| add_big_fragments(core::fragment::FragSetOP newval) | protocols::hybridization::HybridizeProtocol | inline |
| add_hetatm_ | protocols::hybridization::HybridizeProtocol | private |
| add_non_init_chunks_ | protocols::hybridization::HybridizeProtocol | private |
| add_small_fragments(core::fragment::FragSetOP newval) | protocols::hybridization::HybridizeProtocol | inline |
| add_template(std::string template_fn, std::string cst_fn, std::string symmdef_file="NULL", core::Real weight=1., core::Real domain_assembly_weight=0., core::Size cluster_id=1, utility::vector1< core::Size > cst_reses=utility::vector1< core::Size >(0)) | protocols::hybridization::HybridizeProtocol | |
| add_template(core::pose::PoseOP template_pose, std::string cst_fn, std::string symmdef_file="NULL", core::Real weight=1., core::Real domain_assembly_weight=0., core::Size cluster_id=1, utility::vector1< core::Size > cst_reses=utility::vector1< core::Size >(0), std::string filename="default") | protocols::hybridization::HybridizeProtocol | |
| align_by_domain(utility::vector1< core::pose::PoseOP > &poses, utility::vector1< Loops > domains, core::pose::PoseOP &ref_pose) | protocols::hybridization::HybridizeProtocol | |
| align_by_domain(core::pose::Pose &pose, core::pose::Pose const &ref_pose, utility::vector1< Loops > domains) | protocols::hybridization::HybridizeProtocol | |
| allowed_to_move_ | protocols::hybridization::HybridizeProtocol | private |
| aln_ | protocols::hybridization::HybridizeProtocol | private |
| apply(Pose &) | protocols::hybridization::HybridizeProtocol | virtual |
| protocols::moves::Mover::apply(core::io::serialization::PipeMap &pmap) | protocols::moves::Mover | virtual |
| auto_frag_insertion_weight_ | protocols::hybridization::HybridizeProtocol | private |
| batch_relax_ | protocols::hybridization::HybridizeProtocol | private |
| big_frag_insertion_weight_ | protocols::hybridization::HybridizeProtocol | private |
| cartfrag_overlap_ | protocols::hybridization::HybridizeProtocol | private |
| check_and_create_fragments(Pose &) | protocols::hybridization::HybridizeProtocol | |
| chunk_insertion_weight_ | protocols::hybridization::HybridizeProtocol | private |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const | protocols::hybridization::HybridizeProtocol | virtual |
| clusterID_map_ | protocols::hybridization::HybridizeProtocol | private |
| create() | protocols::moves::Mover | virtual |
| disulf_file_ | protocols::hybridization::HybridizeProtocol | private |
| domain_assembly_ | protocols::hybridization::HybridizeProtocol | private |
| domain_assembly_weights_ | protocols::hybridization::HybridizeProtocol | private |
| domains_ | protocols::hybridization::HybridizeProtocol | private |
| expand_domains_to_full_length(utility::vector1< utility::vector1< Loops > > all_domains, Size ref_domains_index, Size n_residues) | protocols::hybridization::HybridizeProtocol | |
| fa_cst_fn_ | protocols::hybridization::HybridizeProtocol | private |
| fa_scorefxn_ | protocols::hybridization::HybridizeProtocol | private |
| filter_templates_ | protocols::hybridization::HybridizeProtocol | private |
| Filters_map typedef | protocols::moves::Mover | |
| frag_1mer_insertion_weight_ | protocols::hybridization::HybridizeProtocol | private |
| frag_weight_aligned_ | protocols::hybridization::HybridizeProtocol | private |
| fragments_big_ | protocols::hybridization::HybridizeProtocol | private |
| fragments_small_ | protocols::hybridization::HybridizeProtocol | private |
| fresh_instance() const | protocols::hybridization::HybridizeProtocol | virtual |
| get_additional_output() | protocols::moves::Mover | virtual |
| get_current_job() const | protocols::moves::Mover | |
| get_current_tag() const | protocols::moves::Mover | inline |
| get_input_pose() const | protocols::moves::Mover | |
| get_last_move_status() const | protocols::moves::Mover | |
| get_name() const | protocols::hybridization::HybridizeProtocol | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| get_type() const | protocols::moves::Mover | inline |
| hcut_ | protocols::hybridization::HybridizeProtocol | private |
| hetatm_prot_cst_weight_ | protocols::hybridization::HybridizeProtocol | private |
| hetatm_self_cst_weight_ | protocols::hybridization::HybridizeProtocol | private |
| HybridizeProtocol() | protocols::hybridization::HybridizeProtocol | |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| init() | protocols::hybridization::HybridizeProtocol | |
| initialize_and_sample_loops(core::pose::Pose &pose, core::pose::PoseOP chosen_templ, protocols::loops::Loops template_contigs_icluster, core::scoring::ScoreFunctionOP scorefxn) | protocols::hybridization::HybridizeProtocol | |
| jump_move_ | protocols::hybridization::HybridizeProtocol | private |
| jump_move_repeat_ | protocols::hybridization::HybridizeProtocol | private |
| keep_pose_constraint_ | protocols::hybridization::HybridizeProtocol | private |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| length_ | protocols::hybridization::HybridizeProtocol | private |
| linmin_only_ | protocols::hybridization::HybridizeProtocol | private |
| max_registry_shift_ | protocols::hybridization::HybridizeProtocol | private |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| Mover(Mover const &other) | protocols::moves::Mover | |
| name() | protocols::moves::Mover | inlinestatic |
| native_ | protocols::hybridization::HybridizeProtocol | private |
| no_global_frame_ | protocols::hybridization::HybridizeProtocol | private |
| nofragbias_ | protocols::hybridization::HybridizeProtocol | private |
| operator=(Mover const &other) | protocols::moves::Mover | |
| pairings_file_ | protocols::hybridization::HybridizeProtocol | private |
| parse_def(utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache) | protocols::moves::Mover | virtual |
| parse_my_tag(TagCOP, basic::datacache::DataMap &, Filters_map const &, Movers_map const &, Pose const &) | protocols::hybridization::HybridizeProtocol | virtual |
| parse_state(SerializableState const &state) | protocols::moves::Mover | virtual |
| pcut_ | protocols::hybridization::HybridizeProtocol | private |
| pick_starting_template(core::Size &initial_template_index, core::Size &initial_template_index_icluster, utility::vector1< core::Size > &template_index_icluster, utility::vector1< core::pose::PoseOP > &templates_icluster, utility::vector1< core::Real > &weights_icluster, utility::vector1< protocols::loops::Loops > &template_chunks_icluster, utility::vector1< protocols::loops::Loops > &template_contigs_icluster) | protocols::hybridization::HybridizeProtocol | |
| Pose typedef | protocols::moves::Mover | |
| PoseCOP typedef | protocols::moves::Mover | |
| random_sheets_ | protocols::hybridization::HybridizeProtocol | private |
| read_template_structures(utility::file::FileName template_list) | protocols::hybridization::HybridizeProtocol | |
| read_template_structures(utility::vector1< utility::file::FileName > const &template_filenames) | protocols::hybridization::HybridizeProtocol | |
| realign_domains_ | protocols::hybridization::HybridizeProtocol | private |
| realign_domains_stage2_ | protocols::hybridization::HybridizeProtocol | private |
| register_options() | protocols::moves::Mover | inlinestatic |
| reinitialize_for_each_job() const | protocols::moves::Mover | virtual |
| reinitialize_for_new_input() const | protocols::moves::Mover | virtual |
| relax_repeats_ | protocols::hybridization::HybridizeProtocol | private |
| reset_status() | protocols::moves::Mover | |
| save_state(SerializableState &state) | protocols::moves::Mover | virtual |
| seqfrags_only_ | protocols::hybridization::HybridizeProtocol | private |
| set_batch_relax(core::Size newval) | protocols::hybridization::HybridizeProtocol | inline |
| set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
| set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inline |
| set_fullatom_scorefxn(core::scoring::ScoreFunctionOP newval) | protocols::hybridization::HybridizeProtocol | inline |
| set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_stage1_increase_cycles(core::Real newval) | protocols::hybridization::HybridizeProtocol | inline |
| set_stage1_scorefxn(core::scoring::ScoreFunctionOP newval) | protocols::hybridization::HybridizeProtocol | inline |
| set_stage2_increase_cycles(core::Real newval) | protocols::hybridization::HybridizeProtocol | inline |
| set_stage2_scorefxn(core::scoring::ScoreFunctionOP newval) | protocols::hybridization::HybridizeProtocol | inline |
| sheets_ | protocols::hybridization::HybridizeProtocol | private |
| show(std::ostream &output=std::cout) const | protocols::moves::Mover | virtual |
| skip_long_min_ | protocols::hybridization::HybridizeProtocol | private |
| small_frag_insertion_weight_ | protocols::hybridization::HybridizeProtocol | private |
| stage1_1_cycles_ | protocols::hybridization::HybridizeProtocol | private |
| stage1_2_cycles_ | protocols::hybridization::HybridizeProtocol | private |
| stage1_3_cycles_ | protocols::hybridization::HybridizeProtocol | private |
| stage1_4_cycles_ | protocols::hybridization::HybridizeProtocol | private |
| stage1_increase_cycles_ | protocols::hybridization::HybridizeProtocol | private |
| stage1_probability_ | protocols::hybridization::HybridizeProtocol | private |
| stage1_scorefxn_ | protocols::hybridization::HybridizeProtocol | private |
| stage25_increase_cycles_ | protocols::hybridization::HybridizeProtocol | private |
| stage2_increase_cycles_ | protocols::hybridization::HybridizeProtocol | private |
| stage2_scorefxn_ | protocols::hybridization::HybridizeProtocol | private |
| starting_templates_ | protocols::hybridization::HybridizeProtocol | private |
| strand_pairs_ | protocols::hybridization::HybridizeProtocol | private |
| Strings typedef | protocols::moves::Mover | |
| symmdef_files_ | protocols::hybridization::HybridizeProtocol | private |
| TagCOP typedef | protocols::moves::Mover | |
| task_ | protocols::hybridization::HybridizeProtocol | private |
| task_factory_ | protocols::hybridization::HybridizeProtocol | private |
| template_chunks_ | protocols::hybridization::HybridizeProtocol | private |
| template_clusterID_ | protocols::hybridization::HybridizeProtocol | private |
| template_contigs_ | protocols::hybridization::HybridizeProtocol | private |
| template_cst_fn_ | protocols::hybridization::HybridizeProtocol | private |
| template_cst_reses_ | protocols::hybridization::HybridizeProtocol | private |
| template_fn_ | protocols::hybridization::HybridizeProtocol | private |
| template_weights_ | protocols::hybridization::HybridizeProtocol | private |
| template_weights_sum_ | protocols::hybridization::HybridizeProtocol | private |
| templates_ | protocols::hybridization::HybridizeProtocol | private |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| type() const | protocols::moves::Mover | inline |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| user_csts_ | protocols::hybridization::HybridizeProtocol | private |
| ~Mover() | protocols::moves::Mover | virtual |
1.8.7