References ObjexxFCL::abs(), oop_conformations::angles, basic::citation_manager::Application, argv, basic::options::OptionKeys::pocket_grid::central_relax_pdb_num, basic::options::OptionKeys::cm::cm, utility::io::oc::cout, basic::options::OptionKeys::fingerprint::darc_shape_only, basic::options::OptionKeys::pocket_grid::dump_pocketGrid, test.T009_Exceptions::e, utility::options::OptionKeys::options::exit, fprintf(), utility::SingletonBase< CitationManager >::get_instance(), create_a3b_hbs::i, basic::init(), create_a3b_hbs::j, lig_res_num, NEW_OPT, option, numeric::constants::r::pi_2, basic::options::OptionKeys::pocket_grid::pocket_grid_size_x, basic::options::OptionKeys::pocket_grid::pocket_grid_size_y, basic::options::OptionKeys::pocket_grid::pocket_grid_size_z, basic::options::OptionKeys::pocket_grid::pocket_grid_spacing, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::stepwise::protein::protein, execute::residues, predPRE::resnum, basic::options::OptionKeys::mp::visualize::spacing, numeric::random::uniform(), basic::options::OptionKeys::inout::dbms::user, kmeans_adaptive_kernel_density_bb_dependent_rotlib::v, x, numeric::xyzVector< T >::x(), numeric::x_rotation_matrix_radians(), predPRE::y, numeric::xyzVector< T >::y(), numeric::y_rotation_matrix_radians(), predPRE::z, numeric::xyzVector< T >::z(), and numeric::z_rotation_matrix_radians().