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)
curContainer.append(aCat)
myDataList.append(curContainer)
ofh = open("test-output-1.cif", "w")
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
#
#
# Read and update the data -
#
myDataList = []
ifh = open("test-output-1.cif", "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 xrange(0, myCat.getRowCount()):
myCat.setValue('some value', 'ref_mon_id', iRow)
myCat.setValue(100, 'ref_mon_num', iRow)
ofh = open("test-output-2.cif", "w")
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
#
except:
traceback.print_exc(file=self.lfh)
self.fail()
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)
curContainer.append(aCat)
myDataList.append(curContainer)
ofh = open("test-output-1.cif", "w")
pdbxW=PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
#
#
# Read and update the data -
#
myDataList=[]
ifh = open("test-output-1.cif", "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 xrange(0,myCat.getRowCount()):
myCat.setValue('some value', 'ref_mon_id',iRow)
myCat.setValue(100, 'ref_mon_num',iRow)
ofh = open("test-output-2.cif", "w")
pdbxW=PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
#
except:
traceback.print_exc(file=self.lfh)
self.fail()
def open_cif(cif_file):
""" Assumes a mmCif file and returns a data block used for subsequent procedures """
# The "usual" procedure to open a mmCIF with pdbX/mmCIF
with open(cif_file) as cif_fh:
data = []
reader = PdbxReader(cif_fh)
reader.read(data)
block = data[0]
return block
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 = "test-simple.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 open_cif(self):
""" Assumes a mmCif file and returns a data block used for subsequent procedures. """
# The "usual" procedure to open a mmCIF with pdbX/mmCIF
try:
with open(self.cif_path) as cif_fh:
data = []
reader = PdbxReader(cif_fh)
reader.read(data)
return data[0]
except:
print "! Unexpected error during open_cif:", sys.exc_info()[0], in_file
return None
def open_cif(self):
""" Assumes a mmCif file and returns a data block used for subsequent procedures. """
# The "usual" procedure to open a mmCIF with pdbX/mmCIF
with open(self.cif_path) as cif_fh:
data = []
reader = PdbxReader(cif_fh)
reader.read(data)
if len(data) == 0:
return None
else:
return data[0]
def open_cif(self):
""" Assumes a mmCif file and returns a data block used for subsequent procedures. """
# The "usual" procedure to open a mmCIF with pdbX/mmCIF
with open(self.cif_path) as cif_fh:
data = []
reader = PdbxReader(cif_fh)
reader.read(data)
if len(data) == 0:
return None
else:
return data[0]
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="test-simple.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 testReadBigDataFile(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.pathBigPdbxDataFile, "r")
pRd=PdbxReader(ifh)
pRd.read(myDataList)
ifh.close()
except:
traceback.print_exc(file=sys.stderr)
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=self.lfh)
self.fail()
def open_cif(self):
""" Assumes a mmCIF or gzipped mmCIF file and returns a data block used for subsequent procedures. """
# The "usual" procedure to open a mmCIF with pdbX/mmCIF
data = []
try:
with gzip.open(self.cif_path) as cif_fh:
reader = PdbxReader(cif_fh)
reader.read(data)
except IOError:
with open(self.cif_path) as cif_fh:
reader = PdbxReader(cif_fh)
reader.read(data)
if len(data) == 0:
return None
else:
return data[0]