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())