| add_hotspot_constraints_to_pose(core::pose::Pose &pose, core::Size const partner, HotspotStubSetOP hotspot_stub_set, core::Real const &CB_force_constant, core::Real const &worst_allowed_stub_bonus, bool const apply_self_energies, core::Real const &bump_cutoff, bool const apply_ambiguous_constraints=false) | protocols::hotspot_hashing::HotspotStubSet | |
| add_hotspot_constraints_to_pose(core::pose::Pose &pose, core::id::AtomID const &fixed_atom, core::pack::task::PackerTaskCOP const packer_task, HotspotStubSetOP hotspot_stub_set, core::Real const &CB_force_constant, core::Real const &worst_allowed_stub_bonus, bool const apply_self_energies, core::Real const &bump_cutoff, bool const apply_ambiguous_constraints=false) | protocols::hotspot_hashing::HotspotStubSet | |
| add_hotspot_constraints_to_wholepose(core::pose::Pose &pose, core::Size const partner, HotspotStubSetOP hotspot_stub_set, core::Real const &CB_force_constant, core::Real const &worst_allowed_stub_bonus, bool const apply_self_energies, core::Real const &bump_cutoff, bool const apply_ambiguous_constraints=false) | protocols::hotspot_hashing::HotspotStubSet | |
| add_hotspot_constraints_to_wholepose(core::pose::Pose &pose, core::id::AtomID const &fixed_atom, core::pack::task::PackerTaskCOP const packer_task, HotspotStubSetOP hotspot_stub_set, core::Real const &CB_force_constant, core::Real const &worst_allowed_stub_bonus, bool const apply_self_energies, core::Real const &bump_cutoff, bool const apply_ambiguous_constraints=false) | protocols::hotspot_hashing::HotspotStubSet | |
| add_stub_(HotspotStubCOP stub) | protocols::hotspot_hashing::HotspotStubSet | |
| add_stub_set(HotspotStubSet const &stubset) | protocols::hotspot_hashing::HotspotStubSet | |
| autofill(core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP scorefxn, core::Size const n_stubs) | protocols::hotspot_hashing::HotspotStubSet | |
| autofill(core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP scorefxn, core::Size const target, core::Real const distance, core::Size const n_stubs) | protocols::hotspot_hashing::HotspotStubSet | |
| begin() const | protocols::hotspot_hashing::HotspotStubSet | inline |
| begin() | protocols::hotspot_hashing::HotspotStubSet | inline |
| chain_to_design_ | protocols::hotspot_hashing::HotspotStubSet | private |
| clear() | protocols::hotspot_hashing::HotspotStubSet | |
| cluster() | protocols::hotspot_hashing::HotspotStubSet | |
| colonyE() | protocols::hotspot_hashing::HotspotStubSet | |
| const_iterator typedef | protocols::hotspot_hashing::HotspotStubSet | |
| constraints() const | protocols::hotspot_hashing::HotspotStubSet | |
| constraints_ | protocols::hotspot_hashing::HotspotStubSet | private |
| create_hotspot_after_pose(core::pose::Pose &pose, std::string const &resname) | protocols::hotspot_hashing::HotspotStubSet | private |
| end() const | protocols::hotspot_hashing::HotspotStubSet | inline |
| end() | protocols::hotspot_hashing::HotspotStubSet | inline |
| evaluate_stub_bumps_(core::conformation::Residue const &placed_stub_residue, core::pose::Pose const &unbound_pose, core::Size const resnum, core::scoring::TenANeighborGraph const &unbound_neighbor_graph, core::scoring::ScoreFunctionCOP const &bump_scorefxn, core::Real const &max_bump_energy) | protocols::hotspot_hashing::HotspotStubSet | private |
| evaluate_stub_self_energy_(core::conformation::Residue const &stub_residue, core::pose::Pose const &unbound_pose, core::Size const resnum, core::scoring::TenANeighborGraph const &unbound_neighbor_graph, core::scoring::ScoreFunctionCOP const &full_scorefxn) | protocols::hotspot_hashing::HotspotStubSet | private |
| fill(core::pose::Pose const &reference_pose, core::scoring::ScoreFunctionCOP scorefxn_in, std::string const &residue_name3, core::Size const n_stubs) | protocols::hotspot_hashing::HotspotStubSet | |
| fill(core::pose::Pose const &reference_pose, core::scoring::ScoreFunctionCOP scorefxn_in, core::Size const target, core::Real const distance, std::string const &residue_name3, core::Size const n_stubs) | protocols::hotspot_hashing::HotspotStubSet | |
| filter(protocols::filters::FilterCOP filter) | protocols::hotspot_hashing::HotspotStubSet | |
| filter_ | protocols::hotspot_hashing::HotspotStubSet | private |
| find_neighboring_stubs(HotspotStubCOP stub) const | protocols::hotspot_hashing::HotspotStubSet | |
| generate_unbound_pose_(core::pose::Pose &pose) | protocols::hotspot_hashing::HotspotStubSet | private |
| get_best_energy_stub() const | protocols::hotspot_hashing::HotspotStubSet | |
| get_nearest_stub(core::conformation::ResidueCOP stub) const | protocols::hotspot_hashing::HotspotStubSet | |
| get_residue_score_(core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP scorefxn, core::Size const seqpos) | protocols::hotspot_hashing::HotspotStubSet | private |
| get_stub(std::string const &residue_name3, core::Real const score) const | protocols::hotspot_hashing::HotspotStubSet | |
| handshake_stub_sets(void) | protocols::hotspot_hashing::HotspotStubSet | private |
| hotspot_length() const | protocols::hotspot_hashing::HotspotStubSet | |
| hotspot_length(core::Size const length) | protocols::hotspot_hashing::HotspotStubSet | |
| hotspot_length_ | protocols::hotspot_hashing::HotspotStubSet | private |
| Hotspots typedef | protocols::hotspot_hashing::HotspotStubSet | |
| HotspotStub class | protocols::hotspot_hashing::HotspotStubSet | friend |
| HotspotStubSet() | protocols::hotspot_hashing::HotspotStubSet | |
| HotspotStubSet(HotspotStubSet const &init) | protocols::hotspot_hashing::HotspotStubSet | |
| HotspotStubSet(HotspotStubSet &&)=default | protocols::hotspot_hashing::HotspotStubSet | |
| Hs_data typedef | protocols::hotspot_hashing::HotspotStubSet | |
| Hs_map typedef | protocols::hotspot_hashing::HotspotStubSet | |
| Hs_vec typedef | protocols::hotspot_hashing::HotspotStubSet | |
| iterator typedef | protocols::hotspot_hashing::HotspotStubSet | |
| operator=(HotspotStubSet &&)=default | protocols::hotspot_hashing::HotspotStubSet | |
| operator=(HotspotStubSet const &rhs) | protocols::hotspot_hashing::HotspotStubSet | inline |
| pair_with_scaffold(core::pose::Pose const &pose, core::Size const partner, protocols::filters::FilterCOP filter) | protocols::hotspot_hashing::HotspotStubSet | |
| pose_ | protocols::hotspot_hashing::HotspotStubSet | private |
| prepare_hashing_packer_task_(core::pose::Pose const &pose, core::Size const chain_to_redesign=2) | protocols::hotspot_hashing::HotspotStubSet | |
| random_stub() | protocols::hotspot_hashing::HotspotStubSet | |
| random_stub(std::string const &resname) | protocols::hotspot_hashing::HotspotStubSet | |
| read_data(std::string const &filename) | protocols::hotspot_hashing::HotspotStubSet | |
| remove_all_hotspot_constraints(core::pose::Pose &pose) const | protocols::hotspot_hashing::HotspotStubSet | |
| remove_random_stubs_from_set(int const num_to_remove) | protocols::hotspot_hashing::HotspotStubSet | |
| remove_stub(HotspotStubCOP stub) | protocols::hotspot_hashing::HotspotStubSet | |
| remove_stubs_from_set(std::set< std::pair< std::string, core::Real > > const &) | protocols::hotspot_hashing::HotspotStubSet | |
| rescore(core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP scorefxn) | protocols::hotspot_hashing::HotspotStubSet | |
| retrieve(std::string const &residue_name3) | protocols::hotspot_hashing::HotspotStubSet | |
| sc_only() const | protocols::hotspot_hashing::HotspotStubSet | |
| sc_only(bool sc_switch) | protocols::hotspot_hashing::HotspotStubSet | |
| sc_only_ | protocols::hotspot_hashing::HotspotStubSet | private |
| score_threshold(core::Real const threshold) | protocols::hotspot_hashing::HotspotStubSet | |
| score_threshold_ | protocols::hotspot_hashing::HotspotStubSet | private |
| set_chain_to_design(core::Size const chain_to_design=2) | protocols::hotspot_hashing::HotspotStubSet | |
| setup_hotspot_foldtree_(core::pose::Pose &pose) | protocols::hotspot_hashing::HotspotStubSet | private |
| size() const | protocols::hotspot_hashing::HotspotStubSet | |
| size(std::string const &resname) | protocols::hotspot_hashing::HotspotStubSet | |
| stub_offset() | protocols::hotspot_hashing::HotspotStubSet | private |
| stub_set_ | protocols::hotspot_hashing::HotspotStubSet | private |
| stub_set_vec_ | protocols::hotspot_hashing::HotspotStubSet | private |
| subset(std::string const &residue_name3, core::Real const scorecut) | protocols::hotspot_hashing::HotspotStubSet | |
| subset(core::Real const scorecut) const | protocols::hotspot_hashing::HotspotStubSet | |
| target_distance_ | protocols::hotspot_hashing::HotspotStubSet | private |
| target_resnum_ | protocols::hotspot_hashing::HotspotStubSet | private |
| write_all(std::string const &filename) const | protocols::hotspot_hashing::HotspotStubSet | |
| write_stub(utility::io::ozstream &outstream, HotspotStubCOP stub, std::string const &tag) const | protocols::hotspot_hashing::HotspotStubSet | |
| ~HotspotStubSet() override | protocols::hotspot_hashing::HotspotStubSet | |
1.8.7