C1 = Atom('C') C2 = Atom('C') C3 = Atom('C') C4 = Atom('C') C5 = Atom('C') C6 = Atom('C') C7 = Atom('C') C8 = Atom('C') b12 = Bond(C1,C2) b23 = Bond(C2,C3) b26 = Bond(C2,C6) b34 = Bond(C3,C4) b48 = Bond(C4,C8) b56 = Bond(C5,C6) b67 = Bond(C6,C7) b78 = Bond(C7,C8) da1 = Dihedral(C1,C2,C3,C4,180*deg) da2 = Dihedral(C1,C2,C6,C5, 60*deg) da3 = Dihedral(C1,C2,C6,C7,180*deg) da4 = Dihedral(C3,C2,C6,C5,180*deg) da5 = Dihedral(C5,C6,C7,C8,180*deg) amber_atom_type = {C1: 'CT', C2: 'CT', C3: 'CT', C4: 'CT', C5: 'CT', C6: 'CT', C7: 'CT', C8: 'CT'} dC1a = DanglingBond(C1, Dihedral(C6,C2,C1,None, 60*deg)) dC1b = DanglingBond(C1, Dihedral(None,C1,C2,C3, 60*deg)) dC1c = DanglingBond(C1, Dihedral(C3,C2,C1,None,180*deg)) dC2a = DanglingBond(C2, Dihedral(C4,C3,C2,None,-60*deg)) dC3a = DanglingBond(C3, Dihedral(C1,C2,C3,None,-60*deg)) dC3b = DanglingBond(C3, Dihedral(C1,C2,C3,None, 60*deg)) dC4a = DanglingBond(C4, Dihedral(None,C4,C3,C2,60*deg)) dC4b = DanglingBond(C4, Dihedral(C2,C3,C4,None,180*deg)) dC5a = DanglingBond(C5, Dihedral(None,C5,C6,C7,180*deg)) dC5b = DanglingBond(C5, Dihedral(C2,C6,C5,None,-60*deg)) dC5c = DanglingBond(C5, Dihedral(C2,C6,C5,None,180*deg)) dC6a = DanglingBond(C6, Dihedral(None,C6,C2,C1,-60*deg)) dC7a = DanglingBond(C7, Dihedral(C4,C8,C7,None,180*deg)) dC7b = DanglingBond(C7, Dihedral(None,C7,C8,C4, 60*deg)) dC8a = DanglingBond(C8, Dihedral(C6,C7,C8,None,180*deg)) dC8b = DanglingBond(C8, Dihedral(None,C8,C7,C6, 60*deg)) hookup = Hook(None, [dC1a,dC3b,dC6a]) hookup_extra = Hook(None, [dC8b]) hookdown = Hook(None, [dC2a,dC4a,dC7b]) hookdown_extra = Hook(None, [dC5b]) hookwest = Hook(None, [dC1b,dC3a]) hookeast = Hook(None, [dC5c,dC7a]) hooknorth = Hook(None, [dC1c,dC5a]) hooksouth = Hook(None, [dC4b,dC8a])