- j -

• j : basic::options::OptionKeys::frags , create_a3b_hbs
• jacobian : build_jacobian
• james : basic::options::OptionKeys::james
• james_debug : options
• jd : demo.D060_Folding , docking , loops , test.Workshop7test , test.Workshop8test
• jd2 : basic::options::OptionKeys::jd2
• jd3 : basic::options::OptionKeys::jd3
• jdist_rerun : basic::options::OptionKeys::abinitio
• jj : beta_nonlocal
• jmp_arr : test.T600_Docking
• job : bin_torsions , cache_trajectory , execute , kic_runner , run_backbone , run_sidechain , score_vs_rmsd , score_vs_time
• job_definition_file : basic::options::OptionKeys::in::file
• job_definition_schema : basic::options::OptionKeys::jd3
• job_definition_script_vars : basic::options::OptionKeys::jd3
• job_id : kic_runner
• job_output : demo.D060_Folding , demo.D070_Refinement , demo.D080_Loop_modeling , demo.D100_Docking , demo.D110_DNA_interface , demo.D120_Ligand_interface
• job_path : average_rmsds
• job_queue_ID : basic::options::OptionKeys::stepwise::rna
• jobdist_miscfile_ext : basic::options::OptionKeys::run
• jobname : basic::options::OptionKeys::lh
• jobs : demo.D060_Folding , demo.D070_Refinement , demo.D080_Loop_modeling , demo.D100_Docking , demo.D110_DNA_interface , demo.D120_Ligand_interface
• jran : basic::options::OptionKeys::run
• jscore_evaluator : basic::options::OptionKeys::evaluation
• json : basic::options::OptionKeys::ddg
• json_cdr : basic::options::OptionKeys::antibody
• jump_change_frequency : basic::options::OptionKeys::rna::denovo
• jump_database : basic::options::OptionKeys::rna::denovo::db
• jump_histogram_binwidth : basic::options::OptionKeys::rna::denovo::out
• jump_histogram_binwidth_rotvector : basic::options::OptionKeys::rna::denovo::out
• jump_histogram_boxsize : basic::options::OptionKeys::rna::denovo::out
• jump_lib : basic::options::OptionKeys::jumps
• jump_library_file : basic::options::OptionKeys::rna::denovo
• jump_move : basic::options::OptionKeys::relax
• jump_nr : basic::options::OptionKeys::evaluation
• jump_num : make_symmdef_file_denovo , test.Workshop7test
• jump_point_pairs : basic::options::OptionKeys::stepwise::rna
• jump_res : basic::options::OptionKeys::full_model
• jump_start : make_symmdef_file_denovo
• jump_stop : make_symmdef_file_denovo
• jumpcut_files : basic::options::OptionKeys::smhybrid
• jumping : basic::options::OptionKeys::cmiles::jumping
• jumps : basic::options::OptionKeys::jumps , basic::options::OptionKeys::resample , docking
• junction_location : enumerate_junctions
• Junction_location_digs : enumerate_junctions
• Junction_location_hyak : enumerate_junctions
• Junction_location_jojo : enumerate_junctions
• Junction_location_short : enumerate_junctions
• junction_run_location : enumerate_junctions
• just_calc_rmsd : basic::options::OptionKeys::score
• just_min_after_mutation_frequency : basic::options::OptionKeys::stepwise::monte_carlo
• just_score : basic::options::OptionKeys::hydrate