Esempio n. 1
0
 def _read_bonds(self, f):
     """ Reads the bond stretching terms """
     self.bond_list = BondList()
     # Eat the next 3 lines
     f.readline()
     f.readline()
     f.readline()
     line = f.readline()
     for i in range(self.pointers['nbond']):
         try:
             int(line[0:6])
             at1 = int(line[9:15]) - 1
             at2 = int(line[15:21]) - 1
             self.bond_list.add(self.atom_list[at1], self.atom_list[at2],
                                line[40:50], line[50:60])
         except ValueError:
             raise TinkerError('Error parsing bonded term')
         line = f.readline()