def test_write_data_file(self):
""" Test writing CIF file """
myDataList = []
ofh = open(self.get_fn("test-output.cif", written=True), "w")
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((1, 2, 3, 4, 5, 6, 7))
aCat.append((1, 2, 3, 4, 5, 6, 7))
aCat.append((1, 2, 3, 4, 5, 6, 7))
aCat.append((1, 2, 3, 4, 5, 6, 7))
curContainer.append(aCat)
myDataList.append(curContainer)
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
self.assertTrue(
diff_files(
self.get_fn('test-output.cif', saved=True),
self.get_fn('test-output.cif', written=True),
))
def test_read_write_data_file(self):
"""Test case - data file read write test
"""
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()
def testReadWriteDataFile(self):
"""Test case - data file read write test
"""
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()
def test_update_data_file(self):
""" Test writing another CIF file """
# Create a initial data file --
#
myDataList = []
ofh = open(self.get_fn("test-output-1.cif", written=True), "w")
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((1, 2, 3, 4, 5, 6, 7))
aCat.append((1, 2, 3, 4, 5, 6, 7))
aCat.append((1, 2, 3, 4, 5, 6, 7))
aCat.append((1, 2, 3, 4, 5, 6, 7))
curContainer.append(aCat)
myDataList.append(curContainer)
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
self.assertTrue(
diff_files(self.get_fn('test-output-1.cif', saved=True),
self.get_fn('test-output-1.cif', written=True)))
#
# Read and update the data -
#
myDataList = []
ifh = open(self.get_fn("test-output-1.cif", written=True), "r")
pRd = PdbxReader(ifh)
pRd.read(myDataList)
ifh.close()
#
myBlock = myDataList[0]
dest = open(self.get_fn('test_write_1.txt', written=True), 'w')
myBlock.printIt(dest)
myCat = myBlock.getObj('pdbx_seqtool_mapping_ref')
myCat.printIt(dest)
dest.close()
for iRow in range(0, myCat.getRowCount()):
myCat.setValue('some value', 'ref_mon_id', iRow)
myCat.setValue(100, 'ref_mon_num', iRow)
ofh = open(self.get_fn("test-output-2.cif", written=True), "w")
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
self.assertTrue(
diff_files(self.get_fn('test-output-2.cif', saved=True),
self.get_fn('test-output-2.cif', written=True)))
self.assertTrue(
diff_files(self.get_fn('test_write_1.txt', saved=True),
self.get_fn('test_write_1.txt', written=True)))
def testWriteDataFile(self):
""" Test writing CIF file """
myDataList=[]
ofh = open(get_fn("test-output.cif", written=True), "w")
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((1,2,3,4,5,6,7))
aCat.append((1,2,3,4,5,6,7))
aCat.append((1,2,3,4,5,6,7))
aCat.append((1,2,3,4,5,6,7))
curContainer.append(aCat)
myDataList.append(curContainer)
pdbxW=PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
self.assertTrue(diff_files(get_saved_fn('test-output.cif'),
get_fn('test-output.cif', written=True)))
def testUpdateDataFile(self):
""" Test writing another CIF file """
# Create a initial data file --
#
myDataList=[]
ofh = open(get_fn("test-output-1.cif", written=True), "w")
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((1,2,3,4,5,6,7))
aCat.append((1,2,3,4,5,6,7))
aCat.append((1,2,3,4,5,6,7))
aCat.append((1,2,3,4,5,6,7))
curContainer.append(aCat)
myDataList.append(curContainer)
pdbxW=PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
self.assertTrue(diff_files(get_saved_fn('test-output-1.cif'),
get_fn('test-output-1.cif', written=True)))
#
# Read and update the data -
#
myDataList=[]
ifh = open(get_fn("test-output-1.cif", written=True), "r")
pRd=PdbxReader(ifh)
pRd.read(myDataList)
ifh.close()
#
myBlock=myDataList[0]
dest = open(get_fn('test_write_1.txt', written=True), 'w')
myBlock.printIt(dest)
myCat=myBlock.getObj('pdbx_seqtool_mapping_ref')
myCat.printIt(dest)
dest.close()
for iRow in range(0,myCat.getRowCount()):
myCat.setValue('some value', 'ref_mon_id',iRow)
myCat.setValue(100, 'ref_mon_num',iRow)
ofh = open(get_fn("test-output-2.cif", written=True), "w")
pdbxW=PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
self.assertTrue(diff_files(get_saved_fn('test-output-2.cif'),
get_fn('test-output-2.cif', written=True)))
self.assertTrue(diff_files(get_saved_fn('test_write_1.txt'),
get_fn('test_write_1.txt', written=True)))