#include <StructFileRep.hh>

Inheritance diagram for core::io::StructFileRep:

Public Types
typedef std::map< std::string, core::Real >	ResidueTemps

typedef std::map< std::string, Vector >	ResidueCoords

typedef std::map< std::string, ResidueCoords >	Coords

typedef utility::vector1< std::string >	Strings

Public Member Functions
	StructFileRep ()
	Constructor. More...

	~StructFileRep () override
	empty destructor in C++ file to reduce number of necessary includes. More...

StructFileRepOP	clone () const
	Create a copy and return an owning pointer to the copy. More...

std::string const &	filename () const
	Access the name of the input/output file, if any. More...

std::string &	filename ()

std::string const &	modeltag () const
	Access the model tag. More...

std::string &	modeltag ()

HeaderInformationCOP	header () const
	Access HEADER, TITLE, EXPDTA, KEYWDS, COMPND, and AUTHOR records. More...

HeaderInformationOP &	header ()

RemarksCOP	remarks () const
	Access PDB remarks. More...

RemarksOP &	remarks ()

std::map< char, utility::vector1< std::string > > const &	chain_sequences () const
	Access the sequences for each chain. More...

std::map< char, utility::vector1< std::string > > &	chain_sequences ()

std::map< std::string, ModifiedResidueInformation > const &	modres_map () const
	Access map for storing MODRES records. More...

std::map< std::string, ModifiedResidueInformation > &	modres_map ()

std::map< std::string, std::string > const &	heterogen_names () const
	Access map for storing HETNAM records. More...

std::map< std::string, std::string > &	heterogen_names ()

std::map< std::string, utility::vector1< std::string > > const &	heterogen_synonyms () const
	Access map for storing HETSYN records. More...

std::map< std::string, utility::vector1< std::string > > &	heterogen_synonyms ()

std::map< std::string, std::string > const &	heterogen_formulae () const
	Access map for storing FORMUL records. More...

std::map< std::string, std::string > &	heterogen_formulae ()

std::map< std::string, std::pair< std::string, std::string > > const &	residue_type_base_names () const
	Access map for storing ResidueType base (non-variant) names; parsed from HETNAM records: More...

std::map< std::string, std::pair< std::string, std::string > > &	residue_type_base_names ()

std::map< std::string, char > const &	default_mainchain_connectivity () const
	Access map for storing the default main-chain connectivity for this residue, if provided by alternate 3-letter code files: More...

std::map< std::string, char > &	default_mainchain_connectivity ()

utility::vector1< HELIXInformation > const &	HELIXInformations () const
	Access map for storing HELIX records. More...

utility::vector1< HELIXInformation > &	HELIXInformations ()

utility::vector1< SHEETInformation > const &	SHEETInformations () const
	Access map for storing SHEET records. More...

utility::vector1< SHEETInformation > &	SHEETInformations ()

std::map< std::string, utility::vector1< SSBondInformation > > const &	ssbond_map () const
	Access map for storing SSBOND records. More...

std::map< std::string, utility::vector1< SSBondInformation > > &	ssbond_map ()

std::map< std::string, utility::vector1< LinkInformation > > const &	link_map () const
	Access map for storing LINK records. More...

std::map< std::string, utility::vector1< LinkInformation > > &	link_map ()

std::map< std::string, CisPeptideInformation > const &	cispep_map () const
	Access map for storing CISPEP records. More...

std::map< std::string, CisPeptideInformation > &	cispep_map ()

CrystInfo const &	crystinfo () const
	Access crystallographic information. More...

CrystInfo &	crystinfo ()

utility::vector0< ChainAtoms > const &	chains () const
	Access the actual atomic coordinates, stored as chains. More...

utility::vector0< ChainAtoms > &	chains ()

std::string const &	foldtree_string () const
	Access the The foldtree, represented as a string. More...

std::string &	foldtree_string ()

std::map< std::string, std::string > const &	pdb_comments () const
	The PDB comments, represented as a map of string->string. More...

std::map< std::string, std::string > &	pdb_comments ()

utility::vector1< std::string > const &	score_table_labels () const
	Pose Energies Table lables. More...

utility::vector1< std::string > &	score_table_labels ()

utility::vector1< core::Real > const &	score_table_weights () const
	Pose Energies Table weights. More...

utility::vector1< core::Real > &	score_table_weights ()

utility::vector1< std::vector< std::string > > const &	score_table_lines () const
	Pose Energies Table lines (Yes, std::vector is appropriate to help for cif writing of the colunns.) More...

utility::vector1< std::vector< std::string > > &	score_table_lines ()

std::string const &	score_table_filename () const
	Pose Energies table filename for PDB output. More...

std::string &	score_table_filename ()

std::map< std::string, std::string > const &	pose_cache_string_data () const
	Pose Cache - String Data. More...

std::map< std::string, std::string > &	pose_cache_string_data ()

std::map< std::string, Real > const &	pose_cache_real_data () const
	Pose Cache - Float Data. More...

std::map< std::string, Real > &	pose_cache_real_data ()

std::string const &	additional_string_output () const
	A catch-all place to store additional data for output. More...

std::string &	additional_string_output ()

simple_metrics::SimpleMetricStruct const &	simple_metric_data () const

simple_metrics::SimpleMetricStruct &	simple_metric_data ()

void	append_to_additional_string_output (std::string const &input_string)
	Append more string data to the additional_string_output_ string in the SFR. More...

Private Attributes
std::string	filename_

std::string	modeltag_

HeaderInformationOP	header_

RemarksOP	remarks_

std::map< char, utility::vector1< std::string > >	chain_sequences_

std::map< std::string, ModifiedResidueInformation >	modres_map_

std::map< std::string, std::string >	heterogen_names_

std::map< std::string, utility::vector1< std::string > >	heterogen_synonyms_

std::map< std::string, std::string >	heterogen_formulae_

std::map< std::string, std::pair< std::string, std::string > >	residue_type_base_names_

std::map< std::string, char >	default_mainchain_connectivity_

utility::vector1< HELIXInformation >	HELIXInformations_

utility::vector1< SHEETInformation >	SHEETInformations_

std::map< std::string, utility::vector1< SSBondInformation > >	ssbond_map_

std::map< std::string, utility::vector1< LinkInformation > >	link_map_

std::map< std::string, CisPeptideInformation >	cispep_map_

CrystInfo	crystinfo_

utility::vector0< ChainAtoms >	chains_

std::string	foldtree_string_

std::map< std::string, std::string >	pdb_comments_

utility::vector1< std::string >	score_table_labels_

utility::vector1< core::Real >	score_table_weights_

utility::vector1< std::vector< std::string > >	score_table_lines_

std::string	score_table_filename_

std::map< std::string, std::string >	pose_cache_string_data_

std::map< std::string, Real >	pose_cache_real_data_

std::string	additional_string_output_

simple_metrics::SimpleMetricStruct	simple_metric_data_

Detailed Description

This class is designed to store information about a structure in a "non-Rosetta" way, such that it can serve as an intermediary between various file formats and a Pose.

Remarks: This class is intended to be light, consisting primarily of simple accessors.

Member Typedef Documentation

◆ Coords

typedef std::map< std::string, ResidueCoords > core::io::StructFileRep::Coords

◆ ResidueCoords

typedef std::map< std::string, Vector > core::io::StructFileRep::ResidueCoords

◆ ResidueTemps

typedef std::map< std::string, core::Real > core::io::StructFileRep::ResidueTemps

◆ Strings

typedef utility::vector1< std::string > core::io::StructFileRep::Strings

Constructor & Destructor Documentation

◆ StructFileRep()

core::io::StructFileRep::StructFileRep ( )

Constructor.

◆ ~StructFileRep()

core::io::StructFileRep::~StructFileRep ( )

overridedefault

empty destructor in C++ file to reduce number of necessary includes.

Member Function Documentation

◆ additional_string_output() [1/2]

std::string& core::io::StructFileRep::additional_string_output ( )

inline

References additional_string_output_.

◆ additional_string_output() [2/2]

std::string const& core::io::StructFileRep::additional_string_output ( ) const

inline

A catch-all place to store additional data for output.

Each file outputter must figure out how to write this out in its output format.

References additional_string_output_.

Referenced by core::io::pdb::create_records_from_sfr().

◆ append_to_additional_string_output()

void core::io::StructFileRep::append_to_additional_string_output ( std::string const & input_string )

Append more string data to the additional_string_output_ string in the SFR.

Retains all string data already added.

References additional_string_output_.

◆ chain_sequences() [1/2]

std::map< char, utility::vector1< std::string > >& core::io::StructFileRep::chain_sequences ( )

inline

References chain_sequences_.

◆ chain_sequences() [2/2]

std::map< char, utility::vector1< std::string > > const& core::io::StructFileRep::chain_sequences ( ) const

inline

Access the sequences for each chain.

References chain_sequences_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::build_pdb_info_1_everything_but_temps(), and core::io::pdb::store_chain_sequence_record_in_sfr().

◆ chains() [1/2]

utility::vector0< ChainAtoms >& core::io::StructFileRep::chains ( )

inline

References chains_.

◆ chains() [2/2]

utility::vector0< ChainAtoms > const& core::io::StructFileRep::chains ( ) const

inline

Access the actual atomic coordinates, stored as chains.

References chains_.

Referenced by core::io::mmtf::aiPose_from_sfr(), core::io::pdb::create_records_from_sfr(), core::io::pdb::create_sfr_from_pdb_records(), core::io::pose_from_sfr::create_working_data(), protocols::electron_density::dump_points_to_search_to_pdb_or_txt(), protocols::chromophore::ReadResidueCoordinatesFromPDB::read_coordinates(), and core::io::mmtf::update_bond_indices().

◆ cispep_map() [1/2]

std::map< std::string, CisPeptideInformation >& core::io::StructFileRep::cispep_map ( )

inline

References cispep_map_.

◆ cispep_map() [2/2]

std::map< std::string, CisPeptideInformation > const& core::io::StructFileRep::cispep_map ( ) const

inline

Access map for storing CISPEP records.

Key is 6-character resID of 1st residue in the peptide bond.

References cispep_map_.

Referenced by core::io::pdb::store_cis_peptide_record_in_sfr().

◆ clone()

StructFileRepOP core::io::StructFileRep::clone ( ) const

Create a copy and return an owning pointer to the copy.

Uses the compiler-default copy constructor.

Referenced by core::import_pose::PDBSilentStruct::init_from_lines(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), and core::import_pose::PDBSilentStruct::struct_file_rep().

◆ crystinfo() [1/2]

CrystInfo& core::io::StructFileRep::crystinfo ( )

inline

References crystinfo_.

◆ crystinfo() [2/2]

CrystInfo const& core::io::StructFileRep::crystinfo ( ) const

inline

Access crystallographic information.

References crystinfo_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::build_pdb_info_1_everything_but_temps(), core::io::pdb::create_records_from_sfr(), and core::io::pdb::store_crystallographic_parameter_record_in_sfr().

◆ default_mainchain_connectivity() [1/2]

std::map< std::string, char >& core::io::StructFileRep::default_mainchain_connectivity ( )

inline

References default_mainchain_connectivity_.

◆ default_mainchain_connectivity() [2/2]

std::map< std::string, char > const& core::io::StructFileRep::default_mainchain_connectivity ( ) const

inline

Access map for storing the default main-chain connectivity for this residue, if provided by alternate 3-letter code files:

key is 6-character resID
value is a char of a single-digit integer

References default_mainchain_connectivity_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::determine_residue_branching_info(), and core::io::pose_from_sfr::PoseFromSFRBuilder::pre_process_residue_type_information().

◆ filename() [1/2]

std::string& core::io::StructFileRep::filename ( )

inline

References filename_.

◆ filename() [2/2]

std::string const& core::io::StructFileRep::filename ( ) const

inline

Access the name of the input/output file, if any.

References filename_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::build_pdb_info_1_everything_but_temps(), core::io::pdb::build_pose_from_pdb_as_is(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_5_note_discarded_atoms(), and core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff().

◆ foldtree_string() [1/2]

std::string& core::io::StructFileRep::foldtree_string ( )

inline

References foldtree_string_.

◆ foldtree_string() [2/2]

std::string const& core::io::StructFileRep::foldtree_string ( ) const

inline

Access the The foldtree, represented as a string.

Each file outputter must figure out how to write this out in its output format.

References foldtree_string_.

Referenced by core::io::pdb::create_records_from_sfr().

◆ header() [1/2]

HeaderInformationOP& core::io::StructFileRep::header ( )

inline

References header_.

◆ header() [2/2]

HeaderInformationCOP core::io::StructFileRep::header ( ) const

inline

Access HEADER, TITLE, EXPDTA, KEYWDS, COMPND, and AUTHOR records.

"header" is a misnomer, as it actually stores HEADER, TITLE, EXPDTA, KEYWDS, COMPND, and AUTHOR records.

References header_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::build_pdb_info_1_everything_but_temps(), core::io::pdb::create_records_from_sfr(), and core::io::pdb::create_sfr_from_pdb_records().

◆ HELIXInformations() [1/2]

utility::vector1< HELIXInformation >& core::io::StructFileRep::HELIXInformations ( )

inline

References HELIXInformations_.

◆ HELIXInformations() [2/2]

utility::vector1< HELIXInformation > const& core::io::StructFileRep::HELIXInformations ( ) const

inline

Access map for storing HELIX records.

These records should be essentially correct, unlike the SHEET records. NOTE that they are NOT read from the PDB by PoseFromStructFileRepConverter, only generated FROM the pose in PoseToStructFileRepConverter.

References HELIXInformations_.

Referenced by core::io::pdb::create_records_from_sfr().

◆ heterogen_formulae() [1/2]

std::map< std::string, std::string >& core::io::StructFileRep::heterogen_formulae ( )

inline

References heterogen_formulae_.

◆ heterogen_formulae() [2/2]

std::map< std::string, std::string > const& core::io::StructFileRep::heterogen_formulae ( ) const

inline

Access map for storing FORMUL records.

key is hetID
value is the chemical formula, including a potential asterisk character

References heterogen_formulae_.

Referenced by core::io::pdb::store_formula_record_in_sfr().

◆ heterogen_names() [1/2]

std::map< std::string, std::string >& core::io::StructFileRep::heterogen_names ( )

inline

References heterogen_names_.

◆ heterogen_names() [2/2]

std::map< std::string, std::string > const& core::io::StructFileRep::heterogen_names ( ) const

inline

Access map for storing HETNAM records.

key is hetID
value is the chemical name field

References heterogen_names_.

Referenced by core::io::pdb::create_records_from_sfr(), and core::io::pdb::store_heterogen_name_record_in_sfr().

◆ heterogen_synonyms() [1/2]

std::map< std::string, utility::vector1< std::string > >& core::io::StructFileRep::heterogen_synonyms ( )

inline

References heterogen_synonyms_.

◆ heterogen_synonyms() [2/2]

std::map< std::string, utility::vector1< std::string > > const& core::io::StructFileRep::heterogen_synonyms ( ) const

inline

Access map for storing HETSYN records.

key is hetID
value is the chemical synonym list field

References heterogen_synonyms_.

Referenced by core::io::pdb::store_heterogen_synonym_record_in_sfr().

◆ link_map() [1/2]

std::map< std::string, utility::vector1< LinkInformation > >& core::io::StructFileRep::link_map ( )

inline

References link_map_.

◆ link_map() [2/2]

std::map< std::string, utility::vector1< LinkInformation > > const& core::io::StructFileRep::link_map ( ) const

inline

Access map for storing LINK records.

Key is 6-character resID of 1st residue in link.

Note: (A vector is needed because a single saccharide residue can have multiple branches.)

References link_map_.

Referenced by core::io::mmtf::add_link_and_ss_information(), core::io::pdb::create_records_from_sfr(), core::pose::get_constraints_from_link_records(), core::io::pose_from_sfr::PoseFromSFRBuilder::lower_terminus_is_occupied_according_to_link_map(), core::io::pose_from_sfr::PoseFromSFRBuilder::pre_process_residue_type_information(), core::io::pose_from_sfr::PoseFromSFRBuilder::setup(), core::io::pdb::store_link_record_in_sfr(), and core::io::pose_from_sfr::PoseFromSFRBuilder::upper_terminus_is_occupied_according_to_link_map().

◆ modeltag() [1/2]

std::string& core::io::StructFileRep::modeltag ( )

inline

References modeltag_.

◆ modeltag() [2/2]

std::string const& core::io::StructFileRep::modeltag ( ) const

inline

Access the model tag.

References modeltag_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::build_pdb_info_1_everything_but_temps(), and core::io::pdb::create_sfr_from_pdb_records().

◆ modres_map() [1/2]

std::map< std::string, ModifiedResidueInformation >& core::io::StructFileRep::modres_map ( )

inline

References modres_map_.

◆ modres_map() [2/2]

std::map< std::string, ModifiedResidueInformation > const& core::io::StructFileRep::modres_map ( ) const

inline

Access map for storing MODRES records.

Key is 6-character resID of the modified residue.

References modres_map_.

Referenced by core::io::pdb::store_mod_res_record_in_sfr().

◆ pdb_comments() [1/2]

std::map< std::string, std::string >& core::io::StructFileRep::pdb_comments ( )

inline

References pdb_comments_.

◆ pdb_comments() [2/2]

std::map< std::string, std::string > const& core::io::StructFileRep::pdb_comments ( ) const

inline

The PDB comments, represented as a map of string->string.

Each file outputter must figure out how to write this out in its output format.

References pdb_comments_.

Referenced by core::io::pdb::create_records_from_sfr(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), and core::io::pdb::store_unknown_records_in_sfr().

◆ pose_cache_real_data() [1/2]

std::map< std::string, Real>& core::io::StructFileRep::pose_cache_real_data ( )

inline

References pose_cache_real_data_.

◆ pose_cache_real_data() [2/2]

std::map< std::string, Real > const& core::io::StructFileRep::pose_cache_real_data ( ) const

inline

Pose Cache - Float Data.

Each file outputter must figure out how to write this out in its output format.

References pose_cache_real_data_.

Referenced by core::io::pdb::create_records_from_sfr(), core::io::pose_data_cache_from_sfr(), and core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose().

◆ pose_cache_string_data() [1/2]

std::map< std::string, std::string >& core::io::StructFileRep::pose_cache_string_data ( )

inline

References pose_cache_string_data_.

◆ pose_cache_string_data() [2/2]

std::map< std::string, std::string > const& core::io::StructFileRep::pose_cache_string_data ( ) const

inline

Pose Cache - String Data.

Each file outputter must figure out how to write this out in its output format.

References pose_cache_string_data_.

Referenced by core::io::pdb::create_records_from_sfr(), core::io::pose_data_cache_from_sfr(), and core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose().

◆ remarks() [1/2]

RemarksOP& core::io::StructFileRep::remarks ( )

inline

References remarks_.

◆ remarks() [2/2]

RemarksCOP core::io::StructFileRep::remarks ( ) const

inline

Access PDB remarks.

References remarks_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::build_pdb_info_1_everything_but_temps(), core::io::pdb::create_records_from_sfr(), and core::io::pdb::create_sfr_from_pdb_records().

◆ residue_type_base_names() [1/2]

std::map< std::string, std::pair< std::string, std::string > >& core::io::StructFileRep::residue_type_base_names ( )

inline

References residue_type_base_names_.

◆ residue_type_base_names() [2/2]

std::map< std::string, std::pair< std::string, std::string > > const& core::io::StructFileRep::residue_type_base_names ( ) const

inline

Access map for storing ResidueType base (non-variant) names; parsed from HETNAM records:

key is 6-character resID
first value of pair is 3-letter-code; second value of pair is the base_name.

References residue_type_base_names_.

Referenced by core::io::pdb::create_records_from_sfr(), core::io::pose_from_sfr::PoseFromSFRBuilder::determine_residue_branching_info(), core::io::pose_from_sfr::PoseFromSFRBuilder::get_rsd_type(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_1_split_and_merge_residues_as_necessary(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_quick_and_dirty_resolve_residue_types(), core::io::pose_from_sfr::PoseFromSFRBuilder::pre_process_residue_type_information(), and core::io::pdb::store_base_residue_type_name_in_sfr().

◆ score_table_filename() [1/2]

std::string& core::io::StructFileRep::score_table_filename ( )

inline

References score_table_filename_.

◆ score_table_filename() [2/2]

std::string const& core::io::StructFileRep::score_table_filename ( ) const

inline

Pose Energies table filename for PDB output.

References score_table_filename_.

Referenced by core::io::pose_energies_from_sfr().

◆ score_table_labels() [1/2]

utility::vector1< std::string >& core::io::StructFileRep::score_table_labels ( )

inline

References score_table_labels_.

◆ score_table_labels() [2/2]

utility::vector1< std::string > const& core::io::StructFileRep::score_table_labels ( ) const

inline

Pose Energies Table lables.

Each file outputter must figure out how to write this out in its output format.

References score_table_labels_.

Referenced by core::io::pdb::create_records_from_sfr(), and core::io::pose_energies_from_sfr().

◆ score_table_lines() [1/2]

utility::vector1< std::vector< std::string > >& core::io::StructFileRep::score_table_lines ( )

inline

References score_table_lines_.

◆ score_table_lines() [2/2]

utility::vector1< std::vector< std::string > > const& core::io::StructFileRep::score_table_lines ( ) const

inline

Pose Energies Table lines (Yes, std::vector is appropriate to help for cif writing of the colunns.)

Each file outputter must figure out how to write this out in its output format.

References score_table_lines_.

Referenced by core::io::pdb::create_records_from_sfr(), and core::io::pose_energies_from_sfr().

◆ score_table_weights() [1/2]

utility::vector1< core::Real >& core::io::StructFileRep::score_table_weights ( )

inline

References score_table_weights_.

◆ score_table_weights() [2/2]

utility::vector1< core::Real > const& core::io::StructFileRep::score_table_weights ( ) const

inline

Pose Energies Table weights.

Each file outputter must figure out how to write this out in its output format.

References score_table_weights_.

Referenced by core::io::pose_energies_from_sfr().

◆ SHEETInformations() [1/2]

utility::vector1< SHEETInformation >& core::io::StructFileRep::SHEETInformations ( )

inline

References SHEETInformations_.

◆ SHEETInformations() [2/2]

utility::vector1< SHEETInformation > const& core::io::StructFileRep::SHEETInformations ( ) const

inline

Access map for storing SHEET records.

These records are cheating on the PDB rules and just storing individual strands as 1-strand sheets. NOTE that they are NOT read from the PDB by PoseFromStructFileRepConverter, only generated FROM the pose in PoseToStructFileRepConverter.

References SHEETInformations_.

Referenced by core::io::pdb::create_records_from_sfr().

◆ simple_metric_data() [1/2]

simple_metrics::SimpleMetricStruct& core::io::StructFileRep::simple_metric_data ( )

inline

References simple_metric_data_.

◆ simple_metric_data() [2/2]

simple_metrics::SimpleMetricStruct const& core::io::StructFileRep::simple_metric_data ( ) const

inline

References simple_metric_data_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose().

◆ ssbond_map() [1/2]

std::map< std::string, utility::vector1< SSBondInformation > >& core::io::StructFileRep::ssbond_map ( )

inline

References ssbond_map_.

◆ ssbond_map() [2/2]

std::map< std::string, utility::vector1< SSBondInformation > > const& core::io::StructFileRep::ssbond_map ( ) const

inline

Access map for storing SSBOND records.

key is 6-character resID of 1st residue in ssbond

Note: (A vector is needed because to futureproof if we ever handle weird disorder situations.)

References ssbond_map_.

Referenced by core::io::mmtf::add_link_and_ss_information(), core::io::pdb::create_records_from_sfr(), core::pose::disulfide_pairs_from_sfr(), and core::io::pdb::store_ssbond_record_in_sfr().

Member Data Documentation

◆ additional_string_output_

std::string core::io::StructFileRep::additional_string_output_

private

Referenced by additional_string_output(), and append_to_additional_string_output().

◆ chain_sequences_

std::map< char, utility::vector1< std::string > > core::io::StructFileRep::chain_sequences_

private

Referenced by chain_sequences().

◆ chains_

utility::vector0< ChainAtoms > core::io::StructFileRep::chains_

private

Referenced by chains().

◆ cispep_map_

std::map< std::string, CisPeptideInformation > core::io::StructFileRep::cispep_map_

private

Referenced by cispep_map().

◆ crystinfo_

CrystInfo core::io::StructFileRep::crystinfo_

private

Referenced by crystinfo().

◆ default_mainchain_connectivity_

std::map< std::string, char > core::io::StructFileRep::default_mainchain_connectivity_

private

Referenced by default_mainchain_connectivity().

◆ filename_

std::string core::io::StructFileRep::filename_

private

Referenced by filename().

◆ foldtree_string_

std::string core::io::StructFileRep::foldtree_string_

private

Referenced by foldtree_string().

◆ header_

HeaderInformationOP core::io::StructFileRep::header_

private

Referenced by header().

◆ HELIXInformations_

utility::vector1< HELIXInformation > core::io::StructFileRep::HELIXInformations_

private

Referenced by HELIXInformations().

◆ heterogen_formulae_

std::map< std::string, std::string > core::io::StructFileRep::heterogen_formulae_

private

Referenced by heterogen_formulae().

◆ heterogen_names_

std::map< std::string, std::string > core::io::StructFileRep::heterogen_names_

private

Referenced by heterogen_names().

◆ heterogen_synonyms_

std::map< std::string, utility::vector1< std::string > > core::io::StructFileRep::heterogen_synonyms_

private

Referenced by heterogen_synonyms().

◆ link_map_

std::map< std::string, utility::vector1< LinkInformation > > core::io::StructFileRep::link_map_

private

Referenced by link_map().

◆ modeltag_

std::string core::io::StructFileRep::modeltag_

private

Referenced by modeltag().

◆ modres_map_

std::map< std::string, ModifiedResidueInformation > core::io::StructFileRep::modres_map_

private

Referenced by modres_map().

◆ pdb_comments_

std::map< std::string, std::string > core::io::StructFileRep::pdb_comments_

private

Referenced by pdb_comments().

◆ pose_cache_real_data_

std::map< std::string, Real > core::io::StructFileRep::pose_cache_real_data_

private

Referenced by pose_cache_real_data().

◆ pose_cache_string_data_

std::map< std::string, std::string > core::io::StructFileRep::pose_cache_string_data_

private

Referenced by pose_cache_string_data().

◆ remarks_

RemarksOP core::io::StructFileRep::remarks_

private

Referenced by remarks().

◆ residue_type_base_names_

std::map< std::string, std::pair< std::string, std::string > > core::io::StructFileRep::residue_type_base_names_

private

Referenced by residue_type_base_names().

◆ score_table_filename_

std::string core::io::StructFileRep::score_table_filename_

private

Referenced by score_table_filename().

◆ score_table_labels_

utility::vector1< std::string > core::io::StructFileRep::score_table_labels_

private

Referenced by score_table_labels().

◆ score_table_lines_

utility::vector1< std::vector < std::string > > core::io::StructFileRep::score_table_lines_

private

Referenced by score_table_lines().

◆ score_table_weights_

utility::vector1< core::Real > core::io::StructFileRep::score_table_weights_

private

Referenced by score_table_weights().

◆ SHEETInformations_

utility::vector1< SHEETInformation > core::io::StructFileRep::SHEETInformations_

private

Referenced by SHEETInformations().

◆ simple_metric_data_

simple_metrics::SimpleMetricStruct core::io::StructFileRep::simple_metric_data_

private

Referenced by simple_metric_data().

◆ ssbond_map_

std::map< std::string, utility::vector1< SSBondInformation > > core::io::StructFileRep::ssbond_map_

private

Referenced by ssbond_map().

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

src/core/io/StructFileRep.hh
src/core/io/StructFileRep.cc

Public Types

Public Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ Coords

◆ ResidueCoords

◆ ResidueTemps

◆ Strings

Constructor & Destructor Documentation

◆ StructFileRep()

◆ ~StructFileRep()

Member Function Documentation

◆ additional_string_output() [1/2]

◆ additional_string_output() [2/2]

◆ append_to_additional_string_output()

◆ chain_sequences() [1/2]

◆ chain_sequences() [2/2]

◆ chains() [1/2]

◆ chains() [2/2]

◆ cispep_map() [1/2]

◆ cispep_map() [2/2]

◆ clone()

◆ crystinfo() [1/2]

◆ crystinfo() [2/2]

◆ default_mainchain_connectivity() [1/2]

◆ default_mainchain_connectivity() [2/2]

◆ filename() [1/2]

◆ filename() [2/2]

◆ foldtree_string() [1/2]

◆ foldtree_string() [2/2]

◆ header() [1/2]

◆ header() [2/2]

◆ HELIXInformations() [1/2]

◆ HELIXInformations() [2/2]

◆ heterogen_formulae() [1/2]

◆ heterogen_formulae() [2/2]

◆ heterogen_names() [1/2]

◆ heterogen_names() [2/2]

◆ heterogen_synonyms() [1/2]

◆ heterogen_synonyms() [2/2]

◆ link_map() [1/2]

◆ link_map() [2/2]

◆ modeltag() [1/2]

◆ modeltag() [2/2]

◆ modres_map() [1/2]

◆ modres_map() [2/2]

◆ pdb_comments() [1/2]

◆ pdb_comments() [2/2]

◆ pose_cache_real_data() [1/2]

◆ pose_cache_real_data() [2/2]

◆ pose_cache_string_data() [1/2]

◆ pose_cache_string_data() [2/2]

◆ remarks() [1/2]

◆ remarks() [2/2]

◆ residue_type_base_names() [1/2]

◆ residue_type_base_names() [2/2]

◆ score_table_filename() [1/2]

◆ score_table_filename() [2/2]

◆ score_table_labels() [1/2]

◆ score_table_labels() [2/2]

◆ score_table_lines() [1/2]

◆ score_table_lines() [2/2]

◆ score_table_weights() [1/2]

◆ score_table_weights() [2/2]

◆ SHEETInformations() [1/2]

◆ SHEETInformations() [2/2]

◆ simple_metric_data() [1/2]

◆ simple_metric_data() [2/2]

◆ ssbond_map() [1/2]

◆ ssbond_map() [2/2]

Member Data Documentation

◆ additional_string_output_

◆ chain_sequences_

◆ chains_

◆ cispep_map_

◆ crystinfo_

◆ default_mainchain_connectivity_

◆ filename_

◆ foldtree_string_