def test09getAtomsFromSegment2(self):
pdbFileName = "../../pdbs/2J9N.pdb"
segmentFileName = "../../pdbs/2J9N_A_101_102.pdb"
chain = " A "
start = 101
stop = 102
startInsertion = ''
stopInsertion = ''
startOrder = True
stopOrder = True
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
segment =[]
#chain, start, stop, startInsertion, stopInsertion, startOder, stopOrder, model=0, onlyBackbone=False):
segment = pdb.getAtomsFromSegment(chain, start, stop, startInsertion, stopInsertion, startOrder, stopOrder)
assert segment is not None
file = open(segmentFileName,"w")
orderedKeys = segment.keys()
orderedKeys.sort()
for lineNumber in orderedKeys:
file.write("%s\n" %(segment[lineNumber].toString(),))
file.write("%s\n" % ("END"+77*" ",))
file.close()
def test05getAtomsFromSegment(self):
pdbFileName = "../../pdbs/1A00.pdb"
chain = " A "
start = 1
stop = 141
startInsertion = ''
stopInsertion = ''
startOrder = True
stopOrder = True
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
segments = pdb.getAtomsFromSegment(chain, start, stop, startInsertion, stopInsertion, startOrder, stopOrder)
assert segments is not None
for (lineNumber, atom) in segments.items():
print "[%d] = %s" %(lineNumber, atom.toString())
