Rosetta Core  2014.35
Static Public Member Functions | List of all members
core::io::pdb::PDB_DReader Class Reference

PDB Reader itself, D - for dynamic approach of type handling. More...

#include <pdb_dynamic_reader.hh>

Static Public Member Functions

static Record mapStringToRecord (const String &s)
 creating record from given string. Also, read Field values from string. More...
 
static String createPDBString (const Record &R)
 Reverse opearation - create PDB string from given Record. More...
 
static std::vector< Record > parse (const String &)
 Parse whole PDB string and return vector of records in order they was in PDB. More...
 
static FileData createFileData (std::vector< Record > &)
 create File data sturcture from array of Records. More...
 
static FileData createFileData (std::vector< Record > &, PDB_DReaderOptions const &options)
 create File data sturcture from array of Records and a set of options. More...
 
static FileData createFileData (const String &data)
 create File data sturcture from string containing PDB information. More...
 
static FileData createFileData (const String &data, PDB_DReaderOptions const &options)
 create File data sturcture from string containing PDB information and a set of options. More...
 
static String createPDBData (FileData const &fd)
 create PDB-like string to represent given FileData object More...
 
static utility::vector1
< std::string > 		createPDBData_vector (FileData const &fd)
 create PDB-like vector of string to represent given FileData object. More...
 
static std::vector< Record > createRecords (FileData const &fd)
 create vector of records for given FileData object. More...
 

Detailed Description

PDB Reader itself, D - for dynamic approach of type handling.

Member Function Documentation

FileData core::io::pdb::PDB_DReader::createFileData ( std::vector< Record > &  VR)
static

create File data sturcture from array of Records.

Create FileData object from a given vector of Records.

References options.

Referenced by core::io::pdb::build_pose_from_pdb_as_is(), createFileData(), core::import_pose::PDBSilentStruct::init_from_lines(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), core::import_pose::pose_from_pdb(), and core::import_pose::pose_from_pdbstring().

FileData core::io::pdb::PDB_DReader::createFileData ( std::vector< Record > &  VR,
PDB_DReaderOptions const &  options 
)
static

create File data sturcture from array of Records and a set of options.

Create FileData object from a given vector of Records.

References core::pose::CrystInfo::alpha(), core::io::pdb::AtomInformation::altLoc, core::pose::CrystInfo::B(), core::pose::CrystInfo::beta(), core::pose::CrystInfo::C(), core::io::pdb::AtomInformation::chainID, core::io::pdb::FileData::chains, core::io::pdb::FileData::crystinfo, core::io::pdb::AtomInformation::element, core::io::pdb::FileData::finalize_header_information(), core::pose::CrystInfo::gamma(), core::io::pdb::AtomInformation::iCode, core::io::pdb::FileData::initialize_header_information(), core::io::pdb::AtomInformation::isHet, core::io::pdb::FileData::modeltag, core::io::pdb::AtomInformation::name, core::io::pdb::PDB_DReaderOptions::new_chain_order(), core::pose::RemarkInfo::num, core::io::pdb::PDB_DReaderOptions::obey_ENDMDL(), core::io::pdb::AtomInformation::occupancy, core::io::pdb::PDB_DReaderOptions::read_link_records(), core::io::pdb::PDB_DReaderOptions::read_pdb_header(), core::io::pdb::FileData::remarks, core::io::pdb::AtomInformation::resName, core::io::pdb::AtomInformation::resSeq, core::io::pdb::AtomInformation::serial, core::pose::CrystInfo::spacegroup(), core::io::pdb::FileData::store_header_record(), core::io::pdb::FileData::store_heterogen_names(), core::io::pdb::FileData::store_link_record(), strip_whitespace(), core::io::pdb::AtomInformation::temperature, core::io::pdb::AtomInformation::terCount, core::io::pdb::TR, utility_exit_with_message, core::pose::RemarkInfo::value, core::io::pdb::AtomInformation::x, core::io::pdb::AtomInformation::y, and core::io::pdb::AtomInformation::z.

FileData core::io::pdb::PDB_DReader::createFileData ( const String &  data)
static

create File data sturcture from string containing PDB information.

Create FileData from a given PDB data (represented as a string).

References createFileData(), and options.

FileData core::io::pdb::PDB_DReader::createFileData ( const String &  data,
PDB_DReaderOptions const &  options 
)
static

create File data sturcture from string containing PDB information and a set of options.

References createFileData(), and parse().

String core::io::pdb::PDB_DReader::createPDBData ( FileData const &  fd)
static

create PDB-like string to represent given FileData object

create PDB file (represented as a string) from FileData object.

References createPDBString(), and createRecords().

Referenced by core::io::pdb::FileData::dump_pdb(), and core::import_pose::PDBSilentStruct::print_conformation().

utility::vector1< std::string > core::io::pdb::PDB_DReader::createPDBData_vector ( FileData const &  fd)
static

create PDB-like vector of string to represent given FileData object.

References createPDBString(), and createRecords().

String core::io::pdb::PDB_DReader::createPDBString ( const Record &  R)
static

Reverse opearation - create PDB string from given Record.

create PDB string from Record data.

References s.

Referenced by createPDBData(), and createPDBData_vector().

std::vector< Record > core::io::pdb::PDB_DReader::createRecords ( FileData const &  fd)
static

create vector of records for given FileData object.

Create vector of Record from given FileData object. Used in PDB writing support.

References core::pose::CrystInfo::alpha(), core::pose::CrystInfo::B(), core::pose::CrystInfo::beta(), core::pose::CrystInfo::C(), core::io::pdb::AtomInformation::chainID, core::io::pdb::LinkInformation::chainID1, core::io::pdb::LinkInformation::chainID2, core::io::pdb::FileData::chains, core::io::pdb::FileData::crystinfo, core::io::pdb::AtomInformation::element, core::io::pdb::FileData::fill_header_records(), core::pose::CrystInfo::gamma(), core::io::pdb::Field::getRecordCollection(), core::io::pdb::FileData::header_information(), core::io::pdb::FileData::heterogen_names, core::io::pdb::AtomInformation::iCode, core::io::pdb::LinkInformation::iCode1, core::io::pdb::LinkInformation::iCode2, core::io::pdb::AtomInformation::isHet, core::io::pdb::LinkInformation::length, core::io::pdb::FileData::link_map, core::io::pdb::AtomInformation::name, core::io::pdb::LinkInformation::name1, core::io::pdb::LinkInformation::name2, core::io::pdb::AtomInformation::occupancy, core::io::pdb::print_d(), core::io::pdb::print_i(), core::io::pdb::FileData::remarks, core::io::pdb::AtomInformation::resName, core::io::pdb::LinkInformation::resName1, core::io::pdb::LinkInformation::resName2, core::io::pdb::AtomInformation::resSeq, core::io::pdb::LinkInformation::resSeq1, core::io::pdb::LinkInformation::resSeq2, core::io::pdb::AtomInformation::serial, core::pose::CrystInfo::spacegroup(), core::io::pdb::AtomInformation::temperature, core::pose::RemarkInfo::value, core::io::pdb::AtomInformation::x, core::io::pdb::AtomInformation::y, and core::io::pdb::AtomInformation::z.

Referenced by createPDBData(), and createPDBData_vector().

Record core::io::pdb::PDB_DReader::mapStringToRecord ( const String &  _s)
static

creating record from given string. Also, read Field values from string.

create Record Object with field collection (depending of the type information in _s), and read fields values.

References core::io::pdb::Field::getRecordCollection(), core::io::pdb::Field::getValueFrom(), s, and core::io::pdb::Field::value.

Referenced by parse(), and core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff().

std::vector< Record > core::io::pdb::PDB_DReader::parse ( const String &  pdb)
static

Parse whole PDB string and return vector of records in order they was in PDB.

Parse given PDB data (represented as a string) into vector of Records.

References mapStringToRecord(), runtime_assert, and core::io::pdb::split().

Referenced by createFileData().

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