Specify atom in second selection of restraints subcommand
#30
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this is important to ensure reproducibility
rvhonorato
deleted the
29-restraint-subcommand-should-likely-specify-ca-for-a-second-selection
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This PR updates
restraint_bodiesto specify the atom for the second selection. It also fixes an issue increate_iter_body_gapsin which thebody_ids: Vec<isize>were not sorted and could affect the reproducibility.