C00 = Atom('C') C01 = Atom('C') C02 = Atom('C') C03 = Atom('C') C04 = Atom('C') C05 = Atom('C') C06 = Atom('C') C07 = Atom('C') C08 = Atom('C') C09 = Atom('C') C10 = Atom('C') C11 = Atom('C') C12 = Atom('C') C13 = Atom('C') C14 = Atom('C') C15 = Atom('C') C16 = Atom('C') C17 = Atom('C') C18 = Atom('C') C19 = Atom('C') C20 = Atom('C') C21 = Atom('C') C22 = Atom('C') C23 = Atom('C') C24 = Atom('C') C25 = Atom('C') C26 = Atom('C') C27 = Atom('C') C28 = Atom('C') C29 = Atom('C') b10 = Bond(C00, C01) b11 = Bond(C01, C02) b12 = Bond(C02, C03) b13 = Bond(C03, C04) b14 = Bond(C04, C05) b15 = Bond(C05, C00) b19 = Bond(C03, C06) b20 = Bond(C06, C07) b21 = Bond(C07, C08) b22 = Bond(C08, C09) b23 = Bond(C09, C10) b24 = Bond(C10, C11) b25 = Bond(C11, C06) b29 = Bond(C09, C12) b30 = Bond(C12, C13) b31 = Bond(C13, C14) b32 = Bond(C14, C15) b33 = Bond(C15, C16) b34 = Bond(C16, C17) b35 = Bond(C17, C12) b39 = Bond(C15, C18) b40 = Bond(C18, C19) b41 = Bond(C19, C20) b42 = Bond(C20, C21) b43 = Bond(C21, C22) b44 = Bond(C22, C23) b45 = Bond(C23, C18) b49 = Bond(C21, C24) b50 = Bond(C24, C25) b51 = Bond(C25, C26) b52 = Bond(C26, C27) b53 = Bond(C27, C28) b54 = Bond(C28, C29) b55 = Bond(C29, C24) b59 = Bond(C27, C00) amber_atom_type = {\ C00 : 'CA',C01 : 'CA',C02 : 'CA',C03 : 'CA',C04 : 'CA',C05 : 'CA',C06 : 'CA', C07 : 'CA',C08 : 'CA',C09 : 'CA',C10 : 'CA',C11 : 'CA',C12 : 'CA',C13 : 'CA', C14 : 'CA',C15 : 'CA',C16 : 'CA',C17 : 'CA',C18 : 'CA',C19 : 'CA',C20 : 'CA', C21 : 'CA',C22 : 'CA',C23 : 'CA',C24 : 'CA',C25 : 'CA',C26 : 'CA',C27 : 'CA', C28 : 'CA',C29 : 'CA'} amber_charge = {\ C00 : 0.0,C01 : 0.0,C02 : 0.0,C03 : 0.0,C04 : 0.0,C05 : 0.0,C06 : 0.0, C07 : 0.0,C08 : 0.0,C09 : 0.0,C10 : 0.0,C11 : 0.0,C12 : 0.0,C13 : 0.0, C14 : 0.0,C15 : 0.0,C16 : 0.0,C17 : 0.0,C18 : 0.0,C19 : 0.0,C20 : 0.0, C21 : 0.0,C22 : 0.0,C23 : 0.0,C24 : 0.0,C25 : 0.0,C26 : 0.0,C27 : 0.0, C28 : 0.0,C29 : 0.0} dtube1a = Dihedral(C01, C02, C03, C06, 138.5*deg) dtube2a = Dihedral(C07, C08, C09, C12, 138.5*deg) dtube3a = Dihedral(C13, C14, C15, C18, 138.5*deg) dtube4a = Dihedral(C19, C20, C21, C24, 138.5*deg) dtube5a = Dihedral(C25, C26, C27, C00, 138.5*deg) dtube1b = Dihedral(C02, C03, C06, C07, 0*deg) dtube2b = Dihedral(C08, C09, C12, C13, 0*deg) dtube3b = Dihedral(C14, C15, C18, C19, 0*deg) dtube4b = Dihedral(C20, C21, C24, C25, 0*deg) dtube5b = Dihedral(C26, C27, C00, C01, 0*deg) dtube1c = Dihedral(C03, C06, C07, C08, -138.5*deg) dtube2c = Dihedral(C09, C12, C13, C14, -138.5*deg) dtube3c = Dihedral(C15, C18, C19, C20, -138.5*deg) dtube4c = Dihedral(C21, C24, C25, C26, -138.5*deg) dtube5c = Dihedral(C27, C00, C01, C02, -138.5*deg) da11 = Dihedral(C01, C02, C03, C04, 0*deg) da12 = Dihedral(C02, C03, C04, C05, 0*deg) da13 = Dihedral(C03, C04, C05, C00, 0*deg) da14 = Dihedral(C04, C05, C00, C01, 0*deg) da21 = Dihedral(C07, C08, C09, C10, 0*deg) da22 = Dihedral(C08, C09, C10, C11, 0*deg) da23 = Dihedral(C09, C10, C11, C06, 0*deg) da24 = Dihedral(C10, C11, C06, C07, 0*deg) da31 = Dihedral(C13, C14, C15, C16, 0*deg) da32 = Dihedral(C14, C15, C16, C17, 0*deg) da33 = Dihedral(C15, C16, C17, C12, 0*deg) da34 = Dihedral(C16, C17, C12, C13, 0*deg) da41 = Dihedral(C19, C20, C21, C22, 0*deg) da42 = Dihedral(C20, C21, C22, C23, 0*deg) da43 = Dihedral(C21, C22, C23, C18, 0*deg) da44 = Dihedral(C22, C23, C18, C19, 0*deg) da50 = Dihedral(C24, C25, C26, C27, 0*deg) da51 = Dihedral(C25, C26, C27, C28, 0*deg) da52 = Dihedral(C26, C27, C28, C29, 0*deg) da53 = Dihedral(C27, C28, C29, C24, 0*deg) da54 = Dihedral(C28, C29, C24, C25, 0*deg) dC01 = DanglingBond(C01, Dihedral(C05,C00,C01,None,180*deg)) dC02 = DanglingBond(C02, Dihedral(None,C02,C01,C00,180*deg)) dC04 = DanglingBond(C04, Dihedral(None,C04,C03,C02,180.0*deg)) dC05 = DanglingBond(C05, Dihedral(None,C05,C00,C01,180*deg)) dC07 = DanglingBond(C07, Dihedral(C03,C06,C07,None,40.9999921286*deg)) dC08 = DanglingBond(C08, Dihedral(C06,C07,C08,None,180*deg)) dC10 = DanglingBond(C10, Dihedral(None,C10,C09,C08,180*deg)) dC11 = DanglingBond(C11, Dihedral(None,C11,C06,C03,-36.8402441955*deg)) dC13 = DanglingBond(C13, Dihedral(None,C13,C12,C09,41*deg)) dC14 = DanglingBond(C14, Dihedral(C12,C13,C14,None,180*deg)) dC16 = DanglingBond(C16, Dihedral(None,C16,C15,C14,180*deg)) dC17 = DanglingBond(C17, Dihedral(C09,C12,C17,None,-37.0687351463*deg)) dC19 = DanglingBond(C19, Dihedral(None,C19,C18,C15,41*deg)) dC20 = DanglingBond(C20, Dihedral(C18,C19,C20,None,180*deg)) dC22 = DanglingBond(C22, Dihedral(C20,C21,C22,None,180*deg)) dC23 = DanglingBond(C23, Dihedral(None,C23,C18,C15,-38.47048891*deg)) dC25 = DanglingBond(C25, Dihedral(C21,C24,C25,None,27.0741411323*deg)) dC26 = DanglingBond(C26, Dihedral(C24,C25,C26,None,175.608887269*deg)) dC28 = DanglingBond(C28, Dihedral(C26,C27,C28,None,169.012703255*deg)) dC29 = DanglingBond(C29, Dihedral(C21,C24,C29,None,-26.9128929845*deg)) hook1 = Hook(None,[dC05, dC04, dC11, dC10, dC17, dC16, dC23, dC22, dC29, dC28]) hook2 = Hook(None,[dC02, dC07, dC08, dC13, dC14, dC19, dC20, dC25, dC26, dC01])