BALL::PDBFile Class Reference
PDB file class. More...#include <PDBFile.h>
Inheritance diagram for BALL::PDBFile:
[legend]
Classes |
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| struct | Default |
| Default values
for PDBFile options. More... |
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| struct | Option |
| Symbolic names for option keys.
More... |
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Public Types |
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typedef HashMap<
PDB::Integer, PDBAtom * > |
PDBAtomMap |
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typedef Quadruple< String, PDB::Character, PDB::Integer, PDB::AChar > |
ResidueQuadruple |
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typedef HashMap < ResidueQuadruple, Residue * > |
ResidueMap |
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typedef std::list < ResidueQuadruple > |
QuadrupleList |
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typedef std::list < SecondaryStructure * > |
SecStructList |
Public Member Functions |
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| virtual bool | hasFormat () |
| Check whether the current file is in
PDB format. |
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|
Constructurs and destructor.
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| PDBFile () | |
| Default
constructor. |
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| PDBFile (const String &filename, File::OpenMode open_mode=std::ios::in) throw (Exception::FileNotFound) | |
| File-like constructor. |
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| PDBFile (const Options &new_options) | |
| Construct with options. |
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| PDBFile (const PDBFile &file) throw (Exception::FileNotFound) | |
| Copy constructor. |
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| virtual | ~PDBFile () |
| Destructor. |
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Assignment.
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| virtual void | clear (int state) |
| Clear the stream state. |
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| virtual void | clear () |
| Clear all members and close the
file. |
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Accessors.
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| virtual float | getVersion () const |
| Returns the version number this
PDB file reader is able to
read. |
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| void | selectModel (Index index) |
| Selects one of multiple models for
reading. |
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| Index | getSelectedModel () const |
| Return the model currently
selected. |
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| void | selectAllModels () |
| Selects all models for
reading. |
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| Index | getCurrentModel () const |
| Returns the number of the model
weare currently reading. (?????). |
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| char * | getRecordString () |
| Return a mutable pointer to the line
buffer. |
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| const char * | getRecordString () const |
| Return a constant pointer to the
line buffer. |
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| Index | getRecordNumber () const |
| Returns the number of the record we
are currently reading. |
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| PDB::RecordType | getRecordType () const |
| Returns the type of the record we
are currently reading. |
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| virtual const char * | getAtomElementSymbol (const PDB::Atom atom_name, PDB::Atom element_symbol) |
| Returns the element symbol of an
atom. |
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| 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. |
|
| virtual short | getAtomBranchDesignator (const PDB::Atom atom_name) |
| Extract the PDB
branch designator of an atom record. |
|
| Size | countRecordFields () const |
| Returns the number of record
fields. |
|
| Size | countRecord (PDB::RecordType record_type, bool from_begin_of_file=true) |
| Returns the number of records of
type record_type in the file being read. |
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| Size | countRecords (bool from_begin_of_file=true) |
| Returns the number of all records in
the file. |
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Methods for parsing individual records.
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| bool | parseLine (const char *line, Size size, const char *format_string,...) |
| Parse a line from a PDBFile. This is a helper function
for readLine(). |
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| bool | readLine (char *line, Size size, bool extract_values) |
| Read and parse a line from a
PDB file. |
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| bool | readFirstRecord (bool read_values=true) |
| Read the firts record of a
file. |
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| bool | readNextRecord (bool read_values=true) |
| Read the next record of a PDB file. |
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| bool | readRecords () |
| Reads all records of a file.
|
|
| virtual bool | readUnknownRecord (const char *line) |
| Called for unknown PDB records. |
|
| virtual bool | readInvalidRecord (const char *line) |
| Called an invalid record by simply
returning true. |
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| bool | skipCurrentRecord () |
| Skip the current record. |
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| virtual bool | interpretRecord (const PDB::RecordANISOU &record) |
| Reads an anisotropic temperature
factor record. |
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| virtual bool | fillRecord (const char *line, Size size, PDB::RecordANISOU &record) |
| virtual bool | parseRecordANISOU (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordATOM &record) |
| Reads an atom record. |
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| virtual bool | fillRecord (const char *line, Size size, PDB::RecordATOM &record) |
| virtual bool | parseRecordATOM (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordAUTHOR &record) |
| Reads an author record. |
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| virtual bool | fillRecord (const char *line, Size size, PDB::RecordAUTHOR &record) |
| virtual bool | parseRecordAUTHOR (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordCAVEAT &record) |
| Reads a caveat record. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordCAVEAT &record) |
| virtual bool | parseRecordCAVEAT (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordCISPEP &record) |
| Reads a record specifying peptides
in cis conformation. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordCISPEP &record) |
| virtual bool | parseRecordCISPEP (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordCOMPND &record) |
| Reads the title record containing
macroscopic compoubd information. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordCOMPND &record) |
| virtual bool | parseRecordCOMPND (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordCONECT &record) |
| Reads a connection
record. |
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| virtual bool | fillRecord (const char *line, Size size, PDB::RecordCONECT &record) |
| virtual bool | parseRecordCONECT (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordCRYST1 &record) |
| Reads the record specifying the unit
cell parameters, space group, and Z value for
crystographically determined structures. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordCRYST1 &record) |
| virtual bool | parseRecordCRYST1 (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordDBREF &record) |
| Reads a record containing database
cross-reference links. |
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| virtual bool | fillRecord (const char *line, Size size, PDB::RecordDBREF &record) |
| virtual bool | parseRecordDBREF (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordEND &record) |
| Reads the record defining the end of
a PDB file. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordEND &record) |
| virtual bool | parseRecordEND (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordENDMDL &record) |
| Reads a model ending
record. |
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| virtual bool | fillRecord (const char *line, Size size, PDB::RecordENDMDL &record) |
| virtual bool | parseRecordENDMDL (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordEXPDTA &record) |
| Reads a record containing data about
the experiment. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordEXPDTA &record) |
| virtual bool | parseRecordEXPDTA (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordFORMUL &record) |
| Reads a record containing the
chemical formula of a non-standard group. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordFORMUL &record) |
| virtual bool | parseRecordFORMUL (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordFTNOTE &record) |
| Reads a record containing a
footnote. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordFTNOTE &record) |
| virtual bool | parseRecordFTNOTE (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordHEADER &record) |
| Reads the header recors which
contains the idCode field, entry classification and
deposition date. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordHEADER &record) |
| virtual bool | parseRecordHEADER (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordHELIX &record) |
| Reads a helix defining
record. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordHELIX &record) |
| virtual bool | parseRecordHELIX (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordHET &record) |
| Reads a record defining a
non-standard residue. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordHET &record) |
| virtual bool | parseRecordHET (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordHETATM &record) |
| Reads atomic coordinates for atoms
in non-standard groups. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordHETATM &record) |
| virtual bool | parseRecordHETATM (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordHETNAM &record) |
| Reads a record defining the name of
a non-standard group. |
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| virtual bool | fillRecord (const char *line, Size size, PDB::RecordHETNAM &record) |
| virtual bool | parseRecordHETNAM (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordHETSYN &record) |
| Reads a record defining synonyms of
a non-standard group. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordHETSYN &record) |
| virtual bool | parseRecordHETSYN (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordHYDBND &record) |
| Reads a record defining a hydrogen
bond. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordHYDBND &record) |
| virtual bool | parseRecordHYDBND (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordJRNL &record) |
| Reads a record containing a journal
reference. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordJRNL &record) |
| virtual bool | parseRecordJRNL (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordKEYWDS &record) |
| Reads a record containing keywords
for this entry. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordKEYWDS &record) |
| virtual bool | parseRecordKEYWDS (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordLINK &record) |
| Reads a record containing
supplemental connectivity information. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordLINK &record) |
| virtual bool | parseRecordLINK (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordMASTER &record) |
| Reads the master record containing
numerous counts for bookkeeping purposes. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordMASTER &record) |
| virtual bool | parseRecordMASTER (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordMODEL &record) |
| Reads a record indicating the
beginning of a new model. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordMODEL &record) |
| virtual bool | parseRecordMODEL (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordMODRES &record) |
| Reads a record identifying residue
modifications. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordMODRES &record) |
| virtual bool | parseRecordMODRES (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordMTRIX1 &record) |
| Reads a record defining
transformations expressing non-crystallographic
symmetry. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordMTRIX1 &record) |
| virtual bool | parseRecordMTRIX1 (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordMTRIX2 &record) |
| Reads a record defining
transformations expressing non-crystallographic
symmetry. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordMTRIX2 &record) |
| virtual bool | parseRecordMTRIX2 (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordMTRIX3 &record) |
| Reads a record defining
transformations expressing non-crystallographic
symmetry. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordMTRIX3 &record) |
| virtual bool | parseRecordMTRIX3 (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordOBSLTE &record) |
| Reads a record indicating that this
structura has been withdrawnform the database. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordOBSLTE &record) |
| virtual bool | parseRecordOBSLTE (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordORIGX1 &record) |
| Reads a record defining the
transformation from the orthogonal coordinates contained in
the entry to the submitted coordinates. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordORIGX1 &record) |
| virtual bool | parseRecordORIGX1 (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordORIGX2 &record) |
| Reads a record defining the
transformation from the orthogonal coordinates contained in
the entry to the submitted coordinates. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordORIGX2 &record) |
| virtual bool | parseRecordORIGX2 (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordORIGX3 &record) |
| Reads a record defining the
transformation from the orthogonal coordinates contained in
the entry to the submitted coordinates. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordORIGX3 &record) |
| virtual bool | parseRecordORIGX3 (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordREMARK &record) |
| Reads a record containing
remarks. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordREMARK &record) |
| virtual bool | parseRecordREMARK (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordREVDAT &record) |
| Reads a record containing a revision
history. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordREVDAT &record) |
| virtual bool | parseRecordREVDAT (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordSCALE1 &record) |
| Reads a scale transformation
record. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordSCALE1 &record) |
| virtual bool | parseRecordSCALE1 (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordSCALE2 &record) |
| Reads a scale transformation
record. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordSCALE2 &record) |
| virtual bool | parseRecordSCALE2 (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordSCALE3 &record) |
| Reads a scale transformation
record. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordSCALE3 &record) |
| virtual bool | parseRecordSCALE3 (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordSEQADV &record) |
| Sequence information conflicts
between atom records and dbref content. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordSEQADV &record) |
| virtual bool | parseRecordSEQADV (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordSEQRES &record) |
| Reads a record containing the
sequence of residues. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordSEQRES &record) |
| virtual bool | parseRecordSEQRES (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordSHEET &record) |
| Reads a record defining a
beta-sheet. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordSHEET &record) |
| virtual bool | parseRecordSHEET (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordSIGATM &record) |
| Reads a record giving the standard
deviation of atomic coordinates. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordSIGATM &record) |
| virtual bool | parseRecordSIGATM (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordSIGUIJ &record) |
| Reads a record giving the standard
deviation of anisotropic temperature factors. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordSIGUIJ &record) |
| virtual bool | parseRecordSIGUIJ (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordSITE &record) |
| Reads a record containing groups
comprising a site. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordSITE &record) |
| virtual bool | parseRecordSITE (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordSLTBRG &record) |
| Reads a record defining a salt
bridge. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordSLTBRG &record) |
| virtual bool | parseRecordSLTBRG (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordSOURCE &record) |
| Reads a record specifies the
chemical/biological source of each molecule in the
entry. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordSOURCE &record) |
| virtual bool | parseRecordSOURCE (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordSPRSDE &record) |
| List of entries this file
supersedes. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordSPRSDE &record) |
| virtual bool | parseRecordSPRSDE (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordSSBOND &record) |
| Reads a record specifying a
disulfide bond. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordSSBOND &record) |
| virtual bool | parseRecordSSBOND (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordTER &record) |
| Reads a record terminating
molecule. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordTER &record) |
| virtual bool | parseRecordTER (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordTITLE &record) |
| Reads a record specifying the title
of the experiment or anaysis. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordTITLE &record) |
| virtual bool | parseRecordTITLE (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordTURN &record) |
| Reads a record specifying a
turn. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordTURN &record) |
| virtual bool | parseRecordTURN (const char *line, Size size) |
| virtual bool | interpretRecord (const PDB::RecordTVECT &record) |
| Reads a record specifying the
translation vector for infinite covalently connected
structures. |
|
| virtual bool | fillRecord (const char *line, Size size, PDB::RecordTVECT &record) |
| virtual bool | parseRecordTVECT (const char *line, Size size) |
|
Reading and writing
|
|
| PDBFile & | operator>> (Protein &protein) throw (Exception::ParseError) |
| Read a protein from the
file. |
|
| PDBFile & | operator>> (Molecule &molecule) throw (Exception::ParseError) |
| Read a molecule from the
file. |
|
| PDBFile & | operator>> (System &system) throw (Exception::ParseError) |
| Stream operator for reading a
system. |
|
| PDBFile & | operator<< (const Protein &protein) throw (File::CannotWrite) |
| Write a protein to the
file. |
|
| PDBFile & | operator<< (const System &system) throw (File::CannotWrite) |
| Stream operator for writing a system
of molecules. |
|
| PDBFile & | operator<< (const Molecule &molecule) throw (File::CannotWrite) |
| Stream operator for writing a system
of molecules. |
|
| bool | read (Protein &protein) throw (Exception::ParseError) |
| bool | read (Molecule &protein) throw (Exception::ParseError) |
| bool | read (System &system) throw (Exception::ParseError) |
| Read a system. |
|
| Molecule * | read () throw (Exception::ParseError) |
| Read a molecule. |
|
| bool | write (const Protein &protein) throw (File::CannotWrite) |
| bool | write (const Molecule &molecule) throw (File::CannotWrite) |
| Write a molecule. |
|
| bool | write (const System &system) throw (File::CannotWrite) |
| Write the molecules of a system.
|
|
| bool | write (const System &system, const PDBInfo &info) throw (File::CannotWrite) |
Public Attributes |
|
|
Options
|
|
| Options | options |
| The options for parsing the
file. |
|
| PDBInfo | info |
| Summary information on the last file
read. |
|
Protected Member Functions |
|
| PDBFile (const File &pdbf) throw (Exception::FileNotFound) | |
| PDBFile & | operator= (const PDBFile &pdbf) |
| void | init_ () |
| void | postprocessSSBonds_ () |
| void | postprocessHelices_ () |
| void | postprocessSheetsTurns_ (QuadrupleList §ruct_list, SecStructList &new_secstruct_list) |
| void | postprocessRandomCoils_ () |
| void | write_ (const AtomContainer &ac, const PDBInfo &info=PDBInfo()) |
| void | writeRecord_ (PDB::RecordType record,...) |
| Write a record to the stream using a
predefined record type. |
|
| void | writeCONECTRecords_ (PDB::Structure::ConectAtomList &cl) |
| void | writeRawRecord_ (const char *format, const char *tag,...) |
| Write a record to the stream using a
predefined format string. |
|
| void | addAllRecords_ (const PDBInfo &info, PDB::RecordType type) |
| Add all records of a specific type
in the info object to the current stream. |
|
| void | writeRecord_ (const PDB::RecordSEQRES &seqres) |
| Write a SEQRES record to the current
stream. |
|
| void | writeRecord_ (const PDB::RecordHELIX &helix) |
| Write a HELIX record to the current
stream. |
|
| void | writeRecord_ (const PDB::RecordSHEET &helix) |
| Write a SHEET record to the current
stream. |
|
| void | writeRecord_ (const PDB::RecordTURN &helix) |
| Write a TURN record to the current
stream. |
|
| void | writeRecord_ (const PDB::RecordSSBOND &helix) |
| Write a SSBOND record to the current
stream. |
|
| void | writeRecord_ (const PDB::RecordCONECT &helix) |
| Write a CONECT record to the current
stream. |
|
| void | writeAtom_ (const PDB::Structure::AtomEntry &atom, PDB::AdditionalAtomInfo &cr, bool hetatm=false) |
| void | writeTitleSection_ (const PDB::Structure &structure, const PDBInfo &info) |
| void | writePrimaryStructureSection_ (const PDB::Structure &structure, const PDBInfo &info) |
| void | writeHeterogenSection_ (const PDB::Structure &structure, const PDBInfo &info) |
| void | writeSecondaryStructureSection_ (const PDB::Structure &structure, const PDBInfo &info) |
| void | writeConnectivityAnnotationSection_ (const PDB::Structure &structure, const PDBInfo &info) |
| void | writeMiscellaneousFeaturesSection_ (const PDB::Structure &structure, const PDBInfo &info) |
| void | writeCrystallographicSection_ (const PDB::Structure &structure, const PDBInfo &info) |
| void | writeCoordinateSection_ (const PDB::Structure &structure, const PDBInfo &info) |
| void | writeConnectivitySection_ (const PDB::Structure &structure, const PDBInfo &info) |
| void | writeBookKeepingSection_ (const PDB::Structure &structure, const PDBInfo &info) |
| void | writeSEQRESSection_ (const std::vector< std::pair< char, String > > &chain_residues) |
| void | writeHELIXSection_ (const PDB::Structure &structure) |
| void | writeSHEETSection_ (const PDB::Structure &structure) |
| void | writeTURNSection_ (const PDB::Structure &structure) |
| void | writeSSBONDSection_ (const PDB::Structure &structure) |
| void | writeHYDBNDSection_ (const PDB::Structure &structure) |
| void | writeSLTBRGSection_ (const PDB::Structure &structure) |
Static Protected Member Functions |
|
| static void | extractStructure_ (const AtomContainer &ac, PDB::Structure &structure) |
| Extract the atom and bond
information from an atom container prior to writing a
PDB file. |
|
| static bool | isHeteroAtom_ (const Atom &atom) |
| Determine whether an atom is a
hetero atom or part of a standard amino acid or nucleotide.
|
|
| static void | updateAdditionalAtomInfo_ (const PDB::Structure::AtomEntry &atom, PDB::AdditionalAtomInfo &cr) |
| Compute the current name and id of
chain and residue. |
|
Protected Attributes |
|
| char | line_buffer_ [PDB::SIZE_OF_PDB_LINE_BUFFER] |
| String | residue_name_ |
| Index | residue_sequence_number_ |
| Index | current_model_ |
| Index | current_record_ |
| Size | record_fields_ |
| PDB::RecordType | current_record_type_ |
| PDB::RecordTypeFormat | compare_record_type_format_ |
| PDBAtomMap | PDB_atom_map_ |
| ResidueMap | residue_map_ |
| QuadrupleList | ssbond_list_ |
| QuadrupleList | helix_list_ |
| QuadrupleList | sheet_list_ |
| QuadrupleList | turn_list_ |
| SecStructList | new_helix_secstruc_list_ |
| SecStructList | new_sheet_secstruc_list_ |
| SecStructList | new_turn_secstruc_list_ |
| PDB::AChar | insertion_code_ |
| PDB::Character | chain_ID_ |
| PDB::Integer | sequence_number_ |
| PDB::AChar | code_ |
| Protein * | current_protein_ |
| const Protein * | current_const_protein_ |
| Chain * | current_chain_ |
| const Chain * | current_const_chain_ |
| Residue * | current_residue_ |
| const Residue * | current_const_residue_ |
| PDBAtom * | current_PDB_atom_ |
| const Atom * | current_const_atom_ |
| String | name_ |
| HashMap< const Atom *, Position > | atom_map_ |
| PDB::BookKeeping | book_keeping_ |
| Book keeping struct for the number
of records written. |
|
| int | verbosity_ |
| _Verbosity level |
|
| bool | strict_line_checking_ |
| Index | selected_model_ |
| The selected model_. |
|
| bool | store_skipped_records_ |
| Store the skipped records in
info? |
|
| bool | ignore_xplor_pseudo_atoms_ |
| Ignore XPLOR pseudo
atoms? |
|
| bool | parse_partial_charges_ |
| Read partial charges from cols
76-80? |
|
Detailed Description
PDB file class.Member Function Documentation
| static void BALL::PDBFile::extractStructure_ | ( | const AtomContainer & | ac, | |
| PDB::Structure & | structure | |||
| ) | [static, protected] |
| virtual const char* BALL::PDBFile::getAtomElementSymbol | ( | const PDB::Atom | atom_name, | |
| PDB::Atom | element_symbol | |||
| ) | [virtual] |
Returns the element symbol of an atom.
If element_symbol is invalid we try to reconstruct the element symbol from the atom name.
| static bool BALL::PDBFile::isHeteroAtom_ | ( | const Atom & | atom | ) | [static, protected] |
Determine whether an atom is a hetero atom or part of a standard amino acid or nucleotide.
This test is performed by checking for the corresponding properties defined in Residue.
| PDBFile& BALL::PDBFile::operator<< | ( | const Molecule & | molecule | ) | throw (File::CannotWrite)
[virtual] |
Stream operator for writing a system of molecules.
Calls write()
Reimplemented from BALL::GenericMolFile.
| PDBFile& BALL::PDBFile::operator<< | ( | const System & | system | ) | throw (File::CannotWrite)
[virtual] |
Stream operator for writing a system of molecules.
Calls write(const System& system) const .
Reimplemented from BALL::GenericMolFile.
| PDBFile& BALL::PDBFile::operator>> | ( | System & | system | ) | throw (Exception::ParseError)
[virtual] |
Stream operator for reading a system.
Calls read(System&) .
Reimplemented from BALL::GenericMolFile.
| Molecule* BALL::PDBFile::read | ( | ) | throw (Exception::ParseError)
[virtual] |
Read a molecule.
This method will load the first (or the next, on subsequent invocation) molecule from the file. If the file format does not support multiple molecules, only the first call to read will be successful. This method will create an instance of molecule and its the user's responsibility to destroy that molecule.
- Returns:
- a pointer to a molecule, 0 if the file was not open, empty, or at its end
- Exceptions:
-
Exception::ParseError if the contents of the file could not be parsed
Reimplemented from BALL::GenericMolFile.
| bool BALL::PDBFile::read | ( | System & | system | ) | throw (Exception::ParseError)
[virtual] |
Read a system.
This method will read all molecules contained in the file and add them to the system.
- The default implementation calls read() until false is returned and adds the molecules read to the system.
- Returns:
- true if anything could be read
- Exceptions:
-
Exception::ParseError if the file could not be parsed while reading a molecule
Reimplemented from BALL::GenericMolFile.
| bool BALL::PDBFile::readRecords | ( | ) |
Reads all records of a file.
- Returns:
-
true if all records were parsed without error
false otherwise
| virtual bool BALL::PDBFile::readUnknownRecord | ( | const char * | line | ) | [virtual] |
Called for unknown PDB records.
The default implementation does nothing, it always returns true.
- Returns:
- true
| void BALL::PDBFile::selectModel | ( | Index | index | ) |
Selects one of multiple models for reading.
Default behaviour is reading model 1. If a file does not contain a MODEL specifier, all coordinates will be assigned to model 1.
| bool BALL::PDBFile::skipCurrentRecord | ( | ) |
Skip the current record.
If storeSkippedRecords is set to true, the records are added to the skipped records of info. Otherwise, they are just ignored. This method should be called by those readRecord methods that want to skip a particular record (this is the default behavior implemented in PDBFile).
- Returns:
- true
| static void BALL::PDBFile::updateAdditionalAtomInfo_ | ( | const PDB::Structure::AtomEntry & | atom, | |
| PDB::AdditionalAtomInfo & | cr | |||
| ) | [static, protected] |
Compute the current name and id of chain and residue.
This method guesses more or less correct values for names and IDs or uses decent default values. It does so only of the pointers to the residue and chain in cr differ from the values in atom.
| bool BALL::PDBFile::write | ( | const System & | system | ) | throw (File::CannotWrite)
[virtual] |
Write the molecules of a system.
If the file format does not support multiple molecules in a single file, a warning should be printed and only the first molecule should be stored.
- The default implementation iterates over the system and calls write(const Molecule& molecule) for each molecule.
Reimplemented from BALL::GenericMolFile.
| bool BALL::PDBFile::write | ( | const Molecule & | molecule | ) | throw (File::CannotWrite)
[virtual] |
Write a molecule.
Repeated invocations of this method append molecules to the same file.
- The default implementation does nothing.
Reimplemented from BALL::GenericMolFile.
| void BALL::PDBFile::writeRawRecord_ | ( | const char * | format, | |
| const char * | tag, | |||
| ... | ||||
| ) | [protected] |
Write a record to the stream using a predefined format string.
You should not use this method unless you know what you are doing. Use writeRecord_ instead, as this method also updates the record book keeping required for the MASTER record. If you use it, you'll have to update the book keeping structure yourself!
| void BALL::PDBFile::writeRecord_ | ( | PDB::RecordType | record, | |
| ... | ||||
| ) | [protected] |
Write a record to the stream using a predefined record type.
This method updates the internal book keeping data structure required for writing the MASTER record.
- See also:
- PDB::RecordType
