| add_big_fragments(core::fragment::FragSetOP newval) | protocols::hybridization::HybridizeProtocol | inline |
| add_fragment_csts(core::pose::Pose &pose) | protocols::hybridization::HybridizeProtocol | |
| add_hetatm_ | protocols::hybridization::HybridizeProtocol | private |
| add_non_init_chunks_ | protocols::hybridization::HybridizeProtocol | private |
| add_null_template(core::pose::PoseOP template_pose, std::string cst_fn, std::string symmdef_file="NULL", core::Real weight=1.) | protocols::hybridization::HybridizeProtocol | |
| add_small_fragments(core::fragment::FragSetOP newval) | protocols::hybridization::HybridizeProtocol | inline |
| add_template(std::string const &template_fn, std::string const &cst_fn, std::string const &symmdef_file="NULL", core::Real const weight=1., utility::vector1< char > const &rand_chains=utility::vector1< core::Size >(0), bool const align_pdb_info=true) | protocols::hybridization::HybridizeProtocol | |
| add_template(core::pose::PoseOP template_pose, std::string const &cst_fn, std::string const &symmdef_file="NULL", core::Real const weight=1., utility::vector1< char > const &rand_chains=utility::vector1< core::Size >(0), std::string const &filename="default", bool const align_pdb_info=true) | protocols::hybridization::HybridizeProtocol | |
| align_by_domain(core::pose::Pose &pose, core::pose::Pose const &ref_pose, utility::vector1< protocols::loops::Loops > domains) | protocols::hybridization::HybridizeProtocol | |
| align_templates_by_domain(core::pose::PoseOP &ref_pose, utility::vector1< protocols::loops::Loops > domains=utility::vector1< protocols::loops::Loops >()) | protocols::hybridization::HybridizeProtocol | |
| aln_ | protocols::hybridization::HybridizeProtocol | private |
| apply(Pose &) override | protocols::hybridization::HybridizeProtocol | 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 |
| cen_cst_in_ | protocols::hybridization::HybridizeProtocol | private |
| cenrot_ | 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 override | protocols::hybridization::HybridizeProtocol | virtual |
| coord_cst_res_ | protocols::hybridization::HybridizeProtocol | private |
| create() | protocols::moves::Mover | virtual |
| csts_from_frags_ | protocols::hybridization::HybridizeProtocol | private |
| detailed_controls_settings_ | protocols::hybridization::HybridizeProtocol | private |
| disulf_file_ | protocols::hybridization::HybridizeProtocol | private |
| do_intrastage_docking(core::pose::Pose &pose) | protocols::hybridization::HybridizeProtocol | |
| domain_parse_templates(core::Size nres) | protocols::hybridization::HybridizeProtocol | |
| domains_all_templ_ | protocols::hybridization::HybridizeProtocol | private |
| fa_cst_fn_ | protocols::hybridization::HybridizeProtocol | private |
| fa_cst_in_ | protocols::hybridization::HybridizeProtocol | private |
| fa_scorefxn_ | protocols::hybridization::HybridizeProtocol | private |
| filter_templates_ | protocols::hybridization::HybridizeProtocol | private |
| 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 |
| fragprob_stage2_ | protocols::hybridization::HybridizeProtocol | private |
| fresh_instance() const override | 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 override | protocols::hybridization::HybridizeProtocol | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| get_self_ptr() const | protocols::moves::Mover | inline |
| get_self_ptr() | protocols::moves::Mover | inline |
| get_self_weak_ptr() const | protocols::moves::Mover | inline |
| get_self_weak_ptr() | protocols::moves::Mover | inline |
| 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 | |
| HybridizeProtocol(utility::vector1< core::pose::PoseOP > templates_in, utility::vector1< core::Real > template_weights_in, core::scoring::ScoreFunctionOP stage1_scorefxn_in, core::scoring::ScoreFunctionOP stage2_scorefxn_in, core::scoring::ScoreFunctionOP fa_scorefxn_in, std::string frag3_fn, std::string frag9_fn, std::string &cen_cst_in, std::string &fa_cst_in) | protocols::hybridization::HybridizeProtocol | |
| include_loop_ss_chunks_ | protocols::hybridization::HybridizeProtocol | private |
| 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_contig_insertion_ | protocols::hybridization::HybridizeProtocol | private |
| max_registry_shift_ | protocols::hybridization::HybridizeProtocol | private |
| min_after_stage1_ | protocols::hybridization::HybridizeProtocol | private |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| mover_name() | protocols::hybridization::HybridizeProtocol | static |
| name() | protocols::moves::Mover | inlinestatic |
| native_ | protocols::hybridization::HybridizeProtocol | private |
| no_global_frame_ | protocols::hybridization::HybridizeProtocol | private |
| non_null_template_indices_ | protocols::hybridization::HybridizeProtocol | private |
| pairings_file_ | protocols::hybridization::HybridizeProtocol | private |
| parse_my_tag(TagCOP, basic::datacache::DataMap &) override | protocols::hybridization::HybridizeProtocol | virtual |
| pcut_ | protocols::hybridization::HybridizeProtocol | private |
| pick_starting_template() | protocols::hybridization::HybridizeProtocol | |
| Pose typedef | protocols::moves::Mover | |
| PoseCOP typedef | protocols::moves::Mover | |
| provide_citation_info(basic::citation_manager::CitationCollectionList &) const | protocols::moves::Mover | virtual |
| provide_xml_schema(utility::tag::XMLSchemaDefinition &xsd) | protocols::hybridization::HybridizeProtocol | static |
| randfragprob_stage2_ | protocols::hybridization::HybridizeProtocol | private |
| random_sheets_ | protocols::hybridization::HybridizeProtocol | private |
| randomize_chains_ | protocols::hybridization::HybridizeProtocol | private |
| 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 | |
| residue_max_registry_shift_ | protocols::hybridization::HybridizeProtocol | private |
| residue_sample_abinitio_ | protocols::hybridization::HybridizeProtocol | private |
| residue_sample_template_ | protocols::hybridization::HybridizeProtocol | private |
| seqfrags_only_ | protocols::hybridization::HybridizeProtocol | private |
| set_add_hetatm(bool add_hetatm) | protocols::hybridization::HybridizeProtocol | inline |
| 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 | inlinevirtual |
| 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 |
| set_stage2min_scorefxn(core::scoring::ScoreFunctionOP newval) | protocols::hybridization::HybridizeProtocol | inline |
| set_stage2pack_scorefxn(core::scoring::ScoreFunctionOP newval) | protocols::hybridization::HybridizeProtocol | inline |
| set_type(std::string const &setting) | protocols::moves::Mover | inline |
| setup_templates_and_sampling_options(core::pose::Pose const &pose) | protocols::hybridization::HybridizeProtocol | |
| sheets_ | protocols::hybridization::HybridizeProtocol | private |
| should_align_pdb_infos_ | 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 |
| stage2_temperature_ | protocols::hybridization::HybridizeProtocol | private |
| stage2min_scorefxn_ | protocols::hybridization::HybridizeProtocol | private |
| stage2pack_scorefxn_ | 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 | |
| template_chunks_ | protocols::hybridization::HybridizeProtocol | private |
| template_contigs_ | protocols::hybridization::HybridizeProtocol | private |
| template_cst_fn_ | protocols::hybridization::HybridizeProtocol | private |
| template_fns_ | protocols::hybridization::HybridizeProtocol | private |
| template_weights_ | protocols::hybridization::HybridizeProtocol | private |
| templates_ | protocols::hybridization::HybridizeProtocol | private |
| templates_aln_ | protocols::hybridization::HybridizeProtocol | private |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| type() const | protocols::moves::Mover | inline |
| update_template(core::Size const template_idx) | protocols::hybridization::HybridizeProtocol | |
| user_csts_ | protocols::hybridization::HybridizeProtocol | private |
| validate_template(std::string const &filename, std::string const &fasta, core::pose::PoseOP template_pose, bool &align_pdb_info) | protocols::hybridization::HybridizeProtocol | |
1.8.7