#include <BALL/FORMAT/HINFile.h>
Public Member Functions | |
Constructors and Destructors | |
| HINFile () | |
| HINFile (const String &filename, File::OpenMode open_mode=std::ios::in) | |
| virtual | ~HINFile () |
Assignment. | |
| const HINFile & | operator= (const HINFile &rhs) |
Reading and Writing of Kernel Datastructures | |
| virtual bool | write (const Molecule &molecule) |
| virtual bool | write (const System &system) |
| virtual Molecule * | read () |
| virtual bool | read (System &system) |
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_ |
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.
| BALL::HINFile::HINFile | ( | ) |
Default constructor
| BALL::HINFile::HINFile | ( | const String & | filename, | |
| File::OpenMode | open_mode = std::ios::in | |||
| ) |
Detailed constructor
| Exception::FileNotFound | if the file could not be opened |
| virtual BALL::HINFile::~HINFile | ( | ) | [virtual] |
Destructor
| SimpleBox3 BALL::HINFile::getPeriodicBoundary | ( | ) | const |
Return the periodic boundary of the file. An empty box is returned if no periodic boundary is defined.
| 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.
| 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.
Assignment operator.
| Exception::FileNotFound | if the file could not be opened |
Reimplemented from BALL::GenericMolFile.
| virtual Molecule* BALL::HINFile::read | ( | ) | [virtual] |
Read a molecule from the HIN file
| Exception::ParseError | if a syntax error was encountered |
Reimplemented from BALL::GenericMolFile.
Write a system to a HIN file. Note that this changes the properties of atoms in the system.
| File::CannotWrite | if writing to the file failed |
Reimplemented from BALL::GenericMolFile.
Write a molecule to a HIN file. Note that this changes the properties of atoms in the system.
| File::CannotWrite | if writing to the file failed |
Reimplemented from BALL::GenericMolFile.
SimpleBox3 BALL::HINFile::box_ [protected] |
float BALL::HINFile::temperature_ [protected] |
1.6.3
