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core::io::StructFileRep Class Reference

#include <StructFileRep.hh>

Inheritance diagram for core::io::StructFileRep:
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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...
 
HeaderInformationOPheader ()
 
RemarksCOP remarks () const
 Access PDB remarks. More...
 
RemarksOPremarks ()
 
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...
 
CrystInfocrystinfo ()
 
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::SimpleMetricStructsimple_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< ChainAtomschains_
 
std::string foldtree_string_
 
std::map< std::string,
std::string > 
pdb_comments_
 
utility::vector1< std::string > score_table_labels_
 
utility::vector1< core::Realscore_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, Realpose_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

typedef std::map< std::string, ResidueCoords > core::io::StructFileRep::Coords
typedef std::map< std::string, Vector > core::io::StructFileRep::ResidueCoords
typedef std::map< std::string, core::Real > core::io::StructFileRep::ResidueTemps
typedef utility::vector1< std::string > core::io::StructFileRep::Strings

Constructor & Destructor Documentation

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

Constructor.

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

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

Member Function Documentation

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().

std::string& core::io::StructFileRep::additional_string_output ( )
inline
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_.

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

References chain_sequences_.

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

References chains_.

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().

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

References cispep_map_.

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

References crystinfo_.

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::pass_2_resolve_residue_types().

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

References filename_.

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().

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

References foldtree_string_.

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(), and core::io::pdb::create_records_from_sfr().

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

References header_.

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().

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

References HELIXInformations_.

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().

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

References heterogen_formulae_.

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().

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

References heterogen_names_.

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().

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

References heterogen_synonyms_.

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

References link_map_.

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

References modeltag_.

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().

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

References modres_map_.

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().

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

References pdb_comments_.

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().

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

References pose_cache_real_data_.

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().

std::map< std::string, std::string >& core::io::StructFileRep::pose_cache_string_data ( )
inline
RemarksCOP core::io::StructFileRep::remarks ( ) const
inline
RemarksOP& core::io::StructFileRep::remarks ( )
inline

References remarks_.

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_2_resolve_residue_types(), and core::io::pdb::store_base_residue_type_name_in_sfr().

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

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

References score_table_filename_.

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().

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

References score_table_labels_.

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().

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

References score_table_lines_.

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().

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

References score_table_weights_.

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().

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

References SHEETInformations_.

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

References simple_metric_data_.

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::initialize_disulfide_bonds(), and core::io::pdb::store_ssbond_record_in_sfr().

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

References ssbond_map_.

Member Data Documentation

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

Referenced by chain_sequences().

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

Referenced by chains().

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

Referenced by cispep_map().

CrystInfo core::io::StructFileRep::crystinfo_
private

Referenced by crystinfo().

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

Referenced by filename().

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

Referenced by foldtree_string().

HeaderInformationOP core::io::StructFileRep::header_
private

Referenced by header().

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

Referenced by HELIXInformations().

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

Referenced by heterogen_formulae().

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

Referenced by heterogen_names().

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

Referenced by heterogen_synonyms().

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

Referenced by link_map().

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

Referenced by modeltag().

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

Referenced by modres_map().

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

Referenced by pdb_comments().

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

Referenced by pose_cache_real_data().

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

Referenced by pose_cache_string_data().

RemarksOP core::io::StructFileRep::remarks_
private

Referenced by remarks().

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

Referenced by residue_type_base_names().

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

Referenced by score_table_filename().

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

Referenced by score_table_labels().

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

Referenced by score_table_lines().

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

Referenced by score_table_weights().

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

Referenced by SHEETInformations().

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

Referenced by simple_metric_data().

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: