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 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 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 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 testPisaAssemblyMergeModelCif(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)
assignPath = os.path.join(self.__testFilePath, "3rer_assembly_assign_P1.cif")
dp.imp(fPath)
dp.addInput(name="pisa_session_name", value="session_3re3-cif")
dp.op("pisa-analysis")
dp.op("pisa-assembly-report-xml")
dp.exp("pisa-assembly-report-cif.xml")
#
cifPath = os.path.join(self.__testFilePath, self.__testFileCifPisa)
dp.imp(cifPath)
#
# assignmentFile = self.__inputParamDict['pisa_assembly_assignment_file_path']
#
dp.addInput(name="pisa_assembly_file_path", value="pisa-assembly-report-cif.xml", type="file")
dp.addInput(name="pisa_assembly_assignment_file_path", value=assignPath, type="file")
dp.op("pisa-assembly-merge-cif")
dp.exp("3rer-updated.cif.gz")
dp.expLog("3rer-updated-cif.log.gz")
# 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 __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 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 testAnnotSiteAndMerge(self):
"""Calculate site environment"""
logger.info("\nStarting")
try:
of = "annot-site-" + self.__testFileAnnotSite # +".gz"
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
inpPath = os.path.join(self.__testFilePath,
self.__testFileAnnotSite)
dp.imp(inpPath)
dp.addInput(name="block_id", value=self.__testIdAnnotSite)
dp.op("annot-site")
dp.expLog("annot-site.log")
dp.exp(of)
inpPath = os.path.join(self.__testFilePath,
self.__testFileAnnotSite)
dp.imp(inpPath)
dp.addInput(name="site_info_file_path", value=of, type="file")
dp.op("annot-merge-struct-site")
dp.exp("annot-site-updated.cif.gz")
dp.expLog("annot-site-updated-cif.log.gz")
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testEm2EmSpider(self):
""" Test mapfix utility
"""
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.__testMapSpider)
of = self.__testMapSpider + "-spider-cnv.map"
dp.imp(inpPath)
pixelSize = 2.54
dp.addInput(name="pixel-spacing-x", value=pixelSize)
dp.addInput(name="pixel-spacing-y", value=pixelSize)
dp.addInput(name="pixel-spacing-z", value=pixelSize)
dp.op("em2em-spider")
dp.expLog("em2em-spider.log")
dp.exp(of)
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def testMapFixRemote(self):
""" Test mapfix utility
"""
self.__lfh.write(
"\nStarting %s %s\n" %
(self.__class__.__name__, sys._getframe().f_code.co_name))
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
#
inpPath = os.path.join(self.__testFilePath, self.__testMapNormal)
of = os.path.join(self.__tmpPath, self.__testMapNormal + "-fix.map")
dp.imp(inpPath)
pixelSize = 2.54
#dp.addInput(name="pixel-spacing-x", value=pixelSize)
#dp.addInput(name="pixel-spacing-y", value=pixelSize)
#dp.addInput(name="pixel-spacing-z", value=pixelSize)
dp.addInput(name="input_map_file_path", value=inpPath)
dp.addInput(name="output_map_file_path", value=of)
dp.addInput(name="label", value='test')
dp.addInput(name="voxel", value='{0} {0} {0}'.format(pixelSize))
# dp.setRunRemote()
ret = dp.op("deposit-update-map-header-in-place")
dp.expLog(os.path.join(self.__tmpPath, "mapfix-big.log"))
dp.exp(of)
# dp.cleanup()
self.assertTrue(ret == 0)
self.assertTrue(os.path.exists(of))
def test_AnnotMergeRemote(self):
""" Test of updating geometrical validation diagnostics -
"""
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)
testFileValidateXyz = pdbId + ".cif"
xyzPath = os.path.abspath(
os.path.join(self.__testFilePath, testFileValidateXyz))
dp = RcsbDpUtility(tmpPath=self.__tmpPath,
siteId=self.__siteId,
verbose=True)
of = os.path.join(self.__tmpPath, "annot-merge-xyz-remote.cif")
dp.imp(xyzPath)
dp.addInput(name="new_coordinate_file_path", value=xyzPath)
dp.addInput(name="new_coordinate_format", value='cif')
# dp.setRunRemote()
ret = dp.op("annot-merge-xyz")
dp.expLog(
os.path.join(self.__tmpPath, "annot-merge-xyz-remote.log"))
dp.exp(of)
# dp.cleanup()
self.assertTrue(ret == 0)
self.assertTrue(os.path.exists(of))
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 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 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 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 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 testCifCheck(self):
""" """
logger.info("\nStarting")
try:
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
cifPath = os.path.join(self.__testFilePath, self.__testFileCif)
dp.imp(cifPath)
dp.op("check-cif")
dp.exp("check-cif-diags.txt")
dp.expLog("check-cif.log")
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testCifToPdb(self):
""" """
logger.info("\nStarting")
try:
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
cifPath = os.path.join(self.__testFilePath, self.__testFileCif)
dp.imp(cifPath)
dp.op("cif2pdb")
dp.exp("myTest1.pdb.gz")
dp.expLog("myLog1.log.gz")
# 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.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)
if out_binary_volume:
if os.path.exists(out_binary_volume):
return True
return False
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 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 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 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 testCifCheckExt(self):
""" """
logger.info("\nStarting")
try:
for name in ["deposit", "archive_current", "archive_next"]:
dp = RcsbDpUtility(tmpPath=self.__tmpPath, siteId=self.__siteId, verbose=True)
cifPath = os.path.join(self.__testFilePath, self.__testFileCif)
dp.imp(cifPath)
dp.addInput(name="dictionary", value=name)
dp.op("check-cif-ext")
dp.exp("check-cif-diags-%s.txt" % name)
dp.expLog("check-cif-%s.log" % name)
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
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 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 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 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
