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BALL::PDBFile Class Reference

#include <PDBFile.h>

Inheritance diagram for BALL::PDBFile:

BALL::GenericMolFile BALL::PropertyManager BALL::LineBasedFile BALL::File

List of all members.


Detailed Description

PDB file class.

Definition at line 76 of file PDBFile.h.


Enums

enum  Transformation { TRANSFORMATION__EXEC = 1, TRANSFORMATION__FILTER = 2, TRANSFORMATION__URL = 3 }
enum  Type {
  TYPE__UNKNOWN = 0, TYPE__DIRECTORY = 1, TYPE__CHAR_SPECIAL_FILE = 2, TYPE__BLOCK_SPECIAL_FILE = 3,
  TYPE__REGULAR_FILE = 4, TYPE__SYMBOLIC_LINK = 5, TYPE__SOCKET = 6, TYPE__FIFO_SPECIAL_FILE = 7
}
static const String TRANSFORMATION_EXEC_PREFIX = "exec:"
 Prefix for filenames that are created through the execution of commands "exec:".
static const String TRANSFORMATION_FILE_PREFIX = "file:"
 Prefix for files (to mimick URL-like behavior) "file:".
static const String TRANSFORMATION_FTP_PREFIX = "ftp://"
 Prefix for FTP-transfers "ftp://".
static const String TRANSFORMATION_HTTP_PREFIX = "http://"
 Prefix for HTTP-transfer "http://".

Accessors

void close ()
bool copyTo (const String &destination_name, Size buffer_size=4096) throw (Exception::FileNotFound)
std::fstream & getFileStream ()
const StringgetName () const
File::OpenMode getOpenMode () const
const StringgetOriginalName () const
Size getSize () throw (Exception::FileNotFound)
Type getType (bool trace_link) const throw (Exception::FileNotFound)
bool moveTo (const String &destination_name) throw (Exception::FileNotFound)
bool open (const String &name, File::OpenMode open_mode=std::ios::in) throw (Exception::FileNotFound)
bool remove ()
bool renameTo (const String &new_path) throw (Exception::FileNotFound)
bool reopen (File::OpenMode open_mode) throw (Exception::FileNotFound)
bool reopen () throw (Exception::FileNotFound)
void setName (const String &name)
bool truncate (Size size=0) throw (Exception::FileNotFound)
static bool copy (String source_name, String destination_name, Size buffer_size=4096) throw (Exception::FileNotFound)
static bool createTemporaryFilename (String &temporary)
static Size getSize (String name) throw (Exception::FileNotFound)
static Type getType (String name, bool trace_link) throw (Exception::FileNotFound)
static bool move (const String &source_name, const String &destination_name) throw (Exception::FileNotFound)
static bool remove (String name)
static bool rename (String old_path, String new_path) throw (Exception::FileNotFound)
static bool truncate (String path, Size size=0) throw (Exception::FileNotFound)

On-the-fly file transformation

See also:
TransformationManager


const TransformationManagergetTransformationManager () const
TransformationManagergetTransformationManager ()
static void disableTransformation (Transformation transformation)
static void enableTransformation (Transformation transformation)
static bool isTransformationEnabled (Transformation transformation)
static void registerTransformation (const String &pattern, const String &exec)
static void unregisterTransformation (const String &pattern)

Predicates

bool isAccessible () const throw (Exception::FileNotFound)
bool isCanonized () const throw (Exception::FileNotFound)
bool isClosed () const
bool isExecutable () const throw (Exception::FileNotFound)
bool isOpen () const
bool isReadable () const throw (Exception::FileNotFound)
bool isWritable () const throw (Exception::FileNotFound)
bool operator!= (const File &file) const
bool operator== (const File &file) const
static bool isAccessible (String name)
static bool isExecutable (String name) throw (Exception::FileNotFound)
static bool isReadable (String name) throw (Exception::FileNotFound)
static bool isWritable (String name) throw (Exception::FileNotFound)

Public Types

typedef HashMap< PDB::Integer,
PDBAtom * > 
PDBAtomMap
typedef std::list
< ResidueQuadruple
QuadrupleList
typedef HashMap
< ResidueQuadruple, Residue * > 
ResidueMap
typedef Quadruple< String,
PDB::Character, PDB::Integer,
PDB::AChar > 
ResidueQuadruple
typedef std::list
< SecondaryStructure * > 
SecStructList
Type definitions
typedef std::ios::openmode OpenMode

Public Member Functions

virtual bool hasFormat ()
 Check whether the current file is in PDB format.
Assignment.
virtual void clear ()
 Clear all members and close the file.
virtual void clear (int state)
 Clear the stream state.
Handling named properties
PropertyManager contains an vector of NamedProperty objects. Each of the NamedProeprty objects has to have a unique name. The setProperty methods ensure the uniqueness of this name. If a setProperty method is called for an existing name, the existing object is destructed prior to the insertion of the new object.

void clearProperty (const string &name)
Size countNamedProperties () const
NamedPropertygetNamedProperty (Position index) throw (Exception::IndexOverflow)
const NamedPropertygetNamedProperty (Position index) const throw (Exception::IndexOverflow)
const NamedPropertygetProperty (const string &name) const
void setProperty (const string &name, const PersistentObject &value)
void setProperty (const string &name, const string &value)
void setProperty (const string &name, double value)
void setProperty (const string &name, float value)
void setProperty (const string &name, unsigned int value)
void setProperty (const string &name, int value)
void setProperty (const string &name, bool value)
void setProperty (const string &name)
void setProperty (const NamedProperty &property)
Handling unnamed bit properties
void clearProperty (Property property)
Size countProperties () const
void setProperty (Property property)
void toggleProperty (Property property)
Accessors.
Size countRecord (PDB::RecordType record_type, bool from_begin_of_file=true)
Size countRecordFields () const
 Returns the number of record fields.
Size countRecords (bool from_begin_of_file=true)
virtual short getAtomBranchDesignator (const PDB::Atom atom_name)
 Extract the PDB branch designator of an atom record.
virtual const char * getAtomElementSymbol (const PDB::Atom atom_name, PDB::Atom element_symbol)
virtual const char * getAtomName (const PDB::Atom atom_name)
 Returns the atom name.
virtual char getAtomRemotenessIndicator (const PDB::Atom atom_name)
 Extract the PDB remoteness indicator of an atom record.
Index getCurrentModel () const
 Returns the number of the model weare currently reading. (?????).
Index getRecordNumber () const
 Returns the number of the record we are currently reading.
const char * getRecordString () const
 Return a constant pointer to the line buffer.
char * getRecordString ()
 Return a mutable pointer to the line buffer.
PDB::RecordType getRecordType () const
 Returns the type of the record we are currently reading.
Index getSelectedModel () const
 Return the model currently selected.
virtual float getVersion () const
 Returns the version number this PDB file reader is able to read.
void selectAllModels ()
 Selects all models for reading.
void selectModel (Index index)
Constructors and Destructors


virtual void destroy ()
 Clears all properties.
Debugging and Diagnostics
void dump (std::ostream &s=std::cout, Size depth=0) const
bool isValid () const
Help-Methods for File Acces
void enableTrimWhitespaces (bool state)
 Set wheter leading and trailing whitespaces in lines shall be removed.
String getField (Index pos=0, const String &quotes="", const String &delimiters=String::CHARACTER_CLASS__WHITESPACE) const throw (Exception::IndexUnderflow)
bool gotoLine (Position line_number) throw (Exception::ParseError)
bool has (const String &text) const
 Return true if the current line contains text.
bool parseColumnFormat (const char *format, Position index, Size length, void *arg)
bool readLine () throw (Exception::ParseError)
void rewind () throw (Exception::ParseError)
bool search (const String &text, const String &stop, bool return_to_start=false) throw (Exception::ParseError)
bool search (const String &text, bool return_to_start=false) throw (Exception::ParseError)
bool skipLines (Size number=1) throw (Exception::ParseError)
bool startsWith (const String &text) const
 Test if the current line starts with text.
Index switchString (const std::vector< String > &data) const
void test (const char *file, int line, bool condition, const String &msg) const throw (Exception::ParseError)
bool trimWhiteSpacesEnabled () const
Methods for parsing individual records.
These methods are typically required if you want to implement your own PDB parser (derived from PDBFile or PDBFile).

virtual bool fillRecord (const char *line, Size size, PDB::RecordTVECT &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordTURN &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordTITLE &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordTER &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordSSBOND &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordSPRSDE &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordSOURCE &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordSLTBRG &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordSITE &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordSIGUIJ &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordSIGATM &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordSHEET &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordSEQRES &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordSEQADV &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordSCALE3 &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordSCALE2 &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordSCALE1 &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordREVDAT &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordREMARK &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordORIGX3 &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordORIGX2 &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordORIGX1 &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordOBSLTE &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordMTRIX3 &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordMTRIX2 &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordMTRIX1 &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordMODRES &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordMODEL &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordMASTER &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordLINK &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordKEYWDS &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordJRNL &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordHYDBND &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordHETSYN &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordHETNAM &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordHETATM &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordHET &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordHELIX &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordHEADER &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordFTNOTE &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordFORMUL &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordEXPDTA &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordENDMDL &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordEND &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordDBREF &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordCRYST1 &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordCONECT &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordCOMPND &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordCISPEP &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordCAVEAT &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordAUTHOR &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordATOM &record)
virtual bool fillRecord (const char *line, Size size, PDB::RecordANISOU &record)
virtual bool interpretRecord (const PDB::RecordTVECT &record)
virtual bool interpretRecord (const PDB::RecordTURN &record)
 Reads a record specifying a turn.
virtual bool interpretRecord (const PDB::RecordTITLE &record)
 Reads a record specifying the title of the experiment or anaysis.
virtual bool interpretRecord (const PDB::RecordTER &record)
 Reads a record terminating molecule.
virtual bool interpretRecord (const PDB::RecordSSBOND &record)
 Reads a record specifying a disulfide bond.
virtual bool interpretRecord (const PDB::RecordSPRSDE &record)
 List of entries this file supersedes.
virtual bool interpretRecord (const PDB::RecordSOURCE &record)
virtual bool interpretRecord (const PDB::RecordSLTBRG &record)
 Reads a record defining a salt bridge.
virtual bool interpretRecord (const PDB::RecordSITE &record)
 Reads a record containing groups comprising a site.
virtual bool interpretRecord (const PDB::RecordSIGUIJ &record)
virtual bool interpretRecord (const PDB::RecordSIGATM &record)
 Reads a record giving the standard deviation of atomic coordinates.
virtual bool interpretRecord (const PDB::RecordSHEET &record)
 Reads a record defining a beta-sheet.
virtual bool interpretRecord (const PDB::RecordSEQRES &record)
 Reads a record containing the sequence of residues.
virtual bool interpretRecord (const PDB::RecordSEQADV &record)
 Sequence information conflicts between atom records and dbref content.
virtual bool interpretRecord (const PDB::RecordSCALE3 &record)
 Reads a scale transformation record.
virtual bool interpretRecord (const PDB::RecordSCALE2 &record)
 Reads a scale transformation record.
virtual bool interpretRecord (const PDB::RecordSCALE1 &record)
 Reads a scale transformation record.
virtual bool interpretRecord (const PDB::RecordREVDAT &record)
 Reads a record containing a revision history.
virtual bool interpretRecord (const PDB::RecordREMARK &record)
 Reads a record containing remarks.
virtual bool interpretRecord (const PDB::RecordORIGX3 &record)
virtual bool interpretRecord (const PDB::RecordORIGX2 &record)
virtual bool interpretRecord (const PDB::RecordORIGX1 &record)
virtual bool interpretRecord (const PDB::RecordOBSLTE &record)
virtual bool interpretRecord (const PDB::RecordMTRIX3 &record)
virtual bool interpretRecord (const PDB::RecordMTRIX2 &record)
virtual bool interpretRecord (const PDB::RecordMTRIX1 &record)
virtual bool interpretRecord (const PDB::RecordMODRES &record)
 Reads a record identifying residue modifications.
virtual bool interpretRecord (const PDB::RecordMODEL &record)
 Reads a record indicating the beginning of a new model.
virtual bool interpretRecord (const PDB::RecordMASTER &record)
virtual bool interpretRecord (const PDB::RecordLINK &record)
 Reads a record containing supplemental connectivity information.
virtual bool interpretRecord (const PDB::RecordKEYWDS &record)
 Reads a record containing keywords for this entry.
virtual bool interpretRecord (const PDB::RecordJRNL &record)
 Reads a record containing a journal reference.
virtual bool interpretRecord (const PDB::RecordHYDBND &record)
 Reads a record defining a hydrogen bond.
virtual bool interpretRecord (const PDB::RecordHETSYN &record)
 Reads a record defining synonyms of a non-standard group.
virtual bool interpretRecord (const PDB::RecordHETNAM &record)
 Reads a record defining the name of a non-standard group.
virtual bool interpretRecord (const PDB::RecordHETATM &record)
 Reads atomic coordinates for atoms in non-standard groups.
virtual bool interpretRecord (const PDB::RecordHET &record)
 Reads a record defining a non-standard residue.
virtual bool interpretRecord (const PDB::RecordHELIX &record)
 Reads a helix defining record.
virtual bool interpretRecord (const PDB::RecordHEADER &record)
virtual bool interpretRecord (const PDB::RecordFTNOTE &record)
 Reads a record containing a footnote.
virtual bool interpretRecord (const PDB::RecordFORMUL &record)
virtual bool interpretRecord (const PDB::RecordEXPDTA &record)
 Reads a record containing data about the experiment.
virtual bool interpretRecord (const PDB::RecordENDMDL &record)
 Reads a model ending record.
virtual bool interpretRecord (const PDB::RecordEND &record)
 Reads the record defining the end of a PDB file.
virtual bool interpretRecord (const PDB::RecordDBREF &record)
 Reads a record containing database cross-reference links.
virtual bool interpretRecord (const PDB::RecordCRYST1 &record)
virtual bool interpretRecord (const PDB::RecordCONECT &record)
 Reads a connection record.
virtual bool interpretRecord (const PDB::RecordCOMPND &record)
 Reads the title record containing macroscopic compoubd information.
virtual bool interpretRecord (const PDB::RecordCISPEP &record)
 Reads a record specifying peptides in cis conformation.
virtual bool interpretRecord (const PDB::RecordCAVEAT &record)
 Reads a caveat record.
virtual bool interpretRecord (const PDB::RecordAUTHOR &record)
 Reads an author record.
virtual bool interpretRecord (const PDB::RecordATOM &record)
 Reads an atom record.
virtual bool interpretRecord (const PDB::RecordANISOU &record)
 Reads an anisotropic temperature factor record.
bool parseLine (const char *line, Size size, const char *format_string,...)
 Parse a line from a PDBFile. This is a helper function for readLine().
virtual bool parseRecordANISOU (const char *line, Size size)
virtual bool parseRecordATOM (const char *line, Size size)
virtual bool parseRecordAUTHOR (const char *line, Size size)
virtual bool parseRecordCAVEAT (const char *line, Size size)
virtual bool parseRecordCISPEP (const char *line, Size size)
virtual bool parseRecordCOMPND (const char *line, Size size)
virtual bool parseRecordCONECT (const char *line, Size size)
virtual bool parseRecordCRYST1 (const char *line, Size size)
virtual bool parseRecordDBREF (const char *line, Size size)
virtual bool parseRecordEND (const char *line, Size size)
virtual bool parseRecordENDMDL (const char *line, Size size)
virtual bool parseRecordEXPDTA (const char *line, Size size)
virtual bool parseRecordFORMUL (const char *line, Size size)
virtual bool parseRecordFTNOTE (const char *line, Size size)
virtual bool parseRecordHEADER (const char *line, Size size)
virtual bool parseRecordHELIX (const char *line, Size size)
virtual bool parseRecordHET (const char *line, Size size)
virtual bool parseRecordHETATM (const char *line, Size size)
virtual bool parseRecordHETNAM (const char *line, Size size)
virtual bool parseRecordHETSYN (const char *line, Size size)
virtual bool parseRecordHYDBND (const char *line, Size size)
virtual bool parseRecordJRNL (const char *line, Size size)
virtual bool parseRecordKEYWDS (const char *line, Size size)
virtual bool parseRecordLINK (const char *line, Size size)
virtual bool parseRecordMASTER (const char *line, Size size)
virtual bool parseRecordMODEL (const char *line, Size size)
virtual bool parseRecordMODRES (const char *line, Size size)
virtual bool parseRecordMTRIX1 (const char *line, Size size)
virtual bool parseRecordMTRIX2 (const char *line, Size size)
virtual bool parseRecordMTRIX3 (const char *line, Size size)
virtual bool parseRecordOBSLTE (const char *line, Size size)
virtual bool parseRecordORIGX1 (const char *line, Size size)
virtual bool parseRecordORIGX2 (const char *line, Size size)
virtual bool parseRecordORIGX3 (const char *line, Size size)
virtual bool parseRecordREMARK (const char *line, Size size)
virtual bool parseRecordREVDAT (const char *line, Size size)
virtual bool parseRecordSCALE1 (const char *line, Size size)
virtual bool parseRecordSCALE2 (const char *line, Size size)
virtual bool parseRecordSCALE3 (const char *line, Size size)
virtual bool parseRecordSEQADV (const char *line, Size size)
virtual bool parseRecordSEQRES (const char *line, Size size)
virtual bool parseRecordSHEET (const char *line, Size size)
virtual bool parseRecordSIGATM (const char *line, Size size)
virtual bool parseRecordSIGUIJ (const char *line, Size size)
virtual bool parseRecordSITE (const char *line, Size size)
virtual bool parseRecordSLTBRG (const char *line, Size size)
virtual bool parseRecordSOURCE (const char *line, Size size)
virtual bool parseRecordSPRSDE (const char *line, Size size)
virtual bool parseRecordSSBOND (const char *line, Size size)
virtual bool parseRecordTER (const char *line, Size size)
virtual bool parseRecordTITLE (const char *line, Size size)
virtual bool parseRecordTURN (const char *line, Size size)
virtual bool parseRecordTVECT (const char *line, Size size)
bool readFirstRecord (bool read_values=true)
 Read the firts record of a file.
virtual bool readInvalidRecord (const char *line)
bool readLine (char *line, Size size, bool extract_values)
 Read and parse a line from a PDB file.
bool readNextRecord (bool read_values=true)
 Read the next record of a PDB file.
bool readRecords ()
virtual bool readUnknownRecord (const char *line)
bool skipCurrentRecord ()
Assignment
void get (PropertyManager &property_manager) const
void set (const PropertyManager &property_manager)
void swap (PropertyManager &property_manager)
Accessors
const BitVectorgetBitVector () const
BitVectorgetBitVector ()
Accessors
StringgetLine ()
 Return the current line.
const StringgetLine () const
 Return the current line.
Position getLineNumber () const
 Get the last line number in the file.
Predicates
bool hasProperty (const string &name) const
 Query for a named property.
bool hasProperty (Property property) const
 Query for an unnamed property.
bool operator!= (const PropertyManager &pm) const
 Inequality operator.
bool operator== (const PropertyManager &pm) const
Debugging and Diagnostics
bool isValid () const
Converters
 operator BitVector & ()
Equality operators
bool operator!= (const LineBasedFile &f)
bool operator== (const LineBasedFile &f)
Reading and writing


PDBFileoperator<< (const Molecule &molecule) throw (File::CannotWrite)
PDBFileoperator<< (const System &system) throw (File::CannotWrite)
PDBFileoperator<< (const Protein &protein) throw (File::CannotWrite)
 Write a protein to the file.
PDBFileoperator>> (System &system) throw (Exception::ParseError)
PDBFileoperator>> (Molecule &molecule) throw (Exception::ParseError)
 Read a molecule from the file.
PDBFileoperator>> (Protein &protein) throw (Exception::ParseError)
 Read a protein from the file.
Moleculeread () throw (Exception::ParseError)
bool read (System &system) throw (Exception::ParseError)
bool read (Molecule &protein) throw (Exception::ParseError)
bool read (Protein &protein) throw (Exception::ParseError)
bool write (const System &system, const PDBInfo &info) throw (File::CannotWrite)
bool write (const System &system) throw (File::CannotWrite)
bool write (const Molecule &molecule) throw (File::CannotWrite)
bool write (const Protein &protein) throw (File::CannotWrite)
Constructurs and destructor.
 PDBFile (const PDBFile &file) throw (Exception::FileNotFound)
 Copy constructor.
 PDBFile (const Options &new_options)
 Construct with options.
 PDBFile (const String &filename, File::OpenMode open_mode=std::ios::in) throw (Exception::FileNotFound)
 File-like constructor.
 PDBFile ()
 Default constructor.
virtual ~PDBFile ()
 Destructor.
Storable Interface
bool read (PersistenceManager &pm)
 Persistent stream reading.
void write (PersistenceManager &pm) const
 Persistent stream writing.

Public Attributes

Options
PDBInfo info
 Summary information on the last file read.
Options options
 The options for parsing the file.

Static Public Attributes

Constants
static const OpenMode MODE_APP = std::ios::app
 Append. Seek to end before each write operation.
static const OpenMode MODE_ATE = std::ios::ate
 Seek to end directly after opening.
static const OpenMode MODE_BINARY = std::ios::binary
 Binary mode.
static const OpenMode MODE_IN = std::ios::in
 Open for input (default).
static const OpenMode MODE_OUT = std::ios::out
 Open for output.
static const OpenMode MODE_TRUNC = std::ios::trunc
 Truncate an existing file.

Protected Member Functions

void addAllRecords_ (const PDBInfo &info, PDB::RecordType type)
 Add all records of a specific type in the info object to the current stream.
void init_ ()
virtual void initRead_ ()
virtual void initWrite_ ()
PDBFileoperator= (const PDBFile &pdbf)
 PDBFile (const File &pdbf) throw (Exception::FileNotFound)
void postprocessHelices_ ()
void postprocessRandomCoils_ ()
void postprocessSheetsTurns_ (QuadrupleList &sectruct_list, SecStructList &new_secstruct_list)
void postprocessSSBonds_ ()
void write_ (const AtomContainer &ac, const PDBInfo &info=PDBInfo())
void writeAtom_ (const PDB::Structure::AtomEntry &atom, PDB::AdditionalAtomInfo &cr, bool hetatm=false)
void writeBookKeepingSection_ (const PDB::Structure &structure, const PDBInfo &info)
void writeCONECTRecords_ (PDB::Structure::ConectAtomList &cl)
void writeConnectivityAnnotationSection_ (const PDB::Structure &structure, const PDBInfo &info)
void writeConnectivitySection_ (const PDB::Structure &structure, const PDBInfo &info)
void writeCoordinateSection_ (const PDB::Structure &structure, const PDBInfo &info)
void writeCrystallographicSection_ (const PDB::Structure &structure, const PDBInfo &info)
void writeHELIXSection_ (const PDB::Structure &structure)
void writeHeterogenSection_ (const PDB::Structure &structure, const PDBInfo &info)
void writeHYDBNDSection_ (const PDB::Structure &structure)
void writeMiscellaneousFeaturesSection_ (const PDB::Structure &structure, const PDBInfo &info)
void writePrimaryStructureSection_ (const PDB::Structure &structure, const PDBInfo &info)
void writeRawRecord_ (const char *format, const char *tag,...)
void writeRecord_ (const PDB::RecordCONECT &helix)
void writeRecord_ (const PDB::RecordSSBOND &helix)
void writeRecord_ (const PDB::RecordTURN &helix)
void writeRecord_ (const PDB::RecordSHEET &helix)
void writeRecord_ (const PDB::RecordHELIX &helix)
void writeRecord_ (const PDB::RecordSEQRES &seqres)
void writeRecord_ (PDB::RecordType record,...)
void writeSecondaryStructureSection_ (const PDB::Structure &structure, const PDBInfo &info)
void writeSEQRESSection_ (const std::vector< std::pair< char, String > > &chain_residues)
void writeSHEETSection_ (const PDB::Structure &structure)
void writeSLTBRGSection_ (const PDB::Structure &structure)
void writeSSBONDSection_ (const PDB::Structure &structure)
void writeTitleSection_ (const PDB::Structure &structure, const PDBInfo &info)
void writeTURNSection_ (const PDB::Structure &structure)

Static Protected Member Functions

static void extractStructure_ (const AtomContainer &ac, PDB::Structure &structure)
static bool isHeteroAtom_ (const Atom &atom)
static void updateAdditionalAtomInfo_ (const PDB::Structure::AtomEntry &atom, PDB::AdditionalAtomInfo &cr)

Protected Attributes

HashMap< const Atom *, Positionatom_map_
PDB::BookKeeping book_keeping_
 Book keeping struct for the number of records written.
PDB::Character chain_ID_
PDB::AChar code_
PDB::RecordTypeFormat compare_record_type_format_
Chaincurrent_chain_
const Atomcurrent_const_atom_
const Chaincurrent_const_chain_
const Proteincurrent_const_protein_
const Residuecurrent_const_residue_
Index current_model_
PDBAtomcurrent_PDB_atom_
Proteincurrent_protein_
Index current_record_
PDB::RecordType current_record_type_
Residuecurrent_residue_
QuadrupleList helix_list_
bool ignore_xplor_pseudo_atoms_
 Ignore XPLOR pseudo atoms?
PDB::AChar insertion_code_
bool is_open_
bool is_temporary_
String line_
 buffer for the line in use
char line_buffer_ [PDB::SIZE_OF_PDB_LINE_BUFFER]
Position line_number_
 line number in the file
String name_
SecStructList new_helix_secstruc_list_
SecStructList new_sheet_secstruc_list_
SecStructList new_turn_secstruc_list_
OpenMode open_mode_
String original_name_
bool parse_partial_charges_
 Read partial charges from cols 76-80?
PDBAtomMap PDB_atom_map_
Size record_fields_
ResidueMap residue_map_
String residue_name_
Index residue_sequence_number_
Index selected_model_
 The selected model_.
PDB::Integer sequence_number_
QuadrupleList sheet_list_
QuadrupleList ssbond_list_
bool store_skipped_records_
 Store the skipped records in info?
bool strict_line_checking_
bool trim_whitespaces_
QuadrupleList turn_list_
int verbosity_
 _Verbosity level

Static Protected Attributes

static TransformationManager transformation_manager_
static Size transformation_methods_

Classes

struct  Default
struct  Option

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

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