| add_chain_ending(Size const seqpos) | core::io::silent::BinarySilentStruct | |
| add_comment(std::string name, std::string value) | core::io::silent::SilentStruct | |
| add_energy(std::string const &scorename, Real value, Real weight=1.0) | core::io::silent::SilentStruct | |
| add_jump(kinematics::Jump jump) | core::io::silent::BinarySilentStruct | inline |
| add_other_struct(SilentStructOP silent_struct) | core::io::silent::SilentStruct | |
| add_parent_remark(std::string const &name, std::string const &value) | core::io::silent::SilentStruct | |
| add_string_value(std::string const &scorename, std::string const &value, int const index=-1) | core::io::silent::SilentStruct | |
| add_submotif_info_from_line(std::istream &line_stream) | core::io::silent::SilentStruct | |
| atm_coords_ | core::io::silent::BinarySilentStruct | private |
| BinarySilentStruct(SilentFileOptions const &opts, Size const nres_in) | core::io::silent::BinarySilentStruct | |
| BinarySilentStruct(SilentFileOptions const &opts) | core::io::silent::BinarySilentStruct | |
| BinarySilentStruct(SilentFileOptions const &opts, core::pose::Pose const &pose, std::string tag="empty_tag") | core::io::silent::BinarySilentStruct | |
| BinarySilentStruct(BinarySilentStruct const &src) | core::io::silent::BinarySilentStruct | |
| bJumps_use_IntraResStub_ | core::io::silent::BinarySilentStruct | private |
| CA_rmsd(BinarySilentStruct other_pss) | core::io::silent::BinarySilentStruct | virtual |
| chain_endings(utility::vector1< Size > const &endings) | core::io::silent::BinarySilentStruct | |
| chain_endings() const | core::io::silent::BinarySilentStruct | inline |
| chain_endings_ | core::io::silent::BinarySilentStruct | private |
| chain_endings_str() const | core::io::silent::BinarySilentStruct | |
| clear_comments() | core::io::silent::SilentStruct | |
| clear_energies() | core::io::silent::SilentStruct | inlinevirtual |
| clone() const override | core::io::silent::BinarySilentStruct | inlinevirtual |
| comment_from_line(std::string const &line) | core::io::silent::SilentStruct | |
| comment_from_line(std::string const &line, bool const include_silentfile_comments) | core::io::silent::SilentStruct | |
| copy_scores(const SilentStruct &src_ss) | core::io::silent::SilentStruct | |
| decoy_tag() const | core::io::silent::SilentStruct | inline |
| decoy_tag(std::string const &tag) | core::io::silent::SilentStruct | inline |
| detect_fullatom(core::Size pos, core::Size natoms, bool &fullatom, bool &well_defined) | core::io::silent::SilentStruct | protected |
| energies() const | core::io::silent::SilentStruct | inline |
| energies_from_pose(core::pose::Pose const &pose) | core::io::silent::SilentStruct | |
| energies_into_pose(core::pose::Pose &pose) const | core::io::silent::SilentStruct | |
| energy_names() const | core::io::silent::SilentStruct | |
| erase_comment(std::string const &name) | core::io::silent::SilentStruct | |
| extract_writeable_cacheable_data(core::pose::Pose const &pose) | core::io::silent::SilentStruct | protected |
| figure_out_residue_numbers_from_line(std::istream &line_stream) | core::io::silent::SilentStruct | |
| figure_out_segment_ids_from_line(std::istream &line_stream) | core::io::silent::SilentStruct | |
| fill_other_struct_list(pose::Pose const &pose) | core::io::silent::SilentStruct | |
| fill_pose(core::pose::Pose &pose, bool const metapatches=true) const override | core::io::silent::BinarySilentStruct | virtual |
| fill_pose(core::pose::Pose &pose, core::chemical::ResidueTypeSet const &residue_set, bool const metapatches=true) const override | core::io::silent::BinarySilentStruct | virtual |
| core::io::silent::SilentStruct::fill_pose(core::pose::Pose &pose, core::chemical::ResidueTypeSetCOP residue_set, bool const metapatches=true) const | core::io::silent::SilentStruct | |
| fill_struct(core::pose::Pose const &pose, std::string tag) override | core::io::silent::BinarySilentStruct | virtual |
| fill_struct_with_residue_numbers(pose::Pose const &pose) | core::io::silent::SilentStruct | |
| fill_struct_with_submotif_info_list(pose::Pose const &pose) | core::io::silent::SilentStruct | |
| finish_pose(core::pose::Pose &pose) const | core::io::silent::SilentStruct | |
| fold_tree(kinematics::FoldTree f) | core::io::silent::BinarySilentStruct | inline |
| fold_tree() const | core::io::silent::BinarySilentStruct | inline |
| fold_tree_ | core::io::silent::BinarySilentStruct | private |
| force_bitflip() const | core::io::silent::SilentStruct | inlinevirtual |
| full_model_info_into_pose(pose::Pose &pose) const | core::io::silent::SilentStruct | |
| full_model_parameters() const | core::io::silent::SilentStruct | inline |
| fullatom() const | core::io::silent::BinarySilentStruct | inline |
| fullatom(bool fullatom) | core::io::silent::BinarySilentStruct | inline |
| fullatom_ | core::io::silent::BinarySilentStruct | private |
| get_all_comments() const | core::io::silent::SilentStruct | |
| get_CA_xyz() const override | core::io::silent::BinarySilentStruct | virtual |
| get_comment(std::string const &name) const | core::io::silent::SilentStruct | |
| get_debug_rmsd() override | core::io::silent::BinarySilentStruct | virtual |
| get_energy(std::string const &scorename) const | core::io::silent::SilentStruct | |
| get_parent_remark(std::string const &name) const | core::io::silent::SilentStruct | |
| get_parent_remark_from_line(std::string const &line) | core::io::silent::SilentStruct | |
| get_self_ptr() const | core::io::silent::SilentStruct | inline |
| get_self_ptr() | core::io::silent::SilentStruct | inline |
| get_silent_energies() | core::io::silent::SilentStruct | inline |
| get_silent_energy(std::string const &scorename) const | core::io::silent::SilentStruct | |
| get_string_value(std::string const &scorename) const | core::io::silent::SilentStruct | |
| has_comment(std::string const &name) const | core::io::silent::SilentStruct | |
| has_energy(std::string const &scorename) const | core::io::silent::SilentStruct | |
| has_parent_remark(std::string const &name) const | core::io::silent::SilentStruct | |
| init_from_lines(utility::vector1< std::string > const &lines, SilentFileData &container) override | core::io::silent::BinarySilentStruct | virtual |
| init_from_lines(utility::vector1< std::string > const &lines, SilentFileData &container, bool const skip_read_from_container) | core::io::silent::BinarySilentStruct | |
| is_symmetric() const | core::io::silent::BinarySilentStruct | inline |
| jump(Size jump_num) const | core::io::silent::BinarySilentStruct | inline |
| jumps_ | core::io::silent::BinarySilentStruct | private |
| mem_footprint() const | core::io::silent::SilentStruct | inlinevirtual |
| noncanonical_residue_connections_ | core::io::silent::BinarySilentStruct | private |
| nonconst_other_struct_list() | core::io::silent::SilentStruct | inline |
| nres() const | core::io::silent::SilentStruct | inlinevirtual |
| nres(Size nres) | core::io::silent::SilentStruct | inline |
| one_letter_sequence() const | core::io::silent::SilentStruct | |
| operator=(BinarySilentStruct const &src) | core::io::silent::BinarySilentStruct | |
| core::io::silent::SilentStruct::operator=(SilentStruct const &) | core::io::silent::SilentStruct | |
| options() const | core::io::silent::SilentStruct | |
| other_struct_list() const | core::io::silent::SilentStruct | inline |
| Parent typedef | core::io::silent::BinarySilentStruct | private |
| parse_chain_endings(std::istream &stream) | core::io::silent::BinarySilentStruct | |
| parse_energies(std::istream &input, utility::vector1< std::string > const &energy_names) | core::io::silent::SilentStruct | |
| precision(core::Size precision) | core::io::silent::SilentStruct | |
| precision() const | core::io::silent::SilentStruct | |
| print_comments(std::ostream &out) const | core::io::silent::SilentStruct | virtual |
| print_conformation(std::ostream &output) const override | core::io::silent::BinarySilentStruct | virtual |
| print_header(std::ostream &out) const override | core::io::silent::BinarySilentStruct | virtual |
| print_parent_remarks(std::ostream &out) const | core::io::silent::SilentStruct | |
| print_residue_numbers(std::ostream &out) const | core::io::silent::SilentStruct | virtual |
| print_score_header(std::ostream &out) const | core::io::silent::SilentStruct | virtual |
| print_scores(std::ostream &out) const | core::io::silent::SilentStruct | virtual |
| print_submotif_info(std::ostream &out) const | core::io::silent::SilentStruct | virtual |
| read_score_headers(std::string const &line, utility::vector1< std::string > &enames, SilentFileData &container) | core::io::silent::SilentStruct | |
| read_sequence(std::string const &line) | core::io::silent::SilentStruct | |
| rename_energies() | core::io::silent::SilentStruct | |
| residue_numbers_into_pose(pose::Pose &pose) const | core::io::silent::SilentStruct | |
| resize(Size const nres_in) | core::io::silent::BinarySilentStruct | |
| scoreline_prefix(std::string const &prefix) | core::io::silent::SilentStruct | |
| scoreline_prefix() const | core::io::silent::SilentStruct | |
| secstruct(unsigned int seqpos) const | core::io::silent::BinarySilentStruct | inline |
| secstruct(unsigned int seqpos, char ss) | core::io::silent::BinarySilentStruct | inline |
| secstruct_ | core::io::silent::BinarySilentStruct | private |
| sequence() const | core::io::silent::SilentStruct | inline |
| sequence(core::sequence::AnnotatedSequence const &sequence) | core::io::silent::SilentStruct | inline |
| set_chains(utility::vector1< char > const &chains) | core::io::silent::SilentStruct | inline |
| set_decoy_tag(std::string const &tag) | core::io::silent::SilentStruct | inline |
| set_force_bitflip(bool const setting) | core::io::silent::SilentStruct | inlinevirtual |
| set_full_model_parameters(core::pose::full_model_info::FullModelParametersCOP setting) | core::io::silent::SilentStruct | inline |
| set_residue_numbers(utility::vector1< int > const &residue_numbers) | core::io::silent::SilentStruct | inline |
| set_segment_IDs(utility::vector1< std::string > const &segids) | core::io::silent::SilentStruct | inline |
| set_tag_from_pose(const core::pose::Pose &pose) | core::io::silent::SilentStruct | |
| set_valid_energies(utility::vector1< std::string > valid) | core::io::silent::SilentStruct | |
| setup_other_poses(core::pose::Pose &pose, core::chemical::ResidueTypeSet const &residue_set) const | core::io::silent::BinarySilentStruct | |
| shared_from_this() | core::io::silent::BinarySilentStruct | inline |
| silent_energies(utility::vector1< SilentEnergy > const &new_se) | core::io::silent::SilentStruct | inline |
| SilentStruct(SilentFileOptions const &opts) | core::io::silent::SilentStruct | |
| SilentStruct(SilentStruct const &) | core::io::silent::SilentStruct | |
| sort_silent_scores() | core::io::silent::SilentStruct | |
| symmetry_info(core::conformation::symmetry::SymmetryInfo &s) | core::io::silent::BinarySilentStruct | inline |
| symmetry_info() const | core::io::silent::BinarySilentStruct | inline |
| symminfo_ | core::io::silent::BinarySilentStruct | private |
| ~BinarySilentStruct() override | core::io::silent::BinarySilentStruct | |
| ~SilentStruct() override | core::io::silent::SilentStruct | |
1.8.7