def testUpdateDataFile(self):
"""Test case - update data file"""
self.lfh.write(
"\nStarting %s %s\n" %
(self.__class__.__name__, sys._getframe().f_code.co_name))
try:
# Create a initial data file --
#
myDataList = []
curContainer = DataContainer("myblock")
aCat = DataCategory("pdbx_seqtool_mapping_ref")
aCat.appendAttribute("ordinal")
aCat.appendAttribute("entity_id")
aCat.appendAttribute("auth_mon_id")
aCat.appendAttribute("auth_mon_num")
aCat.appendAttribute("pdb_chain_id")
aCat.appendAttribute("ref_mon_id")
aCat.appendAttribute("ref_mon_num")
aCat.append([9, 2, 3, 4, 5, 6, 7])
aCat.append([10, 2, 3, 4, 5, 6, 7])
aCat.append([11, 2, 3, 4, 5, 6, 7])
aCat.append([12, 2, 3, 4, 5, 6, 7])
# self.lfh.write("Assigned data category state-----------------\n")
# aCat.dumpIt(fh=self.lfh)
tmpf = tempname(suffix=".cif")
curContainer.append(aCat)
myDataList.append(curContainer)
ofh = open(tmpf, "w")
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
#
#
# Read and update the data -
#
myDataList = []
ifh = open(tmpf, "r")
pRd = PdbxReader(ifh)
pRd.read(myDataList)
ifh.close()
#
myBlock = myDataList[0]
myBlock.printIt()
myCat = myBlock.getObj("pdbx_seqtool_mapping_ref")
myCat.printIt()
for iRow in range(0, myCat.getRowCount()):
myCat.setValue("some value", "ref_mon_id", iRow)
myCat.setValue(100, "ref_mon_num", iRow)
ofh = open(tempname(suffix=".cif"), "w")
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
#
except:
traceback.print_exc(file=self.lfh)
self.fail()
def testSimpleInitialization(self):
"""Test case - Simple initialization of a data category and data block
"""
self.lfh.write(
"\nStarting %s %s\n" %
(self.__class__.__name__, sys._getframe().f_code.co_name))
try:
#
fn = tempname(suffix='.cif')
attributeNameList = [
'aOne', 'aTwo', 'aThree', 'aFour', 'aFive', 'aSix', 'aSeven',
'aEight', 'aNine', 'aTen'
]
rowList = [[1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10]]
nameCat = 'myCategory'
#
#
curContainer = DataContainer("myblock")
aCat = DataCategory(nameCat, attributeNameList, rowList)
aCat.printIt()
curContainer.append(aCat)
curContainer.printIt()
#
myContainerList = []
myContainerList.append(curContainer)
ofh = open(fn, "w")
pdbxW = PdbxWriter(ofh)
pdbxW.write(myContainerList)
ofh.close()
myContainerList = []
ifh = open(fn, "r")
pRd = PdbxReader(ifh)
pRd.read(myContainerList)
ifh.close()
for container in myContainerList:
for objName in container.getObjNameList():
name, aList, rList = container.getObj(objName).get()
self.lfh.write("Recovered data category %s\n" % name)
self.lfh.write("Attribute list %r\n" %
repr(aList))
self.lfh.write("Row list %r\n" %
repr(rList))
except:
traceback.print_exc(file=self.lfh)
self.fail()
def testReadSFDataFile(self):
"""Test case - read PDB structure factor data file and compute statistics on f/sig(f).
"""
self.lfh.write(
"\nStarting %s %s\n" %
(self.__class__.__name__, sys._getframe().f_code.co_name))
try:
#
myContainerList = []
ifh = open(self.pathSFDataFile, "r")
pRd = PdbxReader(ifh)
pRd.read(myContainerList)
c0 = myContainerList[0]
#
catObj = c0.getObj("refln")
if catObj is None:
return False
nRows = catObj.getRowCount()
#
# Get column name index.
#
itDict = {}
itNameList = catObj.getItemNameList()
for idxIt, itName in enumerate(itNameList):
itDict[str(itName).lower()] = idxIt
#
idf = itDict['_refln.f_meas_au']
idsigf = itDict['_refln.f_meas_sigma_au']
minR = 100
maxR = -1
sumR = 0
icount = 0
for row in catObj.getRowList():
try:
f = float(row[idf])
sigf = float(row[idsigf])
ratio = sigf / f
#self.lfh.write(" %f %f %f\n" % (f,sigf,ratio))
maxR = max(maxR, ratio)
minR = min(minR, ratio)
sumR += ratio
icount += 1
except:
continue
ifh.close()
self.lfh.write("f/sig(f) min %f max %f avg %f count %d\n" %
(minR, maxR, sumR / icount, icount))
except:
traceback.print_exc(file=sys.stderr)
self.fail()
def testReadDataFile(self):
"""Test case - read data file"""
self.lfh.write(
"\nStarting %s %s\n" %
(self.__class__.__name__, sys._getframe().f_code.co_name))
try:
#
myDataList = []
ifh = open(self.pathPdbxDataFile, "r")
pRd = PdbxReader(ifh)
pRd.read(myDataList)
ifh.close()
except:
traceback.print_exc(file=self.lfh)
self.fail()
def testReadWriteDataFile(self):
"""Test case - data file read write test"""
self.lfh.write(
"\nStarting %s %s\n"
% (self.__class__.__name__, sys._getframe().f_code.co_name)
)
try:
#
myDataList = []
ifh = open(self.pathPdbxDataFile, "r")
pRd = PdbxReader(ifh)
pRd.read(myDataList)
ifh.close()
ofh = open(self.pathOutputFile, "w")
pWr = PdbxWriter(ofh)
pWr.write(myDataList)
ofh.close()
except:
traceback.print_exc(file=sys.stderr)
self.fail()
