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 pdbx2Assemblies(self, idCode, inpFilePath, outPath=".", indexFilePath=None):
"""Create model assemby files from input PDBx model file."""
try:
pdbxPath = inpFilePath
logPath = os.path.join(self.__sessionPath, "pdbx-assembly.log")
# indexFilePath=os.path.join(self.__sessionPath,"pdbx-assembly-index.txt")
#
dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
dp.imp(pdbxPath)
if idCode is not None:
dp.addInput(name="deposition_data_set_id", value=idCode, type="param")
if indexFilePath is not None:
dp.addInput(name="index_file_path", value=indexFilePath, type="param")
dp.op("annot-gen-assem-pdbx")
dp.expLog(logPath)
pthList = dp.getResultPathList()
# wrkPath = dp.getWorkingDir()
for pth in pthList:
if os.access(pth, os.R_OK):
(_t, fn) = os.path.split(pth)
shutil.copyfile(pth, os.path.join(outPath, fn))
# if (not self.__debug):
# dp.cleanup()
#
if self.__verbose:
self.__lfh.write("+DataFileAdapter.pdbx2Assemblies() - input model file path: %s\n" % inpFilePath)
self.__lfh.write("+DataFileAdapter.pdbx2Assemblies() - assembly output paths: %r\n" % pthList)
return True
except: # noqa: E722 pylint: disable=bare-except
self.__lfh.write("+DataFileAdapter.pdbx2Assemblies() - failing for input file path %s output path %s\n" % (inpFilePath, outPath))
traceback.print_exc(file=self.__lfh)
return False
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 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 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 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 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 testAnnotSiteAndMerge(self):
""" Calculate site environment
"""
logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
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 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 testAnnotLigandMapCalc(self):
""" Test create density maps --
"""
logger.info("\nStarting %s %s\n" % (self.__class__.__name__, sys._getframe().f_code.co_name))
try:
for pdbId in ['3of4']:
# 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)
outMapPath = '.'
outMapPathFull = os.path.abspath(outMapPath)
#
dp.imp(xyzPath)
dp.addInput(name="sf_file_path", value=sfPath)
dp.addInput(name="output_map_file_path", value=outMapPathFull)
dp.op("annot-make-ligand-maps")
dp.expLog(pdbId + "-annot-make-ligand-maps.log")
# dp.expList(dstPathList=[of2fofc,offofc])
# dp.cleanup()
except Exception as e:
logger.exception("Failing with %s" % str(e))
self.fail()
def testAnnotValidateListXrayTest(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:
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 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 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 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 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 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 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 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 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 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 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 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 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()
