BALL::XYZFile Class Reference
[Molecular structure file formats]
#include <BALL/FORMAT/XYZFile.h>
Public Member Functions | |
Constructors and Destructors | |
| XYZFile () | |
| XYZFile (const String &filename, File::OpenMode open_mode=std::ios::in) throw (Exception::FileNotFound) | |
| XYZFile (const XYZFile &file) throw (Exception::FileNotFound) | |
| virtual | ~XYZFile () |
Destructor. | |
Reading and Writing of Kernel Datastructures | |
| String | comment_ |
| virtual bool | write (const AtomContainer &ac) throw (File::CannotWrite) |
| virtual bool | write (const System &system) throw (File::CannotWrite) |
| virtual bool | write (const Molecule &mol) throw (File::CannotWrite) |
| virtual bool | read (System &system) throw (Exception::ParseError) |
| virtual Molecule * | read () throw (Exception::ParseError) |
| const XYZFile & | operator= (const XYZFile &file) |
| BALL_DEPRECATED const String & | getComent () const |
| const String & | getComment () const |
Detailed Description
XYZ file class. This class enables BALL to read and write XMol XYZ files. The XYZ format is a very simple molecular file format. In general it contains only the atom type (i.e., the element) and the cartesian coordinates of the structure. Newer versions of this file format also contain bonds (without bond order) and atom names.
- The first line of each XYZ file contains a single integer number: the number of atoms in the file. The second line is just a comment line. When reading a XYZ file, BALL stores this comment as the name attribute of the system read. Similarly, on writing the system, it's name is written to this comment line. All remaining lines contain the element symbol and the three coordinates in free format.
Constructor & Destructor Documentation
| BALL::XYZFile::XYZFile | ( | ) |
Default constructor
| BALL::XYZFile::XYZFile | ( | const String & | filename, | |
| File::OpenMode | open_mode = std::ios::in | |||
| ) | throw (Exception::FileNotFound) |
Detailed constructor. Create a XYZ file and open it with mode open_mode (reading is default)
- Parameters:
-
filename the filename open_mode the openmode - default is File::IN
| BALL::XYZFile::XYZFile | ( | const XYZFile & | file | ) | throw (Exception::FileNotFound) |
Copy constructor
| virtual BALL::XYZFile::~XYZFile | ( | ) | [virtual] |
Destructor.
Member Function Documentation
| BALL_DEPRECATED const String& BALL::XYZFile::getComent | ( | ) | const [inline] |
- Deprecated:
- Instead of this method use XYZFile::getComment()
| const String& BALL::XYZFile::getComment | ( | ) | const [inline] |
References BALL::File::operator=().
| virtual Molecule* BALL::XYZFile::read | ( | ) | throw (Exception::ParseError) [virtual] |
Read a molecule from the XYZ file
Reimplemented from BALL::GenericMolFile.
| virtual bool BALL::XYZFile::read | ( | System & | system | ) | throw (Exception::ParseError) [virtual] |
Read a system from the XYZ file
Reimplemented from BALL::GenericMolFile.
| virtual bool BALL::XYZFile::write | ( | const Molecule & | mol | ) | throw (File::CannotWrite) [virtual] |
Write a molecule to the XYZ file
Reimplemented from BALL::GenericMolFile.
| virtual bool BALL::XYZFile::write | ( | const System & | system | ) | throw (File::CannotWrite) [virtual] |
Write a system to the XYZ file
Reimplemented from BALL::GenericMolFile.
| virtual bool BALL::XYZFile::write | ( | const AtomContainer & | ac | ) | throw (File::CannotWrite) [virtual] |
Write an AtomContainer to the XYZ file
Member Data Documentation
String BALL::XYZFile::comment_ [private] |