References ObjexxFCL::format::A(), basic::options::OptionKeys::hotspot::angle, numeric::angle_radians(), job_manager::app, argv, base_name(), utility::io::oc::cerr, data, numeric::conversions::degrees(), numeric::dihedral(), numeric::dihedral_radians(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::dis, ObjexxFCL::distance(), test.T009_Exceptions::e, ObjexxFCL::format::F(), lactamize::filename, get_tenA_neighbor_residues(), ObjexxFCL::getline(), create_a3b_hbs::i, ObjexxFCL::format::I(), basic::init(), create_a3b_hbs::j, create_a3b_hbs::k, kk, basic::options::OptionKeys::in::file::l, basic::options::OptionKeys::magnesium::ligand_res, line, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::out::file::o, basic::options::option, erraser_single_res_analysis::out, lactamize::outfile, create_a3b_hbs::pdb_info, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, oop_conformations::scorefxn, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.