- j -

• j : basic::options::OptionKeys::frags
• james : basic::options::OptionKeys::james
• james_debug : options
• jd : app::surface_docking::surface_docking , demo::D060_Folding , docking , loops , test::Workshop7test , test::Workshop8test
• jd1 : app::surface_docking::surface_docking
• jd2 : basic::options::OptionKeys::jd2
• jdist_rerun : basic::options::OptionKeys::abinitio
• jmp_arr : test::T600_Docking
• job_definition_file : basic::options::OptionKeys::in::file
• job_output : demo::D060_Folding , demo::D070_Refinement , demo::D080_Loop_modeling , demo::D100_Docking , demo::D110_DNA_interface , demo::D120_Ligand_interface
• job_queue_ID : basic::options::OptionKeys::stepwise::rna
• jobdist_miscfile_ext : basic::options::OptionKeys::run
• jobname : basic::options::OptionKeys::lh
• Jobs : BuildBindings
• jobs : demo::D060_Folding , demo::D070_Refinement , demo::D080_Loop_modeling , demo::D100_Docking , demo::D110_DNA_interface , demo::D120_Ligand_interface
• JobTuple : BuildPackagedBindings
• join : extract_scores_and_constraints
• join2 : extract_scores_and_constraints
• jran : basic::options::OptionKeys::run
• jscore_evaluator : basic::options::OptionKeys::evaluation
• jump_change_frequency : basic::options::OptionKeys::rna::farna
• jump_database : basic::options::OptionKeys::rna::farna::db
• jump_lib : basic::options::OptionKeys::jumps
• jump_library_file : basic::options::OptionKeys::rna::farna
• 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
• just_calc_rmsd : basic::options::OptionKeys::score
• just_min_after_mutation_frequency : basic::options::OptionKeys::stepwise::monte_carlo