name ='cytosine'

N_1 = Atom('N')
C_6 = Atom('C')
H_6 = Atom('H')
C_5 = Atom('C')
H_5 = Atom('H')
C_4 = Atom('C')
N_4 = Atom('N')
H_41 = Atom('H')
H_42 = Atom('H')
N_3 = Atom('N')
C_2 = Atom('C')
O_2 = Atom('O')

bonds = [Bond(C_6, N_1), Bond(H_6, C_6), Bond(C_5, C_6), Bond(H_5, C_5), Bond(C_4, C_5), Bond(N_4, C_4), Bond(H_41, N_4), Bond(H_42, N_4), Bond(N_3, C_4), Bond(C_2, N_3), Bond(O_2, C_2), Bond(C_2, N_1), ]

pdbmap = [('C', {"C6": C_6, "H41": H_41, "H42": H_42, "C5": C_5, "C2": C_2, "C4": C_4, "N3": N_3, "N1": N_1, "N4": N_4, "O2": O_2, "H5": H_5, "H6": H_6, })]

amber_atom_type = {C_6: 'CM', H_41: 'H', H_42: 'H', C_5: 'CM', C_2: 'C', C_4: 'CA', N_3: 'NC', N_1: 'N*', N_4: 'N2', O_2: 'O', H_5: 'HA', H_6: 'H4', }

amber12_atom_type = amber_atom_type
