cg_openmm
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shirtsgroup
Make the native contact symmetry checks more general
Right now, we can scan the forward and reverse orientations of a linear homopolymer chain which has end-to-end symmetry by setting homopolymer_sym=True in the fraction_native_contacts function, and the higher of the two native contact fractions is used. The symmetry check is needed because the particle indices in the native structure may be the reverse of that in the current structure.
There are checks in place on the cgmodel that only allow this option to be used for linear homopolymer chains, since it currently does not work for models with sidechains. It would be useful to make the symmetry check more general - this would require some parsing of the topology, and determining what the particle indices in the reversed structure are.
