name = 'diamond4carbon' C1 = Atom('C') C2 = Atom('C') C3 = Atom('C') C4 = Atom('C') b12 = Bond(C1,C2) b23 = Bond(C2,C3) b34 = Bond(C3,C4) da1 = Dihedral(C1,C2,C3,C4,180*deg) amber_atom_type = {C1: 'CT', C2: 'CT', C3: 'CT', C4: 'CT' } #mm3_atom_type = {C1: 1, C2: 1, C3: 1, C4: 1 } dC1a = DanglingBond(C1, Dihedral(None,C1,C2,C3, 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(None,C2,C3,C4,-60*deg)) dC2b = DanglingBond(C2, Dihedral(None,C2,C3,C4, 60*deg)) dC3a = DanglingBond(C3, Dihedral(C1,C2,C3,None, 60*deg)) dC3b = DanglingBond(C3, Dihedral(None,C3,C2,C1,-60*deg)) dC4a = DanglingBond(C4, Dihedral(C2,C3,C4,None, 60*deg)) dC4b = DanglingBond(C4, Dihedral(C2,C3,C4,None,-60*deg)) dC4c = DanglingBond(C4, Dihedral(C2,C3,C4,None,180*deg)) hooknorth = Hook(None, [dC1c]) hooksouth = Hook(None, [dC4c]) hookup = Hook(None, [dC2b, dC4b]) hookdown = Hook(None, [dC1a, dC3b]) hookeast = Hook(None, [dC2a, dC4a]) hookwest = Hook(None, [dC1b, dC3a])