| add_big_fragments(core::fragment::FragSetOP newval) | protocols::hybridization::HybridizeSetup | inline |
| add_fragments_big(core::fragment::FragSetOP v) | protocols::hybridization::HybridizeSetup | inline |
| add_fragments_small(core::fragment::FragSetOP v) | protocols::hybridization::HybridizeSetup | inline |
| add_hetatm() const | protocols::hybridization::HybridizeSetup | inline |
| add_hetatm_ | protocols::hybridization::HybridizeSetup | private |
| add_non_init_chunks_ | protocols::hybridization::HybridizeSetup | private |
| add_small_fragments(core::fragment::FragSetOP newval) | protocols::hybridization::HybridizeSetup | inline |
| add_starting_templates(core::Size t) | protocols::hybridization::HybridizeSetup | 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., utility::vector1< core::Size > cst_reses=utility::vector1< core::Size >(0)) | protocols::hybridization::HybridizeSetup | |
| 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., utility::vector1< core::Size > cst_reses=utility::vector1< core::Size >(0), std::string name="default") | protocols::hybridization::HybridizeSetup | |
| align_by_domain(utility::vector1< core::pose::PoseOP > &poses, utility::vector1< Loops > domains, core::pose::PoseCOP &ref_pose) | protocols::hybridization::HybridizeSetup | |
| align_by_domain(core::pose::Pose &pose, core::pose::Pose const &ref_pose, utility::vector1< Loops > domains) | protocols::hybridization::HybridizeSetup | |
| align_domains_to_pose_ | protocols::hybridization::HybridizeSetup | private |
| align_domains_to_template_ | protocols::hybridization::HybridizeSetup | private |
| aln_ | protocols::hybridization::HybridizeSetup | private |
| auto_frag_insertion_weight_ | protocols::hybridization::HybridizeSetup | private |
| big_frag_insertion_weight_ | protocols::hybridization::HybridizeSetup | private |
| cartfrag_overlap_ | protocols::hybridization::HybridizeSetup | private |
| check_and_create_fragments(core::pose::Pose const &) | protocols::hybridization::HybridizeSetup | |
| clone() const | protocols::hybridization::HybridizeSetup | virtual |
| disulf_file_ | protocols::hybridization::HybridizeSetup | private |
| domain_assembly() const | protocols::hybridization::HybridizeSetup | inline |
| domain_assembly_ | protocols::hybridization::HybridizeSetup | private |
| domain_assembly_weights() const | protocols::hybridization::HybridizeSetup | inline |
| domain_assembly_weights_ | protocols::hybridization::HybridizeSetup | private |
| domains_ | protocols::hybridization::HybridizeSetup | private |
| expand_domains_to_full_length(utility::vector1< utility::vector1< Loops > > all_domains, Size ref_domains_index, Size n_residues) | protocols::hybridization::HybridizeSetup | |
| filter_templates_ | protocols::hybridization::HybridizeSetup | private |
| frag_1mer_insertion_weight_ | protocols::hybridization::HybridizeSetup | private |
| frag_weight_aligned_ | protocols::hybridization::HybridizeSetup | private |
| fragments_big() const | protocols::hybridization::HybridizeSetup | inline |
| fragments_big_ | protocols::hybridization::HybridizeSetup | private |
| fragments_small() const | protocols::hybridization::HybridizeSetup | inline |
| fragments_small_ | protocols::hybridization::HybridizeSetup | private |
| hcut_ | protocols::hybridization::HybridizeSetup | private |
| hetatm_prot_cst_weight() const | protocols::hybridization::HybridizeSetup | inline |
| hetatm_prot_cst_weight_ | protocols::hybridization::HybridizeSetup | private |
| hetatm_self_cst_weight() const | protocols::hybridization::HybridizeSetup | inline |
| hetatm_self_cst_weight_ | protocols::hybridization::HybridizeSetup | private |
| HybridizeSetup() | protocols::hybridization::HybridizeSetup | |
| init() | protocols::hybridization::HybridizeSetup | |
| initial_template_index() const | protocols::hybridization::HybridizeSetup | inline |
| initial_template_index_ | protocols::hybridization::HybridizeSetup | private |
| length_ | protocols::hybridization::HybridizeSetup | private |
| max_registry_shift_ | protocols::hybridization::HybridizeSetup | private |
| native_ | protocols::hybridization::HybridizeSetup | private |
| nres_protein_asu() const | protocols::hybridization::HybridizeSetup | inline |
| nres_protein_tgt_ | protocols::hybridization::HybridizeSetup | private |
| nres_tgt_ | protocols::hybridization::HybridizeSetup | private |
| nres_tgt_asu() const | protocols::hybridization::HybridizeSetup | inline |
| pairings_file_ | protocols::hybridization::HybridizeSetup | private |
| pcut_ | protocols::hybridization::HybridizeSetup | private |
| pick_starting_template() | protocols::hybridization::HybridizeSetup | |
| random_sheets_ | protocols::hybridization::HybridizeSetup | private |
| realign_templates(core::pose::PoseCOP ref_pose) | protocols::hybridization::HybridizeSetup | |
| run_domain_assembly() | protocols::hybridization::HybridizeSetup | |
| set_add_hetatm(bool v) | protocols::hybridization::HybridizeSetup | inline |
| set_align_domains_to_pose(bool v) | protocols::hybridization::HybridizeSetup | inline |
| set_align_domains_to_template(bool v) | protocols::hybridization::HybridizeSetup | inline |
| set_domain_assembly(bool v) | protocols::hybridization::HybridizeSetup | inline |
| set_domain_hcut(core::Real v) | protocols::hybridization::HybridizeSetup | inline |
| set_domain_length(core::Size v) | protocols::hybridization::HybridizeSetup | inline |
| set_domain_pcut(core::Real v) | protocols::hybridization::HybridizeSetup | inline |
| set_hetatm_prot_cst_weight(core::Real v) | protocols::hybridization::HybridizeSetup | inline |
| set_hetatm_self_cst_weight(core::Real v) | protocols::hybridization::HybridizeSetup | inline |
| set_nres_protein(core::Size nres_protein_tgt_in) | protocols::hybridization::HybridizeSetup | inline |
| set_nres_tgt(core::Size nres_tgt_in) | protocols::hybridization::HybridizeSetup | inline |
| sheets_ | protocols::hybridization::HybridizeSetup | private |
| small_frag_insertion_weight_ | protocols::hybridization::HybridizeSetup | private |
| starting_templates_ | protocols::hybridization::HybridizeSetup | private |
| strand_pairs_ | protocols::hybridization::HybridizeSetup | private |
| symmdef_files() const | protocols::hybridization::HybridizeSetup | inline |
| symmdef_files_ | protocols::hybridization::HybridizeSetup | private |
| template_chunks() const | protocols::hybridization::HybridizeSetup | inline |
| template_chunks_ | protocols::hybridization::HybridizeSetup | private |
| template_contigs() const | protocols::hybridization::HybridizeSetup | inline |
| template_contigs_ | protocols::hybridization::HybridizeSetup | private |
| template_cst_fn() const | protocols::hybridization::HybridizeSetup | inline |
| template_cst_fn_ | protocols::hybridization::HybridizeSetup | private |
| template_cst_reses_ | protocols::hybridization::HybridizeSetup | private |
| template_file_names() | protocols::hybridization::HybridizeSetup | inline |
| template_fn_ | protocols::hybridization::HybridizeSetup | private |
| template_poses() const | protocols::hybridization::HybridizeSetup | inline |
| template_weights_ | protocols::hybridization::HybridizeSetup | private |
| template_weights_sum_ | protocols::hybridization::HybridizeSetup | private |
| template_wts() const | protocols::hybridization::HybridizeSetup | inline |
| templates_ | protocols::hybridization::HybridizeSetup | private |
1.8.7