| add_complementary_sequence(ResTypeSequence &) | protocols::dna::DnaInterfacePacker | private |
| allowed_types() const | protocols::dna::DnaInterfacePacker | |
| allowed_types_ | protocols::dna::DnaInterfacePacker | private |
| apply(Pose &) | protocols::dna::DnaInterfacePacker | virtual |
| protocols::moves::Mover::apply(core::io::serialization::PipeMap &pmap) | protocols::moves::Mover | virtual |
| base_only_ | protocols::dna::DnaInterfacePacker | private |
| binding_E_ | protocols::dna::DnaInterfacePacker | private |
| calculate_specificity(Pose const &, ResTypeSequence const &, SequenceScores const &) | protocols::dna::DnaInterfacePacker | private |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clear_initialization() | protocols::dna::DnaInterfacePacker | |
| clone() const | protocols::dna::DnaInterfacePacker | virtual |
| create() | protocols::moves::Mover | virtual |
| current_dna_design_string(Pose const &) const | protocols::dna::DnaInterfacePacker | |
| current_working_sequence(Pose const &) const | protocols::dna::DnaInterfacePacker | |
| dna_chains_ | protocols::dna::DnaInterfacePacker | private |
| dna_seq_tag(Pose const &, ResTypeSequence const &) const | protocols::dna::DnaInterfacePacker | |
| dna_sequences_ | protocols::dna::DnaInterfacePacker | private |
| DnaInterfacePacker() | protocols::dna::DnaInterfacePacker | |
| DnaInterfacePacker(ScoreFunctionOP, bool minimize=false, std::string filename_root="dnapacker") | protocols::dna::DnaInterfacePacker | |
| filename_root_ | protocols::dna::DnaInterfacePacker | private |
| Filters_map typedef | protocols::moves::Mover | |
| fresh_instance() const | protocols::dna::DnaInterfacePacker | 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::dna::DnaInterfacePacker | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| get_targeted_sequence(Pose const &) const | protocols::dna::DnaInterfacePacker | |
| get_type() const | protocols::moves::Mover | inline |
| ig() const | protocols::simple_moves::PackRotamersMover | |
| include_dna_potentials_in_specificity_calculations_ | protocols::dna::DnaInterfacePacker | private |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| init_standard(Pose &) | protocols::dna::DnaInterfacePacker | private |
| initialization_state_ | protocols::dna::DnaInterfacePacker | private |
| initialized() const | protocols::dna::DnaInterfacePacker | |
| InteractionGraphBaseCOP typedef | protocols::simple_moves::PackRotamersMover | |
| InteractionGraphBaseOP typedef | protocols::simple_moves::PackRotamersMover | |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| make_dna_sequence_combinations() | protocols::dna::DnaInterfacePacker | private |
| measure_bp_specificities(Pose &) | protocols::dna::DnaInterfacePacker | |
| measure_specificities(Pose &, ResTypeSequences const &) | protocols::dna::DnaInterfacePacker | |
| measure_specificity(Pose &) | protocols::dna::DnaInterfacePacker | |
| min_movemap_ | protocols::dna::DnaInterfacePacker | private |
| minimize_ | protocols::dna::DnaInterfacePacker | private |
| minimize_options_ | protocols::dna::DnaInterfacePacker | 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 |
| nloop(core::Size nloop_in) | protocols::simple_moves::PackRotamersMover | |
| nloop() const | protocols::simple_moves::PackRotamersMover | inline |
| note_packertask_settings(Pose const &) | protocols::simple_moves::PackRotamersMover | protectedvirtual |
| num_repacks_ | protocols::dna::DnaInterfacePacker | private |
| operator=(Mover const &other) | protocols::moves::Mover | |
| PackerTaskCOP typedef | protocols::simple_moves::PackRotamersMover | |
| PackRotamersMover() | protocols::simple_moves::PackRotamersMover | |
| PackRotamersMover(std::string const &) | protocols::simple_moves::PackRotamersMover | |
| PackRotamersMover(ScoreFunctionCOP scorefxn, PackerTaskCOP task=0, core::Size nloop=1) | protocols::simple_moves::PackRotamersMover | |
| PackRotamersMover(PackRotamersMover const &other) | protocols::simple_moves::PackRotamersMover | |
| parse_def(utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, protocols::moves::MoverCacheSP cache) | protocols::simple_moves::PackRotamersMover | virtual |
| parse_my_tag(TagCOP, basic::datacache::DataMap &, protocols::filters::Filters_map const &, moves::Movers_map const &, Pose const &) | protocols::dna::DnaInterfacePacker | virtual |
| parse_score_function(TagCOP, basic::datacache::DataMap const &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &) | protocols::simple_moves::PackRotamersMover | virtual |
| parse_state(SerializableState const &state) | protocols::moves::Mover | virtual |
| parse_task_operations(TagCOP, basic::datacache::DataMap const &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &) | protocols::simple_moves::PackRotamersMover | virtual |
| pdbname() | protocols::dna::DnaInterfacePacker | inline |
| pdbname_ | protocols::dna::DnaInterfacePacker | private |
| pdboutput(PDBOutputOP) | protocols::dna::DnaInterfacePacker | |
| pdboutput_ | protocols::dna::DnaInterfacePacker | private |
| Pose typedef | protocols::moves::Mover | |
| PoseCOP typedef | protocols::moves::Mover | |
| post_packing(Pose &, ResTypeSequence const &, Size) | protocols::dna::DnaInterfacePacker | private |
| probe_specificity_ | protocols::dna::DnaInterfacePacker | private |
| protein_scan(Pose &) | protocols::dna::DnaInterfacePacker | private |
| protein_scan_ | protocols::dna::DnaInterfacePacker | private |
| reference_pose(Pose const &) | protocols::dna::DnaInterfacePacker | |
| reference_pose() const | protocols::dna::DnaInterfacePacker | |
| reference_pose_ | protocols::dna::DnaInterfacePacker | private |
| reference_residue_types_ | protocols::dna::DnaInterfacePacker | 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 |
| reset_status() | protocols::moves::Mover | |
| reversion_scan(Pose &, core::Real bound_score=0., core::Real binding_score=0., std::pair< core::Real, core::Real > specificities=std::make_pair(0., 0.)) | protocols::dna::DnaInterfacePacker | |
| reversion_scan_ | protocols::dna::DnaInterfacePacker | private |
| rotamer_sets() const | protocols::simple_moves::PackRotamersMover | |
| RotamerSetsCOP typedef | protocols::simple_moves::PackRotamersMover | |
| RotamerSetsOP typedef | protocols::simple_moves::PackRotamersMover | |
| run(Pose &pose, utility::vector0< int > rot_to_pack=utility::vector0< int >()) const | protocols::simple_moves::PackRotamersMover | protectedvirtual |
| save_state(SerializableState &state) | protocols::moves::Mover | virtual |
| score_function(ScoreFunctionCOP sf) | protocols::simple_moves::PackRotamersMover | |
| score_function() const | protocols::simple_moves::PackRotamersMover | |
| ScoreFunctionCOP typedef | protocols::simple_moves::PackRotamersMover | |
| ScoreFunctionOP typedef | protocols::dna::DnaInterfacePacker | |
| set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
| set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inline |
| set_filename_root(std::string const &name) | protocols::dna::DnaInterfacePacker | 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_type(std::string const &setting) | protocols::moves::Mover | inline |
| setup(Pose &pose) | protocols::simple_moves::PackRotamersMover | protectedvirtual |
| show(std::ostream &output=std::cout) const | protocols::simple_moves::PackRotamersMover | virtual |
| specificity_repacks_ | protocols::dna::DnaInterfacePacker | private |
| standard_packing(Pose &) | protocols::dna::DnaInterfacePacker | private |
| Strings typedef | protocols::moves::Mover | |
| TagCOP typedef | protocols::dna::DnaInterfacePacker | |
| targeted_dna(DnaDesignDefOPs const &) | protocols::dna::DnaInterfacePacker | |
| targeted_dna() const | protocols::dna::DnaInterfacePacker | |
| targeted_dna_ | protocols::dna::DnaInterfacePacker | private |
| task(PackerTaskCOP t) | protocols::simple_moves::PackRotamersMover | |
| task() const | protocols::simple_moves::PackRotamersMover | |
| task_factory(TaskFactoryCOP tf) | protocols::simple_moves::PackRotamersMover | |
| task_factory() const | protocols::simple_moves::PackRotamersMover | |
| task_is_valid(Pose const &pose) const | protocols::simple_moves::PackRotamersMover | |
| TaskFactoryCOP typedef | protocols::simple_moves::PackRotamersMover | |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| type() const | protocols::moves::Mover | inline |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| unbound_score(Pose const &, bool output_pdb=false, std::string pdbname="") | protocols::dna::DnaInterfacePacker | |
| ~DnaInterfacePacker() | protocols::dna::DnaInterfacePacker | virtual |
| ~Mover() | protocols::moves::Mover | virtual |
| ~PackRotamersMover() | protocols::simple_moves::PackRotamersMover | virtual |
1.8.7