BALL::HINFile Class Reference
[Molecular structure file formats]
#include <BALL/FORMAT/HINFile.h>
Public Member Functions | |
Constructors and Destructors | |
| HINFile () | |
| HINFile (const String &filename, File::OpenMode open_mode=std::ios::in) throw (Exception::FileNotFound) | |
| virtual | ~HINFile () |
Assignment. | |
| const HINFile & | operator= (const HINFile &rhs) throw (Exception::FileNotFound) |
Reading and Writing of Kernel Datastructures | |
| virtual bool | write (const Molecule &molecule) throw (File::CannotWrite) |
| virtual bool | write (const System &system) throw (File::CannotWrite) |
| virtual Molecule * | read () throw (Exception::ParseError) |
| virtual bool | read (System &system) throw (Exception::ParseError) |
Accessors | |
| bool | hasPeriodicBoundary () const |
| SimpleBox3 | getPeriodicBoundary () const |
| float | getTemperature () const |
Protected Member Functions | |
| virtual void | initRead_ () |
| Initialize temperature and box dimensions prior to reading a system. | |
| void | writeAtom_ (const Atom &atom, Size number, Size atom_offset) |
Protected Attributes | |
| SimpleBox3 | box_ |
| float | temperature_ |
Detailed Description
HyperChem file class. This class enables BALL to read and write HyperChem HIN files.
Note: HIN defines a Molecule as a connected component in the molecule graph If you read e.g. a protein from a PDBFile, such that no bonds are set each atom will be placed into its own molecule. To prevent this from happening use the FragmentDB to build missing bonds.
Definition at line 29 of file HINFile.h.
Constructor & Destructor Documentation
| BALL::HINFile::HINFile | ( | ) |
Default constructor
| BALL::HINFile::HINFile | ( | const String & | filename, | |
| File::OpenMode | open_mode = std::ios::in | |||
| ) | throw (Exception::FileNotFound) |
Detailed constructor
| virtual BALL::HINFile::~HINFile | ( | ) | [virtual] |
Destructor
Member Function Documentation
| SimpleBox3 BALL::HINFile::getPeriodicBoundary | ( | ) | const |
Return the periodic boundary of the file. An emptry box is returned if no periodic boundary is defined.
- Returns:
- the boundary box
| float BALL::HINFile::getTemperature | ( | ) | const |
Return the temperature stored in the file. HIN files may contain a sys entry containing the temperature of the last simulation step. If it is set, it is returned. Otherwise 0 is returned.
- Returns:
- the final simulation temperature
| bool BALL::HINFile::hasPeriodicBoundary | ( | ) | const |
Check for a periodic boundary in the file.
| virtual void BALL::HINFile::initRead_ | ( | ) | [protected, virtual] |
Initialize temperature and box dimensions prior to reading a system.
Reimplemented from BALL::GenericMolFile.
| const HINFile& BALL::HINFile::operator= | ( | const HINFile & | rhs | ) | throw (Exception::FileNotFound) |
Assignment operator.
| virtual bool BALL::HINFile::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.
| virtual Molecule* BALL::HINFile::read | ( | ) | throw (Exception::ParseError) [virtual] |
Read a system from the HIN file
Reimplemented from BALL::GenericMolFile.
| virtual bool BALL::HINFile::write | ( | const System & | system | ) | throw (File::CannotWrite) [virtual] |
Write a system to a HIN file. Note that this changes the properties of atoms in the system.
Reimplemented from BALL::GenericMolFile.
| virtual bool BALL::HINFile::write | ( | const Molecule & | molecule | ) | throw (File::CannotWrite) [virtual] |
Write a molecule to a HIN file. Note that this changes the properties of atoms in the system.
Reimplemented from BALL::GenericMolFile.
Member Data Documentation
SimpleBox3 BALL::HINFile::box_ [protected] |
float BALL::HINFile::temperature_ [protected] |
