def testReadMapHeaderPygal(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)
#
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 len x %d len y %d \n" %
(len(x), len(logy)))
nL = int(len(x) / 10)
#
if False:
bar_chart = pygal.Bar(x_label_rotation=20,
show_minor_x_labels=False,
style=LightColorizedStyle)
bar_chart = pygal.Bar(x_label_rotation=20,
show_minor_x_labels=False,
style=LightGreenStyle)
bar_chart.title = 'Map density distribution'
bar_chart.x_labels = map(str, [int(t) for t in x])
bar_chart.x_labels_major = map(str, [int(t) for t in x[::nL]])
bar_chart.add('Voxels (log(10)', logy)
plotFileName = "map-density-plot-pygal.svg"
bar_chart.render_to_file(plotFileName)
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 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 rcsb2Pdbx(self,
inpPath,
outPath,
stripFlag=False,
stripEntityFlag=False):
""" RCSB CIF -> PDBx conversion (Using the smaller application in the annotation package)
"""
try:
dp = RcsbDpUtility(tmpPath=self.__sessionPath,
siteId=self.__siteId,
verbose=self.__verbose,
log=self.__lfh)
dp.imp(inpPath)
if stripFlag:
if stripEntityFlag:
dp.op("annot-rcsb2pdbx-strip-plus-entity")
else:
dp.op("annot-rcsb2pdbx-strip")
else:
dp.op("annot-rcsb2pdbx")
logPath = os.path.join(self.__sessionPath, "annot-rcsb2pdbx.log")
dp.expLog(logPath)
dp.exp(outPath)
if (not self.__debug):
dp.cleanup()
except:
traceback.print_exc(file=self.__lfh)
return False
#
return True
def testPisaAssemblyDownloadModelPdb(self):
"""
"""
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)
fPath = os.path.join(self.__testFilePath, self.__testFileCifPisa)
dp.imp(fPath)
dp.addInput(name="pisa_session_name", value="session_3re3_cif")
dp.op("pisa-analysis")
dp.expLog("pisa-anal-assembly-cif.log.gz")
dp.op("pisa-assembly-report-xml")
dp.exp("pisa-assembly-report-cif.xml")
dp.expLog("pisa-report-xml-cif.log.gz")
#
for assemId in ['1', '2', '3', '4', '5']:
dp.addInput(name="pisa_assembly_id", value=assemId)
oFileName = '3rer-assembly-' + assemId + '.pdb.gz'
oLogName = '3rer-assembly-' + assemId + '-pdb.log.gz'
dp.op("pisa-assembly-coordinates-pdb")
dp.exp(oFileName)
dp.expLog(oLogName)
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 rcsbEps2Pdbx(self,
inpPath,
outPath,
stripFlag=False,
stripEntityFlag=False):
""" RCSB CIFEPS -> PDBx conversion (This still requires using the full maxit application)
"""
try:
dp = RcsbDpUtility(tmpPath=self.__sessionPath,
siteId=self.__siteId,
verbose=self.__verbose,
log=self.__lfh)
dp.imp(inpPath)
if stripFlag:
if stripEntityFlag:
dp.op("annot-rcsbeps2pdbx-strip-plus-entity")
else:
dp.op("annot-rcsbeps2pdbx-strip")
else:
dp.op("annot-cif2cif")
logPath = os.path.join(self.__sessionPath,
"annot-rcsbeps2pdbx.log")
dp.expLog(logPath)
dp.exp(outPath)
if (not self.__debug):
dp.cleanup()
except:
traceback.print_exc(file=self.__lfh)
return False
#
return True
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 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 testPisaAssemblyDownloadModelPdb(self):
""" """
logger.info("\nStarting")
try:
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
fPath = os.path.join(self.__testFilePath, self.__testFileCifPisa)
dp.imp(fPath)
dp.addInput(name="pisa_session_name", value="session_3re3_cif")
dp.op("pisa-analysis")
dp.expLog("pisa-anal-assembly-cif.log.gz")
dp.op("pisa-assembly-report-xml")
dp.exp("pisa-assembly-report-cif.xml")
dp.expLog("pisa-report-xml-cif.log.gz")
#
for assemId in ["1", "2", "3", "4", "5"]:
dp.addInput(name="pisa_assembly_id", value=assemId)
oFileName = "3rer-assembly-" + assemId + ".pdb.gz"
oLogName = "3rer-assembly-" + assemId + "-pdb.log.gz"
dp.op("pisa-assembly-coordinates-pdb")
dp.exp(oFileName)
dp.expLog(oLogName)
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
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 testSpecialPosition(self):
"""Test for atom on special position"""
logger.info("\nStarting")
try:
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
#
# dp.setDebugMode(True)
#
inpPath = os.path.join(self.__testFilePath,
self.__testFileValidateXyz)
dp.imp(inpPath)
dp.op("annot-dcc-special-position")
dp.expLog("special-position.log")
dp.exp("special-position-output.log")
f = open("special-position-output.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-special-position")
dp.expLog("special-position2.log")
dp.exp("special-position-output2.log")
f = open("special-position-output2.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 testPisaAnalysisCif(self):
"""
"""
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)
cifPath = os.path.join(self.__testFilePath, self.__testFileCifPisa)
dp.imp(cifPath)
dp.addInput(name="pisa_session_name", value="session_test_cif")
dp.op("pisa-analysis")
dp.expLog("pisa-anal-cif.log.gz")
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def cif2Pdbx(self, inpPath, outPath):
"""CIF -> PDBx conversion (public subset with PDBid conversion)"""
try:
dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
dp.imp(inpPath)
dp.op("cif2pdbx-public")
logPath = os.path.join(self.__sessionPath, "annot-cif2pdbx.log")
dp.expLog(logPath)
dp.exp(outPath)
if not self.__debug:
dp.cleanup()
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
return False
#
return True
def testAnnotSecondaryStructure(self):
""" Calculate secondary structure for a complicated case where pro-motif will fail.
"""
logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
of = "annot-ss-" + self.__testFileAnnotSS + ".gz"
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
inpPath = os.path.join(self.__testFilePath, self.__testFileAnnotSS)
dp.imp(inpPath)
dp.op("annot-secondary-structure")
dp.expLog("annot-secondary-structure.log")
dp.exp(of)
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def rcsb2PdbxWithPdbId(self, inpPath, outPath):
"""RCSB CIF -> PDBx conversion (converting to PDB ID entry/datablock id.)"""
try:
dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
dp.imp(inpPath)
dp.op("annot-rcsb2pdbx-withpdbid")
logPath = os.path.join(self.__sessionPath, "annot-rcsb2pdbx.log")
dp.expLog(logPath)
dp.exp(outPath)
if not self.__debug:
dp.cleanup()
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
return False
#
return True
def testAnnotValidation(self):
""" Calculate geometrical validation -
"""
logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
of = "annot-validation-" + self.__testFileAnnotValidate + ".gz"
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
inpPath = os.path.join(self.__testFilePath, self.__testFileAnnotValidate)
dp.imp(inpPath)
dp.op("annot-validation")
dp.expLog("annot-validation.log")
dp.exp(of)
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def testAnnotLinkSSBond(self):
""" Calculate link and ss-bond features -
"""
logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
of = "annot-link-" + self.__testFileAnnotLink + ".gz"
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
inpPath = os.path.join(self.__testFilePath, self.__testFileAnnotLink)
dp.imp(inpPath)
dp.op("annot-link-ssbond")
dp.expLog("annot-link-ssbond.log")
dp.exp(of)
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def convert_em_volume(self, in_em_volume, out_binary_volume, working_dir):
logging.info("Converting EM maps to binary cif")
logging.debug(working_dir)
rdb = RcsbDpUtility(tmpPath=working_dir,
siteId=self.__site_id,
verbose=True)
rdb.imp(in_em_volume)
rdb.op("em-density-bcif")
rdb.exp(out_binary_volume)
rdb.cleanup()
if out_binary_volume:
if os.path.exists(out_binary_volume):
return True
return False
def testAnnotRepositionSolventPlusDerived(self):
""" Calculate distant solvent followed by computing key derived categories --
"""
logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
of = "annot-reposition-add-derived-" + self.__testFileAnnotSolvent
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
inpPath = os.path.join(self.__testFilePath, self.__testFileAnnotSolvent)
dp.imp(inpPath)
dp.op("annot-reposition-solvent-add-derived")
dp.expLog("annot-reposition-solvent-plus-derived.log")
dp.exp(of)
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def testPisaAnalysisPdb(self):
""" """
logger.info("\nStarting")
try:
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
pdbPath = os.path.join(self.__testFilePath, self.__testFilePdbPisa)
dp.imp(pdbPath)
dp.addInput(name="pisa_session_name", value="session_3re3_pdb")
dp.op("pisa-analysis")
dp.expLog("pisa-anal-pdb.log.gz")
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def cif2Pdb(self, inpPath, outPath):
"""CIF -> PDB conversion (Using the smaller application in the annotation package)"""
try:
dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
dp.imp(inpPath)
dp.op("annot-cif2pdb")
logPath = os.path.join(self.__sessionPath, "annot-cif2pdb.log")
dp.expLog(logPath)
dp.exp(outPath)
if not self.__debug:
dp.cleanup()
except: # noqa: E722 pylint: disable=bare-except
traceback.print_exc(file=self.__lfh)
return False
#
return True
def testAnnotRcsb2PdbxStrip(self):
""" RCSB CIF -> PDBx conversion (Using the smaller application in the annotation package)
"""
logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
of = "annot-rcsb2pdbx-strip-" + self.__testFileAnnotRcsb
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
inpPath = os.path.join(self.__testFilePath, self.__testFileAnnotRcsb)
dp.imp(inpPath)
dp.op("annot-rcsb2pdbx-strip")
dp.expLog("annot-rcsb2pdbx-strip.log")
dp.exp(of)
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def testAnnotBasePair(self):
"""Calculate base pairing"""
logger.info("\nStarting")
try:
of = "annot-base-pair-" + self.__testFileAnnotNA + ".gz"
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
inpPath = os.path.join(self.__testFilePath, self.__testFileAnnotNA)
dp.imp(inpPath)
dp.op("annot-base-pair-info")
dp.expLog("annot-base-pair.log")
dp.exp(of)
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testAnnotUpdateDepositorAssembly(self):
""" Update deposition provided assembly info into model (need better test example)
"""
logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
of = "annot-update-assembly-" + self.__testDepAssembly
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
inpPath = os.path.join(self.__testFilePath, self.__testDepAssembly)
dp.imp(inpPath)
dp.op("annot-update-dep-assembly-info")
dp.expLog("annot-update-dep-assembly.log")
dp.exp(of)
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def testPisaAssemblyReportXmlPdb(self):
"""
"""
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)
fPath = os.path.join(self.__testFilePath, self.__testFilePdbPisa)
dp.imp(fPath)
dp.addInput(name="pisa_session_name", value="session_3re3_cif")
dp.op("pisa-analysis")
dp.expLog("pisa-anal-assembly-pdb.log.gz")
dp.op("pisa-assembly-report-xml")
dp.exp("pisa-assembly-report-pdb.xml")
dp.expLog("pisa-report-xml-pdb.log.gz")
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def testAnnotRepositionSolvent(self):
"""Calculate distant solvent"""
logger.info("\nStarting")
try:
of = "annot-reposition-" + self.__testFileAnnotSolvent
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
inpPath = os.path.join(self.__testFilePath,
self.__testFileAnnotSolvent)
dp.imp(inpPath)
dp.op("annot-reposition-solvent")
dp.expLog("annot-reposition-solvent.log")
dp.exp(of)
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testAnnotCisPeptide(self):
"""Calculate cis-peptide linkages -"""
logger.info("\nStarting")
try:
of = "annot-link-" + self.__testFileAnnotCisPeptide + ".gz"
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
inpPath = os.path.join(self.__testFilePath,
self.__testFileAnnotCisPeptide)
dp.imp(inpPath)
dp.op("annot-cis-peptide")
dp.expLog("annot-cis-peptide.log")
dp.exp(of)
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testAnnotConsolidatedTasksWithTopology(self):
""" Calculate annotation tasks in a single step including supporting topology data.
"""
logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
of = "annot-consolidated-top-" + self.__testFileAnnotSS + ".gz"
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
inpPath = os.path.join(self.__testFilePath, self.__testFileAnnotSS)
dp.imp(inpPath)
topPath = os.path.abspath(os.path.join(self.__testFilePath, self.__testFileAnnotSSTop))
dp.addInput(name="ss_topology_file_path", value=topPath)
dp.op("annot-consolidated-tasks")
dp.expLog("annot-consolidated-w-top.log")
dp.exp(of)
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def testAnnotSecondaryStructureWithTopology(self):
""" Calculate secondary structure with a supporting topology file.
"""
logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
of = "annot-ss-with-top-" + self.__testFileAnnotSS + ".gz"
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
inpPath = os.path.join(self.__testFilePath, self.__testFileAnnotSS)
dp.imp(inpPath)
topPath = os.path.abspath(os.path.join(self.__testFilePath, self.__testFileAnnotSSTop))
dp.addInput(name="ss_topology_file_path", value=topPath)
dp.op("annot-secondary-structure")
dp.expLog("annot-secondary-structure-w-top.log")
dp.exp(of)
dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
