def __init__(self, filename, recSpecs): PdbParser.__init__(self, filename) assert isinstance(recSpecs, AtomRecFieldSpecs) self.recSpecs = recSpecs # what type of parsing, by column or by index self.specType = recSpecs.specType self.atomCounter = 0 # what about model??? i think it's ok self.residueCounter = 0 self.HOHCounter = 0 self.chaincounter = 0