- j -

• jacobi() : core::scoring , protocols::toolbox
• jacobi3() : core::scoring , protocols::cluster::calibur
• JD2_BOGUS_JOB() : protocols::jd2
• jd2_used() : protocols::jd2
• JobDistributorTracer() : protocols::jobdist
• jobname_dirhash() : protocols::canonical_sampling
• jobs_tracer() : protocols::jobdist
• judge_facing() : protocols::features::strand_assembly
• jump_distance() : core::kinematics
• jump_dofs() : protocols::environment
• jump_from_internal_coords() : core::kinematics::inverse
• jump_num_sym_dof() : core::pose::symmetry
• jump_which_partitions() : core::kinematics
• jumpfunc() : protocols::protein_interface_design::movers
• jumps_and_cuts_from_pose() : protocols::forge::methods
• jumps_connected_to_position() : protocols::forge::methods
• jumps_from_pose() : core::pose
• jumpsfunc() : protocols::protein_interface_design::movers
• just_modeling_RNA() : core::import_pose , core::pose
• just_protein() : protocols::stepwise::modeler::protein
• just_rna() : protocols::stepwise::modeler::rna