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core::io::pose_from_sfr::PoseFromSFRBuilder Class Reference

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_merge_residues_as_necessary ()
 
void pass_2_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...
 
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...
 
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 (core::pose::Pose const &pose, conformation::ResidueCOP metal_rsd)
 
bool last_residue_was_recognized (Size seqpos) const
 
void output_ignore_water_warning_once ()
 Tell user about ancient Rosetta choice to ignore HOH waters if -ignore_unrecognized_res is set. More...
 

Private Attributes

chemical::ResidueTypeSetCOP residue_type_set_
 
StructFileRep sfr_
 
StructFileRepOptions options_
 
id::AtomID_Mask missing_
 
utility::vector1
< core::io::ResidueInformation
rinfos_
 
std::map< std::string, core::Sizeresid_to_index_
 
id::NamedAtomID_Mask coordinates_assigned_
 
utility::vector1< Sizepose_to_rinfo_
 
utility::vector1
< StructFileRep::ResidueTemps
pose_temps_
 
utility::vector1
< core::pose::UnrecognizedAtomRecord
unrecognized_atoms_
 
StructFileRep::Strings branch_lower_termini_
 
StructFileRep::Strings branch_lower_termini_extra_
 
utility::vector1
< chemical::merge_residue_behavior
merge_behaviors_
 
utility::vector1< std::map
< std::string, std::string > > 
merge_atom_maps_
 
utility::vector1< core::Sizeglycan_positions_
 
utility::vector1< std::string > glycan_tree_roots_
 
utility::vector1
< chemical::ResidueTypeCOP
residue_types_
 
utility::vector1< NameBimapremapped_atom_names_
 
utility::vector1< boolis_lower_terminus_
 
utility::vector1< boolsame_chain_prev_
 
utility::vector1< boolresidue_was_recognized_
 
std::map< std::string,
std::map< std::string,
std::pair< std::string,
std::string > > > 
known_links_
 
bool outputted_ignored_water_warning_
 
core::Size nfix_
 Used for nucleic acid input. More...
 
bool showed_nfix_warning_
 Used for nucleic acid input. More...
 

Detailed Description

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 MergeBehaviorManager. 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.

Constructor & Destructor Documentation

core::io::pose_from_sfr::PoseFromSFRBuilder::PoseFromSFRBuilder ( chemical::ResidueTypeSetCOP  rts,
StructFileRepOptions const &  options 
)
core::io::pose_from_sfr::PoseFromSFRBuilder::~PoseFromSFRBuilder ( )
default

Member Function Documentation

void core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose ( pose::Pose pose)
private

References core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), protocols::loops::chainID, core::io::pose_from_sfr::check_and_correct_sister_atoms(), core::pose::Pose::conformation(), core::conformation::Conformation::contains_carbohydrate_residues(), coordinates_assigned_, determine_check_Ntermini_for_this_chain(), core::sequence::end, find_atom_tree_root_for_metal_ion(), core::chemical::ResidueTypeBase::has_variant_type(), core::conformation::Conformation::insert_chain_ending(), core::chemical::ResidueType::is_carbohydrate(), is_lower_terminus_, core::chemical::ResidueTypeBase::is_polymer(), core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueTypeBase::is_RNA(), core::chemical::ResidueType::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_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), residue_types_, rinfos_, core::chemical::ResidueType::ring_conformer_set(), same_chain_prev_, core::pose::Pose::size(), core::io::pose_from_sfr::TR(), core::chemical::UPPER_TERMINUS_VARIANT, core::chemical::UPPERTERM_TRUNC_VARIANT, and protocols::kinmatch::xyz().

Referenced by build_pose().

void core::io::pose_from_sfr::PoseFromSFRBuilder::build_pdb_info_1_everything_but_temps ( pose::Pose pose)
private
void core::io::pose_from_sfr::PoseFromSFRBuilder::build_pdb_info_2_temps ( pose::Pose pose)
private
void core::io::pose_from_sfr::PoseFromSFRBuilder::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.

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(), pass_1_merge_residues_as_necessary(), 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().

void core::io::pose_from_sfr::PoseFromSFRBuilder::convert_nucleic_acid_residue_info_to_standard ( )
private
bool core::io::pose_from_sfr::PoseFromSFRBuilder::determine_check_Ctermini_for_this_chain ( char  chainID) const
private
bool core::io::pose_from_sfr::PoseFromSFRBuilder::determine_check_Ntermini_for_this_chain ( char  chainID) const
private
void core::io::pose_from_sfr::PoseFromSFRBuilder::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 
)
private

This function uses linkage information to determine main-chain and branch polymer connectivity.

This function does three separate things that are related:

  • It determines which atoms on this residue are listed as chemically connected to other residues
  • It assigns main-chain connectivity to carbohydrate ResidueType base names.
  • It turns off implicit connections to the next residue for carbohydrates where we don't know linkage information.

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_resolve_residue_types().

bool core::io::pose_from_sfr::PoseFromSFRBuilder::determine_same_chain_next ( Size  resid,
bool  separate_chemical_entity 
) const
private
bool core::io::pose_from_sfr::PoseFromSFRBuilder::determine_same_chain_prev ( Size  resid,
bool  separate_chemical_entity 
) const
private
bool core::io::pose_from_sfr::PoseFromSFRBuilder::determine_separate_chemical_entity ( char  chainID) const
private
void core::io::pose_from_sfr::PoseFromSFRBuilder::fill_name_map ( Size  seqpos)
private
Size core::io::pose_from_sfr::PoseFromSFRBuilder::find_atom_tree_root_for_metal_ion ( core::pose::Pose const &  pose,
conformation::ResidueCOP  metal_rsd 
)
private
chemical::ResidueTypeCOP core::io::pose_from_sfr::PoseFromSFRBuilder::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 
)
private
bool core::io::pose_from_sfr::PoseFromSFRBuilder::is_residue_type_recognized ( Size const  pdb_residue_index,
std::string const &  rosetta_residue_name3,
core::chemical::ResidueTypeCOPs const &  rsd_type_list 
)
private
bool core::io::pose_from_sfr::PoseFromSFRBuilder::is_residue_type_recognized ( Size const  pdb_residue_index,
std::string const &  rosetta_residue_name3,
bool is_chemical_component_derived 
)
private

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().

bool core::io::pose_from_sfr::PoseFromSFRBuilder::last_residue_was_recognized ( Size  seqpos) const
private
bool core::io::pose_from_sfr::PoseFromSFRBuilder::lower_terminus_is_occupied_according_to_link_map ( std::string const &  resid)
private
id::AtomID_Mask const & core::io::pose_from_sfr::PoseFromSFRBuilder::missing_atoms ( ) const

not present in the SFR

References missing_.

Referenced by pass_5_note_discarded_atoms().

Size core::io::pose_from_sfr::PoseFromSFRBuilder::next_residue_skipping_merges ( Size  resid) const
private

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::mrb_merge_w_prev, and rinfos_.

Referenced by determine_residue_branching_info(), and determine_same_chain_next().

Size core::io::pose_from_sfr::PoseFromSFRBuilder::next_residue_skipping_null_residue_types ( Size  resid) const
private

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().

void core::io::pose_from_sfr::PoseFromSFRBuilder::output_ignore_water_warning_once ( )
private

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().

void core::io::pose_from_sfr::PoseFromSFRBuilder::pass_1_merge_residues_as_necessary ( )
private
void core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_resolve_residue_types ( )
private

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::add_glycan_links_to_map(), core::io::StructFileRepOptions::auto_detect_glycan_connections(), protocols::vip::base_name(), core::io::ResidueInformation::chainID(), protocols::loops::chainID, core::io::StructFileRep::default_mainchain_connectivity(), core::chemical::detect_ld_chirality_from_polymer_residue(), determine_check_Ctermini_for_this_chain(), determine_check_Ntermini_for_this_chain(), core::io::determine_glycan_links(), determine_residue_branching_info(), determine_same_chain_next(), determine_same_chain_prev(), determine_separate_chemical_entity(), core::sequence::end, core::io::explicit_links_from_sfr_linkage(), fill_name_map(), core::io::fix_glycan_order(), get_rsd_type(), glycan_positions_, core::pose::is_lower_terminus(), is_lower_terminus_, is_residue_type_recognized(), core::pose::is_upper_terminus(), known_links_, last_residue_was_recognized(), core::io::StructFileRep::link_map(), lower_terminus_is_occupied_according_to_link_map(), core::io::StructFileRepOptions::maintain_links(), merge_behaviors_, core::chemical::mrb_merge_w_next, core::chemical::mrb_merge_w_prev, options_, core::io::ResidueInformation::resid(), resid_to_index_, core::io::StructFileRep::residue_type_base_names(), residue_types_, residue_was_recognized_, core::io::ResidueInformation::resName(), rinfos_, core::io::ResidueInformation::rosetta_resName(), same_chain_prev_, sfr_, 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().

void core::io::pose_from_sfr::PoseFromSFRBuilder::pass_3_verify_sufficient_backbone_atoms ( )
private

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_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().

void core::io::pose_from_sfr::PoseFromSFRBuilder::pass_4_redo_termini ( )
private

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(), protocols::stepwise::modeler::is_protein(), 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().

void core::io::pose_from_sfr::PoseFromSFRBuilder::pass_5_note_discarded_atoms ( )
private
Size core::io::pose_from_sfr::PoseFromSFRBuilder::prev_residue_skipping_merges ( Size  resid) const
private

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::mrb_merge_w_next.

Referenced by determine_same_chain_prev(), and last_residue_was_recognized().

Size core::io::pose_from_sfr::PoseFromSFRBuilder::prev_residue_skipping_null_residue_types ( Size  resid) const
private

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().

void core::io::pose_from_sfr::PoseFromSFRBuilder::randomize_missing_coords ( AtomInformation ai) const
private
void core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose ( pose::Pose pose)
private

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::conformation::Residue::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::conformation::Residue::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::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), known_links_, missing_, core::chemical::ResidueTypeBase::mode(), core::chemical::ResidueTypeBase::name(), core::conformation::Residue::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().

void core::io::pose_from_sfr::PoseFromSFRBuilder::setup ( StructFileRep const &  sfr)
private
bool core::io::pose_from_sfr::PoseFromSFRBuilder::update_atom_information_based_on_occupancy ( AtomInformation ai) const
private
bool core::io::pose_from_sfr::PoseFromSFRBuilder::upper_terminus_is_occupied_according_to_link_map ( std::string const &  resid)
private

Member Data Documentation

StructFileRep::Strings core::io::pose_from_sfr::PoseFromSFRBuilder::branch_lower_termini_
private
StructFileRep::Strings core::io::pose_from_sfr::PoseFromSFRBuilder::branch_lower_termini_extra_
private
id::NamedAtomID_Mask core::io::pose_from_sfr::PoseFromSFRBuilder::coordinates_assigned_
private

Referenced by build_initial_pose(), and refine_pose().

utility::vector1< core::Size > core::io::pose_from_sfr::PoseFromSFRBuilder::glycan_positions_
private
utility::vector1< std::string > core::io::pose_from_sfr::PoseFromSFRBuilder::glycan_tree_roots_
private
utility::vector1< bool > core::io::pose_from_sfr::PoseFromSFRBuilder::is_lower_terminus_
private
std::map< std::string, std::map< std::string, std::pair< std::string, std::string > > > core::io::pose_from_sfr::PoseFromSFRBuilder::known_links_
private
utility::vector1< std::map< std::string, std::string > > core::io::pose_from_sfr::PoseFromSFRBuilder::merge_atom_maps_
private
utility::vector1< chemical::merge_residue_behavior > core::io::pose_from_sfr::PoseFromSFRBuilder::merge_behaviors_
private
id::AtomID_Mask core::io::pose_from_sfr::PoseFromSFRBuilder::missing_
private

Referenced by missing_atoms(), refine_pose(), and setup().

core::Size core::io::pose_from_sfr::PoseFromSFRBuilder::nfix_
private

Used for nucleic acid input.

Referenced by convert_nucleic_acid_residue_info_to_standard().

StructFileRepOptions core::io::pose_from_sfr::PoseFromSFRBuilder::options_
private
bool core::io::pose_from_sfr::PoseFromSFRBuilder::outputted_ignored_water_warning_
private
utility::vector1< StructFileRep::ResidueTemps> core::io::pose_from_sfr::PoseFromSFRBuilder::pose_temps_
private

Referenced by build_initial_pose().

utility::vector1< Size > core::io::pose_from_sfr::PoseFromSFRBuilder::pose_to_rinfo_
private
utility::vector1< NameBimap > core::io::pose_from_sfr::PoseFromSFRBuilder::remapped_atom_names_
private
std::map< std::string, core::Size > core::io::pose_from_sfr::PoseFromSFRBuilder::resid_to_index_
private
chemical::ResidueTypeSetCOP core::io::pose_from_sfr::PoseFromSFRBuilder::residue_type_set_
private
utility::vector1< chemical::ResidueTypeCOP > core::io::pose_from_sfr::PoseFromSFRBuilder::residue_types_
private
utility::vector1< bool > core::io::pose_from_sfr::PoseFromSFRBuilder::residue_was_recognized_
private
utility::vector1< core::io::ResidueInformation > core::io::pose_from_sfr::PoseFromSFRBuilder::rinfos_
private
utility::vector1< bool > core::io::pose_from_sfr::PoseFromSFRBuilder::same_chain_prev_
private
StructFileRep core::io::pose_from_sfr::PoseFromSFRBuilder::sfr_
private
bool core::io::pose_from_sfr::PoseFromSFRBuilder::showed_nfix_warning_
private

Used for nucleic acid input.

Referenced by convert_nucleic_acid_residue_info_to_standard().

utility::vector1< core::pose::UnrecognizedAtomRecord > core::io::pose_from_sfr::PoseFromSFRBuilder::unrecognized_atoms_
private

The documentation for this class was generated from the following files: