name ='thymine'

N_1 = Atom('N')
C_6 = Atom('C')
H_6 = Atom('H')
C_5 = Atom('C')
C_7 = Atom('C')
H_71 = Atom('H')
H_72 = Atom('H')
H_73 = Atom('H')
C_4 = Atom('C')
O_4 = Atom('O')
N_3 = Atom('N')
H_3 = Atom('H')
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(C_7, C_5), Bond(H_71, C_7), Bond(H_72, C_7), Bond(H_73, C_7), Bond(C_4, C_5), Bond(O_4, C_4), Bond(N_3, C_4), Bond(H_3, N_3), Bond(C_2, N_3), Bond(O_2, C_2), Bond(C_2, N_1), ]

pdbmap = [('T', {"C6": C_6, "C7": C_7, "C4": C_4, "C5": C_5, "H71": H_71, "H73": H_73, "H72": H_72, "N3": N_3, "C2": C_2, "N1": N_1, "O2": O_2, "H3": H_3, "O4": O_4, "H6": H_6, })]
pdb_alternative = {'C5M': 'C7', 'H51': 'H71', 'H52': 'H72', 'H53': 'H73'}

amber_atom_type = {C_6: 'CM', C_7: 'CT', C_4: 'C', C_5: 'CM', H_71: 'HC', H_73: 'HC', H_72: 'HC', N_3: 'NA', C_2: 'C', N_1: 'N*', O_2: 'O', H_3: 'H', O_4: 'O', H_6: 'H4', }

