pdb_reader.cc File Reference

Function definitions for reading of .pdb files. More...

#include <core/io/pdb/pdb_reader.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/io/pdb/Field.hh>
#include <core/io/pdb/RecordCollection.hh>
#include <core/io/StructFileRep.hh>
#include <core/io/StructFileReaderOptions.hh>
#include <core/io/HeaderInformation.hh>
#include <core/io/Remarks.hh>
#include <utility/string_constants.hh>
#include <utility/string_util.hh>
#include <basic/Tracer.hh>
#include <ObjexxFCL/string.functions.hh>
#include <algorithm>
#include <sstream>
#include <map>
#include <core/io/AtomInformation.hh>

Namespaces
	core
	A class for reading in the atom type properties.
	core::io
	core::io::pdb

Functions
static basic::Tracer	TR ("core.io.pdb.pdb_reader")
Record	core::io::pdb::create_record_from_pdb_line (std::string const &line)
	Convert a .pdb file line into a Record data structure. More...
utility::vector1< Record >	core::io::pdb::create_records_from_pdb_lines (utility::vector1< std::string > const &lines)
	Create a list of .pdb format records from the lines from a .pdb file. More...
utility::vector1< Record >	core::io::pdb::create_records_from_pdb_file_contents (std::string const &pdb_contents)
	Create a list of .pdb format records from the entire contents of a .pdb file. More...
StructFileRep	core::io::pdb::create_sfr_from_pdb_records (utility::vector1< Record > &records, StructFileReaderOptions const &options)
	Create a representation of structural file data from a list of .pdb format records with options. More...
StructFileRep	core::io::pdb::create_sfr_from_pdb_records (utility::vector1< Record > &records)
	Create a representation of structural file data from a list of .pdb format records. More...
StructFileRep	core::io::pdb::create_sfr_from_pdb_file_contents (std::string const &pdb_contents, StructFileReaderOptions const &options)
	Create a representation of structural file data from .pdb file contents with options. More...
StructFileRep	core::io::pdb::create_sfr_from_pdb_file_contents (std::string const &pdb_contents)
	Create a representation of structural file data from .pdb file contents. More...
void	core::io::pdb::store_chain_sequence_record_in_sfr (Record seqres_record, StructFileRep &sfr)
	Create a representation of structural file data from a .pdb file by file. More...
void	core::io::pdb::store_mod_res_record_in_sfr (Record modres_record, StructFileRep &sfr)
	Convert .pdb MODRES record into SFR data. More...
void	core::io::pdb::store_base_residue_type_name_in_sfr (std::string const &hetID, std::string const &text_field, StructFileRep &sfr)
	Parse .pdb HETNAM text field to extract full resID and convert into SFR data. More...
void	core::io::pdb::store_heterogen_name_record_in_sfr (Record hetnam_record, StructFileRep &sfr)
	Convert .pdb HETNAM record into SFR data. More...
void	core::io::pdb::store_heterogen_synonym_record_in_sfr (Record hetsyn_record, StructFileRep &sfr)
	Convert .pdb HETSYN record into SFR data. More...
void	core::io::pdb::store_formula_record_in_sfr (Record formul_record, StructFileRep &sfr)
	Convert .pdb FORMUL record into SFR data. More...
void	core::io::pdb::store_ssbond_record_in_sfr (Record ssbond_record, StructFileRep &sfr)
	Convert .pdb SSBOND record into SFR data. More...
void	core::io::pdb::store_link_record_in_sfr (Record link_record, StructFileRep &sfr)
	Convert .pdb LINK record into SFR data. More...
void	core::io::pdb::store_cis_peptide_record_in_sfr (Record cispep_record, StructFileRep &sfr)
	Convert .pdb CISPEP record into SFR data. More...
void	core::io::pdb::store_crystallographic_parameter_record_in_sfr (Record crystal_record, StructFileRep &sfr)
	Convert .pdb CRYST1 record into SFR data. More...
void	core::io::pdb::store_unknown_records_in_sfr (utility::vector1< Record > unknown_records, StructFileRep &sfr)
	Parse and store unknown record types into SFR data. More...

Detailed Description

Function definitions for reading of .pdb files.

Author

Sergey Lyskov (Serge.nosp@m.y.Ly.nosp@m.skov@.nosp@m.jhu..nosp@m.edu)

Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

Note

We may perhaps decide in the future to wrap this functionality in a class. ~Labonte

Function Documentation

TR()

static basic::Tracer TR ( "core.io.pdb.pdb_reader"  )

static