReport(inputPath=chkPath, verbose=self.__verbose, log=self.__lfh)
status = csr.getStatus()
logger.info("Status code: %s\n" % status)
warnings = csr.getWarnings()
logger.info("\n\nWarning count : %d\n %s\n" % (len(warnings), ('\n').join(warnings)))
#
errors = csr.getErrors()
logger.info("\n\nError count : %d\n %s\n" % (len(errors), ('\n').join(errors)))
#
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def __getLoadFile(self, sessionPath, listfile, sqlfile, logfile):
fn = os.path.join(self.__sessionPath, listfile)
mapping = self.__cIcommon.get_site_da_internal_schema_path()
self.__lfh.write(
"DbLoadUtil::__getLoadFile(): listfile %s sqlfile %s logfile %s\n"
% (fn, sqlfile, logfile))
try:
dp = RcsbDpUtility(tmpPath=sessionPath,
siteId=self.__siteId,
verbose=self.__verbose,
log=self.__lfh)
dp.setDebugMode()
dp.imp(fn)
dp.addInput(name="mapping_file", value=mapping, type="file")
dp.addInput(name="file_list", value=True)
# This code handles model files
dp.addInput(name="first_block", value=True)
dp.op("db-loader")
dp.expLog(logfile)
dp.exp(sqlfile)
dp.cleanup()
return
except: # noqa: E722 pylint: disable=bare-except
self.__lfh.write(
"DbLoadUtil::__getLoadFile(): failing, with exception.\n")
traceback.print_exc(file=self.__lfh)
def testAnnotLigandMapCalc(self):
""" Test create non-polymer local density maps --
"""
logger.info("\nStarting %s %s\n" %
(self.__class__.__name__, sys._getframe().f_code.co_name))
try:
for pdbId in ['3of4']:
testFileXyz = pdbId + ".cif"
testFileSf = pdbId + "-sf.cif"
#
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
dp.setDebugMode(flag=True)
xyzPath = os.path.join(self.__testFilePath, testFileXyz)
sfPath = os.path.join(self.__testFilePath, testFileSf)
#
outDataPath = os.path.join(self.__tmpPath, 'np-cc-maps')
outIndexPath = os.path.join(self.__tmpPath, 'np-cc-maps',
'np-cc-maps-index.cif')
#
dp.imp(xyzPath)
dp.addInput(name="sf_file_path", value=sfPath)
dp.addInput(name="output_data_path", value=outDataPath)
dp.addInput(name="output_index_path", value=outIndexPath)
dp.op("annot-make-ligand-maps")
dp.expLog(pdbId + "-annot-make-ligand-maps.log")
#
if (False):
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
dp.setDebugMode(flag=True)
xyzPath = os.path.join(self.__testFilePath, testFileXyz)
sfPath = os.path.join(self.__testFilePath, testFileSf)
#
outDataPath = os.path.join(self.__tmpPath,
'np-cc-omit-maps')
outIndexPath = os.path.join(self.__tmpPath,
'np-cc-omit-maps',
'np-cc-omit-maps-index.cif')
#
dp.imp(xyzPath)
dp.addInput(name="omit_map", value=True)
dp.addInput(name="sf_file_path", value=sfPath)
dp.addInput(name="output_data_path", value=outDataPath)
dp.addInput(name="output_index_path", value=outIndexPath)
dp.op("annot-make-ligand-maps")
dp.expLog(pdbId + "-annot-make-ligand-omit-maps.log")
#
# This application
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def testReadMapHeader(self):
""" Test read map header -- export JSON packet and plot density distribution -
"""
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)
dp.setDebugMode(flag=True)
#
inpPath = os.path.join(self.__testFilePath, self.__testMapNormal)
of = self.__testMapNormal + "_map-header-data_P1.json"
dp.imp(inpPath)
dp.op("annot-read-map-header")
dp.expLog("annot-read-map-header.log")
dp.exp(of)
# dp.cleanup()
#
mD = json.load(open(of, 'r'))
logger.info("Map header keys: %r\n" % mD.keys())
logger.info("Map header: %r\n" % mD.items())
logger.info("Input header keys: %r\n" % mD['input_header'].keys())
logger.info("Output header keys: %r\n" %
mD['output_header'].keys())
#
x = mD['input_histogram_categories']
y = mD['input_histogram_values']
logy = []
for v in y:
if float(v) <= 0.0:
logy.append(math.log10(.1))
else:
logy.append(math.log10(float(v)))
#
width = float(x[-1] - x[0]) / float(len(x))
#width = 2.0
logger.info("Starting plot\n")
plt.bar(x, y, width, color="r", log=True)
logger.info("Loaded data\n")
plt.title('Map density distribution')
logger.info("set title\n")
plt.ylabel('Voxels (log(10))')
plt.xlabel('Density')
logger.info("set labels\n")
plotFileName = "map-density-plot-mpl.svg"
plt.savefig(plotFileName, format="svg")
logger.info("saved figure\n")
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def testAnnotLigandMapCalc(self):
"""Test create non-polymer local density maps --"""
logger.info("\nStarting")
try:
for pdbId in ["3of4"]:
testFileXyz = pdbId + ".cif"
testFileSf = pdbId + "-sf.cif"
#
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
dp.setDebugMode(flag=True)
xyzPath = os.path.join(self.__testFilePath, testFileXyz)
sfPath = os.path.join(self.__testFilePath, testFileSf)
#
outDataPath = os.path.join(self.__tmpPath, "np-cc-maps")
outIndexPath = os.path.join(self.__tmpPath, "np-cc-maps", "np-cc-maps-index.cif")
#
dp.imp(xyzPath)
dp.addInput(name="sf_file_path", value=sfPath)
dp.addInput(name="output_data_path", value=outDataPath)
dp.addInput(name="output_index_path", value=outIndexPath)
dp.op("annot-make-ligand-maps")
dp.expLog(pdbId + "-annot-make-ligand-maps.log")
#
if False: # pylint: disable=using-constant-test
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
dp.setDebugMode(flag=True)
xyzPath = os.path.join(self.__testFilePath, testFileXyz)
sfPath = os.path.join(self.__testFilePath, testFileSf)
#
outDataPath = os.path.join(self.__tmpPath, "np-cc-omit-maps")
outIndexPath = os.path.join(self.__tmpPath, "np-cc-omit-maps", "np-cc-omit-maps-index.cif")
#
dp.imp(xyzPath)
dp.addInput(name="omit_map", value=True)
dp.addInput(name="sf_file_path", value=sfPath)
dp.addInput(name="output_data_path", value=outDataPath)
dp.addInput(name="output_index_path", value=outIndexPath)
dp.op("annot-make-ligand-maps")
dp.expLog(pdbId + "-annot-make-ligand-omit-maps.log")
#
# This application
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testAnnotGetCorresInfo(self):
""" Test running GetCorresInfo to get correspondance info -
"""
logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
of = os.path.join(self.__tmpPath, "annot-get-corres-info-check.cif")
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
dp.setDebugMode(True)
inpPath = os.path.join(self.__testFilePath, self.__testFileAnnotSite)
dp.imp(inpPath)
dp.op("annot-get-corres-info")
dp.expLog(os.path.join(self.__tmpPath, "annot-get-corres-info-check-pdbx.log"))
dp.exp(of)
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
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()
def testUploadShiftOneCheck(self):
""" Test upload check of one CS file --- upload single file
"""
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)
dp.setDebugMode(flag=True)
inpPath = os.path.join(self.__testFilePath, self.__testFileStarCs)
outPath = "output-cs-file-full.cif"
chkPath = "cs-diag-upload-check-1.cif"
dp.addInput(name="chemical_shifts_file_path_list", value=[inpPath])
dp.addInput(name="chemical_shifts_auth_file_name_list", value=['cs_file_1'])
dp.addInput(name="chemical_shifts_upload_check_file_path", value=chkPath)
dp.op("annot-chem-shifts-upload-check")
dp.expLog("annot-chem-shifts-upload-check.log")
dp.exp(outPath)
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def testChemicalShiftCoordinateCheck(self):
""" Test upload check of one CS file --- Using a PDB Archive STAR file -- (Does not work)
"""
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)
dp.setDebugMode(flag=True)
inpPath = os.path.join(self.__testFilePath, self.__testFileStarCs)
xyzPath = os.path.abspath(os.path.join(self.__testFilePath, self.__testFileNmrModel))
outPath = "output-cs-file.cif"
chkPath = "cs-diag-atom-name-check.cif"
dp.imp(inpPath)
dp.addInput(name="coordinate_file_path", value=xyzPath)
dp.addInput(name="chemical_shifts_coord_check_file_path", value=chkPath)
dp.op("annot-chem-shifts-atom-name-check")
dp.expLog("annot-chem-shifts-atom-name-check.log")
dp.exp(outPath)
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
