| abrelax_checkpoints_ | protocols::abinitio::JumpSpecificAbrelax | private |
| add_constraints(core::pose::Pose &pose) | protocols::abinitio::JumpSpecificAbrelax | |
| add_evaluation(evaluation::PoseEvaluatorOP) | protocols::abinitio::JumpSpecificAbrelax | |
| bRelax_ | protocols::abinitio::JumpSpecificAbrelax | private |
| check_filters(core::pose::Pose &pose) | protocols::abinitio::JumpSpecificAbrelax | |
| close_loops(core::pose::Pose &pose, core::scoring::ScoreFunctionOP scorefxn, std::string const &tag) | protocols::abinitio::JumpSpecificAbrelax | |
| constraint_forest_ | protocols::abinitio::JumpSpecificAbrelax | private |
| copy_native_structure(core::pose::Pose &extended_pose) const | protocols::abinitio::JumpSpecificAbrelax | private |
| copy_structure(core::pose::Pose &extended_pose, core::pose::Pose &desired_pose) const | protocols::abinitio::JumpSpecificAbrelax | private |
| cstset_ | protocols::abinitio::JumpSpecificAbrelax | private |
| do_distributed_rerun() | protocols::abinitio::JumpSpecificAbrelax | |
| do_rerun() | protocols::abinitio::JumpSpecificAbrelax | |
| evaluator_ | protocols::abinitio::JumpSpecificAbrelax | private |
| fold() | protocols::abinitio::JumpSpecificAbrelax | |
| fragset_large_ | protocols::abinitio::JumpSpecificAbrelax | private |
| fragset_small_ | protocols::abinitio::JumpSpecificAbrelax | private |
| fragset_templates_ | protocols::abinitio::JumpSpecificAbrelax | private |
| generate_extended_pose(core::pose::Pose &extended_pose, std::string const &sequence) const | protocols::abinitio::JumpSpecificAbrelax | private |
| generate_scorefxn(bool fullatom=false) | protocols::abinitio::JumpSpecificAbrelax | private |
| init_pose_obj_ | protocols::abinitio::JumpSpecificAbrelax | private |
| initialize_constraint_forest(core::pose::Pose &pose) | protocols::abinitio::JumpSpecificAbrelax | private |
| insert_template_frags(core::pose::Pose &, core::kinematics::MoveMapOP movemap, std::string tag) const | protocols::abinitio::JumpSpecificAbrelax | private |
| jump_def_ | protocols::abinitio::JumpSpecificAbrelax | private |
| JumpSpecificAbrelax() | protocols::abinitio::JumpSpecificAbrelax | |
| loops_in_ | protocols::abinitio::JumpSpecificAbrelax | private |
| multi_fast_relax(Protocol &abinitio_protocol, core::scoring::ScoreFunctionOP, jobdist::PlainSilentFileJobDistributor jobdist, int &curr_nstruct, jobdist::BasicJobOP &curr_job) | protocols::abinitio::JumpSpecificAbrelax | |
| native_pose_ | protocols::abinitio::JumpSpecificAbrelax | private |
| pca_ | protocols::abinitio::JumpSpecificAbrelax | private |
| process_decoy(core::pose::Pose &pose, core::scoring::ScoreFunction const &, std::string tag, core::io::silent::ProteinSilentStruct &) const | protocols::abinitio::JumpSpecificAbrelax | |
| register_options() | protocols::abinitio::JumpSpecificAbrelax | static |
| relax(core::pose::Pose &pose, core::scoring::ScoreFunctionOP, std::string const &tag) | protocols::abinitio::JumpSpecificAbrelax | |
| run() | protocols::abinitio::JumpSpecificAbrelax | |
| sequence_ | protocols::abinitio::JumpSpecificAbrelax | private |
| setup() | protocols::abinitio::JumpSpecificAbrelax | |
| setup_fold(core::pose::Pose &extended_pose, ProtocolOP &prot_ptr) | protocols::abinitio::JumpSpecificAbrelax | private |
| setup_fragments() | protocols::abinitio::JumpSpecificAbrelax | private |
| setup_jumps(core::pose::Pose const &extended_pose) | protocols::abinitio::JumpSpecificAbrelax | private |
| setup_templates() | protocols::abinitio::JumpSpecificAbrelax | private |
| silent_score_file_ | protocols::abinitio::JumpSpecificAbrelax | private |
| ss_def_ | protocols::abinitio::JumpSpecificAbrelax | private |
| templates_ | protocols::abinitio::JumpSpecificAbrelax | private |
