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Rosetta
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The PoseFromSFRBuilder is responsible for taking a partially-processed representation of a structure file, a structure-file repersentation or StructFileRep, and it constructs a Pose from it. Its primary output is a Pose, but it also keeps track of the "missing atoms:" the set of atoms in the Pose whose coordinates were not given in the original file. More...
#include <PoseFromSFRBuilder.hh>
Public Member Functions | |
| PoseFromSFRBuilder (chemical::ResidueTypeSetCOP rts, StructFileRepOptions const &options) | |
| ~PoseFromSFRBuilder () | |
| void | build_pose (StructFileRep const &sfr, pose::Pose &pose) |
| Build a Pose from an SFR using the ResidueTypeSet and the StructFileReaderOptions object that were passed in to the Builder in it's constructor. More... | |
| id::AtomID_Mask const & | missing_atoms () const |
| not present in the SFR More... | |
Private Member Functions | |
| void | setup (StructFileRep const &sfr) |
| void | pass_1_split_and_merge_residues_as_necessary () |
| void | pass_2_resolve_residue_types () |
| void | pass_2_quick_and_dirty_resolve_residue_types () |
| void | pass_3_verify_sufficient_backbone_atoms () |
| void | pass_4_redo_termini () |
| void | pass_5_note_discarded_atoms () |
| void | build_initial_pose (pose::Pose &pose) |
| void | refine_pose (pose::Pose &pose) |
| void | build_pdb_info_1_everything_but_temps (pose::Pose &pose) |
| void | build_pdb_info_2_temps (pose::Pose &pose) |
| bool | update_atom_information_based_on_occupancy (AtomInformation &ai) const |
| void | randomize_missing_coords (AtomInformation &ai) const |
| randomize missing density More... | |
| void | 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) |
| This function uses linkage information to determine main-chain and branch polymer connectivity. More... | |
| void | pre_process_residue_type_information () |
| bool | is_residue_type_recognized (Size const pdb_residue_index, std::string const &rosetta_residue_name3, core::chemical::ResidueTypeCOPs const &rsd_type_list) |
| bool | is_residue_type_recognized (Size const pdb_residue_index, std::string const &rosetta_residue_name3, bool &is_chemical_component_derived) |
| Query the ResidueTypeSet using the residue-type-finder for a potential match based on the name3 that has possibly been remapped by Rosetta through the Nomenclature manager. More... | |
| bool | d_l_threeletter_codes_are_same_for_aa (std::string const &name3, bool const error_on_unrecognized) const |
| Given an amino acid three-letter code, retrive a residue. If the residue is an alpha- or beta-amino acid, also retrieve its mirrored type. Return true if the three-letter codes are the same, false if they differ. If no resiude type could be loaded or there is no mirror type, throw if error_on_unrecognized is true, and return false otherwise. More... | |
| chemical::ResidueTypeCOP | 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) |
| bool | lower_terminus_is_occupied_according_to_link_map (std::string const &resid) |
| bool | upper_terminus_is_occupied_according_to_link_map (std::string const &resid) |
| void | convert_nucleic_acid_residue_info_to_standard () |
| Size | prev_residue_skipping_merges (Size resid) const |
| Returns the input resid if it's either the first residue or it's the second residue and the first residue has a mrb_merge_w_next behavior specified. More... | |
| Size | prev_residue_skipping_null_residue_types (Size resid) const |
| Returns the input resid if it's the first residue that has a non-null-pointing entry in the residue_types_ array. More... | |
| Size | next_residue_skipping_merges (Size resid) const |
| Returns the input resid if it's either the last residue or it's the second-to-last residue and the last residue has a mrb_merge_w_prev behavior specified. More... | |
| Size | next_residue_skipping_null_residue_types (Size resid) const |
| Returns the input resid if it's the last residue that has a non-null-pointing entry in the residue_types_ array. More... | |
| bool | determine_separate_chemical_entity (char chainID) const |
| bool | determine_same_chain_prev (Size resid, bool separate_chemical_entity) const |
| bool | determine_same_chain_next (Size resid, bool separate_chemical_entity) const |
| bool | determine_check_Ntermini_for_this_chain (char chainID) const |
| bool | determine_check_Ctermini_for_this_chain (char chainID) const |
| void | fill_name_map (Size seqpos) |
| Size | find_atom_tree_root_for_metal_ion (utility::vector1< core::conformation::ResidueOP > const &context, conformation::ResidueCOP metal_rsd) |
| bool | last_residue_was_recognized (Size seqpos) const |
| void | remember_unrecognized_res (core::Size rinfo_index) |
| void | output_ignore_water_warning_once () |
| Tell user about ancient Rosetta choice to ignore HOH waters if -ignore_unrecognized_res is set. More... | |
| core::conformation::ResidueOP | add_variant_type_to_residue (core::conformation::ResidueOP rsd, core::chemical::VariantType const variant_type, core::pose::Pose const &pose) |
The PoseFromSFRBuilder is responsible for taking a partially-processed representation of a structure file, a structure-file repersentation or StructFileRep, and it constructs a Pose from it. Its primary output is a Pose, but it also keeps track of the "missing atoms:" the set of atoms in the Pose whose coordinates were not given in the original file.
The construction involves renaming some atoms, for example, the O2* atom in RNA would be renamed O2', and resolving the chain- and branch-connectivity. It uses the ResidueTypeFinder to select the best-fit ResidueType for each residue.
This code handles n-terminal acetylation, and some other similar chemical modifications, by merging the atoms in the "ACE" residue with the next residue. Instructions of what residue types to merge and how to rename the atoms to avoid naming collisions are read in from the database by the MergeAndSplitBehaviorManager. After the atoms are merged and renamed, the appropriate AcetylatedNtermProteinFull is applied to that next residue.
The process of building a pose is handled in four passes.
| core::io::pose_from_sfr::PoseFromSFRBuilder::PoseFromSFRBuilder | ( | chemical::ResidueTypeSetCOP | rts, |
| StructFileRepOptions const & | options | ||
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References core::conformation::ResidueFactory::create_residue(), and core::pose::Pose::residue_type_set_for_pose().
Referenced by build_initial_pose().
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References add_variant_type_to_residue(), core::pose::Pose::append_residues(), protocols::loops::chainID, core::io::pose_from_sfr::check_and_correct_sister_atoms(), core::pose::Pose::conformation(), coordinates_assigned_, determine_check_Ntermini_for_this_chain(), core::sequence::end, find_atom_tree_root_for_metal_ion(), core::conformation::Conformation::insert_chain_ending(), core::chemical::ResidueType::is_lower_terminus(), is_lower_terminus_, core::chemical::ResidueType::is_upper_terminus(), core::pose::is_upper_terminus(), last_residue_was_recognized(), core::sequence::left, core::chemical::LOWER_TERMINUS_VARIANT, core::chemical::LOWERTERM_TRUNC_VARIANT, core::io::StructFileRepOptions::missing_dens_as_jump(), core::chemical::ResidueType::n_rings(), core::chemical::ResidueTypeBase::name(), core::chemical::ResidueTypeBase::name3(), options_, pose_temps_, pose_to_rinfo_, remapped_atom_names_, residue_types_, rinfos_, core::chemical::ResidueType::ring_conformer_set(), same_chain_prev_, core::io::pose_from_sfr::TR(), core::chemical::UPPER_TERMINUS_VARIANT, core::chemical::UPPERTERM_TRUNC_VARIANT, and protocols::kinmatch::xyz().
Referenced by build_pose().
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References core::io::StructFileRep::chain_sequences(), core::io::ResidueInformation::chainID(), core::io::StructFileRep::crystinfo(), core::io::StructFileRep::filename(), core::io::StructFileRep::header(), core::io::ResidueInformation::iCode(), core::io::StructFileRep::modeltag(), options_, core::pose::Pose::pdb_info(), pose_to_rinfo_, core::io::StructFileRepOptions::preserve_crystinfo(), core::io::StructFileRepOptions::preserve_header(), core::io::StructFileRep::remarks(), core::io::ResidueInformation::resSeq(), rinfos_, core::io::ResidueInformation::segmentID(), sfr_, core::pose::Pose::size(), and unrecognized_atoms_.
Referenced by refine_pose().
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Now that the final residue types have been set for the Pose, it is safe to set the temperature data in the PDBInfo.
References core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::has(), core::pose::Pose::pdb_info(), pose_to_rinfo_, remapped_atom_names_, core::pose::Pose::residue_type(), rinfos_, core::pose::Pose::size(), and core::io::pose_from_sfr::TR().
Referenced by refine_pose().
| void core::io::pose_from_sfr::PoseFromSFRBuilder::build_pose | ( | StructFileRep const & | sfr, |
| pose::Pose & | pose | ||
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Build a Pose from an SFR using the ResidueTypeSet and the StructFileReaderOptions object that were passed in to the Builder in it's constructor.
The process of building a Pose occurs in several phases. First, in the setup() function, the builder converts the SFR into a vector of ResidueInformation objects – renaming some atoms along the way. The next five phases involve five passes over this ResidueInformation vector.
References build_initial_pose(), core::pose::Pose::clear(), core::pose::Pose::conformation(), core::io::StructFileRepOptions::fast_restyping(), options_, pass_1_split_and_merge_residues_as_necessary(), pass_2_quick_and_dirty_resolve_residue_types(), pass_2_resolve_residue_types(), pass_3_verify_sufficient_backbone_atoms(), pass_4_redo_termini(), pass_5_note_discarded_atoms(), refine_pose(), core::conformation::Conformation::reset_residue_type_set_for_conf(), residue_type_set_, and setup().
Referenced by core::import_pose::build_pose_as_is(), core::io::pdb::build_pose_from_pdb_as_is(), and core::io::pose_from_pose().
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References core::io::ResidueInformation::atoms(), core::io::StructFileRepOptions::guarantee_no_DNA(), core::io::NomenclatureManager::is_old_DNA(), core::io::NomenclatureManager::is_old_RNA(), core::io::pose_from_sfr::missing_O2prime(), core::io::AtomInformation::name, nfix_, options_, core::io::ResidueInformation::rename_atom(), core::io::ResidueInformation::resName(), rinfos_, core::io::StructFileRepOptions::show_all_fixes(), showed_nfix_warning_, and core::io::pose_from_sfr::TR().
Referenced by pass_1_split_and_merge_residues_as_necessary().
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Given an amino acid three-letter code, retrive a residue. If the residue is an alpha- or beta-amino acid, also retrieve its mirrored type. Return true if the three-letter codes are the same, false if they differ. If no resiude type could be loaded or there is no mirror type, throw if error_on_unrecognized is true, and return false otherwise.
References core::chemical::ResidueTypeFinder::get_representative_type(), core::chemical::ResidueTypeFinder::name3(), and residue_type_set_.
Referenced by pass_2_resolve_residue_types().
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This function uses linkage information to determine main-chain and branch polymer connectivity.
This function does three separate things that are related:
References core::chemical::carbohydrates::CarbohydrateInfoManager::anomeric_position_from_code(), protocols::loops::chainID, core::io::StructFileRep::default_mainchain_connectivity(), core::chemical::carbohydrates::CarbohydrateInfoManager::is_valid_sugar_code(), next_residue_skipping_merges(), resid_to_index_, core::io::StructFileRep::residue_type_base_names(), protocols::loops::resSeq, rinfos_, same_chain_prev_, sfr_, and core::io::pose_from_sfr::TR().
Referenced by pass_2_quick_and_dirty_resolve_residue_types(), and pass_2_resolve_residue_types().
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References next_residue_skipping_merges(), rinfos_, and same_chain_prev_.
Referenced by pass_2_quick_and_dirty_resolve_residue_types(), and pass_2_resolve_residue_types().
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modifies the remapped_atom_names_ bimap at position seqpos given the names that are in residue_types_[ seqpos ]
References core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atom_name(), core::io::ResidueInformation::atoms(), core::chemical::ResidueType::has(), core::chemical::ResidueTypeBase::name3(), options_, core::io::pose_from_sfr::remap_names_on_geometry(), core::chemical::ResidueTypeBase::remap_pdb_atom_names(), remapped_atom_names_, residue_types_, core::io::StructFileRepOptions::residues_for_atom_name_remapping(), rinfos_, and core::io::ResidueInformation::xyz().
Referenced by pass_2_quick_and_dirty_resolve_residue_types(), pass_2_resolve_residue_types(), and pass_4_redo_termini().
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References core::chemical::ResidueTypeFinder::check_nucleic_acid_virtual_phosphates(), core::chemical::ResidueTypeFinder::connect_atoms(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::chemical::D_AA, core::chemical::DEPROTONATED, core::chemical::ResidueTypeFinder::disallow_variants(), core::chemical::ResidueTypeFinder::discouraged_properties(), core::chemical::DISULFIDE_BONDED, core::chemical::ResidueTypeFinder::get_best_match_residue_type_for_atom_names(), core::chemical::ResidueTypeFinder::ignore_atom_named_H(), core::pose::is_lower_terminus(), core::pose::is_upper_terminus(), core::io::StructFileRepOptions::keep_input_protonation_state(), core::chemical::L_AA, core::chemical::LOWER_TERMINUS, core::chemical::ResidueTypeFinder::name3(), options_, core::chemical::ResidueTypeFinder::patch_names(), core::chemical::ResidueTypeFinder::preferred_properties(), core::chemical::PROTONATED, core::chemical::ResidueTypeFinder::residue_base_name(), core::io::StructFileRep::residue_type_base_names(), residue_type_set_, rinfos_, sfr_, core::chemical::UPPER_TERMINUS, update_ResidueType_enum_files::variants, core::chemical::ResidueTypeFinder::variants(), and protocols::kinmatch::xyz().
Referenced by pass_2_resolve_residue_types().
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Query the ResidueTypeSet using the residue-type-finder for a potential match based on the name3 that has possibly been remapped by Rosetta through the Nomenclature manager.
References core::chemical::ResidueTypeFinder::get_representative_type(), is_residue_type_recognized(), and core::chemical::ResidueTypeFinder::name3().
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Look at a list of potential residue types and finding the best one, and record the set of unrecognized atoms.
References core::io::StructFileRepOptions::ignore_unrecognized_res(), core::io::StructFileRepOptions::ignore_waters(), core::chemical::carbohydrates::CarbohydrateInfoManager::is_valid_sugar_code(), options_, output_ignore_water_warning_once(), core::io::StructFileRepOptions::remember_unrecognized_res(), remember_unrecognized_res(), and core::io::StructFileRepOptions::remember_unrecognized_water().
Referenced by is_residue_type_recognized(), and pass_2_resolve_residue_types().
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References prev_residue_skipping_merges(), and residue_was_recognized_.
Referenced by build_initial_pose(), and pass_2_resolve_residue_types().
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| id::AtomID_Mask const & core::io::pose_from_sfr::PoseFromSFRBuilder::missing_atoms | ( | ) | const |
not present in the SFR
References missing_.
Referenced by core::import_pose::build_pose_as_is(), and pass_5_note_discarded_atoms().
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Returns the input resid if it's either the last residue or it's the second-to-last residue and the last residue has a mrb_merge_w_prev behavior specified.
References merge_behaviors_, core::chemical::io::mrb_merge_w_prev, and rinfos_.
Referenced by determine_residue_branching_info(), and determine_same_chain_next().
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Returns the input resid if it's the last residue that has a non-null-pointing entry in the residue_types_ array.
References residue_types_.
Referenced by pass_4_redo_termini().
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Tell user about ancient Rosetta choice to ignore HOH waters if -ignore_unrecognized_res is set.
References core::io::StructFileRepOptions::ignore_unrecognized_res(), core::io::StructFileRepOptions::ignore_waters(), options_, outputted_ignored_water_warning_, and core::io::pose_from_sfr::TR().
Referenced by is_residue_type_recognized(), and pass_2_quick_and_dirty_resolve_residue_types().
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References core::io::ResidueInformation::append_atom(), core::io::ResidueInformation::atoms(), core::io::ResidueInformation::chainID(), convert_nucleic_acid_residue_info_to_standard(), core::io::pose_from_sfr::create_working_data(), core::sequence::end, core::io::ResidueInformation::iCode(), is_lower_terminus_, merge_atom_maps_, merge_behaviors_, core::chemical::io::mrb_do_not_merge, core::chemical::io::mrb_merge_w_next, core::chemical::io::mrb_merge_w_prev, core::io::AtomInformation::name, options_, remapped_atom_names_, core::io::ResidueInformation::resid(), resid_to_index_, core::io::StructFileRep::residue_type_base_names(), residue_type_set_, residue_types_, residue_was_recognized_, core::io::ResidueInformation::resName(), core::io::ResidueInformation::resSeq(), rinfos_, same_chain_prev_, core::io::ResidueInformation::segmentID(), sfr_, core::io::ResidueInformation::terCount(), core::id::to_string(), and core::io::pose_from_sfr::TR().
Referenced by build_pose().
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Like the pass_2_resolve_residue_types() function above. However, we assume that if the three letter code corresponds to a (full!) name of the ResidueType, unless we have the full name of the ResidueType specified in the HETNAM records (this should be written by the PDB writer). Failing that, we assume that the residue comes from the CCD.
References protocols::cluster::calibur::aa, core::chemical::aa_from_name(), core::chemical::aa_his, core::io::ResidueInformation::chainID(), protocols::loops::chainID, core::chemical::ResidueTypeFinder::connect_atoms(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, determine_check_Ctermini_for_this_chain(), determine_check_Ntermini_for_this_chain(), determine_residue_branching_info(), determine_same_chain_next(), determine_same_chain_prev(), determine_separate_chemical_entity(), fill_name_map(), core::io::pose_from_sfr::find_restype(), core::chemical::FULL_ATOM_t, core::chemical::full_name_from_aa(), core::chemical::ResidueTypeFinder::get_representative_type(), core::io::StructFileRepOptions::ignore_unrecognized_res(), core::io::StructFileRepOptions::ignore_waters(), core::chemical::is_aa_name_unknown(), core::pose::is_lower_terminus(), is_lower_terminus_, core::pose::is_upper_terminus(), core::chemical::carbohydrates::CarbohydrateInfoManager::is_valid_sugar_code(), known_links_, core::chemical::LOWER_TERMINUS, lower_terminus_is_occupied_according_to_link_map(), core::chemical::ResidueTypeFinder::name3(), options_, output_ignore_water_warning_once(), pre_process_residue_type_information(), update_ResidueType_enum_files::properties, core::chemical::ResidueTypeFinder::properties(), core::io::StructFileRepOptions::remember_unrecognized_res(), remember_unrecognized_res(), core::io::StructFileRepOptions::remember_unrecognized_water(), core::io::ResidueInformation::resid(), core::chemical::ResidueTypeFinder::residue_base_name(), core::io::StructFileRep::residue_type_base_names(), residue_type_set_, residue_types_, residue_was_recognized_, rinfos_, core::io::ResidueInformation::rosetta_resName(), same_chain_prev_, sfr_, core::id::to_string(), core::io::pose_from_sfr::TR(), core::chemical::UPPER_TERMINUS, upper_terminus_is_occupied_according_to_link_map(), update_ResidueType_enum_files::variants, core::chemical::ResidueTypeFinder::variants(), core::chemical::VIRTUAL_DNA_PHOSPHATE, core::chemical::VIRTUAL_PHOSPHATE, and core::io::ResidueInformation::xyz().
Referenced by build_pose().
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at the end of this pass, the residue_types_ array will have a pointer to the ResidueType used for each entry in the rinfos_ array. Any null pointer entry in this array should be interpreted as an unrecognized, unreadable, or otherwise unread residue.
References core::io::ResidueInformation::chainID(), protocols::loops::chainID, d_l_threeletter_codes_are_same_for_aa(), core::chemical::detect_ld_chirality_from_polymer_residue(), determine_check_Ctermini_for_this_chain(), determine_check_Ntermini_for_this_chain(), determine_residue_branching_info(), determine_same_chain_next(), determine_same_chain_prev(), determine_separate_chemical_entity(), fill_name_map(), get_rsd_type(), core::pose::is_lower_terminus(), is_lower_terminus_, is_residue_type_recognized(), core::pose::is_upper_terminus(), known_links_, last_residue_was_recognized(), lower_terminus_is_occupied_according_to_link_map(), merge_behaviors_, core::chemical::io::mrb_merge_w_next, core::chemical::io::mrb_merge_w_prev, pre_process_residue_type_information(), core::io::ResidueInformation::resid(), residue_types_, residue_was_recognized_, rinfos_, core::io::ResidueInformation::rosetta_resName(), same_chain_prev_, core::id::to_string(), core::io::pose_from_sfr::TR(), upper_terminus_is_occupied_according_to_link_map(), core::io::ResidueInformation::xyz(), and protocols::kinmatch::xyz().
Referenced by build_pose().
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Check for missing mainchain atoms; if there is no contiguous block of 3 mainchain atoms that are not missing, then we will be unable to build an initial stub, or to fill in the coordinates of those missing atoms, so, we will have to reject the residue.
References core::chemical::ResidueType::atom_being_shadowed(), core::chemical::ResidueType::atom_name(), core::io::StructFileRepOptions::exit_if_missing_heavy_atoms(), core::chemical::ResidueTypeBase::is_polymer(), core::chemical::ResidueType::mainchain_atoms(), core::chemical::ResidueTypeBase::name(), options_, remapped_atom_names_, residue_types_, residue_was_recognized_, rinfos_, core::io::pose_from_sfr::TR(), and protocols::kinmatch::xyz().
Referenced by build_pose().
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Now take another pass over the residue types and for those residues that are now the first residue of their chain (because the residue(s) before them had insufficient backbone atoms) add the lower- or upper-termini variants to their residue types. This behavior means that Rosetta will end up modeling chemistry that isn't there – and so this is more than a little questionable. Alternatively, this code could and maybe should add the truncation variants to the residue types.
References core::io::ResidueInformation::chainID(), protocols::loops::chainID, core::chemical::CUTPOINT_UPPER, determine_check_Ctermini_for_this_chain(), determine_check_Ntermini_for_this_chain(), fill_name_map(), core::pose::is_lower_terminus(), core::pose::is_upper_terminus(), known_links_, core::chemical::LOWER_TERMINUS_VARIANT, next_residue_skipping_null_residue_types(), prev_residue_skipping_null_residue_types(), core::io::ResidueInformation::resid(), residue_type_set_, residue_types_, rinfos_, core::io::pose_from_sfr::TR(), and core::chemical::UPPER_TERMINUS_VARIANT.
Referenced by build_pose().
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References core::io::StructFileRep::filename(), is_lower_terminus_, core::sequence::left, missing_atoms(), remapped_atom_names_, residue_types_, rinfos_, sfr_, core::io::pose_from_sfr::TR(), and protocols::kinmatch::xyz().
Referenced by build_pose().
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Common code from the pass_2 functions which do some (not computationally intensive) ResidueType annotation.
References core::io::add_glycan_links_to_map(), core::io::StructFileRepOptions::auto_detect_glycan_connections(), protocols::vip::base_name(), core::io::StructFileRep::default_mainchain_connectivity(), core::io::determine_glycan_links(), core::sequence::end, core::io::explicit_links_from_sfr_linkage(), core::io::fix_glycan_order(), glycan_positions_, core::chemical::carbohydrates::CarbohydrateInfoManager::is_valid_sugar_code(), known_links_, core::io::StructFileRep::link_map(), core::io::StructFileRepOptions::maintain_links(), options_, core::io::ResidueInformation::resid(), resid_to_index_, core::io::StructFileRep::residue_type_base_names(), core::io::ResidueInformation::resName(), rinfos_, same_chain_prev_, sfr_, and core::io::pose_from_sfr::TR().
Referenced by pass_2_quick_and_dirty_resolve_residue_types(), and pass_2_resolve_residue_types().
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Returns the input resid if it's either the first residue or it's the second residue and the first residue has a mrb_merge_w_next behavior specified.
References merge_behaviors_, and core::chemical::io::mrb_merge_w_next.
Referenced by determine_same_chain_prev(), and last_residue_was_recognized().
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Returns the input resid if it's the first residue that has a non-null-pointing entry in the residue_types_ array.
References residue_types_.
Referenced by pass_4_redo_termini().
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randomize missing density
Referenced by core::io::pose_from_sfr::update_atom_information_based_on_occupancy().
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References core::pose::add_comment(), core::chemical::ICoorAtomID::atom_id(), core::conformation::Residue::atom_index(), core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atom_is_hydrogen(), core::chemical::ResidueType::atom_name(), core::id::AtomID::BOGUS_ATOM_ID(), core::chemical::AtomICoor::build(), build_pdb_info_1_everything_but_temps(), build_pdb_info_2_temps(), core::pose::Pose::conformation(), core::io::StructFileRepOptions::constraints_from_link_records(), core::conformation::Conformation::contains_carbohydrate_residues(), coordinates_assigned_, core::conformation::Conformation::declare_chemical_bond(), core::chemical::AtomICoor::depends_on_polymer_lower(), core::chemical::AtomICoor::depends_on_polymer_upper(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_pseudobonds(), core::conformation::Conformation::fill_missing_atoms(), core::scoring::cryst::fix_bfactorsH(), core::scoring::cryst::fix_bfactorsMissing(), core::pose::get_constraints_from_link_records(), core::simple_metrics::get_sm_data(), core::chemical::ResidueType::has(), core::simple_metrics::SimpleMetricStruct::has_data(), core::conformation::Residue::has_incomplete_connection(), core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueType::icoor(), core::conformation::Residue::icoor(), core::pose::initialize_atomid_map(), core::pose::initialize_disulfide_bonds(), core::pose::ncbb::initialize_ncbbs(), core::chemical::ResidueType::is_carbohydrate(), core::io::pose_from_sfr::is_connected(), core::chemical::ResidueTypeBase::is_DNA(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueType::is_upper_terminus(), known_links_, missing_, core::chemical::ResidueTypeBase::mode(), core::chemical::ResidueTypeBase::name(), core::chemical::ResidueType::natoms(), core::io::StructFileRepOptions::no_detect_pseudobonds(), options_, core::chemical::PATCH_LINKER, core::io::mmtf::pdb_comments, core::io::StructFileRep::pdb_comments(), core::pose::Pose::pdb_info(), core::io::StructFileRep::pose_cache_real_data(), core::io::StructFileRep::pose_cache_string_data(), pose_to_rinfo_, core::io::StructFileRepOptions::preserve_crystinfo(), core::pose::replace_pose_residue_copying_existing_coordinates(), resid_to_index_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), rinfos_, core::conformation::Conformation::set_xyz(), core::pose::setPoseExtraScore(), core::conformation::Conformation::setup_glycan_trees(), sfr_, core::io::pose_from_sfr::show_residue_connections(), core::io::StructFileRep::simple_metric_data(), core::pose::Pose::size(), core::chemical::AtomICoor::stub_atom1(), core::chemical::AtomICoor::stub_atom2(), core::chemical::AtomICoor::stub_atom3(), core::io::pose_from_sfr::TR(), core::conformation::Residue::type(), unrecognized_atoms_, and core::chemical::VIRTUAL_DNA_PHOSPHATE.
Referenced by build_pose().
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References rinfos_, core::io::ResidueInformation::rosetta_resName(), core::io::ResidueInformation::temps(), core::io::pose_from_sfr::TR(), unrecognized_atoms_, core::io::ResidueInformation::xyz(), and protocols::kinmatch::xyz().
Referenced by is_residue_type_recognized(), and pass_2_quick_and_dirty_resolve_residue_types().
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References core::chemical::ResidueTypeFinder::get_representative_type(), core::io::StructFileRepOptions::ignore_sugars(), core::io::NomenclatureManager::is_metal(), core::io::NomenclatureManager::is_sugar(), core::io::StructFileRep::link_map(), missing_, core::chemical::ResidueTypeFinder::name3(), options_, core::id::AtomID_Map< T >::resize(), sfr_, and core::io::pose_from_sfr::TR().
Referenced by build_pose().
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Referenced by core::io::pose_from_sfr::create_working_data().
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Referenced by build_initial_pose(), and refine_pose().
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Referenced by pre_process_residue_type_information().
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Referenced by pass_1_split_and_merge_residues_as_necessary().
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Referenced by missing_atoms(), refine_pose(), and setup().
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Used for nucleic acid input.
Referenced by convert_nucleic_acid_residue_info_to_standard().
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Referenced by build_initial_pose(), build_pdb_info_1_everything_but_temps(), build_pose(), convert_nucleic_acid_residue_info_to_standard(), determine_check_Ctermini_for_this_chain(), determine_check_Ntermini_for_this_chain(), determine_separate_chemical_entity(), fill_name_map(), get_rsd_type(), is_residue_type_recognized(), output_ignore_water_warning_once(), pass_1_split_and_merge_residues_as_necessary(), pass_2_quick_and_dirty_resolve_residue_types(), pass_3_verify_sufficient_backbone_atoms(), pre_process_residue_type_information(), refine_pose(), and setup().
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Referenced by output_ignore_water_warning_once().
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Referenced by build_initial_pose().
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Referenced by build_initial_pose(), build_pdb_info_1_everything_but_temps(), build_pdb_info_2_temps(), and refine_pose().
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Referenced by build_initial_pose(), fill_name_map(), next_residue_skipping_null_residue_types(), pass_1_split_and_merge_residues_as_necessary(), pass_2_quick_and_dirty_resolve_residue_types(), pass_2_resolve_residue_types(), pass_3_verify_sufficient_backbone_atoms(), pass_4_redo_termini(), pass_5_note_discarded_atoms(), and prev_residue_skipping_null_residue_types().
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Referenced by build_initial_pose(), build_pdb_info_1_everything_but_temps(), build_pdb_info_2_temps(), convert_nucleic_acid_residue_info_to_standard(), determine_residue_branching_info(), determine_same_chain_next(), determine_same_chain_prev(), fill_name_map(), get_rsd_type(), next_residue_skipping_merges(), pass_1_split_and_merge_residues_as_necessary(), pass_2_quick_and_dirty_resolve_residue_types(), pass_2_resolve_residue_types(), pass_3_verify_sufficient_backbone_atoms(), pass_4_redo_termini(), pass_5_note_discarded_atoms(), pre_process_residue_type_information(), refine_pose(), and remember_unrecognized_res().
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Referenced by build_initial_pose(), determine_residue_branching_info(), determine_same_chain_next(), determine_same_chain_prev(), pass_1_split_and_merge_residues_as_necessary(), pass_2_quick_and_dirty_resolve_residue_types(), pass_2_resolve_residue_types(), and pre_process_residue_type_information().
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Referenced by build_pdb_info_1_everything_but_temps(), determine_residue_branching_info(), get_rsd_type(), lower_terminus_is_occupied_according_to_link_map(), pass_1_split_and_merge_residues_as_necessary(), pass_2_quick_and_dirty_resolve_residue_types(), pass_5_note_discarded_atoms(), pre_process_residue_type_information(), refine_pose(), setup(), and upper_terminus_is_occupied_according_to_link_map().
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Used for nucleic acid input.
Referenced by convert_nucleic_acid_residue_info_to_standard().
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Referenced by build_pdb_info_1_everything_but_temps(), refine_pose(), and remember_unrecognized_res().
1.9.1