BALL::SDFile Class Reference
[Molecular structure file formats]
#include <BALL/FORMAT/SDFile.h>
Public Member Functions | |
Constructors and Destructors | |
| SDFile () | |
| SDFile (const String &filename, File::OpenMode open_mode=std::ios::in) throw (Exception::FileNotFound) | |
| SDFile (const SDFile &file) throw (Exception::FileNotFound) | |
| virtual | ~SDFile () |
Destructor. | |
Reading and Writing of Kernel Datastructures | |
| virtual bool | write (const System &system) throw (File::CannotWrite) |
| virtual bool | write (const Molecule &molecule) throw (File::CannotWrite) |
| virtual bool | read (System &system) throw (Exception::ParseError) |
| virtual Molecule * | read () throw (Exception::ParseError) |
| void | disableAtoms () |
| void | enableAtoms () |
| const SDFile & | operator= (const SDFile &file) |
Protected Member Functions | |
| void | readPropertyBlock_ (Molecule &molecule) |
| void | writePropertyBlock_ (const Molecule &molecule) |
Protected Attributes | |
| bool | read_atoms_ |
Detailed Description
MDL SD file class. This class enables BALL to read and write MDL SD files.
- A description of this file format (and the related MOLFile format) can be obtained from the MDL webpage http://www.mdli.com
Constructor & Destructor Documentation
| BALL::SDFile::SDFile | ( | ) |
Default constructor
| BALL::SDFile::SDFile | ( | const String & | filename, | |
| File::OpenMode | open_mode = std::ios::in | |||
| ) | throw (Exception::FileNotFound) |
Detailed constructor.
| BALL::SDFile::SDFile | ( | const SDFile & | file | ) | throw (Exception::FileNotFound) |
Copy constructor
| virtual BALL::SDFile::~SDFile | ( | ) | [virtual] |
Destructor.
Member Function Documentation
| void BALL::SDFile::disableAtoms | ( | ) |
Do not read atoms and bonds. This (seemingly strange) option allows the user to read the properties of the molecules only. Since SD files can contain all kinds of information besides the molecular structure and reading the structure can be rather time and space consuming, you can disable it with this option. The read and write methods will still create molecules, but they will be empty. However, the NamedProperties of the molecules contain the optional information contained in the SD file.
| void BALL::SDFile::enableAtoms | ( | ) |
Read atoms and bonds.
- See also:
- disableAtoms
| virtual Molecule* BALL::SDFile::read | ( | ) | throw (Exception::ParseError) [virtual] |
Read a single molecule from an SD file.
Reimplemented from BALL::MOLFile.
| virtual bool BALL::SDFile::read | ( | System & | system | ) | throw (Exception::ParseError) [virtual] |
Read a system from the SD file
Reimplemented from BALL::MOLFile.
| void BALL::SDFile::readPropertyBlock_ | ( | Molecule & | molecule | ) | [protected] |
Read the property block of an SD file. The values are stored as named properties in the molecule read.
| virtual bool BALL::SDFile::write | ( | const Molecule & | molecule | ) | throw (File::CannotWrite) [virtual] |
Append a single molecule to the SD file.
Reimplemented from BALL::MOLFile.
| virtual bool BALL::SDFile::write | ( | const System & | system | ) | throw (File::CannotWrite) [virtual] |
Write a system to the SD file. Write all molecules contained in the system to the SD file. All named properties are included in the property section.
Reimplemented from BALL::MOLFile.
| void BALL::SDFile::writePropertyBlock_ | ( | const Molecule & | molecule | ) | [protected] |
Read the propertyblock of an SD file. The values are stored as named properties in the molecule read.
Member Data Documentation
bool BALL::SDFile::read_atoms_ [protected] |
Whether atoms and bonds should be read