BALL
1.4.1
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#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.
Default constructor
BALL::HINFile::HINFile | ( | const String & | filename, |
File::OpenMode | open_mode = std::ios::in |
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) |
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 |
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.
virtual bool BALL::HINFile::read | ( | System & | system | ) | [virtual] |
Reimplemented from BALL::GenericMolFile.
virtual bool BALL::HINFile::write | ( | const Molecule & | molecule | ) | [virtual] |
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.
virtual bool BALL::HINFile::write | ( | const System & | system | ) | [virtual] |
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.
void BALL::HINFile::writeAtom_ | ( | const Atom & | atom, |
Size | number, | ||
Size | atom_offset | ||
) | [protected] |
SimpleBox3 BALL::HINFile::box_ [protected] |
float BALL::HINFile::temperature_ [protected] |