def testWriteDataFile(self):
"""Test case - write data file
"""
try:
#
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((1, 2, 3, 4, "55555555555555555555555555555555555555555555", 6, 7))
aCat.append((1, 2, 3, 4, "5555", 6, 7))
aCat.append((1, 2, 3, 4, "5555555555", 6, 7))
aCat.append((1, 2, 3, 4, "5", 6, 7))
curContainer.append(aCat)
myDataList.append(curContainer)
with open(self.__pathOutputFile1, "w") as ofh:
pdbxW = PdbxWriter(ofh)
pdbxW.setAlignmentFlag(flag=True)
pdbxW.write(myDataList)
self.assertEqual(len(myDataList), 1)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def __writeFile(
self,
ofh,
containerList,
maxLineLength=900,
columnAlignFlag=True,
lastInOrder=None,
selectOrder=None,
useStopTokens=False,
formattingStep=None,
enforceAscii=False,
cnvCharRefs=False,
):
"""Internal method mapping arguments to PDBxWriter API."""
#
pdbxW = PdbxWriter(ofh)
pdbxW.setUseStopTokens(flag=useStopTokens)
pdbxW.setMaxLineLength(numChars=maxLineLength)
pdbxW.setAlignmentFlag(flag=columnAlignFlag)
pdbxW.setRowPartition(numParts=formattingStep)
pdbxW.setConvertCharRefs(flag=cnvCharRefs)
pdbxW.setSetEnforceAscii(enforceAscii)
pdbxW.write(containerList,
lastInOrder=lastInOrder,
selectOrder=selectOrder)
def _createfile1(pathout):
my_data_list = []
cur_container = DataContainer("myblock")
acat = DataCategory("pdbx_item_enumeration")
acat.appendAttribute("name")
acat.appendAttribute("value")
acat.appendAttribute("detail")
acat.append(('1', '2', '3'))
cur_container.append(acat)
acat = DataCategory("exptl")
acat.appendAttribute('absorpt_coefficient_mu')
acat.appendAttribute('entry_id')
acat.appendAttribute('method')
acat.appendAttribute('details')
acat.append(('?', 'D_12345', 'X-RAY DIFFRACTION', 'some details'))
cur_container.append(acat)
acat = DataCategory("struct")
acat.appendAttribute('title')
acat.appendAttribute('pdbx_descriptor')
acat.append(('Start title', 'Start Descriptor'))
cur_container.append(acat)
my_data_list.append(cur_container)
# Second block
cur_container = DataContainer("secondblock")
acat = DataCategory("pdbx_item_enumeration")
acat.appendAttribute("name")
acat.appendAttribute("value")
acat.appendAttribute("detail")
acat.append(('3', '2', '1'))
cur_container.append(acat)
my_data_list.append(cur_container)
with open(pathout, "w") as ofh:
pdbxw = PdbxWriter(ofh)
pdbxw.setAlignmentFlag(flag=True)
pdbxw.write(my_data_list)
def _createfile1(pathout):
my_data_list = []
cur_container = DataContainer("myblock")
acat = DataCategory("pdbx_item_enumeration")
acat.appendAttribute("name")
acat.appendAttribute("value")
acat.appendAttribute("detail")
acat.append(("1", "2", "3"))
cur_container.append(acat)
acat = DataCategory("exptl")
acat.appendAttribute("absorpt_coefficient_mu")
acat.appendAttribute("entry_id")
acat.appendAttribute("method")
acat.appendAttribute("details")
acat.append(("?", "D_12345", "X-RAY DIFFRACTION", "some details"))
cur_container.append(acat)
acat = DataCategory("struct")
acat.appendAttribute("title")
acat.appendAttribute("pdbx_descriptor")
acat.append(("Start title", "Start Descriptor"))
cur_container.append(acat)
my_data_list.append(cur_container)
# Second block
cur_container = DataContainer("secondblock")
acat = DataCategory("pdbx_item_enumeration")
acat.appendAttribute("name")
acat.appendAttribute("value")
acat.appendAttribute("detail")
acat.append(("3", "2", "1"))
cur_container.append(acat)
my_data_list.append(cur_container)
with open(pathout, "w") as ofh:
pdbxw = PdbxWriter(ofh)
pdbxw.setAlignmentFlag(flag=True)
pdbxw.write(my_data_list)
def _createfile2(pathout):
my_data_list = []
cur_container = DataContainer("test")
acat = DataCategory("new")
acat.appendAttribute("item")
acat.append(('1',))
cur_container.append(acat)
acat = DataCategory("second_category")
acat.appendAttribute('row')
acat.appendAttribute('rowb')
acat.append(('1', '2'))
cur_container.append(acat)
acat = DataCategory("third")
acat.appendAttribute('id')
acat.appendAttribute('val')
acat.append(('1', 'a'))
acat.append(('2', 'b'))
acat.append(('3', 'c'))
cur_container.append(acat)
acat = DataCategory("exptl")
acat.appendAttribute('method')
acat.appendAttribute('entry_id')
acat.append(('NEW', 'something'))
cur_container.append(acat)
acat = DataCategory("struct")
acat.appendAttribute('new')
acat.appendAttribute('pdbx_descriptor')
acat.append(('Something to add', 'Override descriptor'))
cur_container.append(acat)
my_data_list.append(cur_container)
with open(pathout, "w") as ofh:
pdbxw = PdbxWriter(ofh)
pdbxw.setAlignmentFlag(flag=True)
pdbxw.write(my_data_list)
def _createfile2(pathout):
my_data_list = []
cur_container = DataContainer("test")
acat = DataCategory("new")
acat.appendAttribute("item")
acat.append(("1",))
cur_container.append(acat)
acat = DataCategory("second_category")
acat.appendAttribute("row")
acat.appendAttribute("rowb")
acat.append(("1", "2"))
cur_container.append(acat)
acat = DataCategory("third")
acat.appendAttribute("id")
acat.appendAttribute("val")
acat.append(("1", "a"))
acat.append(("2", "b"))
acat.append(("3", "c"))
cur_container.append(acat)
acat = DataCategory("exptl")
acat.appendAttribute("method")
acat.appendAttribute("entry_id")
acat.append(("NEW", "something"))
cur_container.append(acat)
acat = DataCategory("struct")
acat.appendAttribute("new")
acat.appendAttribute("pdbx_descriptor")
acat.append(("Something to add", "Override descriptor"))
cur_container.append(acat)
my_data_list.append(cur_container)
with open(pathout, "w") as ofh:
pdbxw = PdbxWriter(ofh)
pdbxw.setAlignmentFlag(flag=True)
pdbxw.write(my_data_list)
def test_write_data_file(self, writer_paths):
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(
(1, 2, 3, 4, '55555555555555555555555555555555555555555555', 6, 7))
aCat.append((1, 2, 3, 4, '5555', 6, 7))
aCat.append((1, 2, 3, 4, '5555555555', 6, 7))
aCat.append((1, 2, 3, 4, '5', 6, 7))
curContainer.append(aCat)
myDataList.append(curContainer)
with open(str(writer_paths['pathOutputFile1']), "w") as ofh:
pdbxW = PdbxWriter(ofh)
pdbxW.setAlignmentFlag(flag=True)
pdbxW.write(myDataList)
assert len(myDataList) == 1