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') b50 = Bond(C29, C19) b51 = Bond(C28, C29) b52 = Bond(C10, C28) b53 = Bond(C27, C11) b54 = Bond(C26, C27) b55 = Bond(C12, C26) b56 = Bond(C25, C13) b57 = Bond(C24, C25) b58 = Bond(C14, C24) b59 = Bond(C23, C15) b60 = Bond(C22, C23) b61 = Bond(C16, C22) b62 = Bond(C21, C17) b63 = Bond(C20, C21) b64 = Bond(C18, C20) b65 = Bond(C09, C11) b66 = Bond(C12, C09) b67 = Bond(C08, C13) b68 = Bond(C14, C08) b69 = Bond(C07, C15) b70 = Bond(C16, C07) b71 = Bond(C06, C17) b72 = Bond(C18, C06) b73 = Bond(C05, C19) b74 = Bond(C10, C05) b75 = Bond(C03, C08) b76 = Bond(C04, C07) b77 = Bond(C06, C00) b78 = Bond(C19, C18) b79 = Bond(C16, C17) b80 = Bond(C14, C15) b81 = Bond(C12, C13) b82 = Bond(C10, C11) b83 = Bond(C02, C09) b84 = Bond(C01, C05) b85 = Bond(C04, C00) b86 = Bond(C03, C04) b87 = Bond(C02, C03) b88 = Bond(C01, C02) b89 = Bond(C00, C01) 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} dC20a = DanglingBond(C20, Dihedral(None,C20,C21,C17,144.856706984*deg)) dC21a = DanglingBond(C21, Dihedral(C06,C17,C21,None,140.709373064*deg)) dC22a = DanglingBond(C22, Dihedral(C15,C23,C22,None,142.938450372*deg)) dC23a = DanglingBond(C23, Dihedral(None,C23,C15,C07,141.400738744*deg)) dC24a = DanglingBond(C24, Dihedral(None,C24,C25,C13,142.649278885*deg)) dC25a = DanglingBond(C25, Dihedral(C08,C13,C25,None,142.1936735*deg)) dC26a = DanglingBond(C26, Dihedral(C11,C27,C26,None,143.723858851*deg)) dC27a = DanglingBond(C27, Dihedral(None,C27,C11,C09,141.162556228*deg)) dC28a = DanglingBond(C28, Dihedral(C19,C29,C28,None,143.120993932*deg)) dC29a = DanglingBond(C29, Dihedral(C05,C19,C29,None,142.499445663*deg)) alldbs = [dC20a, dC21a, dC22a, dC23a, dC24a, dC25a, dC26a, dC27a, dC28a, dC29a] hook1 = Hook(None, alldbs) alldbs2 = alldbs[1:] + [alldbs[0]] # rotate by 1 alldbs2.reverse() hook2 = Hook(None, alldbs2) configurations = { 'default' : Cartesian({ C00 : (0.022426609094483*Ang, 1.8752544214456*Ang, -3.4007996639713*Ang), C01 : (1.1512995918111*Ang, 2.6495195729795*Ang, -2.598708545398*Ang), C02 : (2.4179789740772*Ang, 1.7147154540948*Ang, -2.5205747481998*Ang), C03 : (2.0860404997325*Ang, 0.36092065139099*Ang, -3.2874697668923*Ang), C04 : (0.60608387409333*Ang, 0.46222015490445*Ang, -3.8199758192258*Ang), C05 : (0.77351228548216*Ang, 3.5509969712007*Ang, -1.4137732389618*Ang), C06 : (-1.4255700230364*Ang, 1.9917929483423*Ang, -2.9955312476464*Ang), C07 : (-0.29610879377116*Ang, -0.78308610108052*Ang, -3.8134867055276*Ang), C08 : (2.604846005198*Ang, -0.97171588071547*Ang, -2.7718538744558*Ang), C09 : (3.2467805949263*Ang, 1.6896484464886*Ang, -1.2382202475234*Ang), C10 : (1.6432691711786*Ang, 3.5413228108245*Ang, -0.093804211226442*Ang), C11 : (2.850916276039*Ang, 2.6067653777954*Ang, -0.015288865495504*Ang), C12 : (3.7600410025801*Ang, 0.30884651973247*Ang, -0.68481513334933*Ang), C13 : (3.445275252173*Ang, -0.99116106552154*Ang, -1.4294272169306*Ang), C14 : (1.6733121142724*Ang, -2.269167292962*Ang, -2.7707276449365*Ang), C15 : (0.24634783824581*Ang, -2.173021690927*Ang, -3.2712338089226*Ang), C16 : (-1.8045428208403*Ang, -0.66222381501763*Ang, -3.3655085997901*Ang), C17 : (-2.3498856424879*Ang, 0.70405480213134*Ang, -2.9629617421814*Ang), C18 : (-1.8093930291125*Ang, 2.9088782919611*Ang, -1.7547250052457*Ang), C19 : (-0.74636612168478*Ang, 3.6773410429349*Ang, -0.99608382140807*Ang), C20 : (-2.9696250901741*Ang, 2.168164766813*Ang, -0.96299746359134*Ang), C21 : (-3.2909583870676*Ang, 0.80077838116632*Ang, -1.6938320401995*Ang), C22 : (-2.1886283525531*Ang, -1.9418232112557*Ang, -2.5229425026006*Ang), C23 : (-0.92702601044008*Ang, -2.8732456994522*Ang, -2.4560691933984*Ang), C24 : (1.9315090628864*Ang, -3.0502411895725*Ang, -1.4106754898822*Ang), C25 : (3.0229329692195*Ang, -2.2576371835023*Ang, -0.59176797041437*Ang), C26 : (3.6909562156065*Ang, 0.37322167149474*Ang, 0.90264066440579*Ang), C27 : (3.1122399286525*Ang, 1.7971600700949*Ang, 1.3168084292087*Ang), C28 : (0.66509588413135*Ang, 3.6752805917837*Ang, 1.1423896720197*Ang), C29 : (-0.8099783082791*Ang, 3.7539243266469*Ang, 0.59349369318477*Ang) }) }