| branch_lower_termini_ | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| branch_lower_termini_extra_ | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| build_initial_pose(pose::Pose &pose) | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| build_pdb_info_1_everything_but_temps(pose::Pose &pose) | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| build_pdb_info_2_temps(pose::Pose &pose) | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| build_pose(StructFileRep const &sfr, pose::Pose &pose) | core::io::pose_from_sfr::PoseFromSFRBuilder | |
| convert_nucleic_acid_residue_info_to_standard() | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| coordinates_assigned_ | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| d_l_threeletter_codes_are_same_for_aa(std::string const &name3, bool const error_on_unrecognized) const | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| determine_check_Ctermini_for_this_chain(char chainID) const | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| determine_check_Ntermini_for_this_chain(char chainID) const | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| determine_residue_branching_info(Size seqpos, utility::vector1< std::string > &known_connect_atoms_on_this_residue, std::map< std::string, std::map< std::string, std::pair< std::string, std::string > > > const &explicit_link_mapping) | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| determine_same_chain_next(Size resid, bool separate_chemical_entity) const | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| determine_same_chain_prev(Size resid, bool separate_chemical_entity) const | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| determine_separate_chemical_entity(char chainID) const | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| fill_name_map(Size seqpos) | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| find_atom_tree_root_for_metal_ion(core::pose::Pose const &pose, conformation::ResidueCOP metal_rsd) | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| get_rsd_type(std::string const &name3, Size seqpos, utility::vector1< std::string > const &known_connect_atoms_on_this_residue, std::string const &resid, bool const is_lower_terminus, bool const is_upper_terminus, bool const is_d_aa, bool const is_l_aa) | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| glycan_positions_ | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| glycan_tree_roots_ | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| is_lower_terminus_ | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| is_residue_type_recognized(Size const pdb_residue_index, std::string const &rosetta_residue_name3, core::chemical::ResidueTypeCOPs const &rsd_type_list) | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| is_residue_type_recognized(Size const pdb_residue_index, std::string const &rosetta_residue_name3, bool &is_chemical_component_derived) | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| known_links_ | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| last_residue_was_recognized(Size seqpos) const | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| lower_terminus_is_occupied_according_to_link_map(std::string const &resid) | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| merge_atom_maps_ | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| merge_behaviors_ | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| missing_ | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| missing_atoms() const | core::io::pose_from_sfr::PoseFromSFRBuilder | |
| next_residue_skipping_merges(Size resid) const | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| next_residue_skipping_null_residue_types(Size resid) const | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| nfix_ | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| options_ | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| output_ignore_water_warning_once() | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| outputted_ignored_water_warning_ | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| pass_1_merge_residues_as_necessary() | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| pass_2_resolve_residue_types() | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| pass_3_verify_sufficient_backbone_atoms() | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| pass_4_redo_termini() | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| pass_5_note_discarded_atoms() | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| pose_temps_ | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| pose_to_rinfo_ | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| PoseFromSFRBuilder(chemical::ResidueTypeSetCOP rts, StructFileRepOptions const &options) | core::io::pose_from_sfr::PoseFromSFRBuilder | |
| prev_residue_skipping_merges(Size resid) const | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| prev_residue_skipping_null_residue_types(Size resid) const | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| randomize_missing_coords(AtomInformation &ai) const | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| refine_pose(pose::Pose &pose) | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| remapped_atom_names_ | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| resid_to_index_ | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| residue_type_set_ | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| residue_types_ | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| residue_was_recognized_ | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| rinfos_ | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| same_chain_prev_ | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| setup(StructFileRep const &sfr) | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| sfr_ | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| showed_nfix_warning_ | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| unrecognized_atoms_ | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| update_atom_information_based_on_occupancy(AtomInformation &ai) const | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| upper_terminus_is_occupied_according_to_link_map(std::string const &resid) | core::io::pose_from_sfr::PoseFromSFRBuilder | private |
| ~PoseFromSFRBuilder() | core::io::pose_from_sfr::PoseFromSFRBuilder | |
1.8.7