BALL::MOLFile Class Reference
[Molecular structure file formats]
#include <BALL/FORMAT/MOLFile.h>
Classes | |
| class | AtomStruct |
| class | BondStruct |
| class | CountsStruct |
| struct | Property |
Public Member Functions | |
Constructors and Destructors | |
| MOLFile () | |
| MOLFile (const String &filename, File::OpenMode open_mode=std::ios::in) throw (Exception::FileNotFound) | |
| virtual | ~MOLFile () |
| Destructor. | |
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 bool | read (System &system) throw (Exception::ParseError) |
| virtual Molecule * | read () throw (Exception::ParseError) |
| const MOLFile & | operator= (const MOLFile &file) |
Protected Member Functions | |
| Molecule * | readCTAB_ (std::vector< Atom * > &atom_map) throw (Exception::ParseError) |
| Read the CTAB of a MOL file and construct a Molecule from its data. | |
| bool | readCountsLine_ (CountsStruct &counts) |
| Read the Counts line of a MOL file. | |
| bool | readAtomLine_ (AtomStruct &atom) |
| Read a line from the atom block. | |
| bool | readBondLine_ (BondStruct &bond) |
| Read a line from the bond block. | |
| void | writeCountsLine_ (const CountsStruct &counts) |
| Write the Counts line. | |
| void | writeAtomLine_ (const AtomStruct &atom) |
| Write a line of the atom block. | |
| void | writeBondLine_ (const BondStruct &bond) |
| Write a line of the bond block. | |
Static Protected Attributes | |
Format definitions | |
| static const String | counts_format_ |
| The format of the counts line. | |
| static const String | atom_format_ |
| The format of an entry of the atom block. | |
| static const String | bond_format_ |
| The format of an entry of the bond block. | |
Detailed Description
MDL MOL file class. This class enables BALL to read and write MDL MOL files.
Definition at line 27 of file MOLFile.h.
Constructor & Destructor Documentation
| BALL::MOLFile::MOLFile | ( | ) |
Default constructor
| BALL::MOLFile::MOLFile | ( | const String & | filename, | |
| File::OpenMode | open_mode = std::ios::in | |||
| ) | throw (Exception::FileNotFound) |
Detailed constructor.
| virtual BALL::MOLFile::~MOLFile | ( | ) | [virtual] |
Destructor.
Member Function Documentation
| virtual Molecule* BALL::MOLFile::read | ( | ) | throw (Exception::ParseError) [virtual] |
Read a single molecule from the file
Reimplemented from BALL::GenericMolFile.
Reimplemented in BALL::SDFile.
| virtual bool BALL::MOLFile::read | ( | System & | system | ) | throw (Exception::ParseError) [virtual] |
Read a system from the MOL file
Reimplemented from BALL::GenericMolFile.
Reimplemented in BALL::SDFile.
| bool BALL::MOLFile::readAtomLine_ | ( | AtomStruct & | atom | ) | [protected] |
Read a line from the atom block.
| bool BALL::MOLFile::readBondLine_ | ( | BondStruct & | bond | ) | [protected] |
Read a line from the bond block.
| bool BALL::MOLFile::readCountsLine_ | ( | CountsStruct & | counts | ) | [protected] |
Read the Counts line of a MOL file.
| Molecule* BALL::MOLFile::readCTAB_ | ( | std::vector< Atom * > & | atom_map | ) | throw (Exception::ParseError) [protected] |
Read the CTAB of a MOL file and construct a Molecule from its data.
| virtual bool BALL::MOLFile::write | ( | const System & | system | ) | throw (File::CannotWrite) [virtual] |
Write a system to the MOL file. Note that this changes the properties of atoms in the system.
Reimplemented from BALL::GenericMolFile.
Reimplemented in BALL::SDFile.
| virtual bool BALL::MOLFile::write | ( | const Molecule & | molecule | ) | throw (File::CannotWrite) [virtual] |
Write a molecule to the file
Reimplemented from BALL::GenericMolFile.
Reimplemented in BALL::SDFile.
| void BALL::MOLFile::writeAtomLine_ | ( | const AtomStruct & | atom | ) | [protected] |
Write a line of the atom block.
| void BALL::MOLFile::writeBondLine_ | ( | const BondStruct & | bond | ) | [protected] |
Write a line of the bond block.
| void BALL::MOLFile::writeCountsLine_ | ( | const CountsStruct & | counts | ) | [protected] |
Write the Counts line.
Member Data Documentation
const String BALL::MOLFile::atom_format_ [static, protected] |
const String BALL::MOLFile::bond_format_ [static, protected] |
const String BALL::MOLFile::counts_format_ [static, protected] |
