References ObjexxFCL::format::A(), argv, basic::options::OptionKeys::in::file::burial, calculate_burial(), utility::io::oc::cout, constraints::cst_weight(), ObjexxFCL::distance(), basic::options::OptionKeys::contactMap::distance_cutoff, test.T009_Exceptions::e, ObjexxFCL::format::F(), create_a3b_hbs::i, ObjexxFCL::format::I(), basic::init(), create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, bin_torsions::output, clean_pdb_keep_ligand::pdbfile, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, pna::resi, basic::options::OptionKeys::cmiles::jumping::resj, in::file::s(), oop_conformations::scorefxn, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.