| apply(components::StructureData &sd) const | protocols::denovo_design::connection::ConnectionArchitect | |
| apply(components::StructureData &sd, core::Real &random) const | protocols::denovo_design::connection::ConnectionArchitect | |
| attributes_for_parse_my_tag(utility::tag::AttributeList &attlist) | protocols::denovo_design::connection::ConnectionArchitect | static |
| available_lower_termini(components::StructureData const &sd) const | protocols::denovo_design::connection::ConnectionArchitect | private |
| available_upper_termini(components::StructureData const &sd) const | protocols::denovo_design::connection::ConnectionArchitect | private |
| bridge_ | protocols::denovo_design::connection::ConnectionArchitect | private |
| chain1_ | protocols::denovo_design::connection::ConnectionArchitect | private |
| chain2_ | protocols::denovo_design::connection::ConnectionArchitect | private |
| choose_motif(MotifOPs const &motifs, core::Real &random) const | protocols::denovo_design::connection::ConnectionArchitect | private |
| class_name() | protocols::denovo_design::connection::ConnectionArchitect | inlinestatic |
| clone() const | protocols::denovo_design::connection::ConnectionArchitect | virtual |
| combine_segment_names(SegmentNames const &seg1s, SegmentNames const &seg2s) const | protocols::denovo_design::connection::ConnectionArchitect | private |
| compute_connection_candidates(components::StructureData const &sd) const | protocols::denovo_design::connection::ConnectionArchitect | |
| compute_connection_candidates(components::StructureData const &sd, AreConnectablePredicate const &connectable) const | protocols::denovo_design::connection::ConnectionArchitect | private |
| connect(components::StructureData &sd, Motif &motif) const | protocols::denovo_design::connection::ConnectionArchitect | private |
| ConnectionArchitect(std::string const &id_value) | protocols::denovo_design::connection::ConnectionArchitect | |
| cutpoints() const | protocols::denovo_design::connection::ConnectionArchitect | private |
| DATA_MAP_NAME | protocols::denovo_design::connection::ConnectionArchitect | static |
| id() const | protocols::denovo_design::architects::StructureArchitect | |
| ideal_abego_ | protocols::denovo_design::connection::ConnectionArchitect | private |
| lengths() const | protocols::denovo_design::connection::ConnectionArchitect | private |
| Lengths typedef | protocols::denovo_design::connection::ConnectionArchitect | |
| LengthSet typedef | protocols::denovo_design::connection::ConnectionArchitect | |
| motifs_ | protocols::denovo_design::connection::ConnectionArchitect | private |
| motifs_for_pair(SegmentPair const &pair, components::StructureData const &sd, LengthSet const &length_set, LengthSet const &cutpoint_set) const | protocols::denovo_design::connection::ConnectionArchitect | private |
| parse_motif_string(std::string const &motifs) const | protocols::denovo_design::connection::ConnectionArchitect | private |
| parse_my_tag(utility::tag::TagCOP tag, basic::datacache::DataMap &data) | protocols::denovo_design::architects::StructureArchitect | |
| parse_tag(utility::tag::TagCOP tag, basic::datacache::DataMap &data) override | protocols::denovo_design::connection::ConnectionArchitect | protectedvirtual |
| segment1_ids() const | protocols::denovo_design::connection::ConnectionArchitect | |
| segment1_ids_ | protocols::denovo_design::connection::ConnectionArchitect | private |
| segment2_ids() const | protocols::denovo_design::connection::ConnectionArchitect | |
| segment2_ids_ | protocols::denovo_design::connection::ConnectionArchitect | private |
| segment_pairs(components::StructureData const &sd) const | protocols::denovo_design::connection::ConnectionArchitect | private |
| SegmentPair typedef | protocols::denovo_design::connection::ConnectionArchitect | |
| SegmentPairs typedef | protocols::denovo_design::connection::ConnectionArchitect | |
| set_bridge(bool const bridge) | protocols::denovo_design::connection::ConnectionArchitect | |
| set_id(std::string const &new_id) | protocols::denovo_design::architects::StructureArchitect | |
| set_ideal_abego(bool const use_ideal_abego, std::string const &extend_ss) | protocols::denovo_design::connection::ConnectionArchitect | |
| set_motifs(std::string const &motif_str, std::string const &cutpoints_str) | protocols::denovo_design::connection::ConnectionArchitect | |
| set_motifs(MotifCOPs const &motifs) | protocols::denovo_design::connection::ConnectionArchitect | |
| set_segment1_ids(std::string const &segment1_str) | protocols::denovo_design::connection::ConnectionArchitect | |
| set_segment1_ids(SegmentNames const &segments) | protocols::denovo_design::connection::ConnectionArchitect | |
| set_segment2_ids(std::string const &segment2_str) | protocols::denovo_design::connection::ConnectionArchitect | |
| set_segment2_ids(SegmentNames const &segments) | protocols::denovo_design::connection::ConnectionArchitect | |
| set_use_hh_abego_rules(bool const use_rules) | protocols::denovo_design::connection::ConnectionArchitect | |
| set_user_chain1(core::Size const chain) | protocols::denovo_design::connection::ConnectionArchitect | |
| set_user_chain2(core::Size const chain) | protocols::denovo_design::connection::ConnectionArchitect | |
| StructureArchitect(std::string const &id) | protocols::denovo_design::architects::StructureArchitect | |
| type() const override | protocols::denovo_design::connection::ConnectionArchitect | virtual |
| user_chain1() const | protocols::denovo_design::connection::ConnectionArchitect | |
| user_chain2() const | protocols::denovo_design::connection::ConnectionArchitect | |
| ~ConnectionArchitect() override | protocols::denovo_design::connection::ConnectionArchitect | |
| ~StructureArchitect() override | protocols::denovo_design::architects::StructureArchitect | |
1.8.7