def testWriteDataFile(self):
"""Test case - write data file
"""
self.lfh.write("\nStarting %s %s\n" % (self.__class__.__name__,
sys._getframe().f_code.co_name))
try:
#
myDataList=[]
ofh = open("test-output.cif", "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])
aCat.append([7,6,5,4,3,2,1])
aCat.printIt()
curContainer.append(aCat)
curContainer.printIt()
#
myDataList.append(curContainer)
pdbxW=PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
except:
traceback.print_exc(file=self.lfh)
self.fail()
def testWriteDataFile(self):
"""Test case - write data file
"""
self.lfh.write(
"\nStarting %s %s\n" %
(self.__class__.__name__, sys._getframe().f_code.co_name))
try:
#
myDataList = []
ofh = open("test-output.cif", "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()
except:
traceback.print_exc(file=sys.stderr)
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 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 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 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 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 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 vis(argv):
# default parameters
color_file_name = None
missing_value = -1.0
discard_missing = False
# read arguments
try:
opts, args = getopt.getopt(argv[1:], "c:m:M")
except getopt.GetoptError as err:
sys.stderr.write("[E::" + __name__ + "] unknown command\n")
return 1
if len(args) == 0:
sys.stderr.write("Usage: dip-c vis [options] <in.3dg>\n")
sys.stderr.write("Options:\n")
sys.stderr.write(
" -c <color.txt> color by a list of locus-color pairs (tab-delimited: homolog, locus, color)\n"
)
sys.stderr.write(
" -m FLOAT color for particles that are missing from the color scheme ["
+ str(missing_value) + "]\n")
sys.stderr.write(
" -M discard particles that are missing from the color scheme\n\n"
)
sys.stderr.write("Output mmCIF format:\n")
sys.stderr.write(
" label_asym_id homolog name (e.g. \"1(mat)\")\n")
sys.stderr.write(
" label_comp_id locus // 1 Mb, 3 digits with leading zeros\n")
sys.stderr.write(" label_seq_id 1\n")
sys.stderr.write(
" label_atom_id locus % 1 Mb // 1 kb, 3 digits with leading zeros\n"
)
sys.stderr.write(" B_iso_or_equiv scalar color\n")
sys.stderr.write(" covale backbone bond\n")
return 1
num_color_schemes = 0
for o, a in opts:
if o == "-m":
missing_value = float(a)
elif o == "-c":
color_file_name = a
elif o == "-M":
discard_missing = True
# read 3DG file
g3d_data = file_to_g3d_data(open(args[0], "rb"))
g3d_data.sort_g3d_particles()
g3d_resolution = g3d_data.resolution()
sys.stderr.write(
"[M::" + __name__ + "] read a 3D structure with " +
str(g3d_data.num_g3d_particles()) + " particles at " +
("N.A." if g3d_resolution is None else str(g3d_resolution)) +
" bp resolution\n")
# read color file
color_data = {}
if not color_file_name is None:
color_file = open(color_file_name, "rb")
for color_file_line in color_file:
hom_name, ref_locus, color = color_file_line.strip().split("\t")
ref_locus = int(ref_locus)
color = float(color)
color_data[(hom_name, ref_locus)] = color
# open mmCIF file to write
myDataList = []
curContainer = DataContainer("myblock")
aCat = DataCategory("atom_site")
aCat.appendAttribute("group_PDB")
aCat.appendAttribute("type_symbol")
aCat.appendAttribute("id")
aCat.appendAttribute("label_asym_id")
aCat.appendAttribute("label_comp_id")
aCat.appendAttribute("label_seq_id")
aCat.appendAttribute("label_atom_id")
aCat.appendAttribute("Cartn_x")
aCat.appendAttribute("Cartn_y")
aCat.appendAttribute("Cartn_z")
aCat.appendAttribute("B_iso_or_equiv")
sCat = DataCategory("struct_conn")
sCat.appendAttribute("id")
sCat.appendAttribute("conn_type_id")
sCat.appendAttribute("ptnr1_label_asym_id")
sCat.appendAttribute("ptnr1_label_comp_id")
sCat.appendAttribute("ptnr1_label_seq_id")
sCat.appendAttribute("ptnr1_label_atom_id")
sCat.appendAttribute("ptnr2_label_asym_id")
sCat.appendAttribute("ptnr2_label_comp_id")
sCat.appendAttribute("ptnr2_label_seq_id")
sCat.appendAttribute("ptnr2_label_atom_id")
# write atoms
atom_id = 0
for g3d_particle in g3d_data.get_g3d_particles():
atom_id += 1
try:
color = color_data[(g3d_particle.get_hom_name(),
g3d_particle.get_ref_locus())]
except KeyError:
if discard_missing:
continue
color = missing_value
aCat.append(g3d_particle_to_atom_data(g3d_particle, atom_id, color))
# write backbond bonds
conn_id = 0
for g3d_particle_tuple in g3d_data.get_adjacent_g3d_particle_tuples(
g3d_resolution):
conn_id += 1
sCat.append(
g3d_particle_tuple_to_conn_data(g3d_particle_tuple, conn_id))
# write output
curContainer.append(sCat)
curContainer.append(aCat)
myDataList.append(curContainer)
pdbxW = PdbxWriter(sys.stdout)
pdbxW.write(myDataList)
return 0
inputPosString = inputPdbLineData[1].rjust(9, '0')
inputPosValue = int(inputPdbLineData[1])
inputPosList = [inputPosString[0:3], 1, inputPosString[3:6]]
# for using position as B factor
#inputBFactor = float(inputPdbLineData[1])/chrLengths[inputDipChr - 1]
# for using external bedgraph file as B factor
inputBFactor = 0
if (inputDipChr, inputPosValue) in bFactorData:
inputBFactor = bFactorData[(inputDipChr, inputPosValue)]
aCat.append(('HETATM', atomId, inputChrName, inputPosList[0],
inputPosList[1], inputPosList[2], inputPdbLineData[2],
inputPdbLineData[3], inputPdbLineData[4], inputBFactor))
atomId += 1
if inputChr == previousChr and inputPosValue - previousPosValue == resolution:
sCat.append(('covale', inputChrName, previousPosList[0],
previousPosList[1], previousPosList[2], inputChrName,
inputPosList[0], inputPosList[1], inputPosList[2]))
previousChr = inputChr
previousPosValue = inputPosValue
previousPosList = copy.copy(inputPosList)
curContainer.append(sCat)
curContainer.append(aCat)
myDataList.append(curContainer)
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
